Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures

DEFF Research Database (Denmark)

Nazir, Rashid; Hansen, Martin A.; Sorensen, Soren

2012-01-01

Burkholderia terrae BS001 is a soil bacterium which was originally isolated from the mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a range of fungus-interacting traits which reveal its propensity to actively interact at fungal interfaces. Here, we present the approximately...

Electricity Generation in Microbial Fuel Cell (MFC) by Bacterium Isolated from Rice Paddy Field Soil

Science.gov (United States)

Fakhirruddin, Fakhriah; Amid, Azura; Salim, Wan Wardatul Amani Wan; Suhaida Azmi, Azlin

2018-03-01

Microbial fuel cell (MFC) is an alternative approach in generating renewable energy by utilising bacteria that will oxidize organic or inorganic substrates, producing electrons yielded as electrical energy. Different species of exoelectrogenic bacteria capable of generating significant amount of electricity in MFC has been identified, using various organic compounds for fuel. Soil sample taken from rice paddy field is proven to contain exoelectrogenic bacteria, thus electricity generation using mixed culture originally found in the soil, and pure culture isolated from the soil is studied. This research will isolate the exoelectrogenic bacterial species in the rice paddy field soil responsible for energy generation. Growth of bacteria isolated from the MFC is observed by measuring the optical density (OD), cell density weight (CDW) and viable cell count. Mixed bacterial species found in paddy field soil generates maximum power of 77.62 μW and 0.70 mA of current. In addition, the research also shows that the pure bacterium in rice paddy field soil can produce maximum power and current at 51.32 μW and 0.28 mA respectively.

Serpentine endophytic bacterium Pseudomonas azotoformans ASS1 accelerates phytoremediation of soil metals under drought stress.

Science.gov (United States)

Ma, Ying; Rajkumar, Mani; Moreno, António; Zhang, Chang; Freitas, Helena

2017-10-01

This study evaluates the potential of serpentine endophytic bacterium to foster phytoremediation efficiency of Trifolium arvense grown on multi-metal (Cu, Zn and Ni) contaminated soils under drought stress. A drought resistant endophytic bacterial strain ASS1 isolated from the leaves of Alyssum serpyllifolium grown in serpentine soils was identified as Pseudomonas azotoformans based on biochemical tests and partial 16S rRNA gene sequencing. P. azotoformans ASS1 possessed abiotic stress resistance (heavy metals, drought, salinity, antibiotics and extreme temperature) and plant growth promoting (PGP) properties (phosphate solubilization, nitrogen fixation, production of 1-aminocyclopropane-1-carboxylate deaminase, siderophore and ammonia). Inoculation of T. arvense with ASS1 considerably increased the plant biomass and leaf relative water content in both roll towel assay and pot experiments in the absence and presence of drought stress (DS). In the pot experiments, ASS1 greatly enhanced chlorophyll content, catalase, peroxidase, superoxide dismutase activities, and proline content (only in the absence of drought) in plant leaves, whereas they decreased the concentrations of malondialdehyde. Irrespective of water stress, ASS1 significantly improved accumulation, total removal, bio-concentration factor and biological accumulation coefficient of metals (Cu, Zn and Ni), while decreased translocation factors of Cu. The effective colonization and survival in the rhizosphere and tissue interior assured improved plant growth and successful metal phytoremediation under DS. These results demonstrate the potential of serpentine endophytic bacterium ASS1 for protecting plants against abiotic stresses and helping plants to thrive in semiarid ecosystems and accelerate phytoremediation process in metal polluted soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Temporal dynamics in microbial soil communities at anthrax carcass sites.

Science.gov (United States)

Valseth, Karoline; Nesbø, Camilla L; Easterday, W Ryan; Turner, Wendy C; Olsen, Jaran S; Stenseth, Nils Chr; Haverkamp, Thomas H A

2017-09-26

Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetative after ingestion by grazing mammals. After killing the host, B. anthracis cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra (Equus quagga) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored B. anthracis throughout the period using cultivation, qPCR and shotgun metagenomic sequencing. The combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow B. anthracis population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the B. cereus group, despite their high sequence similarity. Vegetative B. anthracis abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g. Frankiales and Rhizobiales species) becomes temporarily dominated by the orders Bacillales and Pseudomonadales, known to contain plant growth-promoting species. Our work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future B. anthracis transmission events at carcass sites may be

Bioaugmentation with endophytic bacterium E6S homologous to Achromobacter piechaudii enhances metal rhizoaccumulation in host Sedum plumbizincicola

Directory of Open Access Journals (Sweden)

Ying eMa

2016-02-01

Full Text Available Application of hyperaccumulator–endophyte symbiotic systems is a potential approach to improve phytoremediation efficiency, since some beneficial endophytic bacteria are able to detoxify heavy metals, alter metal solubility in soil and facilitate plant growth. The objective of this study was to isolate multi-metal resistant and plant beneficial endophytic bacteria and to evaluate their role in enhancing plant growth and metal accumulation/translocation. The metal resistant endophytic bacterial strain E6S was isolated from stems of the Zn/Cd hyperaccumulator plant Sedum plumbizincicola growing in metalliferous mine soils using Dworkin and Foster salts minimal agar medium with 1-aminocyclopropane-1-carboxylate (ACC as the sole nitrogen source, and identified as homologous to Achromobacter piechaudii based on morphological and biochemical characteristics, partial 16S rDNA sequence and phylogenetic analysis. Strain E6S showed high level of resistance to various metals (Cd, Zn and Pb. Besides utilizing ACC, strain E6S exhibited plant beneficial traits, such as solubilization of phosphate and production of indole-3-acetic acid. Inoculation with E6S significantly increased the bioavailability of Cd, Zn and Pb in soil. In addition, bacterial cells bound considerable amounts of metal ions in the following order: Zn ˃ Cd ˃ Pb. Inoculation of E6S significantly stimulated plant biomass, uptake and bioaccumulation of Cd, Zn and Pb. However, E6S greatly reduced the root to shoot translocation of Cd and Zn, indicating that bacterial inoculation assisted the host plant to uptake and store heavy metals in its root system. Inoculation with the endophytic bacterium E6S homologous to A. piechaudii can improve phytostabilization of metalliferous soils due to its effective ability to enhance in situ metal rhizoaccumulation in plants.

Soil eukaryotic microorganism succession as affected by continuous cropping of peanut--pathogenic and beneficial fungi were selected.

Directory of Open Access Journals (Sweden)

Mingna Chen

Full Text Available Peanut is an important oil crop worldwide and shows considerable adaptability but growth and yield are negatively affected by continuous cropping. Soil micro-organisms are efficient bio-indicators of soil quality and plant health and are critical to the sustainability of soil-based ecosystem function and to successful plant growth. In this study, 18S rRNA gene clone library analyses were employed to study the succession progress of soil eukaryotic micro-organisms under continuous peanut cultivation. Eight libraries were constructed for peanut over three continuous cropping cycles and its representative growth stages. Cluster analyses indicated that soil micro-eukaryotic assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. Six eukaryotic groups were found and fungi predominated in all libraries. The fungal populations showed significant dynamic change and overall diversity increased over time under continuous peanut cropping. The abundance and/or diversity of clones affiliated with Eurotiales, Hypocreales, Glomerales, Orbiliales, Mucorales and Tremellales showed an increasing trend with continuous cropping but clones affiliated with Agaricales, Cantharellales, Pezizales and Pyxidiophorales decreased in abundance and/or diversity over time. The current data, along with data from previous studies, demonstrated that the soil microbial community was affected by continuous cropping, in particular, the pathogenic and beneficial fungi that were positively selected over time, which is commonplace in agro-ecosystems. The trend towards an increase in fungal pathogens and simplification of the beneficial fungal community could be important factors contributing to the decline in peanut growth and yield over many years of continuous cropping.

Exo- and surface proteomes of the probiotic bacterium Lactobacillus acidophilus NCFM

DEFF Research Database (Denmark)

Celebioglu, Hasan Ufuk; Svensson, Birte

2017-01-01

Lactobacillus acidophilus NCFM is a well-known probiotic bacterium extensively studied for its beneficial health effects. Exoproteome (proteins exported into culture medium) and surface proteome (proteins attached to S-layer) of this probiotic were identified by using 2DE followed by MALDI TOF MS...

Toxicity evaluation of textile effluents and role of native soil bacterium in biodegradation of a textile dye.

Science.gov (United States)

Khan, Sana; Malik, Abdul

2018-02-01

Water pollution caused by the discharge of hazardous textile effluents is a serious environmental problem worldwide. In order to assess the pollution level of the textile effluents, various physico-chemical parameters were analyzed in the textile wastewater and agricultural soil irrigated with the wastewater (contaminated soil) using atomic absorption spectrophotometer and gas chromatography-mass spectrometry (GC-MS) analysis that demonstrated the presence of several toxic heavy metals (Ni, Cu, Cr, Pb, Cd, and Zn) and a large number of organic compounds. Further, in order to get a comprehensive idea about the toxicity exerted by the textile effluent, mung bean seed germination test was performed that indicated the reduction in percent seed germination and radicle-plumule growth. The culturable microbial populations were also enumerated and found to be significantly lower in the wastewater and contaminated soil than the ground water irrigated soil, thus indicating the biotic homogenization of indigenous microflora. Therefore, the study was aimed to develop a cost effective and ecofriendly method of textile waste treatment using native soil bacterium, identified as Arthrobacter soli BS5 by 16S rDNA sequencing that showed remarkable ability to degrade a textile dye reactive black 5 with maximum degradation of 98% at 37 °C and pH in the range of 5-9 after 120 h of incubation.

Effects of Some Beneficial Bacteria in Casing Soil on Growth and Yield of Cultivated Mushroom Agaricus bisporus

Directory of Open Access Journals (Sweden)

Mehmet Çetin

2016-03-01

Full Text Available This research was carried out to determine the interaction between some bacteria naturally existing in casing soil and Agaricus bisporus (Sylvan Hauser A15 hypha in laboratory (in vitro and cultivation (in vivo conditions, and to confirm its effects on mushroom yield. Totally 32 bacteria (3 Gram (+ and 29 Fluorescent Pseudomonads was isolated from casing soil and healthy sporophores. As a result of in vitro experiment carried out to determine the effects of bacteria on mycelium growth of A. bisporus, 24 bacterial isolates were found more effective at the rate of 2 to 115% than control treatment. To determine the effects of bacterium, chosen at the end of in vitro experiments, on mushroom yield in cultivation conditions, three experiments were established in March, May and July in 2008. At the end of experiments, bacterial isolates provided 8 – 40 % increase in total yield. Population density and change in population number related to time was observed during growing period, after the inoculation of bacterial isolates into casing soil. According to the results, Pseudomonas fluorescens (T 4/2 and Ş 8, P.putida (Ş 2/1 and Ş 10 and Bacillus mycoides (T 7/2 bacterial isolates were colonized successfully both in casing soil and sporophores.

State of the Science Review: Potential for Beneficial Use of Waste By-Products for In-situ Remediation of Metal-Contaminated Soil and Sediment

Science.gov (United States)

Metal and metalloid contamination of soil and sediment is a widespread problem both in urban and rural areas throughout the United States (U.S. EPA, 2014). Beneficial use of waste by-products as amendments to remediate metal-contaminated soils and sediments can provide major eco...

Interactions between Pteris vittata L. genotypes and a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium (Alcaligenes sp.) in arsenic uptake and PAH-dissipation.

Science.gov (United States)

Sun, Lu; Zhu, Ganghui; Liao, Xiaoyong; Yan, Xiulan

2017-11-01

The effects of two Pteris vittata L. accessions and a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium (Alcaligenes sp.) on arsenic (As) uptake and phenanthrene dissipation were studied. The Alcaligenes sp. survived in the rhizosphere and improved soil As bioavailability with co-exposure. However, bacterial inoculation altered Pteris vittata L. stress tolerance, and substantially affected the As distribution in the rhizosphere of the two P. vittata accessions. Bacterial inoculation was beneficial to protect the Guangxi accession against the toxic effects, and significantly increased plant As and phenanthrene removal ratios by 27.8% and 2.89%, respectively. In contrast, As removal was reduced by 29.8% in the Hunan accession, when compared with corresponding non-inoculated treatments. We conclude that plant genotype selection is critically important for successful microorganism-assisted phytoremediation of soil co-contaminated with As and PAHs, and appropriate genotype selection may enhance remediation efficiency. Copyright © 2017 Elsevier Ltd. All rights reserved.

Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5

Science.gov (United States)

Idogawa, Nao; Amamoto, Ryuta; Murata, Kousaku; Kawai, Shigeyuki

2014-01-01

Gluconacetobacter diazotrophicus is a gram-negative and endophytic nitrogen-fixing bacterium that has several beneficial effects in host plants; thus, utilization of this bacterium as a biofertilizer in agriculture may be possible. G. diazotrophicus synthesizes levan, a D-fructofuranosyl polymer with β-(2→6) linkages, as an exopolysaccharide and the synthesized levan improves the stress tolerance of the bacterium. In this study, we found that phosphate enhances levan production by G. diazotrophicus Pal5, a wild type strain that showed a stronger mucous phenotype on solid medium containing 28 mM phosphate than on solid medium containing 7 mM phosphate. A G. diazotrophicus Pal5 levansucrase disruptant showed only a weak mucous phenotype regardless of the phosphate concentration, indicating that the mucous phenotype observed on 28 mM phosphate medium was caused by levan. To our knowledge, this is the first report of the effect of a high concentration of phosphate on exopolysaccharide production. PMID:24717418

Complete genome of Martelella sp. AD-3, a moderately halophilic polycyclic aromatic hydrocarbons-degrading bacterium.

Science.gov (United States)

Cui, Changzheng; Li, Zhijie; Qian, Jiangchao; Shi, Jie; Huang, Ling; Tang, Hongzhi; Chen, Xin; Lin, Kuangfei; Xu, Ping; Liu, Yongdi

2016-05-10

Martelella sp. strain AD-3, a moderate halophilic bacterium, was isolated from a petroleum-contaminated soil with high salinity in China. Here, we report the complete genome of strain AD-3, which contains one circular chromosome and two circular plasmids. An array of genes related to metabolism of polycyclic aromatic hydrocarbons and halophilic mechanism in this bacterium was identified by the whole genome analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Biochemical and molecular characterization of potential phosphate-solubilizing bacteria in acid sulfate soils and their beneficial effects on rice growth.

Directory of Open Access Journals (Sweden)

Qurban Ali Panhwar

Full Text Available A study was conducted to determine the total microbial population, the occurrence of growth promoting bacteria and their beneficial traits in acid sulfate soils. The mechanisms by which the bacteria enhance rice seedlings grown under high Al and low pH stress were investigated. Soils and rice root samples were randomly collected from four sites in the study area (Kelantan, Malaysia. The topsoil pH and exchangeable Al ranged from 3.3 to 4.7 and 1.24 to 4.25 cmol(c kg(-1, respectively, which are considered unsuitable for rice production. Total bacterial and actinomycetes population in the acidic soils were found to be higher than fungal populations. A total of 21 phosphate-solubilizing bacteria (PSB including 19 N2-fixing strains were isolated from the acid sulfate soil. Using 16S rRNA gene sequence analysis, three potential PSB strains based on their beneficial characteristics were identified (Burkholderia thailandensis, Sphingomonas pituitosa and Burkholderia seminalis. The isolated strains were capable of producing indoleacetic acid (IAA and organic acids that were able to reduce Al availability via a chelation process. These PSB isolates solubilized P (43.65% existing in the growth media within 72 hours of incubation. Seedling of rice variety, MR 219, grown at pH 4, and with different concentrations of Al (0, 50 and 100 µM was inoculated with these PSB strains. Results showed that the bacteria increased the pH with a concomitant reduction in Al concentration, which translated into better rice growth. The improved root volume and seedling dry weight of the inoculated plants indicated the potential of these isolates to be used in a bio-fertilizer formulation for rice cultivation on acid sulfate soils.

Jeotgalibacillus soli sp. nov., a Gram-stain-positive bacterium isolated from soil.

Science.gov (United States)

Cunha, Sofia; Tiago, Igor; Paiva, Gabriel; Nobre, Fernanda; da Costa, Milton S; Veríssimo, António

2012-03-01

A Gram-staining-positive, motile, rod-shaped, spore-forming bacterium, designated P9(T), was isolated from soil in Portugal. This organism was aerobic and catalase- and oxidase-positive. It had an optimum growth temperature of about 35 °C and an optimum growth pH of about 8.0-8.5, and grew in medium with 0-9% (w/v) NaCl. The cell-wall peptidoglycan was of the A1α type, with L-lysine as the diagnostic diamino acid. The major respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C(15:0) (45.4%), iso-C(15:0) (22.0%) and anteiso-C(17:0) (11.2%). The genomic DNA G+C content was about 39.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain P9(T) was most closely related to Jeotgalibacillus campisalis DSM 18983(T) (96.8%) and Jeotgalibacillus marinus DSM 1297(T) (96.5%). These two recognized species formed a coherent cluster with strain P9(T) that was supported by a bootstrap value of 99%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, strain P9(T) (=DSM 23228(T)=LMG 25523(T)) represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus soli sp. nov. is proposed.

Antioxidants keep the potentially probiotic but highly oxygen-sensitive human gut bacterium Faecalibacterium prausnitzii alive at ambient air

NARCIS (Netherlands)

Khan, M. Tanweer; van Dijl, Jan Maarten; Harmsen, Hermie J M

2014-01-01

The beneficial human gut microbe Faecalibacterium prausnitzii is a 'probiotic of the future' since it produces high amounts of butyrate and anti-inflammatory compounds. However, this bacterium is highly oxygen-senstive, making it notoriously difficult to cultivate and preserve. This has so far

Characteristics of cesium accumulation in the filamentous soil bacterium Streptomyces sp. K202

International Nuclear Information System (INIS)

Kuwahara, Chikako; Fukumoto, Atsushi; Nishina, Masami; Sugiyama, Hideo; Anzai, Yojiro; Kato, Fumio

2011-01-01

A filamentous soil bacterium, strain K202, was isolated from soil where an edible mushroom (Boletopsis leucomelas) was growing and identified as belonging to the genus Streptomyces on the basis of its morphological characteristics and the presence of LL-2, 6-diaminopimelic acid. We studied the existence states of Cs and its migration from extracellular to intracellular fluid in the mycelia of Streptomyces sp. K202. The results indicated that Cs accumulated in the cells through at least 2 steps: in the first step, Cs + was immediately and non-specifically adsorbed on the negatively charged cell surface, and in the second step, this adsorbed Cs + was taken up into the cytoplasm, and a part of the Cs entering the cytoplasm was taken up by an energy-dependent transport system(s). Further, we confirmed that a part of the Cs + was taken up into the mycelia competitively with K + , because K + uptake into the intact mycelia of the strain was significantly inhibited by the presence of Cs + in the culture media. This suggested that part of the Cs is transported by the potassium transport system. Moreover, 133 Cs-NMR spectra and SEM-EDX spectra of the mycelia that accumulated Cs showed the presence of at least 2 intracellular Cs states: Cs + trapped by intercellular materials such as polyphosphate and Cs + present in a cytoplasmic pool. - Research highlights: → Cs was taken up into the cells of Streptomyces sp. K202 via 2 steps. → The existence states of Cs accumulated in strain K202 were at least 2 types. → The localized Cs in the cells would be trapped by granules such as polyphosphate. → The localized Cs in the cells might involve in Cs detoxification of strain K202.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Energy Technology Data Exchange (ETDEWEB)

Xie, Gary [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Phosphorus uptake of an arbuscular mycorrhizal fungus is not effected by the biocontrol bacterium ¤Burkholderia cepacia¤

DEFF Research Database (Denmark)

Ravnskov, S.; Larsen, J.; Jakobsen, I.

2002-01-01

The biocontrol bacterium Burkholderia cepacia is known to suppress a broad range of root pathogenic fungi, while its impact on other beneficial non-target organisms such as arbuscular mycorrhizal (AM) fungi is unknown. Direct interactions between five B. cepacia strains and the AM fungus, Glomus ...

Toxicity of fungal-generated silver nanoparticles to soil-inhabiting Pseudomonas putida KT2440, a rhizospheric bacterium responsible for plant protection and bioremediation

Energy Technology Data Exchange (ETDEWEB)

Gupta, Indarchand R. [Nanobiotechnology Laboratory, Department of Biotechnology, S.G.B. Amravati University, Amravati 444602, Maharashtra (India); Department of Biotechnology, Institute of Science, Nipat Niranjan Nagar, Caves Road, Aurangabad 431004, Maharashtra (India); Anderson, Anne J. [Department of Biology, Utah State University, Logan, Utah 84321 (United States); Rai, Mahendra, E-mail: mahendrarai@sgbau.ac.in [Nanobiotechnology Laboratory, Department of Biotechnology, S.G.B. Amravati University, Amravati 444602, Maharashtra (India); Laboratório de Química Biológica, Instituto de Química, UNICAMP, Cidade Universitária “Zefferino Vaz” Barão Geraldo, CEP 13083-970, Caixa Postal 6150, Campinas, SP (Brazil)

2015-04-09

Highlights: • This study incorporates the mycosynthesis of AgNPs and their characterisation by various methods. • A first attempt demonstrating the toxicity assessment of AgNPs on beneficial soil microbe. • Use of biosensor in Pseudomonas putida KT2440, gave accurate antimicrobial results. - Abstract: Silver nanoparticles have attracted considerable attention due to their beneficial properties. But toxicity issues associated with them are also rising. The reports in the past suggested health hazards of silver nanoparticles at the cellular, molecular, or whole organismal level in eukaryotes. Whereas, there is also need to examine the exposure effects of silver nanoparticle to the microbes, which are beneficial to humans as well as environment. The available literature suggests the harmful effects of physically and chemically synthesised silver nanoparticles. The toxicity of biogenically synthesized nanoparticles has been less studied than physically and chemically synthesised nanoparticles. Hence, there is a greater need to study the toxic effects of biologically synthesised silver nanoparticles in general and mycosynthesized nanoparticles in particular. In the present study, attempts have been made to assess the risk associated with the exposure of mycosynthesized silver nanoparticles on a beneficial soil microbe Pseudomonas putida. KT2440. The study demonstrates mycosynthesis of silver nanoparticles and their characterisation by UV–vis spectrophotometry, FTIR, X-ray diffraction, nanosight LM20 – a particle size distribution analyzer and TEM. Silver nanoparticles obtained herein were found to exert the hazardous effect at the concentration of 0.4 μg/ml, which warrants further detailed investigations concerning toxicity.

Toxicity of fungal-generated silver nanoparticles to soil-inhabiting Pseudomonas putida KT2440, a rhizospheric bacterium responsible for plant protection and bioremediation

International Nuclear Information System (INIS)

Gupta, Indarchand R.; Anderson, Anne J.; Rai, Mahendra

2015-01-01

Highlights: • This study incorporates the mycosynthesis of AgNPs and their characterisation by various methods. • A first attempt demonstrating the toxicity assessment of AgNPs on beneficial soil microbe. • Use of biosensor in Pseudomonas putida KT2440, gave accurate antimicrobial results. - Abstract: Silver nanoparticles have attracted considerable attention due to their beneficial properties. But toxicity issues associated with them are also rising. The reports in the past suggested health hazards of silver nanoparticles at the cellular, molecular, or whole organismal level in eukaryotes. Whereas, there is also need to examine the exposure effects of silver nanoparticle to the microbes, which are beneficial to humans as well as environment. The available literature suggests the harmful effects of physically and chemically synthesised silver nanoparticles. The toxicity of biogenically synthesized nanoparticles has been less studied than physically and chemically synthesised nanoparticles. Hence, there is a greater need to study the toxic effects of biologically synthesised silver nanoparticles in general and mycosynthesized nanoparticles in particular. In the present study, attempts have been made to assess the risk associated with the exposure of mycosynthesized silver nanoparticles on a beneficial soil microbe Pseudomonas putida. KT2440. The study demonstrates mycosynthesis of silver nanoparticles and their characterisation by UV–vis spectrophotometry, FTIR, X-ray diffraction, nanosight LM20 – a particle size distribution analyzer and TEM. Silver nanoparticles obtained herein were found to exert the hazardous effect at the concentration of 0.4 μg/ml, which warrants further detailed investigations concerning toxicity

Effect of Azospirillum brasilense inoculation on urease activity in soil and gamma-sterilized soil

International Nuclear Information System (INIS)

Perotti, E.B.R.; Pidello, A.

1999-01-01

Azospirillum spp. is considered a PGPR (plant growth promoting rhyzobacteria) bacterium, besides this interest, there is little information about its effects on other functional microbial groups or on soil enzymes. In this paper, the impact that Azospirillum brasilense 7001 inoculation has on urease activity expression in a Typic Argiudoll was studied. Evolution of urease activity of soil and of gamma irradiation (25 KGy) sterilized soil, and the inoculated strain survival were tested. The relation between soil urease activity and soil NH 4 +-N was also determined. In γ-sterilized soil, urease activity of inoculated soil increased with time, showing significant differences with regard to the control soil without inoculum at day 15. In non-sterile soil, urease activity decreased during the studied period in all treatments; in inoculated soil, it showed higher or lower values than the control depending on sampling time. Azospirillum survival was important and different according to soil condition conditions. The negative relation between NH 4 +-N concentration and soil urease activity (r 2 = 0.62) was observed in inoculated soil. The role of the addition of autoclaved inoculum in the urease activity expression is discussed. The research proves that in both studied situations Azospirillum modified soil urease activity, and that the competition with native microorganisms and soil NH 4 +-N may affect this bacterium capacity. (author)

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Energy Technology Data Exchange (ETDEWEB)

Rhee, Mun Su [University of Florida, Gainesville; Moritz, Brelan E. [University of Florida, Gainesville; Xie, Gary [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Patel, Milind [University of Florida, Gainesville; Ou, Mark [University of Florida, Gainesville; Harbrucker, Roberta [University of Florida, Gainesville; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Science.gov (United States)

Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil.

Science.gov (United States)

Li, Qin-Fen; Sun, Li-Na; Kwon, Soon-Wo; Chen, Qing; He, Jian; Li, Shun-Peng; Zhang, Jun

2014-06-01

A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8(T), was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97% sequence similarity to strains of the environmental species Xenophilus azovorans, Xenophilus aerolatus, Simplicispira metamorpha, Variovorax soli, and Xylophilus ampelinus. However, the phylogenetic tree indicated that strain YW8(T) formed a separate clade from Xenophilus azovorans. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain YW8(T) and its closest phylogenetic neighbours were below 24.2-35.5%, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8(T) were C(16 : 0), C(17 : 0) cyclo, C(18 : 1)ω7c, and summed feature 3(C(16 : 1)ω6c and/or C(16 : 1)ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA-DNA hybridization and chemotaxonomic data, strain YW8(T) is considered to represent a novel species of the genus Xenophilus, for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8(T) ( = CCTCC AB2012103(T) = KACC 16853(T)). © 2014 IUMS.

Volatiles produced by the mycophagous soil bacterium Collimonas

NARCIS (Netherlands)

Garbeva, P.; Hordijk, C.; Gerards, S.; Boer, de W.

2014-01-01

It is increasingly recognized that volatile organic compounds play an import role during interactions between soil microorganisms. Here, we examined the possible involvement of volatiles in the interaction of Collimonas bacteria with soil fungi. The genus Collimonas is known for its ability to grow

Plant-associated fluorescent Pseudomonas from red lateritic soil: Beneficial characteristics and their impact on lettuce growth.

Science.gov (United States)

Maroniche, Guillermo A; Rubio, Esteban J; Consiglio, Adrián; Perticari, Alejandro

2016-11-25

Fluorescent Pseudomonas are ubiquitous soil bacteria that usually establish mutualistic associations with plants, promoting their growth and health by several mechanisms. This makes them interesting candidates for the development of crop bio-inoculants. In this work, we isolated phosphate-solubilizing fluorescent Pseudomonas from the rhizosphere and inner tissues of different plant species growing in red soil from Misiones, Argentina. Seven isolates displaying strong phosphate solubilization were selected for further studies. Molecular identification by rpoD genotyping indicated that they belong to different species within the P. fluorescens and P. putida phylogenetic groups. Screening for in vitro traits such as phosphate solubilization, growth regulators synthesis or degradation, motility and antagonism against phytopathogens or other bacteria, revealed a unique profile of characteristics for each strain. Their plant growth-promoting potential was assayed using lettuce as a model for inoculation under controlled and greenhouse conditions. Five of the strains increased the growth of lettuce plants. Overall, the strongest lettuce growth promoter under both conditions was strain ZME4, isolated from inner tissues of maize. No clear association between lettuce growth promotion and in vitro beneficial traits was detected. In conclusion, several phosphate solubilizing pseudomonads from red soil were isolated that display a rich array of plant growth promotion traits, thus showing a potential for the development of new inoculants.

Selectivity lists of pesticides to beneficial arthropods for IPM programs in carrot--first results.

Science.gov (United States)

Hautier, L; Jansen, J-P; Mabon, N; Schiffers, B

2005-01-01

In order to improve IPM programs in carrot, 7 fungicides, 12 herbicides and 9 insecticides commonly used in Belgium were tested for their toxicity towards five beneficial arthropods representative of most important natural enemies encountered in carrot: parasitic wasps - Aphidius rhopalosiphi (De Stefani-Perez) (Hym., Aphidiidae), ladybirds - Adalia bipunctata (L.) (Col., Coccinellidae), hoverfly - Episyrphus balteatus (Dipt.. Syrphidae), rove beetle - Aleochara bilineata (Col., Staphylinidae) and carabid beetle - Bembidion lampros (Col., Carabidae). Initialy, all plant protection products were tested on inert substrate glass plates or sand according to the insect. Products with a corrected mortality (CM) or a parasitism reduction (PR) lower than 30% were kept for the constitution of positive list (green list). The other compounds were further tested on plant for A. rhopalosiphi, A. bipunctata, E. balteatus and soil for B. lampros and A. bilineata. With these extended laboratory tests results, products were listed in toxicity class: green category [CM or PR harmless to beneficials except Tebuconazole, which was slightly harmful for A. bipunctata. Herbicides were also harmless for soil beneficials, except Chlorpropham. This product was very toxic on sand towards A. bilineata and must be tested on soil. All soil insecticides tested were very toxic for ground beneficials and considered as non-selective. Their use in IPM is subject to questioning in view of negative impacts on beneficials. Among foliar insecticides, Dimethoate and Deltamethrin are not recommended for IPM because their high toxicity for all beneficials. The other foliar insecticides were more selective; any of them were harmless for all species tested.

No apparent costs for facultative antibiotic production by the soil bacterium Pseudomonas fluorescens Pf0-1.

Science.gov (United States)

Garbeva, Paolina; Tyc, Olaf; Remus-Emsermann, Mitja N P; van der Wal, Annemieke; Vos, Michiel; Silby, Mark; de Boer, Wietse

2011-01-01

Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the co-existence of antibiotic-producing and non-antibiotic producing strains. However, so far studies quantifying the costs of antibiotic production by bacteria are scarce. The current study reports on possible costs, for antibiotic production by Pseudomonas fluorescens Pf0-1, a soil bacterium that is induced to produce a broad-spectrum antibiotic when it is confronted with non-related bacterial competitors or supernatants of their cultures. We measured the possible cost of antibiotic production for Pseudomonas fluorescens Pf0-1 by monitoring changes in growth rate with and without induction of antibiotic production by supernatant of a bacterial competitor, namely Pedobacter sp.. Experiments were performed in liquid as well as on semi-solid media under nutrient-limited conditions that are expected to most clearly reveal fitness costs. Our results did not reveal any significant costs for production of antibiotics by Pseudomonas fluorescens Pf0-1. Comparison of growth rates of the antibiotic-producing wild-type cells with those of non-antibiotic producing mutants did not reveal costs of antibiotic production either. Based on our findings we propose that the facultative production of antibiotics might not be selected to mitigate metabolic costs, but instead might be advantageous because it limits the risk of competitors evolving resistance, or even the risk of competitors feeding on the compounds produced.

Bacillus tamaricis sp. nov., an alkaliphilic bacterium isolated from a Tamarix cone soil.

Science.gov (United States)

Zhang, Yong-Guang; Zhou, Xing-Kui; Guo, Jian-Wei; Xiao, Min; Wang, Hong-Fei; Wang, Yun; Bobodzhanova, Khursheda; Li, Wen-Jun

2018-02-01

A Gram-stain-positive, alkaliphilic bacterium, designated EGI 80668 T , was isolated from a Tamarix cone soil in Xinjiang, north-west China. Cells were facultatively anaerobic, terminal endospore-forming and motile by means of peritrichous flagella. Colonies were yellowish and the cells showed oxidase-negative and catalase-positive reactions. Strain EGI 80668 T grew at pH 8.0-10.0 and with 0-10 % (w/v) NaCl (optimally at pH 9.0 and with 1-2 % NaCl) on marine agar 2216. The predominant menaquinone was MK-7. The major fatty acids were anteiso-C17 : 0 and anteiso-C15 : 0. The cellular polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown aminophospholipid. The G+C content of the genomic DNA was 38.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80668 T was affiliated to the genus Bacillus. The highest 16S rRNA gene sequence similarity between strain EGI 80668 T and a member of the genus Bacillus was 96.83 % with Bacillus cellulosilyticus JCM 9156 T . A polyphasic taxonomic study based on morphological, physiological, biochemical and phylogenetic data indicated that strain EGI 80668 T represents a novel species of the genus Bacillus, for which the name Bacillus tamaricis sp. nov. (type strain EGI 80668 T =KCTC 33703 T =CGMCC 1.15917 T ) is proposed.

Conservation Farming and Changing Climate: More Beneficial than Conventional Methods for Degraded Ugandan Soils

Directory of Open Access Journals (Sweden)

Drake N. Mubiru

2017-06-01

Full Text Available The extent of land affected by degradation in Uganda ranges from 20% in relatively flat and vegetation-covered areas to 90% in the eastern and southwestern highlands. Land degradation has adversely affected smallholder agro-ecosystems including direct damage and loss of critical ecosystem services such as agricultural land/soil and biodiversity. This study evaluated the extent of bare grounds in Nakasongola, one of the districts in the Cattle Corridor of Uganda and the yield responses of maize (Zea mays and common bean (Phaseolus vulgaris L. to different tillage methods in the district. Bare ground was determined by a supervised multi-band satellite image classification using the Maximum Likelihood Classifier (MLC. Field trials on maize and bean grain yield responses to tillage practices used a randomized complete block design with three replications, evaluating conventional farmer practice (CFP; permanent planting basins (PPB; and rip lines, with or without fertilizer in maize and bean rotations. Bare ground coverage in the Nakasongola District was 187 km2 (11% of the 1741 km2 of arable land due to extreme cases of soil compaction. All practices, whether conventional or the newly introduced conservation farming practices in combination with fertilizer increased bean and maize grain yields, albeit with minimal statistical significance in some cases. The newly introduced conservation farming tillage practices increased the bean grain yield relative to conventional practices by 41% in PPBs and 43% in rip lines. In maize, the newly introduced conservation farming tillage practices increased the grain yield by 78% on average, relative to conventional practices. Apparently, conservation farming tillage methods proved beneficial relative to conventional methods on degraded soils, with the short-term benefit of increasing land productivity leading to better harvests and food security.

Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens

Energy Technology Data Exchange (ETDEWEB)

Köberl, Martina; White, Richard A.; Erschen, Sabine; El-Arabi, Tarek F.; Jansson, Janet K.; Berg, Gabriele

2015-08-06

Streptomyces sp. strain Wb2n-11, isolated from native desert soil, exhibited broad-spectrum antagonism against plant pathogenic fungi, bacteria and nematodes. The 8.2 Mb draft genome reveals genes putatively responsible for its promising biocontrol activity and genes which enable the soil bacterium to directly interact beneficially with plants.

Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9

Science.gov (United States)

Liu, Jin-liang; Hu, Xiao-min

2013-01-01

Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus. PMID:23618713

No apparent costs for facultative antibiotic production by the soil bacterium Pseudomonas fluorescens Pf0-1.

Directory of Open Access Journals (Sweden)

Paolina Garbeva

Full Text Available BACKGROUND: Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the co-existence of antibiotic-producing and non-antibiotic producing strains. However, so far studies quantifying the costs of antibiotic production by bacteria are scarce. The current study reports on possible costs, for antibiotic production by Pseudomonas fluorescens Pf0-1, a soil bacterium that is induced to produce a broad-spectrum antibiotic when it is confronted with non-related bacterial competitors or supernatants of their cultures. METHODOLOGY AND PRINCIPAL FINDINGS: We measured the possible cost of antibiotic production for Pseudomonas fluorescens Pf0-1 by monitoring changes in growth rate with and without induction of antibiotic production by supernatant of a bacterial competitor, namely Pedobacter sp.. Experiments were performed in liquid as well as on semi-solid media under nutrient-limited conditions that are expected to most clearly reveal fitness costs. Our results did not reveal any significant costs for production of antibiotics by Pseudomonas fluorescens Pf0-1. Comparison of growth rates of the antibiotic-producing wild-type cells with those of non-antibiotic producing mutants did not reveal costs of antibiotic production either. SIGNIFICANCE: Based on our findings we propose that the facultative production of antibiotics might not be selected to mitigate metabolic costs, but instead might be advantageous because it limits the risk of competitors evolving resistance, or even the risk of competitors feeding on the compounds produced.

Frequent beneficial mutations during single-colony serial transfer of Streptococcus pneumoniae.

Directory of Open Access Journals (Sweden)

Kathleen E Stevens

2011-08-01

Full Text Available The appearance of new mutations within a population provides the raw material for evolution. The consistent decline in fitness observed in classical mutation accumulation studies has provided support for the long-held view that deleterious mutations are more common than beneficial mutations. Here we present results of a study using a mutation accumulation design with the bacterium Streptococcus pneumoniae in which the fitness of the derived populations increased. This rise in fitness was associated specifically with adaptation to survival during brief stationary phase periods between single-colony population bottlenecks. To understand better the population dynamics behind this unanticipated adaptation, we developed a maximum likelihood model describing the processes of mutation and stationary-phase selection in the context of frequent population bottlenecks. Using this model, we estimate that the rate of beneficial mutations may be as high as 4.8×10(-4 events per genome for each time interval corresponding to the pneumococcal generation time. This rate is several orders of magnitude higher than earlier estimates of beneficial mutation rates in bacteria but supports recent results obtained through the propagation of small populations of Escherichia coli. Our findings indicate that beneficial mutations may be relatively frequent in bacteria and suggest that in S. pneumoniae, which develops natural competence for transformation, a steady supply of such mutations may be available for sampling by recombination.

Perturbation of an arctic soil microbial community by metal nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Kumar, Niraj [Department of Biology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada); Shah, Vishal [Department of Biology, Dowling College, Oakdale, NY 11769 (United States); Walker, Virginia K., E-mail: walkervk@queensu.ca [Department of Biology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada); Department of Biology, School of Environmental Studies and Department of Microbiology and Immunology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada)

2011-06-15

Highlights: {yields} Silver, copper and silica nanoparticles had an impact on arctic soil {yields} A microbial community toxicity indicator was developed {yields} Community surveys using pyrosequencing confirmed a shift in bacterial biodiversity {yields} Troublingly, silver nanoparticles were highly toxic to a plant beneficial bacterium - Abstract: Technological advances allowing routine nanoparticle (NP) manufacture have enabled their use in electronic equipment, foods, clothing and medical devices. Although some NPs have antibacterial activity, little is known about their environmental impact and there is no information on the influence of NPs on soil in the possibly vulnerable ecosystems of polar regions. The potential toxicity of 0.066% silver, copper or silica NPs on a high latitude (>78{sup o}N) soil was determined using community level physiological profiles (CLPP), fatty acid methyl ester (FAME) assays and DNA analysis, including sequencing and denaturing gradient gel electrophoresis (DGGE). The results of these different investigations were amalgamated in order to develop a community toxicity indicator, which revealed that of the three NPs examined, silver NPs could be classified as highly toxic to these arctic consortia. Subsequent culture-based studies confirmed that one of the community-identified plant-associating bacteria, Bradyrhizobium canariense, appeared to have a marked sensitivity to silver NPs. Thus, NP contamination of arctic soils particularly by silver NPs is a concern and procedures for mitigation and remediation of such pollution should be a priority for investigation.

Perturbation of an arctic soil microbial community by metal nanoparticles

International Nuclear Information System (INIS)

Kumar, Niraj; Shah, Vishal; Walker, Virginia K.

2011-01-01

Highlights: → Silver, copper and silica nanoparticles had an impact on arctic soil → A microbial community toxicity indicator was developed → Community surveys using pyrosequencing confirmed a shift in bacterial biodiversity → Troublingly, silver nanoparticles were highly toxic to a plant beneficial bacterium - Abstract: Technological advances allowing routine nanoparticle (NP) manufacture have enabled their use in electronic equipment, foods, clothing and medical devices. Although some NPs have antibacterial activity, little is known about their environmental impact and there is no information on the influence of NPs on soil in the possibly vulnerable ecosystems of polar regions. The potential toxicity of 0.066% silver, copper or silica NPs on a high latitude (>78 o N) soil was determined using community level physiological profiles (CLPP), fatty acid methyl ester (FAME) assays and DNA analysis, including sequencing and denaturing gradient gel electrophoresis (DGGE). The results of these different investigations were amalgamated in order to develop a community toxicity indicator, which revealed that of the three NPs examined, silver NPs could be classified as highly toxic to these arctic consortia. Subsequent culture-based studies confirmed that one of the community-identified plant-associating bacteria, Bradyrhizobium canariense, appeared to have a marked sensitivity to silver NPs. Thus, NP contamination of arctic soils particularly by silver NPs is a concern and procedures for mitigation and remediation of such pollution should be a priority for investigation.

Multiple approaches towards decolorization and reuse of a textile dye (VB-B) by a marine bacterium Shewanella decolorationis

Digital Repository Service at National Institute of Oceanography (India)

SatheeshBabu, S.; Mohandass, C.; VijayRaj, A.S.; Rajasabapathy, R.; Dhale, M.A.

stream_size 41279 stream_content_type text/plain stream_name Water_Air_Soil_Pollut_224_1500a.pdf.txt stream_source_info Water_Air_Soil_Pollut_224_1500a.pdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8...     1    Author version: Water Air Soil Pollut., vol.224(4); 2013; 1500 Multiple approaches towards decolorization and reuse of a textile dye (VB-B) by a marine bacterium Shewanella decolorationis S. Satheesh Babu, C.Mohandass*, A.S.Vijay Raj, R...

Plant-beneficial elements status assessment in soil-plant system in the vicinity of a chemical industry complex: shedding light on forage grass safety issues.

Science.gov (United States)

Anjum, Naser A; Duarte, Armando C; Pereira, Eduarda; Ahmad, Iqbal

2015-02-01

Human health is closely linked with soils via plants, grazers, or plant-based products. This study estimated plant-beneficial elements (macronutrients: K, P; secondary macronutrients: Ca, Mg; micronutrients: Mo, Mn, Na, Ni, Se) in both soils and shoots of two forage grass species (Eriophorum angustifolium and Lolium perenne) prevalent in the vicinity of a chemical industry complex (Estarreja, Portugal). Both soils and plants from the chemical industrial areas exhibited differential concentrations of the studied elements. In soils, the role of contamination was evidenced as insignificant in context of its impact on all the tested macro and secondary macronutrients except P, and micronutrients such as Mo and Ni. In forage grass plant shoots, the role of contamination was evidenced as insignificant in relation to its impact on all the tested macro and secondary macronutrients except K. Between the two forage grass plants, high Se-harboring L. perenne cannot be recommended for its use as animal feed.

Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila

Directory of Open Access Journals (Sweden)

Patrice D. Cani

2017-09-01

Full Text Available Metabolic disorders associated with obesity and cardiometabolic disorders are worldwide epidemic. Among the different environmental factors, the gut microbiota is now considered as a key player interfering with energy metabolism and host susceptibility to several non-communicable diseases. Among the next-generation beneficial microbes that have been identified, Akkermansia muciniphila is a promising candidate. Indeed, A. muciniphila is inversely associated with obesity, diabetes, cardiometabolic diseases and low-grade inflammation. Besides the numerous correlations observed, a large body of evidence has demonstrated the causal beneficial impact of this bacterium in a variety of preclinical models. Translating these exciting observations to human would be the next logic step and it now appears that several obstacles that would prevent the use of A. muciniphila administration in humans have been overcome. Moreover, several lines of evidence indicate that pasteurization of A. muciniphila not only increases its stability but more importantly increases its efficacy. This strongly positions A. muciniphila in the forefront of next-generation candidates for developing novel food or pharma supplements with beneficial effects. Finally, a specific protein present on the outer membrane of A. muciniphila, termed Amuc_1100, could be strong candidate for future drug development. In conclusion, as plants and its related knowledge, known as pharmacognosy, have been the source for designing drugs over the last century, we propose that microbes and microbiomegnosy, or knowledge of our gut microbiome, can become a novel source of future therapies.

Disease-induced assemblage of a plant-beneficial bacterial consortium

DEFF Research Database (Denmark)

Berendsen, Roeland L.; Vismans, Gilles; Yu, Ke

2018-01-01

Disease suppressive soils typically develop after a disease outbreak due to the subsequent assembly of protective microbiota in the rhizosphere. The role of the plant immune system in the assemblage of a protective rhizosphere microbiome is largely unknown. In this study, we demonstrate...... in a second population of plants growing in the same soil. Together our results indicate that plants can adjust their root microbiome upon pathogen infection and specifically recruit a group of disease resistance-inducing and growth-promoting beneficial microbes, therewith potentially maximizing the chance...

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates.

Science.gov (United States)

Yi, Yanglei; de Jong, Anne; Frenzel, Elrike; Kuipers, Oscar P

2017-01-01

Plant root secreted compounds alter the gene expression of associated microorganisms by acting as signal molecules that either stimulate or repel the interaction with beneficial or harmful species, respectively. However, it is still unclear whether two distinct groups of beneficial bacteria, non-plant-associated (soil) strains and plant-associated (endophytic) strains, respond uniformly or variably to the exposure with root exudates. Therefore, Bacillus mycoides , a potential biocontrol agent and plant growth-promoting bacterium, was isolated from the endosphere of potatoes and from soil of the same geographical region. Confocal fluorescence microscopy of plants inoculated with GFP-tagged B. mycoides strains showed that the endosphere isolate EC18 had a stronger plant colonization ability and competed more successfully for the colonization sites than the soil isolate SB8. To dissect these phenotypic differences, the genomes of the two strains were sequenced and the transcriptome response to potato root exudates was compared. The global transcriptome profiles evidenced that the endophytic isolate responded more pronounced than the soil-derived isolate and a higher number of significant differentially expressed genes were detected. Both isolates responded with the alteration of expression of an overlapping set of genes, which had previously been reported to be involved in plant-microbe interactions; including organic substance metabolism, oxidative reduction, and transmembrane transport. Notably, several genes were specifically upregulated in the endosphere isolate EC18, while being oppositely downregulated in the soil isolate SB8. These genes mainly encoded membrane proteins, transcriptional regulators or were involved in amino acid metabolism and biosynthesis. By contrast, several genes upregulated in the soil isolate SB8 and downregulated in the endosphere isolate EC18 were related to sugar transport, which might coincide with the different nutrient availability

Degradation of thiram in soil

International Nuclear Information System (INIS)

Raghu, K.; Murthy, N.B.K.; Kumarsamy, R.

1975-01-01

Determination of the residual 35 S labelled tetramethylthiuram disulfide showed that the fungicide persisted longer in sterilized than in unsterilized soil, while the chloroform extractable radioactivity decreased, the water extractable radioactivity increased with increase in time. However, in sterilized soil the water extractable radioactivity remained more or less constant. Degradation of the fungicide was further demonstrated by the release of C 35 S 2 from soil treated with labelled thiram. Dimethylamine was found to be one of the degradation products. A bacterium isolated from thiram-enriched soil could degrade the fungicide in shake culture. The degradation pathways of thiram in sterilized and unsterilized soils are discussed. (author)

Application of Sodium Silicate Enhances Cucumber Resistance to Fusarium Wilt and Alters Soil Microbial Communities

Directory of Open Access Journals (Sweden)

Xingang Zhou

2018-05-01

Full Text Available Exogenous silicates can enhance plant resistance to pathogens and change soil microbial communities. However, the relationship between changes in soil microbial communities and enhanced plant resistance remains unclear. Here, effects of exogenous sodium silicate on cucumber (Cucumis sativus L. seedling resistance to Fusarium wilt caused by the soil-borne pathogen Fusarium oxysporum f.sp. cucumerinum Owen (FOC were investigated by drenching soil with 2 mM sodium silicate. Soil bacterial and fungal community abundances and compositions were estimated by real-time PCR and high-throughput amplicon sequencing; then, feedback effects of changes in soil biota on cucumber seedling resistance to FOC were assessed. Moreover, effects of sodium silicate on the growth of FOC and Streptomyces DHV3-2, an antagonistic bacterium to FOC, were investigated both in vitro and in the soil environment. Results showed that exogenous sodium silicate enhanced cucumber seedling growth and resistance to FOC. In bare soil, sodium silicate increased bacterial and fungal community abundances and diversities. In cucumber-cultivated soil, sodium silicate increased bacterial community abundances, but decreased fungal community abundances and diversities. Sodium silicate also changed soil bacterial and fungal communality compositions, and especially, decreased the relative abundances of microbial taxa containing plant pathogens but increased these with plant-beneficial potentials. Moreover, sodium silicate increased the abundance of Streptomyces DHV3-2 in soil. Soil biota from cucumber-cultivated soil treated with sodium silicate decreased cucumber seedling Fusarium wilt disease index, and enhanced cucumber seedling growth and defense-related enzyme activities in roots. Sodium silicate at pH 9.85 inhibited FOC abundance in vitro, but did not affect FOC abundance in soil. Overall, our results suggested that, in cucumber-cultivated soil, sodium silicate increased cucumber seedling

Nano titania aided clustering and adhesion of beneficial bacteria to plant roots to enhance crop growth and stress management

Science.gov (United States)

Palmqvist, N. G. M.; Bejai, S.; Meijer, J.; Seisenbaeva, G. A.; Kessler, V. G.

2015-05-01

A novel use of Titania nanoparticles as agents in the nano interface interaction between a beneficial plant growth promoting bacterium (Bacillus amyloliquefaciens UCMB5113) and oilseed rape plants (Brassica napus) for protection against the fungal pathogen Alternaria brassicae is presented. Two different TiO2 nanoparticle material were produced by the Sol-Gel approach, one using the patented Captigel method and the other one applying TiBALDH precursor. The particles were characterized by transmission electron microscopy, thermogravimetric analysis, X-ray diffraction, dynamic light scattering and nano particle tracking analysis. Scanning electron microscopy showed that the bacterium was living in clusters on the roots and the combined energy-dispersive X-ray spectroscopy analysis revealed that titanium was present in these cluster formations. Confocal laser scanning microscopy further demonstrated an increased bacterial colonization of Arabidopsis thaliana roots and a semi-quantitative microscopic assay confirmed an increased bacterial adhesion to the roots. An increased amount of adhered bacteria was further confirmed by quantitative fluorescence measurements. The degree of infection by the fungus was measured and quantified by real-time-qPCR. Results showed that Titania nanoparticles increased adhesion of beneficial bacteria on to the roots of oilseed rape and protected the plants against infection.

Thermally treated grass fibers as colonizable substrate for beneficial bacterial inoculum

NARCIS (Netherlands)

Trifonova, R.D.; Postma, J.; Ketelaars, J.J.M.H.; Elsas, van J.D.

2008-01-01

This study investigates how thermally treated (i.e., torrefied) grass, a new prospective ingredient of potting soils, is colonized by microorganisms. Torrefied grass fibers (TGF) represent a specific colonizable niche, which is potentially useful to establish a beneficial microbial community that

Biochar application does not improve the soil hydrological function of a sandy soil

NARCIS (Netherlands)

Jeffery, S.; Meinders, M.B.C.; Stoof, C.R.; Bezemer, T.M.; Van de Voorde, T.F.J.; Mommer, Liesje; Van Groenigen, J.W.

2015-01-01

Biochar application to soil is currently being widely posited as a means to improve soil quality and thereby increase crop yield. Next to beneficial effects on soil nutrient availability and retention, biochar is assumed to improve soil water retention. However, evidence for such an effect in the

Impact of spatial organization on a novel auxotrophic interaction among soil microbes.

Science.gov (United States)

Jiang, Xue; Zerfaß, Christian; Feng, Song; Eichmann, Ruth; Asally, Munehiro; Schäfer, Patrick; Soyer, Orkun S

2018-06-01

A key prerequisite to achieve a deeper understanding of microbial communities and to engineer synthetic ones is to identify the individual metabolic interactions among key species and how these interactions are affected by different environmental factors. Deciphering the physiological basis of species-species and species-environment interactions in spatially organized environments requires reductionist approaches using ecologically and functionally relevant species. To this end, we focus here on a defined system to study the metabolic interactions in a spatial context among the plant-beneficial endophytic fungus Serendipita indica, and the soil-dwelling model bacterium Bacillus subtilis. Focusing on the growth dynamics of S. indica under defined conditions, we identified an auxotrophy in this organism for thiamine, which is a key co-factor for essential reactions in the central carbon metabolism. We found that S. indica growth is restored in thiamine-free media, when co-cultured with B. subtilis. The success of this auxotrophic interaction, however, was dependent on the spatial and temporal organization of the system; the beneficial impact of B. subtilis was only visible when its inoculation was separated from that of S. indica either in time or space. These findings describe a key auxotrophic interaction in the soil among organisms that are shown to be important for plant ecosystem functioning, and point to the potential importance of spatial and temporal organization for the success of auxotrophic interactions. These points can be particularly important for engineering of minimal functional synthetic communities as plant seed treatments and for vertical farming under defined conditions.

Using the soil and water assessment tool to estimate achievable water quality targets through implementation of beneficial management practices in an agricultural watershed.

Science.gov (United States)

Yang, Qi; Benoy, Glenn A; Chow, Thien Lien; Daigle, Jean-Louis; Bourque, Charles P-A; Meng, Fan-Rui

2012-01-01

Runoff from crop production in agricultural watersheds can cause widespread soil loss and degradation of surface water quality. Beneficial management practices (BMPs) for soil conservation are often implemented as remedial measures because BMPs can reduce soil erosion and improve water quality. However, the efficacy of BMPs may be unknown because it can be affected by many factors, such as farming practices, land-use, soil type, topography, and climatic conditions. As such, it is difficult to estimate the impacts of BMPs on water quality through field experiments alone. In this research, the Soil and Water Assessment Tool was used to estimate achievable performance targets of water quality indicators (sediment and soluble P loadings) after implementation of combinations of selected BMPs in the Black Brook Watershed in northwestern New Brunswick, Canada. Four commonly used BMPs (flow diversion terraces [FDTs], fertilizer reductions, tillage methods, and crop rotations), were considered individually and in different combinations. At the watershed level, the best achievable sediment loading was 1.9 t ha(-1) yr(-1) (89% reduction compared with default scenario), with a BMP combination of crop rotation, FDT, and no-till. The best achievable soluble P loading was 0.5 kg ha(-1) yr(-1) (62% reduction), with a BMP combination of crop rotation and FDT and fertilizer reduction. Targets estimated through nonpoint source water quality modeling can be used to evaluate BMP implementation initiatives and provide milestones for the rehabilitation of streams and rivers in agricultural regions. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Thermal-treated soil for mercury removal: Soil and phytotoxicity tests

Energy Technology Data Exchange (ETDEWEB)

Roh, Y.; Edwards, N.T.; Lee, S.Y.; Stiles, C.A.; Armes, S.; Foss, J.E.

2000-04-01

Mercury (Hg) contamination of soils and sediments is one of many environmental problems at the Oak Ridge Reservation, Oak Ridge, TN. Mercury-contaminated soil from the Lower East Fork Poplar Creek (LEFPC) at the Oak Ridge Reservation was treated thermally to reduce Hg concentration to a below target level (20 mg kg{sup {minus}1}) as a pilot scale thermal treatment demonstration. As a part of performance evaluation, the soil characteristics and plant growth response of the untreated and treated soil were examined. The soil treated at 350 C retained most of its original soil properties, but the soil treated at 600 C exhibited considerable changes in mineralogical composition and physicochemical characteristics. Growth and physiological response of the three plant species radish (Raphanus sativus L.), fescue (Festuca arundinacea Schreb.), and oat (Avena sativa L.) indicated adverse effects of the thermal treatment. The addition of N fertilizer had beneficial effects in the 350 C treated soil, but had little beneficial effect in the 600 C treated soil. Some changes of soil characteristics induced by thermal treatment cannot be avoided. Soil characteristics and phytotoxicity test results strongly suggest that changes occurring following the 350 C treatment do not limit the use of the treated soil to refill the excavated site for full-scale remediation. The only problem with the 350 C treatment is that small amounts of Hg compounds (<15 mg kg{sup {minus}1}) remain in the soil and a processing cost of $45/Mg.

Biodegradation of cyanide using Serratia sp. isolated from contaminated soil of gold mine in Takab

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Mojtaba Mohseni

2014-07-01

Full Text Available   Introduction : Cyanide is a toxic and hazardous compound for all organisms which is produced enormously by human being and causes the environment pollution. Biodegradation is the best method for cyanide elimination in industrial wastewater. The aims of this study were isolation of cyanide degrading bacteria from contaminated soil and investigation of their ability for cyanide degradation.   Materials and methods: After soil samples collection, enrichment of cyanide degrading bacteria was performed in a minimal medium containing 0.5 mM potassium cyanide. The ability of isolated bacterium to utilize the cyanide as sole carbon and nitrogen source was investigated. Cyanide degradation and ammonium production was determined in growth medium using picric acid and Nessler’s regent methods. Toxicity effect of different cyanide compounds on bacterial growth was determined using minimum inhibitory concentration. In addition, the ability of the isolated bacterium to utilize different cyanide compounds was investigated . Identification of the isolate was undertaken using morphological, physiological and biochemical characteristics and molecular analysis .   Results : A bacterium with ability to degrade cyanide as sole carbon and nitrogen source was isolated from soil. This bacterium named as isolate MF1. MF1 degraded cyanide in growth medium in alkaline condition after 40 hours. Moreover this isolate tolerated more than 7 mM potassium cyanide. The results showed that there was a direct relation between decreasing of cyanide concentration, increasing of ammonia concentration and growth of MF1. In addition, the isolated bacterium demonstrated the ability to utilize different cyanide compounds as sole carbon and nitrogen source. The results of morphological and physiological characteristics showed that this bacterium belonged to the Serratia sp. Moreover, 16S rDNA sequencing and phylogenetic analyses exhibited that MF1 strain was similar to Serratia

NATURAL ATTENUATION OF COPPER IN SOILS AND SOIL MINERALS - II

Science.gov (United States)

The bioabailability and toxicity of Cu in soils is controlled by a number of soil properties and processes. Some of these such as pH, adsorption/desorption and competition with beneficial cations have been extensively studied. However, the effects of natural attenuation (or aging...

Co-metabolism of DDT by the newly isolated bacterium, Pseudoxanthomonas sp. wax

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Guangli Wang

2010-06-01

Full Text Available Microbial degradation of 1,1,1-trichloro-2,2-bis(p-chlorophenylethane (DDT is the most promising way to clean up DDT residues found in the environment. In this paper, a bacterium designated as wax, which was capable of co-metabolizing DDT with other carbon sources, was isolated from a long-term DDT-contaminated soil sample by an enrichment culture technique. The new isolate was identified as a member of the Pseudoxanthomonas sp., based on its morphological, physiological and biochemical properties, as well as by 16S rRNA gene analysis. In the presence of 100 mg l-1 glucose, the wax strain could degrade over 95% of the total DDT, at a concentration of 20 mg l-1, in 72 hours, and could degrade over 60% of the total DDT, at a concentration of 100 mg l-1, in 144 hours. The wax strain had the highest degradation efficiency among all of the documented DDT-degrading bacteria. The wax strain could efficiently degrade DDT at temperatures ranging from 20 to 37ºC, and with initial pH values ranging from 7 to 9. The bacterium could also simultaneously co-metabolize 1,1-dichloro-2,2-bis(p-chlorophenylethane (DDD, 2,2-bis(p-chlorophenyl-1,1-dichlorethylene (DDE, and other organochlorine compounds. The wax strain could also completely remove 20 mg kg-1 of DDT from both sterile and non-sterile soils in 20 days. This study demonstrates the significant potential use of Pseudoxanthomonas sp. wax for the bioremediation of DDT in the environment.

An evaluation of the ability of Dichelobacter nodosus to survive in soil

DEFF Research Database (Denmark)

Cederlöf, Sara Ellinor; Hansen, Tomas; Klaas, Ilka Christine

2013-01-01

Background Dichelobacter nodosus is the causative agent of footrot in sheep. The survival of the bacterium in soil is of importance for the epidemiology of the disease. The investigation evaluates the survival of D. nodosus in soil with and without added hoof powder stored under different tempera...

[Response of mineralization of dissolved organic carbon to soil moisture in paddy and upland soils in hilly red soil region].

Science.gov (United States)

Chen, Xiang-Bi; Wang, Ai-Hua; Hu, Le-Ning; Huang, Yuan; Li, Yang; He, Xun-Yang; Su, Yi-Rong

2014-03-01

Typical paddy and upland soils were collected from a hilly subtropical red-soil region. 14C-labeled dissolved organic carbon (14C-DOC) was extracted from the paddy and upland soils incorporated with 14C-labeled straw after a 30-day (d) incubation period under simulated field conditions. A 100-d incubation experiment (25 degrees C) with the addition of 14C-DOC to paddy and upland soils was conducted to monitor the dynamics of 14C-DOC mineralization under different soil moisture conditions [45%, 60%, 75%, 90%, and 105% of the field water holding capacity (WHC)]. The results showed that after 100 days, 28.7%-61.4% of the labeled DOC in the two types of soils was mineralized to CO2. The mineralization rates of DOC in the paddy soils were significantly higher than in the upland soils under all soil moisture conditions, owing to the less complex composition of DOC in the paddy soils. The aerobic condition was beneficial for DOC mineralization in both soils, and the anaerobic condition was beneficial for DOC accumulation. The biodegradability and the proportion of the labile fraction of the added DOC increased with the increase of soil moisture (45% -90% WHC). Within 100 days, the labile DOC fraction accounted for 80.5%-91.1% (paddy soil) and 66.3%-72.4% (upland soil) of the cumulative mineralization of DOC, implying that the biodegradation rate of DOC was controlled by the percentage of labile DOC fraction.

Can vineyard biodiversity be beneficial for viticulture and tourism?

Science.gov (United States)

Hervé, Morgane; Kratschmer, Sophie; Gregorich, Claudia; Silvia, Winter; Montembault, David; Zaller, Johann G.; Guernion, Muriel; Jung, Vincent; Schuette, Rebekka; Paredes, Daniel; Guzman Diaz, Gema; Cabezas Luque, Jose Manuel; Hoble, Adela; Popescu, Daniela; Burel, Françoise; Cluzeau, Daniel; Bergmann, Holger; Potthoff, Martin; Nicolai, Annegret

2017-04-01

The European research BiodivERsA project VineDivers aims to link ecosystem services and vine production, in an integrative approach that considers both landscape structure and cultural practices (cover-crops versus bare soils), in vineyards of Austria, France, Romania and Spain. Such services studied are (i) provisioning and regulation services by soil biota and pollinators, and (ii) landscape cultural services. In this study, we want to know if landscape beneficial for biodiversity providing ecosystem services at a plot scale also have an aesthetical value. An interdisciplinary approach was chosen to include both ecological and sociological data. First, we analyzed the influence of soil management practices and landscape complexity on soil biota, inter-row flora and bees. Second, we implemented a questionnaire based on photographs about biodiversity perception and visual aesthetic evaluation. Our results highlighted the effect of landscape complexity and soil management intensity on biodiversity and their ecological and cultural ecosystem services. This allows us to discuss the global importance of biodiversity for a wine-producing region. Further analysis within the VineDivers project will focus on an assessment of the biodiversity importance for local viticulture economy.

Fourier transform infrared spectroscopic study of intact cells of the nitrogen-fixing bacterium Azospirillum brasilense

Science.gov (United States)

Kamnev, A. A.; Ristić, M.; Antonyuk, L. P.; Chernyshev, A. V.; Ignatov, V. V.

1997-06-01

The data of Fourier transform infrared (FTIR) spectroscopic measurements performed on intact cells of the soil nitrogen-fixing bacterium Azospirillum brasilense grown in a standard medium and under the conditions of an increased metal uptake are compared and discussed. The structural FTIR information obtained is considered together with atomic absorption spectrometry (AAS) data on the content of metal cations in the bacterial cells. Some methodological aspects concerning preparation of bacterial cell samples for FTIR measurements are also discussed.

Cloning, expression and biochemical characterization of a β-carbonic anhydrase from the soil bacterium Enterobacter sp. B13.

Science.gov (United States)

Eminoğlu, Ayşenur; Vullo, Daniela; Aşık, Aycan; Çolak, Dilşat Nigar; Supuran, Claudiu T; Çanakçı, Sabriye; Osman Beldüz, Ali

2016-12-01

A recombinant carbonic anhydrase (CA, EC 4.2.1.1) from the soil-dwelling bacterium Enterobacter sp. B13 was cloned and purified by Co(2+) affinity chromatography. Bioinformatic analysis showed that the new enzyme (denominated here B13-CA) belongs to the β-class CAs and to possess 95% homology with the ortholog enzyme from Escherichia coli encoded by the can gene, whereas its sequence homology with the other such enzyme from E. coli (encoded by the cynT gene) was of 33%. B13-CA was characterized kinetically as a catalyst for carbon dioxide hydration to bicarbonate and protons. The enzyme shows a significant catalytic activity, with the following kinetic parameters at 20 °C and pH of 8.3: kcat of 4.8 × 10(5) s(-1) and kcat/Km of 5.6 × 10(7) M(-1) × s(-1). This activity was potently inhibited by acetazolamide which showed a KI of 78.9 nM. Although only this compound was investigated for the moment as B13-CA inhibitor, further studies may reveal new classes of inhibitors/activators of this enzyme which may show biomedical or environmental applications, considering the posssible role of this enzyme in CaCO3 biomineralization processes.

Bacterium oxidizing carbon monoxide

Energy Technology Data Exchange (ETDEWEB)

Kistner, A

1953-01-01

Present-day knowledge of the microbiological oxidation of carbon monoxide is based on doubtful observations and imperfect experimental procedures. By making use of shake cultures in contact with gas mixtures containing high concentrations of CO and by employing liquid enrichment media with a low content of organic matter and solid media of the same composition with not more than 1.2% agar, it proved possible to isolate a co-oxidizing bacterium of the genus hydrogenomonas from sewage sludge. For the first time irrefutable proof has been given of the oxidation of carbon monoxide by a pure culture of a bacterium, both in growing cultures and in resting cell suspensions. 12 references.

Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria.

Science.gov (United States)

Raaijmakers, Jos M; Mazzola, Mark

2012-01-01

Soil- and plant-associated environments harbor numerous bacteria that produce antibiotic metabolites with specific or broad-spectrum activities against coexisting microorganisms. The function and ecological importance of antibiotics have long been assumed to yield a survival advantage to the producing bacteria in the highly competitive but resource-limited soil environments through direct suppression. Although specific antibiotics may enhance producer persistence when challenged by competitors or predators in soil habitats, at subinhibitory concentrations antibiotics exhibit a diversity of other roles in the life history of the producing bacteria. Many processes modulated by antibiotics may be inherently critical to the producing bacterium, such as the acquisition of substrates or initiation of developmental changes that will ensure survival under stressful conditions. Antibiotics may also have roles in more complex interactions, including in virulence on host plants or in shaping the outcomes of multitrophic interactions. The innate functions of antibiotics to producing bacteria in their native ecosystem are just beginning to emerge, but current knowledge already reveals a breadth of activities well beyond the historical perspective of antibiotics as weaponry in microbial conflicts.

Plant growth and development vs. high and low levels of plant-beneficial heavy metal ions

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Namira Arif

2016-11-01

Full Text Available Heavy metals (HMs exists in the environment in both forms as essential and non-essential. These HM ions enter in soil biota from various sources like natural and anthropogenic. Essential HMs such as cobalt (Co, copper (Cu, iron (Fe, manganese (Mn, molybdenum (Mo, nickel (Ni, and zinc (Zn plays a beneficial role in plant growth and development. At optimum level these beneficial elements improves the plant’s nutritional level and also several mechanisms essential for the normal growth and better yield of plants. The range of their optimality for land plants is varied. Plant uptake heavy metals as a soluble component or solubilized them by root exudates. While their presence in excess become toxic for plants that switches the plant’s ability to uptake and accumulate other nonessential elements. The increased amount of HMs within the plant tissue displays direct and indirect toxic impacts. Such direct effects are the generation of oxidative stress which further aggravates inhibition of cytoplasmic enzymes and damage to cell structures. Although, indirect possession is the substitution of essential nutrients at plant’s cation exchange sites. These ions readily influence role of various enzymes and proteins, arrest metabolism, and reveal phytotoxicity. On account of recent advancements on beneficial HMs ions Co, Cu, Fe, Mn, Mo, Ni, and Zn in soil-plant system, the present paper: overview the sources of HMs in soils and their uptake and transportation mechanism, here we have discussed the role of metal transporters in transporting the essential metal ions from soil to plants. The role played by Co, Cu, Fe, Mn, Mo, Ni, and Zn at both low and high level on the plant growth and development and the mechanism to alleviate metal toxicity at high level have been also discussed. At the end, on concluding the article we have also discussed the future perspective in respect to beneficial HM ions interaction with plant at both levels.

Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil.

Science.gov (United States)

Lee, Yunho; Jeon, Che Ok

2018-04-01

A Gram-stain-negative, facultatively aerobic, aromatic hydrocarbon-degrading bacterium, designated strain BN5 T , was isolated from gasoline-contaminated soil. Cells were motile and slightly curved rods with a single flagellum showing catalase and oxidase activities. Growth was observed at 20-37 °C (optimum, 25-30 °C), pH 3-7 (optimum, pH 5-6) and 0-2 % NaCl (optimum, 0 %). Ubiquinone-8 was the predominant respiratory quinone. The major fatty acids were C16 : 0, cyclo-C19 : 0ω8c and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phosphoamino lipid, three unidentified amino lipids and eight unidentified lipids were the identified polar lipids. The DNA G+C content was 62.93 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BN5 T formed a phylogenic lineage with members of the genus Paraburkholderia and showed the highest 16S rRNA gene sequence similarities to Paraburkholderia phytofirmans PsJN T (99.4 %), Paraburkholderia dipogonis DL7 T (98.8 %) and Paraburkholderia insulsa PNG-April T (98.8 %). The average nucleotide identity and in silico DNA-DNA hybridization (DDH) values between strain BN5 T and P. phytofirmans PsJN T were 88.5 and 36.5 %, respectively. The DDH values for strain BN5 T with P. dipogonis LMG 28415 T and P. insulsa DSM 28142 T were 41.0±4.9 % (reciprocal, 33.0±4.3 %) and 47.1±6.6 % (reciprocal, 51.7±5.4 %), respectively. Based on its physiological, chemotaxonomic and phylogenetic features, we conclude that strain BN5 T is a novel species of the genus Paraburkholderia, for which the name Paraburkholderia aromaticivorans sp. nov. is proposed. The type strain is BN5 T (=KACC 19419 T =JCM 32303 T ).

Lunar Soil Particle Separator, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — The Lunar Soil Particle Separator (LSPS) is an innovative method to beneficiate soil prior to in-situ resource utilization (ISRU). The LSPS improves ISRU oxygen...

What drives the occurrence of the melioidosis bacterium Burkholderia pseudomallei in domestic gardens?

Directory of Open Access Journals (Sweden)

Mirjam Kaestli

2015-03-01

Full Text Available Melioidosis is an often fatal infectious disease affecting humans and animals in tropical regions and is caused by the saprophytic environmental bacterium Burkholderia pseudomallei. Domestic gardens are not only a common source of exposure to soil and thus to B. pseudomallei, but they also have been found to contain more B. pseudomallei than other environments. In this study we addressed whether anthropogenic manipulations common to gardens such as irrigation or fertilizers change the occurrence of B. pseudomallei. We conducted a soil microcosm experiment with a range of fertilizers and soil types as well as a longitudinal interventional study over three years on an experimental fertilized field site in an area naturally positive for B. pseudomallei. Irrigation was the only consistent treatment to increase B. pseudomallei occurrence over time. The effects of fertilizers upon these bacteria depended on soil texture, physicochemical soil properties and biotic factors. Nitrates and urea increased B. pseudomallei load in sand while phosphates had a positive effect in clay. The high buffering and cation exchange capacities of organic material found in a commercial potting mix led to a marked increase in soil salinity with no survival of B. pseudomallei after four weeks in the potting mix sampled. Imported grasses were also associated with B. pseudomallei occurrence in a multivariate model. With increasing population density in endemic areas these findings inform the identification of areas in the anthropogenic environment with increased risk of exposure to B. pseudomallei.

Biological Control of Meloidogyne hapla Using an Antagonistic Bacterium

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Jiyeong Park

2014-09-01

Full Text Available We examined the efficacy of a bacterium for biocontrol of the root-knot nematode (RKN Meloidogyne hapla in carrot (Daucus carota subsp. sativus and tomato (Solanum lycopersicum. Among 542 bacterial isolates from various soils and plants, the highest nematode mortality was observed for treatments with isolate C1-7, which was identified as Bacillus cereus based on cultural and morphological characteristics, the Biolog program, and 16S rRNA sequencing analyses. The population density and the nematicidal activity of B. cereus C1-7 remained high until the end of culture in brain heart infusion broth, suggesting that it may have sustainable biocontrol potential. In pot experiments, the biocontrol efficacy of B. cereus C1-7 was high, showing complete inhibition of root gall or egg mass formation by RKN in carrot and tomato plants, and subsequently reducing RKN damage and suppressing nematode population growth, respectively. Light microscopy of RKN-infected carrot root tissues treated with C1-7 showed reduced formation of gall cells and fully developed giant cells, while extensive gall cells and fully mature giant cells with prominent cell wall ingrowths formed in the untreated control plants infected with RKNs. These histopathological characteristics may be the result of residual or systemic biocontrol activity of the bacterium, which may coincide with the biocontrol efficacies of nematodes in pots. These results suggest that B. cereus C1-7 can be used as a biocontrol agent for M. hapla.

Lunar Soil Particle Separator, Phase II

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National Aeronautics and Space Administration — The Lunar Soil Particle Separator (LSPS) is an innovative method to beneficiate soil prior to in-situ resource utilization (ISRU). The LSPS can improve ISRU oxygen...

Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov.

Science.gov (United States)

Bach, Evelise; Sant'Anna, Fernando Hayashi; Magrich Dos Passos, João Frederico; Balsanelli, Eduardo; de Baura, Valter Antonio; Pedrosa, Fábio de Oliveira; de Souza, Emanuel Maltempi; Passaglia, Luciane Maria Pereira

2017-08-31

The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Conceptual Framework for Soil management and its effect on Soil Biodiversity in Organic and Low Input Farming

OpenAIRE

Koopmans, Dr. C.J.; Smeding, Dr. F.W.

2008-01-01

Learning how to manage beneficial soil biological processes may be a key step towards developing sustainable agricultural systems. We designed a conceptual framework linking soil management practices to important soil-life groups and soil fertility services like nutrient cycling, soil structure and disease suppression. We selected a necessary parameter set to gain insight between management, soil life and soil support services. The findings help to develop management practices that optimise y...

[Genetic variability of the bacterium Ralstonia solanacearum (Burkholderiales: Burholderiaceae) in the banana-growing region of Uraba (Colombia)].

Science.gov (United States)

Cardozo, Carolina; Rodríguez, Paola; Cotes, José Miguel; Marín, Mauricio

2010-03-01

The banana moko disease, caused by the bacterium Ralstonia solanacearum, is one of the most important phytopathological problems of the banana agribusiness in tropical countries. In Uraba and Magdalena (Colombia), the main exporting regions of banana in Colombia, this disease causes a destruction estimated in 16.5 ha/year. The bacterium presents an extremely high level of genetic variation that affects control measures. This is the first study of its variation in Colombia and was done with AFLP molecular markers on a population of 100 isolates from banana plants, soils and "weeds". The high level of genetic diversity, with Nei and Shannon indexes of h=0.32 and I=0.48, respectively, and the AMOVA, showed that this population is subestructured (Fst=0.66): the host is the main factor of differentiation. Even so, previous tests show that all varieties have pathogenicity on Musa.

Tryptophan Oxidative Metabolism Catalyzed by : A Thermophile Isolated from Kuwait Soil Contaminated with Petroleum Hydrocarbons

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Jassim M. Al-Hassan

2011-01-01

Full Text Available Tryptophan metabolism has been extensively studied in humans as well as in soil. Its metabolism takes place mainly through kynurenine pathway yielding hydroxylated, deaminated and many other products of physiological significance. However, tryptophan metabolism has not been studied in an isolated thermophilic bacterium. Geobacillus stearothermophilus is a local thermophile isolated from Kuwait desert soil contaminated with petroleum hydrocarbons. The bacterium grows well at 65 °C in 0.05 M phosphate buffer (pH 7, when supplied with organic compounds as a carbon source and has a good potential for transformation of steroids and related molecules. In the present study, we used tryptophan ethyl ester as a carbon source for the bacterium to study the catabolism of the amino acid at pH 5 and pH 7. In this endeavor, we have resolved twenty one transformation products of tryptophan by GC/LC and have identified them through their mass spectral fragmentation.

Isolation and identification of soil fungi isolates from forest soil for flooded soil recovery

Science.gov (United States)

Hazwani Aziz, Nor; Zainol, Norazwina

2018-04-01

Soil fungi have been evaluated for their ability in increasing and recovering nitrogen, phosphorus and potassium content in flooded soil and in promoting the growth of the host plant. Host plant was cultivated in a mixture of fertile forest soil (nutrient-rich soil) and simulated flooded soil (nutrient-poor soil) in an optimized soil condition for two weeks. The soil sample was harvested every day until two weeks of planting and was tested for nitrogen, phosphorus and potassium concentration. Soil fungi were isolated by using dilution plating technique and was identified by Biolog’s Microbial Systems. The concentration of nitrogen, phosphorus, and potassium was found to be increasing after two weeks by two to three times approximately from the initial concentration recorded. Two fungi species were identified with probability more than 90% namely Aspergillus aculeatus and Paecilomyces lilacinus. Both identified fungi were found to be beneficial in enhancing plant growth and increasing the availability of nutrient content in the soil and thus recovering the nutrient content in the flooded soil.

Antioxidants keep the potentially probiotic but highly oxygen-sensitive human gut bacterium Faecalibacterium prausnitzii alive at ambient air.

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M Tanweer Khan

Full Text Available The beneficial human gut microbe Faecalibacterium prausnitzii is a 'probiotic of the future' since it produces high amounts of butyrate and anti-inflammatory compounds. However, this bacterium is highly oxygen-senstive, making it notoriously difficult to cultivate and preserve. This has so far precluded its clinical application in the treatment of patients with inflammatory bowel diseases. The present studies were therefore aimed at developing a strategy to keep F. prausnitzii alive at ambient air. Our previous research showed that F. prausnitzii can survive in moderately oxygenized environments like the gut mucosa by transfer of electrons to oxygen. For this purpose, the bacterium exploits extracellular antioxidants, such as riboflavin and cysteine, that are abundantly present in the gut. We therefore tested to what extent these antioxidants can sustain the viability of F. prausnitzii at ambient air. The present results show that cysteine can facilitate the survival of F. prausnitzii upon exposure to air, and that this effect is significantly enhanced the by addition of riboflavin and the cryoprotectant inulin. The highly oxygen-sensitive gut bacterium F. prausnitzii can be kept alive at ambient air for 24 h when formulated with the antioxidants cysteine and riboflavin plus the cryoprotectant inulin. Improved formulations were obtained by addition of the bulking agents corn starch and wheat bran. Our present findings pave the way towards the biomedical exploitation of F. prausnitzii in redox-based therapeutics for treatment of dysbiosis-related inflammatory disorders of the human gut.

MODELING OF MIXED CHEMOSTAT CULTURES OF AN AEROBIC BACTERIUM, COMAMONAS-TESTOSTERONI, AND AN ANAEROBIC BACTERIUM, VEILLONELLA-ALCALESCENS - COMPARISON WITH EXPERIMENTAL-DATA

NARCIS (Netherlands)

GERRITSE, J; SCHUT, F; GOTTSCHAL, JC

A mathematical model of mixed chemostat cultures of the obligately aerobic bacterium Comamonas testosteroni and the anaerobic bacterium Veillonella alcalescens grown under dual limitation Of L-lactate and oxygen was constructed. The model was based on Michaelis-Menten-type kinetics for the

Effects of Chromolaena and Tithonia Mulches on Soil Properties

African Journals Online (AJOL)

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2 Department of Crop, Soil and Pest Management, Federal University of Technology, P.M.B. ... Chromolaena mulch produced higher values of soil chemical properties, leaf nutrient concentrations, ..... increased activities of beneficial soil fauna.

Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24.

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Sang-Yeop Lee

Full Text Available Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs, including benzene, toluene, and xylene (BTX, as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX.

Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24

Science.gov (United States)

Yun, Sung Ho; Choi, Chi-Won; Yi, Yoon-Sun; Kim, Jonghyun; Chung, Young-Ho; Park, Edmond Changkyun; Kim, Seung Il

2016-01-01

Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX. PMID:27124467

Engineering a wild fast-growing Mycoplasma bacterium to generate ...

International Development Research Centre (IDRC) Digital Library (Canada)

2018-01-12

Jan 12, 2018 ... The CCPP bacterium causes sick animals to experience severe symptoms ... because antibiotic treatment does not eliminate the responsible bacterium. ... To develop a fast growing CCPP vaccine for cheaper production and ...

Zymomonas mobilis: a bacterium for ethanol production

Energy Technology Data Exchange (ETDEWEB)

Baratti, J.C.; Bu' Lock, J.D.

1986-01-01

Zymomonas mobilis is a facultative anaerobic gram negative bacterium first isolated in tropical countries from alcoholic beverages like the African palm wine, the Mexican pulque and also as a contaminant of cider (cider sickness) or beer in the European countries. It is one of the few facultative anaerobic bacteria degrading glucose by the Entner-Doudoroff pathway usually found in strictly aerobic microorganisms. Some work was devoted to this bacterium in the 50s and 60s and was reviewed by Swings and De Ley in their classical paper published in 1977. During the 70s there was very little work on the bacterium until 1979 and the first report by the Australian group of P.L. Rogers on the great potentialities of Z. mobilis for ethanol production. At that time the petroleum crisis had led the developed countries to search for alternative fuel from renewable resources. The Australian group clearly demonstrated the advantages of the bacterium compared to the yeasts traditionally used for the alcoholic fermentation. As a result, there was a considerable burst in the Zymomonas literature which started from nearly zero in the late 70s to attain 70 papers published in the field in 1984. In this article, papers published from 1982 to 1986 are reviewed.

Microbial degradation of metalaxyl in soil

International Nuclear Information System (INIS)

Musumeci, M.R.; Ruegg, E.F.

1984-01-01

The behaviour of the fungicide metalaxyl in purple latosol soil was investigated using a ring - 14 C labelled compound under laboratory conditions. In nonsterile soil samples under aerobic conditions, metalaxyl was degrated into two metabolites. After 60 days, 60% of the radiocarbon on TLC plates corresponded to the parent fungicide, 22% to its metabolite N-(2-methoxyacetyl)-N-(2,6-xylyl)-DL-alanine, and 2.7% to a second and unidentified metabolite. The U.V. absorbance value of metalaxyl decreased after seven days incubation with a soil microorganisms suspension. Incubation of 14 C-metalaxyl for 50 days with a bacterium or a fungus isolated from that suspension resulted in metalaxyl gradual disappearance from the medium, but not metabolites were detected during this period. (Author) [pt

Microbial degradation of metalaxyl in soil

Energy Technology Data Exchange (ETDEWEB)

Musumeci, M.R.; Ruegg, E.F. (Instituto Biologico, Sao Paulo (Brazil). Centro de Radioisotopos)

1984-10-01

The behaviour of the fungicide metalaxyl in purple latosol soil was investigated using a ring - /sup 14/C labelled compound under laboratory conditions. In nonsterile soil samples under aerobic conditions, metalaxyl was degraded into two metabolites. After 60 days, 60% of the radiocarbon on TLC plates corresponded to the parent fungicide, 22% to its metabolite N-(2-methoxyacetyl)-N-(2,6-xylyl)-DL-alanine, and 2.7% to a second and unidentified metabolite. The U.V. absorbance value of metalaxyl decreased after seven days incubation with a soil microorganisms suspension. Incubation of /sup 14/C-metalaxyl for 50 days with a bacterium or a fungus isolated from that suspension resulted in metalaxyl gradual disappearance from the medium, but not metabolites were detected during this period.

Degradation of pyrene in soil and in vitro by a Bacillus lentus strain ...

African Journals Online (AJOL)

A bacterium isolated from an asphalt plant soil and identified as a strain of Bacillus lentus was tested in vitro and in sterilized and native soils for ability to survive and sustain pyrene degradation over a period of 63 days. The exponential growth rate in vitro was 0.049 d-1 and the doubling time 2.65 d. In the control flask ...

Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

Energy Technology Data Exchange (ETDEWEB)

Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

1994-06-01

The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

Microflora of urogenital tract in pregnancy with asymptomatic bacterium

International Nuclear Information System (INIS)

Abdullaeva, R.A.

2006-01-01

The article contains results of research interrelationship from colonization of vagina and urinary tract diseases. E.coli one of the main factors in development asymptomatic bacterium. Presented high effects of penicillin medicaments and nitrofurans in treatment of asymptomatic bacterium

Chemical composition and Zn bioavailability of the soil solution extracted from Zn amended variable charge soils.

Science.gov (United States)

Zampella, Mariavittoria; Adamo, Paola

2010-01-01

A study on variable charge soils (volcanic Italian and podzolic Scottish soils) was performed to investigate the influence of soil properties on the chemical composition of soil solution. Zinc speciation, bioavailability and toxicity in the soil solution were examined. The soils were spiked with increasing amounts of Zn (0, 100, 200, 400 and 1000 mg/kg) and the soil solutions were extracted using rhizon soil moisture samplers. The pH, total organic carbon (TOC), base cations, anions, total Zn and free Zn2+ in soil solution were analysed. A rapid bioassay with the luminescent bacterium Escherichia coli HB101 pUCD607 was performed to assess Zn toxicity. The influence of soil type and Zn treatments on the chemical composition of soil solution and on Zn toxicity was considered and discussed. Different trends of total and free Zn concentrations, base cations desorption and luminescence of E. coli HB101 pUCD607 were observed. The soil solution extracted from the volcanic soils had very low total and free Zn concentrations and showed specific Zn2+/Ca2+ exchange. The soil solution from the podzolic soil had much higher total and free Zn concentrations and showed no evidence of specific Zn2+/Ca2+ exchange. In comparison with the subalkaline volcanic soils, the acidic podzol showed enhanced levels of toxic free Zn2+ and consequently stronger effects on E. coli viability.

Low nitrogen stress stimulating the indole-3-acetic acid biosynthesis of Serratia sp. ZM is vital for the survival of the bacterium and its plant growth-promoting characteristic.

Science.gov (United States)

Ouyang, Liming; Pei, Haiyan; Xu, Zhaohui

2017-04-01

Serratia sp. ZM is a plant growth-promoting (PGP) bacterial strain isolated from the rhizospheric soil of Populus euphratica in northwestern China. In this study, low nitrogen supply significantly stimulated the production of indole-3-acetic acid (IAA) in Serratia sp.ZM. The inoculation of the bacterium to wheat seedlings improved plant growth compared with the uninoculated group, and the stimulating effect was more prominent under low nitrogen stress. Inactivation of the predicted key gene in the IAA biosynthesis pathway impaired IAA production and significantly hampered mutant growth in poor medium. Furthermore, the IAA-deficient mutant lost the PGP effect under either normal or low nitrogen conditions in plant experiments. This study revealed the significant impact of environmental nitrogen levels on IAA production in the PGP strain and the vital effect of IAA on resistance physiology of both the bacterium and host plant. The characteristics of Serratia sp. ZM also indicated its application potential as a biofertilizer for plants, especially those suffering from poor nitrogen soil.

Effect of fertilization and soil treatment on the soybean nodulation

International Nuclear Information System (INIS)

Abdel aziz, H.A.

1993-01-01

Soybean (Glycine max L. ) is one of the most important leguminosae crops all over the world. It is considered one of the most important protein sources for human and animals. During the last 20 years, soybean was introduced to Egypt, however the nodulation of soybean under field conditions remains a problem because the egyptian soils were void of soybean rhizobia. Since soybean is a leguminosae crop, symbiosis with root - nodule R hizobium might play a significant role in the management of its production . Nevertheless, soybean suffers from poor nodulation in egypt, hence nitrogenase fertilization for legume is a logical practice. Soybean can utilize both soil -N or applied N and symbiotically fixed atmospheric nitrogen under normal field condition. The fixation of atmospheric N by the legume/Rhizobium symbiosis is an integrated process in which the host plant ( macrosymbiont) supplies the bacterium (microsymbiont) with energy and the bacterium supplies the plant with reduced N. figs.,172 refs

Biodegradation of pentachloronitrobenzene by Cupriavidus sp. YNS-85 and its potential for remediation of contaminated soils.

Science.gov (United States)

Teng, Ying; Wang, Xiaomi; Zhu, Ye; Chen, Wei; Christie, Peter; Li, Zhengao; Luo, Yongming

2017-04-01

Pentachloronitrobenzene (PCNB) is a toxic chlorinated nitroaromatic compound. However, only a few bacteria have been reported to be able to utilize PCNB. In the present study, one pentachloronitrobenzene (PCNB)-degrading bacterium, Cupriavidus sp. YNS-85, was isolated from a contaminated Panax notoginseng plantation. The strain co-metabolized 200 mg L -1 PCNB in aqueous solution with a removal rate of 73.8% after 5 days. The bacterium also degraded PCNB effectively under acid conditions (pH 4-6) and showed resistance to toxic trace elements (arsenic, copper, and cadmium). Its ability to utilize proposed PCNB intermediates as sole carbon sources was also confirmed. The soil microcosm experiment further demonstrated that bacterial bioaugmentation enhanced the removal of PCNB (37.8%) from soil and the accumulation of pentachloroaniline (89.3%) after 30 days. Soil enzyme activity and microbial community functional diversity were positively influenced after bioremediation. These findings indicate that Cupriavidus sp. YNS-85 may be a suitable inoculant for in situ bioremediation of PCNB-polluted sites, especially those with acid soils co-contaminated with heavy metal(loid)s.

Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein

NARCIS (Netherlands)

Sanders, Jan Willem; Kok, Jan; Venema, Gerard; Ledeboer, Adrianus Marinus

1998-01-01

The invention provides a salt-inducible promoter present in SEQ ID NO: 10 and derivable from a lactic acid bacterium in isolation from the coding sequence normally controlled by said promoter in a wild-type lactic acid bacterium, with modifications and important parts thereof. Also provided are a

Soil application of ash produced by low-temperature fluidized bed gasification: effects on soil nutrient dynamics and crop response

DEFF Research Database (Denmark)

Müller-Stöver, Dorette Sophie; Ahrenfeldt, Jesper; Holm, Jens Kai

2012-01-01

not significantly altered after ash application. SA was generally able to increase the levels of Olsen-P and of the ammonium acetate/acetic acid-extractable K in soil as well as to improve the yield of barley and maize, whereas faba bean did not react positively to ash amendment. CP did not show beneficial effects......Recycling of residual products of bioenergy conversion processes is important for adding value to the technologies and as a potential beneficial soil fertility amendment. In this study, two different ash materials originating from low temperature circulating fluidized bed (LT-CFB) gasification...... of either wheat straw (SA) or residue fibers mainly from citrus peels (CP) were tested regarding their potential to be used as fertilizer on agricultural soils. A soil incubation study, a greenhouse experiment with barley and faba bean, and an accompanying outdoor experiment with maize were carried out...

Nutrients can enhance the abundance and expression of alkane hydroxylase CYP153 gene in the rhizosphere of ryegrass planted in hydrocarbon-polluted soil.

Directory of Open Access Journals (Sweden)

Muhammad Arslan

Full Text Available Plant-bacteria partnership is a promising strategy for the remediation of soil and water polluted with hydrocarbons. However, the limitation of major nutrients (N, P and K in soil affects the survival and metabolic activity of plant associated bacteria. The objective of this study was to explore the effects of nutrients on survival and metabolic activity of an alkane degrading rhizo-bacterium. Annual ryegrass (Lolium multiflorum was grown in diesel-contaminated soil and inoculated with an alkane degrading bacterium, Pantoea sp. strain BTRH79, in greenhouse experiments. Two levels of nutrients were applied and plant growth, hydrocarbon removal, and gene abundance and expression were determined after 100 days of sowing of ryegrass. Results obtained from these experiments showed that the bacterial inoculation improved plant growth and hydrocarbon degradation and these were further enhanced by nutrients application. Maximum plant biomass production and hydrocarbon mineralization was observed by the combined use of inoculum and higher level of nutrients. The presence of nutrients in soil enhanced the colonization and metabolic activity of the inoculated bacterium in the rhizosphere. The abundance and expression of CYP153 gene in the rhizosphere of ryegrass was found to be directly associated with the level of applied nutrients. Enhanced hydrocarbon degradation was associated with the population of the inoculum bacterium, the abundance and expression of CYP153 gene in the rhizosphere of ryegrass. It is thus concluded that the combination between vegetation, inoculation with pollutant-degrading bacteria and nutrients amendment was an efficient approach to reduce hydrocarbon contamination.

Nutrients Can Enhance the Abundance and Expression of Alkane Hydroxylase CYP153 Gene in the Rhizosphere of Ryegrass Planted in Hydrocarbon-Polluted Soil

Science.gov (United States)

Arslan, Muhammad; Afzal, Muhammad; Amin, Imran; Iqbal, Samina; Khan, Qaiser M.

2014-01-01

Plant-bacteria partnership is a promising strategy for the remediation of soil and water polluted with hydrocarbons. However, the limitation of major nutrients (N, P and K) in soil affects the survival and metabolic activity of plant associated bacteria. The objective of this study was to explore the effects of nutrients on survival and metabolic activity of an alkane degrading rhizo-bacterium. Annual ryegrass (Lolium multiflorum) was grown in diesel-contaminated soil and inoculated with an alkane degrading bacterium, Pantoea sp. strain BTRH79, in greenhouse experiments. Two levels of nutrients were applied and plant growth, hydrocarbon removal, and gene abundance and expression were determined after 100 days of sowing of ryegrass. Results obtained from these experiments showed that the bacterial inoculation improved plant growth and hydrocarbon degradation and these were further enhanced by nutrients application. Maximum plant biomass production and hydrocarbon mineralization was observed by the combined use of inoculum and higher level of nutrients. The presence of nutrients in soil enhanced the colonization and metabolic activity of the inoculated bacterium in the rhizosphere. The abundance and expression of CYP153 gene in the rhizosphere of ryegrass was found to be directly associated with the level of applied nutrients. Enhanced hydrocarbon degradation was associated with the population of the inoculum bacterium, the abundance and expression of CYP153 gene in the rhizosphere of ryegrass. It is thus concluded that the combination between vegetation, inoculation with pollutant-degrading bacteria and nutrients amendment was an efficient approach to reduce hydrocarbon contamination. PMID:25360680

Sustainable stabilization of sulfate-bearing soils with expansive soil-rubber technology.

Science.gov (United States)

2013-03-01

The beneficial use of scrap tire rubber mixed with expansive soils is of interest to civil engineering : applications since the swell percent and the swell pressure can be potentially reduced with no deleterious : effect to the shear strength of the ...

Biodegradation of Mexican Diesel for a bacteria consortium of an agricultural soil

International Nuclear Information System (INIS)

Cardona, Santiago; Iturbe, Rosario

2003-01-01

The biodegradation of diesel in water was done by means of the microorganisms present in an agriculture soil. The kinetics of biodegradation and adsorption of diesel were determined in order to applying the procedure in soil and water resources contaminated with diesel. The methodology and results of biodegradation and adsorption of diesel in synthetic water is presented with a soil characterization. Degradation takes place using the original microorganisms present in the soil but giving nitrogen as nutrient. As oxygen source the hydrogen peroxide was used. The kinetics of diesel volatility is presented too. Kinetics equations for degradation, adsorption and speed constant were determined with the obtained results biodegradation, diesel, agriculture soil, bacterium group

Beneficial reuse '97

International Nuclear Information System (INIS)

Anon.

1997-01-01

The annual Beneficial Reuse Conference was conducted in Knoxville, Tennessee from August 5-7, 1997. Now in its fifth year, this conference has become the national forum for discussing the beneficial reuse and recycle of contaminated buildings, equipment and resources, and the fabrication of useful products from such resources. As in the past, the primary goal of Beneficial Reuse ''97 was to provide a forum for the practitioners of pollution prevention, decontamination and decommissioning, waste minimization, reindustrialization, asset management, privatization and recycling to share their successes and failures, as well as their innovative strategies and operational experiences with the assembled group of stakeholders. Separate abstracts have been indexed into the database for contributions to this conference proceedings

Whole-Genome Sequence of the Soil Bacterium Micrococcus sp. KBS0714.

Science.gov (United States)

Kuo, V; Shoemaker, W R; Muscarella, M E; Lennon, J T

2017-08-10

We present here a draft genome assembly of Micrococcus sp. KBS0714, which was isolated from agricultural soil. The genome provides insight into the strategies that Micrococcus spp. use to contend with environmental stressors such as desiccation and starvation in environmental and host-associated ecosystems. Copyright © 2017 Kuo et al.

A novel interaction between plant-beneficial rhizobacteria and roots: colonization induces corn resistance against the root herbivore Diabrotica speciosa.

Science.gov (United States)

Santos, Franciele; Peñaflor, Maria Fernanda G V; Paré, Paul W; Sanches, Patrícia A; Kamiya, Aline C; Tonelli, Mateus; Nardi, Cristiane; Bento, José Mauricio S

2014-01-01

A number of soil-borne microorganisms, such as mycorrhizal fungi and rhizobacteria, establish mutualistic interactions with plants, which can indirectly affect other organisms. Knowledge of the plant-mediated effects of mutualistic microorganisms is limited to aboveground insects, whereas there is little understanding of what role beneficial soil bacteria may play in plant defense against root herbivory. Here, we establish that colonization by the beneficial rhizobacterium Azospirillum brasilense affects the host selection and performance of the insect Diabrotica speciosa. Root larvae preferentially orient toward the roots of non-inoculated plants versus inoculated roots and gain less weight when feeding on inoculated plants. As inoculation by A. brasilense induces higher emissions of (E)-β-caryophyllene compared with non-inoculated plants, it is plausible that the non-preference of D. speciosa for inoculated plants is related to this sesquiterpene, which is well known to mediate belowground insect-plant interactions. To the best of our knowledge, this is the first study showing that a beneficial rhizobacterium inoculant indirectly alters belowground plant-insect interactions. The role of A. brasilense as part of an integrative pest management (IPM) program for the protection of corn against the South American corn rootworm, D. speciosa, is considered.

Limited Impact of a Fall-Seeded, Spring-Terminated Rye Cover Crop on Beneficial Arthropods.

Science.gov (United States)

Dunbar, Mike W; Gassmann, Aaron J; O'Neal, Matthew E

2017-04-01

Cover crops are beneficial to agroecosystems because they decrease soil erosion and nutrient loss while increasing within-field plant diversity. Greater plant diversity within cropping systems can positively affect beneficial arthropod communities. We hypothesized that increasing plant diversity within annually rotated corn and soybean with the addition of a rye cover crop would positively affect the beneficial ground and canopy-dwelling communities compared with rotated corn and soybean grown without a cover crop. From 2011 through 2013, arthropod communities were measured at two locations in Iowa four times throughout each growing season. Pitfall traps were used to sample ground-dwelling arthropods within the corn and soybean plots and sweep nets were used to measure the beneficial arthropods in soybean canopies. Beneficial arthropods captured were identified to either class, order, or family. In both corn and soybean, community composition and total community activity density and abundance did not differ between plots that included the rye cover crop and plots without the rye cover crop. Most taxa did not significantly respond to the presence of the rye cover crop when analyzed individually, with the exceptions of Carabidae and Gryllidae sampled from soybean pitfall traps. Activity density of Carabidae was significantly greater in soybean plots that included a rye cover crop, while activity density of Gryllidae was significantly reduced in plots with the rye cover crop. Although a rye cover crop may be agronomically beneficial, there may be only limited effects on beneficial arthropods when added within an annual rotation of corn and soybean. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mitigation of salt stress in white clover (Trifolium repens) by Azospirillum brasilense and its inoculation effect.

Science.gov (United States)

Khalid, Muhammad; Bilal, Muhammad; Hassani, Danial; Iqbal, Hafiz M N; Wang, Hang; Huang, Danfeng

2017-12-01

Salinity is one of the increasingly serious environmental problems worldwide for cultivating agricultural crops. The present study was aimed to ascertain the potential of beneficial soil bacterium Azospirillum brasilense to alleviate saline stress in Trifolium repens. Experimental plants (white clover) were grown from seeds and inoculated with or without A. brasilense bacterial strain supplemented with 0, 40, 80, or 120 mM NaCl into soil. The growth attributes including, shoot heights, root lengths, fresh and dry weights, leaf area and chlorophyll content were significantly enhanced in T. repens plants grown in A. brasilense inoculated soil than un-inoculated controls, particularly under elevated salinity conditions (40, 80 and 120 mM NaCl). Malondialdehyde content of leaf was recorded to be declined under saline conditions. Moreover, the K + /Na + ratio was also improved in bacterium-inoculated plants, since A. brasilense significantly reduced the root and shoot Na + level under high salty environment. Results revealed that soil inoculation with A. brasilense could significantly promote T. repens growth under both non-saline and saline environments, and this study might be extended to other vegetables and crops for the germination and growth enhancement.

Effect of a controlled burn on the thermophysical properties of a dry soil using a new model of soil heat flow and a new high temperature heat flux sensor

Science.gov (United States)

W. J. Massman; J. M. Frank

2004-01-01

Some fires can be beneficial to soils but, if a fire is sufficiently intense, soil can be irreversible altered. We measured soil temperatures and heat fluxes at several soil depths before, during, and after a controlled surface burn at Manitou Experimental Forest (southern Colorado, USA) to evaluate its effects on the soil's thermophysical properties (thermal...

Beneficial Insects: Beetles

OpenAIRE

Hodgson, Erin W.; Patterson, Ron

2007-01-01

There are many beneficial beetles in Utah besides lady beetles or ladybugs. Beetles can significantly reduce common insect and weed problems and in some cases eliminate the need for chemical control. Examples of beneficial beetles include: ground beetles, rove beetles, tiger beetles and tortoise beetles. Many of these beetles are native to Utah, while others have been purposely introduced to help control damage from exotic insect and weed pests.

A Sequential Statistical Approach towards an Optimized Production of a Broad Spectrum Bacteriocin Substance from a Soil Bacterium Bacillus sp. YAS 1 Strain

Directory of Open Access Journals (Sweden)

Amira M. Embaby

2014-01-01

Full Text Available Bacteriocins, ribosomally synthesized antimicrobial peptides, display potential applications in agriculture, medicine, and industry. The present study highlights integral statistical optimization and partial characterization of a bacteriocin substance from a soil bacterium taxonomically affiliated as Bacillus sp. YAS 1 after biochemical and molecular identifications. A sequential statistical approach (Plackett-Burman and Box-Behnken was employed to optimize bacteriocin (BAC YAS 1 production. Using optimal levels of three key determinants (yeast extract (0.48% (w/v, incubation time (62 hrs, and agitation speed (207 rpm in peptone yeast beef based production medium resulted in 1.6-fold enhancement in BAC YAS 1 level (470 AU/mL arbitrary units against Erwinia amylovora. BAC YAS 1 showed activity over a wide range of pH (1–13 and temperature (45–80°C. A wide spectrum antimicrobial activity of BAC YAS 1 against the human pathogens (Clostridium perfringens, Staphylococcus epidermidis, Campylobacter jejuni, Enterobacter aerogenes, Enterococcus sp., Proteus sp., Klebsiella sp., and Salmonella typhimurium, the plant pathogen (E. amylovora, and the food spoiler (Listeria innocua was demonstrated. On top and above, BAC YAS 1 showed no antimicrobial activity towards lactic acid bacteria (Lactobacillus bulgaricus, L. casei, L. lactis, and L. reuteri. Promising characteristics of BAC YAS 1 prompt its commercialization for efficient utilization in several industries.

Soil-Plant-Microbe Interactions in Stressed Agriculture Management: A Review

Institute of Scientific and Technical Information of China (English)

Shobhit Raj VIMAL; Jay Shankar SINGH; Naveen Kumar ARORA; Surendra SINGH

2017-01-01

The expected rise in temperature and decreased precipitation owing to climate change and unabated anthropogenic activities add complexity and uncertainty to agro-industry.The impact of soil nutrient imbalance,mismanaged use of chemicals,high temperature,flood or drought,soil salinity,and heavy metal pollutions,with regard to food security,is increasingly being explored worldwide.This review describes the role of soil-plant-microbe interactions along with organic manure in solving stressed agriculture problems.Beneficial microbes associated with plants are known to stimulate plant growth and enhance plant resistance to biotic (diseases) and abiotic (salinity,drought,pollutions,etc.) stresses.The plant growth-promoting rhizobacteria (PGPR) and mycorrhizae,a key component of soil microbiota,could play vital roles in the maintenance of plant fitness and soil health under stressed environments.The application of organic manure as a soil conditioner to stressed soils along with suitable microbial strains could further enhance the plant-microbe associations and increase the crop yield.A combination of plant,stress-tolerant microbe,and organic amendment represents the tripartite association to offer a favourable environment to the proliferation of beneficial rhizosphere microbes that in turn enhance the plant growth performance in disturbed agro-ecosystem.Agriculture land use patterns with the proper exploitation of plant-microbe associations,with compatible beneficial microbial agents,could be one of the most effective strategies in the management of the concerned agriculture lands owing to climate change resilience.However,the association of such microbes with plants for stressed agriculture management still needs to be explored in greater depth.

IMPROVED RISK ASSESSMENT AND REMEDIATION OF SOIL METALS BASED ON BIOAVAILABILITY MEASUREMENTS

Science.gov (United States)

Heavy metals in soils can comprise risk through plant uptake or soil ingestion. Recent research results and progress in understandings of risks and methods for soil metal remediation will be presented. Beneficial use of composts/bosolids plus limestone to remediate metal killed e...

[Degradation characteristics of naphthalene with a Pseudomonas aeruginosa strain isolated from soil contaminated by diesel].

Science.gov (United States)

Liu, Wen-Chao; Wu, Bin-Bin; Li, Xiao-Sen; Lu, Dian-Nan; Liu, Yong-Min

2015-02-01

Abstract: A naphthalene-degrading bacterium (referred as HD-5) was isolated from the diesel-contaminated soil and was assigned to Pseudomonas aeruginosa according to 16S rDNA sequences analysis. Gene nah, which encodes naphthalene dioxygenase, was identified from strain HD-5 by PCR amplification. Different bioremediation approaches, including nature attenuation, bioaugmentation with strain Pseudomonas aeruginosa, biostimulation, and an integrated degradation by bioaugmentation and biostimulation, were evaluated for their effectiveness in the remediating soil containing 5% naphthalene. The degradation rates of naphthalene in the soil were compared among the different bioremediation approaches, the FDA and dehydrogenase activity in bioremediation process were measured, and the gene copy number of 16S rRNA and nah in soil were dynamically monitored using real-time PCR. It was shown that the naphthalene removal rate reached 71.94%, 62.22% and 83.14% in approaches of bioaugmentation (B), biostimulation(S) and integrated degradation composed of bioaugmentation and biostimulation (BS), respectively. The highest removal rate of naphthalene was achieved by using BS protocol, which also gives the highest FDA and dehydrogenase activity. The gene copy number of 16S rRNA and nah in soil increased by about 2.67 x 10(11) g(-1) and 8.67 x 10(8) g(-1) after 31 days treatment using BS protocol. Above-mentioned results also demonstrated that the screened bacterium, Pseudomonas aeruginosa, could grow well in naphthalene-contaminated soil and effectively degrade naphthalene, which is of fundamental importance for bioremediation of naphthalene-contaminated soil.

Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems

Directory of Open Access Journals (Sweden)

Qisong Li

2018-02-01

Full Text Available Intercropping has been widely used to control disease and improve yield in agriculture. In this study, maize and peanut were used for non-separation intercropping (NS, semi-separation intercropping (SS using a nylon net, and complete separation intercropping (CS using a plastic sheet. In field experiments, two-year land equivalent ratios (LERs showed yield advantages due to belowground interactions when using NS and SS patterns as compared to monoculture. In contrast, intercropping without belowground interactions (CS showed a yield disadvantage. Meanwhile, in pot experiments, belowground interactions (found in NS and SS improved levels of soil-available nutrients (nitrogen (N and phosphorus (P and enzymes (urease and acid phosphomonoesterase as compared to intercropping without belowground interactions (CS. Soil bacterial community assay showed that soil bacterial communities in the NS and SS crops clustered together and were considerably different from the CS crops. The diversity of bacterial communities was significantly improved in soils with NS and SS. The abundance of beneficial bacteria, which have the functions of P-solubilization, pathogen suppression, and N-cycling, was improved in maize and peanut soils due to belowground interactions through intercropping. Among these bacteria, numbers of Bacillus, Brevibacillus brevis, and Paenibacillus were mainly increased in the maize rhizosphere. Burkholderia, Pseudomonas, and Rhizobium were mainly increased in the peanut rhizosphere. In conclusion, using maize and peanut intercropping, belowground interactions increased the numbers of beneficial bacteria in the soil and improved the diversity of the bacterial community, which was conducive to improving soil nutrient (N and P supply capacity and soil microecosystem stability.

Sporosalibacterium faouarense gen. nov., sp. nov., a moderately halophilic bacterium isolated from oil-contaminated soil.

Science.gov (United States)

Rezgui, Raja; Ben Ali Gam, Zouhaier; Ben Hamed, Said; Fardeau, Marie-Laure; Cayol, Jean-Luc; Maaroufi, Abderrazak; Labat, Marc

2011-01-01

A novel strictly anaerobic, moderately halophilic and mesophilic bacterium, designated strain SOL3f37(T), was isolated from a hydrocarbon-polluted soil surrounding a deep petroleum environment located in south Tunisia. Cells of strain SOL3f37(T) stained Gram-positive and were motile, straight and spore-forming. Strain SOL3f37(T) had a typical Gram-positive-type cell-wall structure, unlike the thick, multilayered cell wall of its closest relative Clostridiisalibacter paucivorans. The major fatty acids were iso-C(15 : 0) (41 %), iso-C(14 : 0) 3-OH and/or iso-C(15 : 0) dimethyl acetal (21.6 %), iso-C(13 : 0) (4.4 %), anteiso-C(15 : 0) (3.9 %) and iso-C(15 : 1) (2.8 %). Strain SOL3f37(T) grew between 20 and 48 °C (optimum 40 °C) and at pH 6.2-8.1 (optimum pH 6.9). Strain SOL3f37(T) required at least 0.5 NaCl l(-1) and grew in the presence of NaCl concentrations up to 150 g l(-1) (optimum 40 g l(-1)). Yeast extract (2 g l(-1)) was required for degradation of pyruvate, fumarate, fructose, glucose and mannitol. Also, strain SOL3f37(T) grew heterotrophically on yeast extract, peptone and bio-Trypticase, but was unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content was 30.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SOL3f37(T) was a member of the family Clostridiaceae in the order Clostridiales; strain SOL3f37(T) was related to members of various genera of the family Clostridiaceae. It exhibited highest 16S rRNA gene sequence similarity (93.4 %) with Clostridiisalibacter paucivorans 37HS60(T), 91.8 % with Thermohalobacter berrensis CTT3(T) and 91.7 % with Caloranaerobacter azorensis MV1087(T). On the basis of genotypic, phenotypic and phylogenetic data, it is suggested that strain SOL3f37(T) represents a novel species in a new genus. The name Sporosalibacterium faouarense gen. nov., sp. nov. is

Spectroscopic characterization of cell membranes and their constituents of the plant-associated soil bacterium Azospirillum brasilense

Science.gov (United States)

Kamnev, A. A.; Antonyuk, L. P.; Matora, L. Yu.; Serebrennikova, O. B.; Sumaroka, M. V.; Colina, M.; Renou-Gonnord, M.-F.; Ignatov, V. V.

1999-05-01

Structural and compositional features of bacterial membranes and some of their isolated constituents (cell surface lipopolysaccharide, phospholipids) of the plant-growth-promoting diazotrophic rhizobacterium Azospirillum brasilense (wild-type strain Sp245) were characterized using Fourier transform infrared (FTIR) spectroscopy and some other techniques. FTIR spectra of the cell membranes were shown to comprise the main vibration modes of the relevant lipopolysaccharide and protein components which are believed to be involved in associative plant-bacterium interactions, as well as of phospholipid constituents. The role and functions of metal cations in the structural organization and physicochemical properties of bacterial cell membranes are also discussed considering their accumulation in the membranes from the culture medium.

Effects of persistent insecticides on beneficial soil arthropod in conventional fields compared to organic fields, puducherry.

Science.gov (United States)

Anbarashan, Padmavathy; Gopalswamy, Poyyamoli

2013-07-15

The usage of synthetic fertilizers/insecticides in conventional farming has dramatically increased over the past decades. The aim of the study was to compare the effects of bio-pesticides and insecticides/pesticides on selected beneficial non targeted arthropods. Orders Collembola, Arachinida/Opiliones, Oribatida and Coleoptera were the main groups of arthropods found in the organic fields and Coleoptera, Oribatida, Gamasida and Collembola in conventional fields. Pesticides/insecticides had a significant effect on non-targeted arthropods order- Collembola, Arachinida/Opiliones, Hymenoptera and Thysonoptera were suppressed after pesticides/insecticides spraying. Bio-insecticides in organic fields had a non-significant effect on non targeted species and they started to increase in abundance after 7 days of spraying, whereas insecticide treatment in conventional fields had a significant long-term effect on non targeted arthropods and short term effect on pests/insects, it started to increase after 21 days of the spraying. These results indicate that insecticide treatment kept non targeted arthropods at low abundance. In conclusion, organic farming does not significantly affected the beneficial-non targeted arthropods biodiversity, whereas preventive insecticide application in conventional fields had significant negative effects on beneficial non targeted arthropods. Therefore, conventional farmers should restrict insecticide applications, unless pest densities reach the thresholds and more desirably can switch to organic farming practices.

Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization

Science.gov (United States)

Varman, Arul M.; He, Lian; Follenfant, Rhiannon; Wu, Weihua; Wemmer, Sarah; Wrobel, Steven A.; Tang, Yinjie J.; Singh, Seema

2016-01-01

Sphingobium sp. SYK-6 is a soil bacterium boasting a well-studied ligninolytic pathway and the potential for development into a microbial chassis for lignin valorization. An improved understanding of its metabolism will help researchers in the engineering of SYK-6 for the production of value-added chemicals through lignin valorization. We used 13C-fingerprinting, 13C metabolic flux analysis (13C-MFA), and RNA-sequencing differential expression analysis to uncover the following metabolic traits: (i) SYK-6 prefers alkaline conditions, making it an efficient host for the consolidated bioprocessing of lignin, and it also lacks the ability to metabolize sugars or organic acids; (ii) the CO2 release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO2 release from the sugar-based metabolism of Escherichia coli; (iii) the vanillin catabolic pathway (which is the converging point of majority of the lignin catabolic pathways) is coupled with the tetrahydrofolate-dependent C1 pathway that is essential for the biosynthesis of serine, histidine, and methionine; (iv) catabolic end products of lignin (pyruvate and oxaloacetate) must enter the tricarboxylic acid (TCA) cycle first and then use phosphoenolpyruvate carboxykinase to initiate gluconeogenesis; and (v) 13C-MFA together with RNA-sequencing differential expression analysis establishes the vanillin catabolic pathway as the major contributor of NAD(P)H synthesis. Therefore, the vanillin catabolic pathway is essential for SYK-6 to obtain sufficient reducing equivalents for its healthy growth; cosubstrate experiments support this finding. This unique energy feature of SYK-6 is particularly interesting because most heterotrophs rely on the transhydrogenase, the TCA cycle, and the oxidative pentose phosphate pathway to obtain NADPH. PMID:27634497

Abundant and stable char residues in soils: implications for soil fertility and carbon sequestration.

Science.gov (United States)

Mao, J-D; Johnson, R L; Lehmann, J; Olk, D C; Neves, E G; Thompson, M L; Schmidt-Rohr, K

2012-09-04

Large-scale soil application of biochar may enhance soil fertility, increasing crop production for the growing human population, while also sequestering atmospheric carbon. But reaching these beneficial outcomes requires an understanding of the relationships among biochar's structure, stability, and contribution to soil fertility. Using quantitative (13)C nuclear magnetic resonance (NMR) spectroscopy, we show that Terra Preta soils (fertile anthropogenic dark earths in Amazonia that were enriched with char >800 years ago) consist predominantly of char residues composed of ~6 fused aromatic rings substituted by COO(-) groups that significantly increase the soils' cation-exchange capacity and thus the retention of plant nutrients. We also show that highly productive, grassland-derived soils in the U.S. (Mollisols) contain char (generated by presettlement fires) that is structurally comparable to char in the Terra Preta soils and much more abundant than previously thought (~40-50% of organic C). Our findings indicate that these oxidized char residues represent a particularly stable, abundant, and fertility-enhancing form of soil organic matter.

Study on screening of anti-predator rhizosphere bacterium against Caenorhabditis elegans and its anti predation mechanism

Directory of Open Access Journals (Sweden)

HE Qingling

2016-08-01

Full Text Available Althoughmicrobial fertilizer is multi-effect,environmental friendly and long-term efficient,its practical application effect is but decreased for being prey by the other creators living in soil frequently.Many bacterium have developed their mechanisms that expel or kill worms to defend themselves from predators.Screening of anti-predator rhizosphere bacterium helps us to find out competitive plant growth promoting rhizobacteria(PGPR.Using Caenorhabditis elegans as sample,this study roughly observed two strains of biocontrol:Pseudomonas aurantiaca JD37 and Pseudomonas fluorescens P13.Using Escherichia coli OP50 as control group,we find the preference order of worms,from highest to lowest,is P13,OP50 and JD37.In slow killing assay,the death rate of worms for JD37 and P13 are 26.12% and 18.66% respectively.The activity and reproduction rate of C.elegans decrease when it is fed on JD37.The results of chemical and micro-biological study show that JD37 cannot produce any currently studied second metabolites which kill worms,while P13 can produce Hydrogen cyanide (HCN.All these results show that JD37 has the ability of anti-predator,and is more competitive under predation pressure,which suggests its broad application prospect as microbial fertilizer.

Glyphosate-Induced Specific and Widespread Perturbations in the Metabolome of Soil Pseudomonas Species

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Ludmilla Aristilde

2017-06-01

Full Text Available Previous studies have reported adverse effects of glyphosate on crop-beneficial soil bacterial species, including several soil Pseudomonas species. Of particular interest is the elucidation of the metabolic consequences of glyphosate toxicity in these species. Here we investigated the growth and metabolic responses of soil Pseudomonas species grown on succinate, a common root exudate, and glyphosate at different concentrations. We conducted our experiments with one agricultural soil isolate, P. fluorescens RA12, and three model species, P. putida KT2440, P. putida S12, and P. protegens Pf-5. Our results demonstrated both species- and strain-dependent growth responses to glyphosate. Following exposure to a range of glyphosate concentrations (up to 5 mM, the growth rate of both P. protegens Pf-5 and P. fluorescens RA12 remained unchanged whereas the two P. putida strains exhibited from 0 to 100% growth inhibition. We employed a 13C-assisted metabolomics approach using liquid chromatography-mass spectrometry to monitor disruptions in metabolic homeostasis and fluxes. Profiling of the whole-cell metabolome captured deviations in metabolite levels involved in the tricarboxylic acid cycle, ribonucleotide biosynthesis, and protein biosynthesis. Altered metabolite levels specifically in the biosynthetic pathway of aromatic amino acids (AAs, the target of toxicity for glyphosate in plants, implied the same toxicity target in the soil bacterium. Kinetic flux experiments with 13C-labeled succinate revealed that biosynthetic fluxes of the aromatic AAs were not inhibited in P. fluorescens Pf-5 in the presence of low and high glyphosate doses but these fluxes were inhibited by up to 60% in P. putida KT2440, even at sub-lethal glyphosate exposure. Notably, the greatest inhibition was found for the aromatic AA tryptophan, an important precursor to secondary metabolites. When the growth medium was supplemented with aromatic AAs, P. putida S12 exposed to a lethal

A novel interaction between plant-beneficial rhizobacteria and roots: colonization induces corn resistance against the root herbivore Diabrotica speciosa.

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Franciele Santos

Full Text Available A number of soil-borne microorganisms, such as mycorrhizal fungi and rhizobacteria, establish mutualistic interactions with plants, which can indirectly affect other organisms. Knowledge of the plant-mediated effects of mutualistic microorganisms is limited to aboveground insects, whereas there is little understanding of what role beneficial soil bacteria may play in plant defense against root herbivory. Here, we establish that colonization by the beneficial rhizobacterium Azospirillum brasilense affects the host selection and performance of the insect Diabrotica speciosa. Root larvae preferentially orient toward the roots of non-inoculated plants versus inoculated roots and gain less weight when feeding on inoculated plants. As inoculation by A. brasilense induces higher emissions of (E-β-caryophyllene compared with non-inoculated plants, it is plausible that the non-preference of D. speciosa for inoculated plants is related to this sesquiterpene, which is well known to mediate belowground insect-plant interactions. To the best of our knowledge, this is the first study showing that a beneficial rhizobacterium inoculant indirectly alters belowground plant-insect interactions. The role of A. brasilense as part of an integrative pest management (IPM program for the protection of corn against the South American corn rootworm, D. speciosa, is considered.

Electrostatic beneficiation of coal

Energy Technology Data Exchange (ETDEWEB)

Mazumder, M.K.; Tennal, K.B.; Lindquist, D.

1994-10-01

Dry physical beneficiation of coal has many advantages over wet cleaning methods and post combustion flue gas cleanup processes. The dry beneficiation process is economically competitive and environmentally safe and has the potential of making vast amounts of US coal reserves available for energy generation. While the potential of the electrostatic beneficiation has been studied for many years in laboratories and in pilot plants, a successful full scale electrostatic coal cleaning plant has not been commercially realized yet. In this paper the authors review some of the technical problems that are encountered in this method and suggest possible solutions that may lead toward its full utilization in cleaning coal.

Dense populations of a giant sulfur bacterium in Namibian shelf sediments

DEFF Research Database (Denmark)

Schulz, HN; Brinkhoff, T.; Ferdelman, TG

1999-01-01

A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system. The bacterium has a spherical cell that exceeds by up to 100-fold the biovolume of the largest known prokaryotes. On the basis of 16S ribosomal DNA...

Produced Water Management and Beneficial Use

International Nuclear Information System (INIS)

Brown, Terry; Frost, Carol; Hayes, Thomas; Heath, Leo; Johnson, Drew; Lopez, David; Saffer, Demian; Urynowicz, Michael; Wheaton, John; Zoback, Mark

2007-01-01

Large quantities of water are associated with the production of coalbed methane (CBM) in the Powder River Basin (PRB) of Wyoming. The chemistry of co-produced water often makes it unsuitable for subsequent uses such as irrigated agriculture. However, co-produced waters have substantial potential for a variety of beneficial uses. Achieving this potential requires the development of appropriate water management strategies. There are several unique characteristics of co-produced water that make development of such management strategies a challenge. The production of CBM water follows an inverse pattern compared to traditional wells. CBM wells need to maintain low reservoir pressures to promote gas production. This need renders the reinjection of co-produced waters counterproductive. The unique water chemistry of co-produced water can reduce soil permeability, making surface disposal difficult. Unlike traditional petroleum operations where co-produced water is an undesirable by-product, co-produced water in the PRB often is potable, making it a highly valued resource in arid western states. This research project developed and evaluated a number of water management options potentially available to CBM operators. These options, which focus on cost-effective and environmentally-sound practices, fall into five topic areas: Minimization of Produced Water, Surface Disposal, Beneficial Use, Disposal by Injection and Water Treatment. The research project was managed by the Colorado Energy Research Institute (CERI) at the Colorado School of Mines (CSM) and involved personnel located at CERI, CSM, Stanford University, Pennsylvania State University, the University of Wyoming, the Argonne National Laboratory, the Gas Technology Institute, the Montana Bureau of Mining and Geology and PVES Inc., a private firm

Produced Water Management and Beneficial Use

Energy Technology Data Exchange (ETDEWEB)

Terry Brown; Carol Frost; Thomas Hayes; Leo Heath; Drew Johnson; David Lopez; Demian Saffer; Michael Urynowicz; John Wheaton; Mark Zoback

2007-10-31

Large quantities of water are associated with the production of coalbed methane (CBM) in the Powder River Basin (PRB) of Wyoming. The chemistry of co-produced water often makes it unsuitable for subsequent uses such as irrigated agriculture. However, co-produced waters have substantial potential for a variety of beneficial uses. Achieving this potential requires the development of appropriate water management strategies. There are several unique characteristics of co-produced water that make development of such management strategies a challenge. The production of CBM water follows an inverse pattern compared to traditional wells. CBM wells need to maintain low reservoir pressures to promote gas production. This need renders the reinjection of co-produced waters counterproductive. The unique water chemistry of co-produced water can reduce soil permeability, making surface disposal difficult. Unlike traditional petroleum operations where co-produced water is an undesirable by-product, co-produced water in the PRB often is potable, making it a highly valued resource in arid western states. This research project developed and evaluated a number of water management options potentially available to CBM operators. These options, which focus on cost-effective and environmentally-sound practices, fall into five topic areas: Minimization of Produced Water, Surface Disposal, Beneficial Use, Disposal by Injection and Water Treatment. The research project was managed by the Colorado Energy Research Institute (CERI) at the Colorado School of Mines (CSM) and involved personnel located at CERI, CSM, Stanford University, Pennsylvania State University, the University of Wyoming, the Argonne National Laboratory, the Gas Technology Institute, the Montana Bureau of Mining and Geology and PVES Inc., a private firm.

Modification of soil nutrients and micro-climate by tree crowns in a ...

African Journals Online (AJOL)

The findings on soil nutrient status are consistent with results from disturbed systems, and challenge the dogma, at least for soil nutrient status, that conservative stocking rates are beneficial. Keywords: botany; crown interception; Matopos Research Station; micro-climate; nutrients; semi-arid; shade-adapted; shading; soil ...

Degradation of phenanthrene and pyrene using genetically engineered dioxygenase producing Pseudomonas putida in soil

Directory of Open Access Journals (Sweden)

Mardani Gashtasb

2016-01-01

Full Text Available Bioremediation use to promote degradation and/or removal of contaminants into nonhazardous or less-hazardous substances from the environment using microbial metabolic ability. Pseudomonas spp. is one of saprotrophic soil bacterium and can be used for biodegradation of polycyclic aromatic hydrocarbons (PAHs but this activity in most species is weak. Phenanthrene and pyrene could associate with a risk of human cancer development in exposed individuals. The aim of the present study was application of genetically engineered P. putida that produce dioxygenase for degradation of phenanthrene and pyrene in spiked soil using high-performance liquid chromatography (HPLC method. The nahH gene that encoded catechol 2,3-dioxygenase (C23O was cloned into pUC18 and pUC18-nahH recombinant vector was generated and transformed into wild P. putida, successfully. The genetically modified and wild types of P. putida were inoculated in soil and pilot plan was prepared. Finally, degradation of phenanthrene and pyrene by this bacterium in spiked soil were evaluated using HPLC measurement technique. The results were showed elimination of these PAH compounds in spiked soil by engineered P. putida comparing to dishes containing natural soil with normal microbial flora and inoculated autoclaved soil by wild type of P. putida were statistically significant (p0.05 but it was few impact on this process (more than 2%. Additional and verification tests including catalase, oxidase and PCR on isolated bacteria from spiked soil were indicated that engineered P. putida was alive and functional as well as it can affect on phenanthrene and pyrene degradation via nahH gene producing. These findings indicated that genetically engineered P. putida generated in this work via producing C23O enzyme can useful and practical for biodegradation of phenanthrene and pyrene as well as petroleum compounds in polluted environments.

Moritella viscosa, a pathogenic bacterium affecting the fillet quality in fish

DEFF Research Database (Denmark)

Ingerslev, Hans-Christian; Nielsen, Michael Engelbrecht

2011-01-01

Moritella viscosa is a bacterium belonging to the family Moritellaceae and was formerly known as Vibrio viscosus. The name ‘viscosa’ originates from the slimy nature of the bacterium. M. viscosa is considered to be the main causative agent of the phenomenon ‘winter ulcer’ or ‘cold-water ulcer......’ which affects various fish species in seawater during cold periods (Lunder et al. 1995). The bacterium is mainly a problem for farmed salmonid species, such as Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), but has also been isolated from other fish species, including Atlantic...... market price because of a quality downgrade caused by textural changes in the fillet....

Persistence of Two Campylobacter jejuni Strains in Soil and on Spinach Plants

International Nuclear Information System (INIS)

Jaderlund, L.; Arthurson, V.; Sessitsch, A.

2011-01-01

There are indications that the more frequent use of untreated organic residues for fertilization results in increased risk of contamination with human pathogens. Here, we evaluate the ability of two different strains of Campylobacter jejuni to persist in manure and soil as well as spread to spinach plants. It was revealed that different strategies for inoculation of C. jejuni contribute to the persistence of the bacterium in soil, roots, and shoots. Upon inoculation of the bacteria into manure prior to soil application, the amount of C. jejuni subsequently recovered in soil was higher than that from treatments involving the addition of C. jejuni cells to the soil after plant emergence. Irrespective of the bacterial inoculation dose and strategy employed, the C. jejuni content in soil remained relatively constant, whereas the majority of C. jejuni cells applied to spinach leaves could be recovered during the whole evaluation period of 21 days.

Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling.

Science.gov (United States)

Lidbury, Ian D E A; Murrell, J Colin; Chen, Yin

2015-03-01

Bacteria of the marine Roseobacter clade are characterised by their ability to utilise a wide range of organic and inorganic compounds to support growth. Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are methylated amines (MA) and form part of the dissolved organic nitrogen pool, the second largest source of nitrogen after N2 gas, in the oceans. We investigated if the marine heterotrophic bacterium, Ruegeria pomeroyi DSS-3, could utilise TMA and TMAO as a supplementary energy source and whether this trait had any beneficial effect on growth. In R. pomeroyi, catabolism of TMA and TMAO resulted in the production of intracellular ATP which in turn helped to enhance growth rate and growth yield as well as enhancing cell survival during prolonged energy starvation. Furthermore, the simultaneous use of two different exogenous energy sources led to a greater enhancement of chemoorganoheterotrophic growth. The use of TMA and TMAO primarily as an energy source resulted in the remineralisation of nitrogen in the form of ammonium, which could cross feed into another bacterium. This study provides greater insight into the microbial metabolism of MAs in the marine environment and how it may affect both nutrient flow within marine surface waters and the flux of these climatically important compounds into the atmosphere.

Fermentation products of solvent tolerant marine bacterium Moraxella spp. MB1 and its biotechnological applications in salicylic acid bioconversion.

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Solimabi Wahidullah

Full Text Available As part of a proactive approach to environmental protection, emerging issues with potential impact on the environment is the subject of ongoing investigation. One emerging area of environmental research concerns pharmaceuticals like salicylic acid, which is the main metabolite of various analgesics including aspirin. It is a common component of sewage effluent and also an intermediate in the degradation pathway of various aromatic compounds which are introduced in the marine environment as pollutants. In this study, biotransformation products of salicylic acid by seaweed, Bryopsis plumosa, associated marine bacterium, Moraxella spp. MB1, have been investigated. Phenol, conjugates of phenol and hydroxy cinnamic acid derivatives (coumaroyl, caffeoyl, feruloyl and trihydroxy cinnamyl with salicylic acid (3-8 were identified as the bioconversion products by electrospray ionization mass spectrometry. These results show that the microorganism do not degrade phenolic acid but catalyses oxygen dependent transformations without ring cleavage. The degradation of salicylic acid is known to proceed either via gentisic acid pathway or catechol pathway but this is the first report of biotransformation of salicylic acid into cinnamates, without ring cleavage. Besides cinnamic acid derivatives (9-12, metabolites produced by the bacterium include antimicrobial indole (13 and β-carbolines, norharman (14, harman (15 and methyl derivative (16, which are beneficial to the host and the environment.

Managing for soil health can suppress pests

Directory of Open Access Journals (Sweden)

Amanda Hodson

2016-08-01

Full Text Available A “healthy” soil can be thought of as one that functions well, both agronomically and ecologically, and one in which soil biodiversity and crop management work in synergy to suppress pests and diseases. UC researchers have pioneered many ways of managing soil biology for pest management, including strategies such as soil solarization, steam treatment and anaerobic soil disinfestation, as well as improvements on traditional methods, such as reducing tillage, amending soil with organic materials, and cover cropping. As managing for soil health becomes more of an explicit focus due to restrictions on the use of soil fumigants, integrated soil health tests will be needed that are validated for use in California. Other research needs include breeding crops for disease resistance and pest suppressive microbial communities as well as knowledge of how beneficial organisms influence plant health.

Effects of different soil management practices on soil properties and microbial diversity

Science.gov (United States)

Gajda, Anna M.; Czyż, Ewa A.; Dexter, Anthony R.; Furtak, Karolina M.; Grządziel, Jarosław; Stanek-Tarkowska, Jadwiga

2018-01-01

The effects of different tillage systems on the properties and microbial diversity of an agricultural soil was investigated. In doing so, soil physical, chemical and biological properties were analysed in 2013-2015, on a long-term field experiment on a loamy sand at the IUNG-PIB Experimental Station in Grabów, Poland. Winter wheat was grown under two tillage treatments: conventional tillage using a mouldboard plough and traditional soil tillage equipment, and reduced tillage based on soil crushing-loosening equipment and a rigid-tine cultivator. Chopped wheat straw was used as a mulch on both treatments. Reduced tillage resulted in increased water content throughout the whole soil profile, in comparison with conventional tillage. Under reduced tillage, the content of readily dispersible clay was also reduced, and, therefore, soil stability was increased in the toplayers, compared with conventional tillage. In addition, the beneficial effects of reduced tillage were reflected in higher soil microbial activity as measured with dehydrogenases and hydrolysis of fluorescein diacetate, compared with conventional tillage. Moreover, the polimerase chain reaction - denaturing gradient gel electrophoresis analysis showed that soil under reduced till-age had greater diversity of microbial communities, compared with conventionally-tilled soil. Finally, reduced tillage increased organic matter content, stability in water and microbial diversity in the top layer of the soil.

Pantoea agglomerans: a marvelous bacterium of evil and good.Part I. Deleterious effects: Dust-borne endotoxins and allergens - focus on cotton dust.

Science.gov (United States)

Dutkiewicz, Jacek; Mackiewicz, Barbara; Lemieszek, Marta Kinga; Golec, Marcin; Milanowski, Janusz

2015-01-01

The ubiquitous Gram-negative bacterium Pantoea agglomerans (synonyms: Enterobacter agglomerans, Erwinia herbicola) is known both as an epiphytic microbe developing on the surface of plants and as an endophytic organism living inside the plants. The bacterium occurs also abundantly in plant and animal products, in the body of arthropods and other animals, in water, soil, dust and air, and occasionally in humans. From the human viewpoint, the role of this organism is ambiguous, both deleterious and beneficial: on one side it causes disorders in people exposed to inhalation of organic dusts and diseases of crops, and on the other side it produces substances effective in the treatment of cancer and other diseases of humans and animals, suppresses the development of various plant pathogens, promotes plant growth, and appears as a potentially efficient biofertilizer and bioremediator. P. agglomerans was identified as a predominant bacterium on cotton plant grown all over the world, usually as an epiphyte, rarely as pathogen. It is particularly numerous on cotton bract after senescence. During processing of cotton in mills, bacteria and their products are released with cotton dust into air and are inhaled by workers, causing respiratory and general disorders, usually defined as byssinosis. The most adverse substance is endotoxin, a heteropolymer macromolecule present in the outermost part of the cell wall, consisting of lipopolysaccharide (LPS) as a major constituent, phospholipids and protein. The numerous experiments carried out in last quarter of XXth century on laboratory animals and human volunteers supported a convincing evidence that the inhaled endotoxin produced by P. agglomerans causes numerous pathologic effects similar to those elicited by cotton dust, such as influx of free lung cells into airways and activation of alveolar macrophages which secrete mediators (prostaglandins, platelet-activating factor, interleukin-1, tumor necrosis factor) that cause

Isolation and Characterization of Burkholderia rinojensis sp. nov., a Non-Burkholderia cepacia Complex Soil Bacterium with Insecticidal and Miticidal Activities

Science.gov (United States)

Fernandez, Lorena E.; Koivunen, Marja; Yang, April; Flor-Weiler, Lina; Marrone, Pamela G.

2013-01-01

Isolate A396, a bacterium isolated from a Japanese soil sample demonstrated strong insecticidal and miticidal activities in laboratory bioassays. The isolate was characterized through biochemical methods, fatty acid methyl ester (FAME) analysis, sequencing of 16S rRNA, multilocus sequence typing and analysis, and DNA-DNA hybridization. FAME analysis matched A396 to Burkholderia cenocepacia, but this result was not confirmed by 16S rRNA or DNA-DNA hybridization. 16S rRNA sequencing indicated closest matches with B. glumae and B. plantarii. DNA-DNA hybridization experiments with B. plantarii, B. glumae, B. multivorans, and B. cenocepacia confirmed the low genetic similarity (11.5 to 37.4%) with known members of the genus. PCR-based screening showed that A396 lacks markers associated with members of the B. cepacia complex. Bioassay results indicated two mechanisms of action: through ingestion and contact. The isolate effectively controlled beet armyworms (Spodoptera exigua; BAW) and two-spotted spider mites (Tetranychus urticae; TSSM). In diet overlay bioassays with BAW, 1% to 4% (vol/vol) dilution of the whole-cell broth caused 97% to 100% mortality 4 days postexposure, and leaf disc treatment bioassays attained 75% ± 22% mortality 3 days postexposure. Contact bioassays led to 50% larval mortality, as well as discoloration, stunting, and failure to molt. TSSM mortality reached 93% in treated leaf discs. Activity was maintained in cell-free supernatants and after heat treatment (60°C for 2 h), indicating that a secondary metabolite or excreted thermostable enzyme might be responsible for the activity. Based on these results, we describe the novel species Burkholderia rinojensis, a good candidate for the development of a biocontrol product against insect and mite pests. PMID:24096416

Soil organism in organic and conventional cropping systems.

OpenAIRE

Bettiol, Wagner; Ghini, Raquel; Galvão, José Abrahão Haddad; Ligo, Marcos Antônio Vieira; Mineiro, Jeferson Luiz de Carvalho

2002-01-01

Despite the recent interest in organic agriculture, little research has been carried out in this area. Thus, the objective of this study was to compare, in a dystrophic Ultisol, the effects of organic and conventional agricultures on soil organism populations, for the tomato (Lycopersicum esculentum) and corn (Zea mays) crops. In general, it was found that fungus, bacterium and actinomycet populations counted by the number of colonies in the media, were similar for the two cropping systems. C...

Beneficial Use of Scrap Tire Rubber in Low-volume Road and Bridge Construction with Expansive Soils

Science.gov (United States)

2010-07-14

Billions of dollars in damages are attributed to expansive soils in the United States (Jones and Jones 1987) and in many other countries each year. Geotechnical design and analyses in/on/with expansive soils may involve additional complications that ...

The Prevalence and Distribution of Neurodegenerative Compound-Producing Soil Streptomyces spp.

Science.gov (United States)

Watkins, Anna L.; Ray, Arpita; R. Roberts, Lindsay; Caldwell, Kim A.; Olson, Julie B.

2016-01-01

Recent work from our labs demonstrated that a metabolite(s) from the soil bacterium Streptomyces venezuelae caused dopaminergic neurodegeneration in Caenorhabditis elegans and human neuroblastoma cells. To evaluate the capacity for metabolite production by naturally occurring streptomycetes in Alabama soils, Streptomyces were isolated from soils under different land uses (agriculture, undeveloped, and urban). More isolates were obtained from agricultural than undeveloped soils; there was no significant difference in the number of isolates from urban soils. The genomic diversity of the isolates was extremely high, with only 112 of the 1509 isolates considered clones. A subset was examined for dopaminergic neurodegeneration in the previously established C. elegans model; 28.3% of the tested Streptomyces spp. caused dopaminergic neurons to degenerate. Notably, the Streptomyces spp. isolates from agricultural soils showed more individual neuron damage than isolates from undeveloped or urban soils. These results suggest a common environmental toxicant(s) within the Streptomyces genus that causes dopaminergic neurodegeneration. It could also provide a possible explanation for diseases such as Parkinson’s disease (PD), which is widely accepted to have both genetic and environmental factors. PMID:26936423

Basic soil benefits from ash utilization

Energy Technology Data Exchange (ETDEWEB)

Martens, D.C.; Plank, C.O.

1970-01-01

The beneficial effects of fly ash application shown herein are expected to encourage future disposal of the material in agricultural soils. It is foreseen, however, that fly ash disposal in agricultural soils would be unsuccessful if adverse effects on crop production result from its misuse. It seems evident, therefore, that quality control measures will be required to insure proper disposal of the material in agricultural soils. It will be necessary to consider differences in chemical properties of various samples of fly ash and in chemical reactions of samples of fly ash and soils. Differences in tolerances of plants to soluble salt damage and to specific nutrient deficiencies and toxicities will also have to be taken into account. 9 tables.

Pantoea agglomerans: a marvelous bacterium of evil and good.Part I. Deleterious effects: Dust-borne endotoxins and allergens – focus on cotton dust

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Jacek Dutkiewicz

2015-12-01

Full Text Available The ubiquitous Gram-negative bacterium Pantoea agglomerans (synonyms: Enterobacter agglomerans, Erwinia herbicola is known both as an epiphytic microbe developing on the surface of plants and as an endophytic organism living inside the plants. The bacterium occurs also abundantly in plant and animal products, in the body of arthropods and other animals, in water, soil, dust and air, and occasionally in humans. From the human viewpoint, the role of this organism is ambiguous, both deleterious and beneficial: on one side it causes disorders in people exposed to inhalation of organic dusts and diseases of crops, and on the other side it produces substances effective in the treatment of cancer and other diseases of humans and animals, suppresses the development of various plant pathogens, promotes plant growth, and appears as a potentially efficient biofertilizer and bioremediator. P. agglomerans was identified as a predominant bacterium on cotton plant grown all over the world, usually as an epiphyte, rarely as pathogen. It is particularly numerous on cotton bract after senescence. During processing of cotton in mills, bacteria and their products are released with cotton dust into air and are inhaled by workers, causing respiratory and general disorders, usually defined as byssinosis. The most adverse substance is endotoxin, a heteropolymer macromolecule present in the outermost part of the cell wall, consisting of lipopolysaccharide (LPS as a major constituent, phospholipids and protein. The numerous experiments carried out in last quarter of XXth century on laboratory animals and human volunteers supported a convincing evidence that the inhaled endotoxin produced by P. agglomerans causes numerous pathologic effects similar to those elicited by cotton dust, such as influx of free lung cells into airways and activation of alveolar macrophages which secrete mediators (prostaglandins, platelet-activating factor, interleukin-1, tumor necrosis factor

Pantoea agglomerans : a marvelous bacterium of evil and good. Part I. Deleterious effects: Dust-borne endotoxins and allergens – focus on cotton dust

Directory of Open Access Journals (Sweden)

Jacek Dutkiewicz

2015-12-01

Full Text Available The ubiquitous Gram-negative bacterium Pantoea agglomerans (synonyms: Enterobacter agglomerans , Erwinia herbicola is known both as an epiphytic microbe developing on the surface of plants and as an endophytic organism living inside the plants. The bacterium occurs also abundantly in plant and animal products, in the body of arthropods and other animals, in water, soil, dust and air, and occasionally in humans. From the human viewpoint, the role of this organism is ambiguous, both deleterious and beneficial: on one side it causes disorders in people exposed to inhalation of organic dusts and diseases of crops, and on the other side it produces substances effective in the treatment of cancer and other diseases of humans and animals, suppresses the development of various plant pathogens, promotes plant growth, and appears as a potentially efficient biofertilizer and bioremediator. P. agglomerans was identified as a predominant bacterium on cotton plant grown all over the world, usually as an epiphyte, rarely as pathogen. It is particularly numerous on cotton bract after senescence. During processing of cotton in mills, bacteria and their products are released with cotton dust into air and are inhaled by workers, causing respiratory and general disorders, usually defined as byssinosis. The most adverse substance is endotoxin, a heteropolymer macromolecule present in the outermost part of the cell wall, consisting of lipopolysaccharide (LPS as a major constituent, phospholipids and protein. The numerous experiments carried out in last quarter of XXth century on laboratory animals and human volunteers supported a convincing evidence that the inhaled endotoxin produced by P. agglomerans causes numerous pathologic effects similar to those elicited by cotton dust, such as influx of free lung cells into airways and activation of alveolar macrophages which secrete mediators (prostaglandins, platelet-activating factor, interleukin-1, tumor necrosis factor

ISOLATION AND CHARACTERIZATION OF A MOLYBDENUM-REDUCING AND AZO-DYE DECOLORIZING SERRATIA MARCESCENS STRAIN NENI-1 FROM INDONESIAN SOIL

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Neni Gusmanizar

2016-01-01

Full Text Available Heavy metals and organic xenobiotics including dyes are important industrial components with their usage amounting to the millions of tonnes yearly. Their presence in the environment is a serious pollution issue globally. Bioremediation of these pollutants using microbes with multiple detoxification capacity is constantly being sought. In this work we screen the ability of a molybdenum-reducing bacterium isolated from contaminated soil to decolorize various azo and triphenyl methane dyes. The bacterium reduces molybdate to molybdenum blue (Mo-blue optimally at pH 6.0, and temperatures of between 25 and 40oC. Glucose was the best electron donor for supporting molybdate reduction followed by sucrose, trehalose, maltose, d-sorbitol, dmannitol, d-mannose, myo-inositol, glycerol and salicin in descending order. Other requirements include a phosphate concentration of between 5.0 and 7.5 mM and a molybdate concentration between 10 and 20 mM. The absorption spectrum of the Moblue produced was similar to previous Mo-reducing bacterium, and closely resembles a reduced phosphomolybdate. Molybdenum reduction was inhibited by copper, silver and mercury at 2 ppm by 43.8%, 42.3% and 41.7%, respectively. We screen for the ability of the bacterium to decolorize various dyes. The bacterium was able to decolorize the dye Congo Red. Biochemical analysis resulted in a tentative identification of the bacterium as Serratia marcescens strain Neni-1. The ability of this bacterium to detoxify molybdenum and decolorize azo dye makes this bacterium an important tool for bioremediation.

Diversity and natural functions of antibiotices produced by beneficial and pathogenic soil bacteria

Science.gov (United States)

Soil and plant-associated environments harbor numerous bacterial species that produce antibiotic metabolites. Many of these bacteria have been exploited for the discovery of clinical antibiotics and other therapeutics. In the field of plant pathology, antibiotic-producing bacteria are used as a reso...

Proposal and Research Direction of Soil Mass Organic Reorganization

Science.gov (United States)

Zhang, Lu; Han, Jichang

2018-01-01

Land engineering as a new discipline has been temporarily outrageous. The proposition of soil body organic reorganization undoubtedly enriches the research content for the construction of land engineering disciplines. Soil body organic reconstruction is designed to study how to realize the ecological ecology of the land by studying the external force of nature, to study the influence of sunlight, wind and water on soil body, how to improve the soil physical structure, to further strengthen the research of biological enzymes and microbes, and promote the release and utilization of beneficial inert elements in soil body. The emerging of frontier scientific research issues with soil body organic reorganization to indicate directions for the future development of soil engineering.

Lactococcus lactis - a diploid bacterium

DEFF Research Database (Denmark)

Michelsen, Ole; Hansen, Flemming G.; Jensen, Peter Ruhdal

the next division. Thus, the regions of the chromosome that are the last to be replicated are haploid even in fast-growing bacteria. In contrast to this general rule for bacteria, we found that Lactococcus lactis, a bacterium which has been exploited for thousands of years for the production of fermented...... milk products, is born with two complete non-replicating chromosomes. L. lactis therefore remain diploid throughout its entire life cycle....

Degradation of 14C-parathion 'in vitro' by microorganisms isolated from a gley humic soil

International Nuclear Information System (INIS)

Andrea, M.M. de; Ruegg, E.F.

1982-01-01

It was determined 'in vitro' the degradation of Parathion by a bacterium and a fungus isolated from a sample of Gley Humic soil previously treated with repeated applications of the insecticide. In a qualitative colorimetric assay hydrolisis of parathion to p-nitrophenol just the bacterium gave a positive answer. In quantitative assays of 14 C-parathion degradation in culture media containing both microorganisms, organic solvents extractions resulted in organic and aqueous phases, which were analysed by liquid scintillation counting and thin-layer chromatography. In a mineral salts medium plus buffer, the bacterium and the fungus behaved differently from the control, because part of the 14 C-insecticide was metabolized to, at least, one metabolite and besides, the microorganisms presented smaller percentages of total recovery. The largest percentage of the radio carbon recovery from the extracts of the medium containing the fungus plus extract of yeast, was obtained from the aqueous phase and the existence of other metabolite was demonstrated by chromatograms of the organic phase. (Author) [pt

An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia.

Science.gov (United States)

Berney, Michael; Greening, Chris; Conrad, Ralf; Jacobs, William R; Cook, Gregory M

2014-08-05

Oxygen availability is a major factor and evolutionary force determining the metabolic strategy of bacteria colonizing an environmental niche. In the soil, conditions can switch rapidly between oxia and anoxia, forcing soil bacteria to remodel their energy metabolism accordingly. Mycobacterium is a dominant genus in the soil, and all its species are obligate aerobes. Here we show that an obligate aerobe, the soil actinomycete Mycobacterium smegmatis, adopts an anaerobe-type strategy by activating fermentative hydrogen production to adapt to hypoxia. This process is controlled by the two-component system DosR-DosS/DosT, an oxygen and redox sensor that is well conserved in mycobacteria. We show that DosR tightly regulates the two [NiFe]-hydrogenases: Hyd3 (MSMEG_3931-3928) and Hyd2 (MSMEG_2719-2718). Using genetic manipulation and high-sensitivity GC, we demonstrate that Hyd3 facilitates the evolution of H2 when oxygen is depleted. Combined activity of Hyd2 and Hyd3 was necessary to maintain an optimal NAD(+)/NADH ratio and enhanced adaptation to and survival of hypoxia. We demonstrate that fermentatively-produced hydrogen can be recycled when fumarate or oxygen become available, suggesting Mycobacterium smegmatis can switch between fermentation, anaerobic respiration, and aerobic respiration. Hydrogen metabolism enables this obligate aerobe to rapidly meet its energetic needs when switching between microoxic and anoxic conditions and provides a competitive advantage in low oxygen environments.

Long-Term Coffee Monoculture Alters Soil Chemical Properties and Microbial Communities.

Science.gov (United States)

Zhao, Qingyun; Xiong, Wu; Xing, Yizhang; Sun, Yan; Lin, Xingjun; Dong, Yunping

2018-04-17

Long-term monoculture severely inhibits coffee plant growth, decreases its yield and results in serious economic losses in China. Here, we selected four replanted coffee fields with 4, 18, 26 and 57 years of monoculture history in Hainan China to investigate the influence of continuous cropping on soil chemical properties and microbial communities. Results showed long-term monoculture decreased soil pH and organic matter content and increased soil EC. Soil bacterial and fungal richness decreased with continuous coffee cropping. Principal coordinate analysis suggested monoculture time was a major determinant of bacterial and fungal community structures. Relative abundances of bacterial Proteobacteria, Bacteroidetes and Nitrospira and fungal Ascomycota phyla decreased over time. At genus level, potentially beneficial microbes such as Nitrospira and Trichoderma, significantly declined over time and showed positive relationships with coffee plant growth in pots. In conclusion, continuous coffee cropping decreased soil pH, organic matter content, potentially beneficial microbes and increased soil EC, which might lead to the poor growth of coffee plants in pots and decline of coffee yields in fields. Thus, developing sustainable agriculture to improve soil pH, organic matter content, microbial activity and reduce the salt stress under continuous cropping system is important for coffee production in China.

Endohyphal bacterium enhances production of indole-3-acetic acid by a foliar fungal endophyte.

Directory of Open Access Journals (Sweden)

Michele T Hoffman

Full Text Available Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA, often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales, but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales. Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions.

Decontamination of hydrocarbon contaminated soil

International Nuclear Information System (INIS)

Smith, A.J.

1991-01-01

This patent describes the method of treating hydrocarbon contaminated soil. It comprises forming the soil into a flowing particulate stream, forming an aqueous liquid mixture of water and treating substance that reacts with hydrocarbon to form CO 2 and water, dispersing the liquid mixture into the particulate soil stream to wet the particulate, allowing the substance to react with the wetted soil particulate to thereby form CO 2 and water, thereby the resultant soil is beneficially treated, the stream being freely projected to dwell at a level and then fall, and the dispersing includes spraying the liquid mixture into the projected stream at the dwell, the substance consisting of natural bacteria, and at a concentration level in the mixture of between 100 to 3,000 PPM of bacteria to water, the soil forming step including impacting the soil to reduce it to particles less than about 1 inches in cross dimension, and including forming the wetting particulate into a first layer on a surface to allow the substance to react

Analysis of soil microbial community structure and enzyme activities associated with negative effects of pseudostellaria heterophylla consecutive monoculture on yield

International Nuclear Information System (INIS)

Lin, S.; Lin, W.X.

2015-01-01

Pseudostellaria heterophylla is an important medicinal plant in China. However, cultivation of P. heterophylla using consecutive monoculture results in significant reductions in yield and quality. In this study, terminal-restriction fragment length polymorphism (T-RFLP) analysis and measurement of soil enzyme activities were used to investigate the regulation of soil micro-ecology to identify ways to overcome the negative effects of P. heterophylla consecutive monoculture. T-RFLP analysis showed that rice/P. heterophylla (RP) and bean/P. heterophylla (BP) crop rotation systems increased the number and diversity of microbial groups in P. heterophylla rhizosphere soil. In particular, the RP and BP crop rotations increased the number and abundance of beneficial bacterial species compared with two-year consecutive monoculture of P. heterophylla. The presence of these beneficial bacteria was positively correlated with soil enzyme activities which increased in rhizosphere soils of the RP and BP crop rotation systems. The results indicated that crop rotation systems could increase activities of key soil enzymes and beneficial microbial groups and improve soil health. This study could provide a theoretical basis to resolve the problems associated with P. heterophylla consecutive monoculture. (author)

Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis.

Science.gov (United States)

Wier, Andrew M; Nyholm, Spencer V; Mandel, Mark J; Massengo-Tiassé, R Prisca; Schaefer, Amy L; Koroleva, Irina; Splinter-Bondurant, Sandra; Brown, Bartley; Manzella, Liliana; Snir, Einat; Almabrazi, Hakeem; Scheetz, Todd E; Bonaldo, Maria de Fatima; Casavant, Thomas L; Soares, M Bento; Cronan, John E; Reed, Jennifer L; Ruby, Edward G; McFall-Ngai, Margaret J

2010-02-02

Mechanisms for controlling symbiont populations are critical for maintaining the associations that exist between a host and its microbial partners. We describe here the transcriptional, metabolic, and ultrastructural characteristics of a diel rhythm that occurs in the symbiosis between the squid Euprymna scolopes and the luminous bacterium Vibrio fischeri. The rhythm is driven by the host's expulsion from its light-emitting organ of most of the symbiont population each day at dawn. The transcriptomes of both the host epithelium that supports the symbionts and the symbiont population itself were characterized and compared at four times over this daily cycle. The greatest fluctuation in gene expression of both partners occurred as the day began. Most notable was an up-regulation in the host of >50 cytoskeleton-related genes just before dawn and their subsequent down-regulation within 6 h. Examination of the epithelium by TEM revealed a corresponding restructuring, characterized by effacement and blebbing of its apical surface. After the dawn expulsion, the epithelium reestablished its polarity, and the residual symbionts began growing, repopulating the light organ. Analysis of the symbiont transcriptome suggested that the bacteria respond to the effacement by up-regulating genes associated with anaerobic respiration of glycerol; supporting this finding, lipid analysis of the symbionts' membranes indicated a direct incorporation of host-derived fatty acids. After 12 h, the metabolic signature of the symbiont population shifted to one characteristic of chitin fermentation, which continued until the following dawn. Thus, the persistent maintenance of the squid-vibrio symbiosis is tied to a dynamic diel rhythm that involves both partners.

Ore microscopy applied to beneficiation

International Nuclear Information System (INIS)

Hagni, R.D.

1978-01-01

Ore microscopy can be an important adjunct to beneficiation, because it can be used not only to predict mill problems of undeveloped ore deposits but to identify the causes for the loss of minerals in the products of operating mines and mills. Mineral distribution among various mill products can be determined by examining polished sections prepared from samples obtained from each step of the beneficiation process. The degree of liberation of each mineral can be quantitatively determined for each mill product by counting locked vs. free particles. For many beneficiation problems, the preparation of a few polished sections of carefully selected mill products can yield useful information, which the mill dressing engineer can effectively use to alleviate those problems

Fourier transform Raman spectroscopic characterisation of cells of the plant-associated soil bacterium Azospirillum brasilense Sp7

Science.gov (United States)

Kamnev, A. A.; Tarantilis, P. A.; Antonyuk, L. P.; Bespalova, L. A.; Polissiou, M. G.; Colina, M.; Gardiner, P. H. E.; Ignatov, V. V.

2001-05-01

Structural and compositional features of bacterial cell samples and of lipopolysaccharide-protein complex isolated from the cell surface of the plant-growth-promoting rhizobacterium Azospirillum brasilense (wild-type strain Sp7) were characterised using Fourier transform (FT) Raman spectroscopy. The structural spectroscopic information obtained is analysed and considered together with analytical data on the content of metal cations (Co 2+, Cu 2+ and Zn 2+) in the bacterial cells grown in a standard medium as well as in the presence of each of the cations (0.2 mM). The latter, being taken up by bacterial cells from the culture medium in significant amounts, were shown to induce certain metabolic changes in the bacterium revealed in FT-Raman spectra, which is discussed from the viewpoint of bacterial response to environmental stresses.

The interactions of bacteria with fungi in soil: emerging concepts.

Science.gov (United States)

Haq, Irshad Ul; Zhang, Miaozhi; Yang, Pu; van Elsas, Jan Dirk

2014-01-01

In this chapter, we review the existing literature on bacterial-fungal interactions in soil, exploring the role fungi may play for soil bacteria as providers of hospitable niches. A focus is placed on the mycosphere, i.e., the narrow zone of influence of fungal hyphae on the external soil milieu, in which hypha-associated bacterial cells dwell. Evidence is brought forward for the contention that the hyphae of both mycorrhizal and saprotrophic fungi serve as providers of ecological opportunities in a grossly carbon-limited soil, as a result of their release of carbonaceous compounds next to the provision of a colonizable surface. Soil bacteria of particular nature are postulated to have adapted to such selection pressures, evolving to the extent that they acquired capabilities that allow them to thrive in the novel habitat created by the emerging fungal hyphae. The mechanisms involved in the interactions and the modes of genetic adaptation of the mycosphere dwellers are discussed, with an emphasis on one key mycosphere-adapted bacterium, Burkholderia terrae BS001. In this discussion, we interrogate the positive interactions between soil fungi and bacteria, and refrain from considering negative interactions. © 2014 Elsevier Inc. All rights reserved.

Acute toxicity assessment of explosive-contaminated soil extracting solution by luminescent bacteria assays.

Science.gov (United States)

Xu, Wenjie; Jiang, Zhenming; Zhao, Quanlin; Zhang, Zhenzhong; Su, Hongping; Gao, Xuewen; Ye, Zhengfang

2016-11-01

Explosive-contaminated soil is harmful to people's health and the local ecosystem. The acute toxicity of its extracting solution was tested by bacterial luminescence assay using three kinds of luminescent bacteria to characterize the toxicity of the soil. An orthogonal test L 16 (4 5 ) was designed to optimize the soil extracting conditions. The optimum extracting conditions were obtained when the ultrasonic extraction time, ultrasonic extraction temperature, and the extraction repeat times were 6 h, 40 °C, and three, respectively. Fourier transform infrared spectroscopy (FTIR) results showed that the main components of the contaminated soil's extracting solution were 2,4-dinitrotoluene-3-sulfonate (2,4-DNT-3-SO 3 - ); 2,4-dinitrotoluene-5-sulfonate (2,4-DNT-5-SO 3 - ); and 2,6-dinitrotoluene (2,6-DNT). Compared with Photobacterium phosphoreum and Vibrio fischeri, Vibrio qinghaiensis sp. Nov. is more suitable for assessing the soil extracting solution's acute toxicity. Soil washing can remove most of the contaminants toxic to luminescent bacterium Vibrio qinghaiensis sp. Nov., suggesting that it may be a potential effective remediation method for explosive-contaminated soil.

Long-term application of winery wastewater - Effect on soil microbial populations and soil chemistry

Science.gov (United States)

Mosse, Kim; Patti, Antonio; Smernik, Ron; Cavagnaro, Timothy

2010-05-01

The ability to reuse winery wastewater (WWW) has potential benefits both with respect to treatment of a waste stream, as well as providing a beneficial water resource in water limited regions such as south-eastern Australia, California and South Africa. Over an extended time period, this practice leads to changes in soil chemistry, and potentially, also to soil microbial populations. In this study, we compared the short term effects of WWW (both treated and untreated) application on soil biology and chemistry in two adjacent paired sites with the same soil type, one of which had received WWW for approximately 30 years, and the other which had not. The paired sites were treated with an industrially relevant quantity of WWW, and the soil microbial activity (measured as soil CO2 efflux) and common soil physicochemical properties were monitored over a 16-day period. In addition, Solid State 13C NMR was employed on whole soil samples from the two sites, to measure and compare the chemical nature of the soil organic matter at the paired sites. The acclimatised soil showed a high level of organic matter and a greater spike in microbial activity following WWW addition, in comparison with the non-acclimatised soil, suggesting differences in soil chemistry and soil microbial communities between the two sites. Soil nitrate and phosphorus levels showed significant differences between WWW treatments; these differences likely to be microbially mediated.

Shifts in the abundance and community structure of soil ammonia oxidizers in a wet sclerophyll forest under long-term prescribed burning.

Science.gov (United States)

Long, Xi-En; Chen, Chengrong; Xu, Zhihong; He, Ji-Zheng

2014-02-01

Fire shapes global biome distribution and promotes the terrestrial biogeochemical cycles. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in the biogeochemical cycling of nitrogen (N). However, behaviors of AOB and AOA under long-term prescribed burning remain unclear. This study was to examine how fire affected the abundances and communities of soil AOB and AOA. A long-term repeated forest fire experiment with three burning treatments (never burnt, B0; biennially burnt, B2; and quadrennially burnt, B4) was used in this study. The abundances and community structure of soil AOB and AOA were determined using quantitative PCR, restriction fragment length polymorphism and clone library. More frequent fires (B2) increased the abundance of bacterium amoA gene, but tended to decrease archaeal amoA genes. Fire also modified the composition of AOA and AOB communities. Canonical correspondence analysis showed soil pH and dissolved organic C (DOC) strongly affected AOB genotypes, while nitrate-N and DOC shaped the AOA distribution. The increased abundance of bacterium amoA gene by fires may imply an important role of AOB in nitrification in fire-affected soils. The fire-induced shift in the community composition of AOB and AOA demonstrates that fire can disturb nutrient cycles. © 2013.

Metagenomic of Actinomycetes Based on 16S rRNA and nifH Genes in Soil and Roots of Four Indonesian Rice Cultivars Using PCR-DGGE

Directory of Open Access Journals (Sweden)

Mahyarudin

2015-07-01

Full Text Available The research was conducted to study the metagenomic of actinomycetes based on 16S ribosomal RNA (rRNA and bacterial nifH genes in soil and roots of four rice cultivars. The denaturing gradient gel electrophoresis profile based on 16S rRNA gene showed that the diversity of actinomycetes in roots was higher than soil samples. The profile also showed that the diversity of actinomycetes was similar in four varieties of rice plant and three types of agroecosystem. The profile was partially sequenced and compared to GenBank database indicating their identity with closely related microbes. The blast results showed that 17 bands were closely related ranging from 93% to 100% of maximum identity with five genera of actinomycetes, which is Geodermatophilus, Actinokineospora, Actinoplanes, Streptomyces and Kocuria. Our study found that Streptomyces species in soil and roots of rice plants were more varied than other genera, with a dominance of Streptomyces alboniger and Streptomyces acidiscabies in almost all the samples. Bacterial community analyses based on nifH gene denaturing gradient gel electrophoresis showed that diversity of bacteria in soils which have nifH gene was higher than that in rice plant roots. The profile also showed that the diversity of those bacteria was similar in four varieties of rice plant and three types of agroecosystem. Five bands were closely related with nifH gene from uncultured bacterium clone J50, uncultured bacterium clone clod-38, and uncultured bacterium clone BG2.37 with maximum identity 99%, 98%, and 92%, respectively. The diversity analysis based on 16S rRNA gene differed from nifH gene and may not correlate with each other. The findings indicated the diversity of actinomycetes and several bacterial genomes analyzed here have an ability to fix nitrogen in soil and roots of rice plant.

Initiation of chromosomal replication in predatory bacterium Bdellovibrio bacteriovorus

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Lukasz Makowski

2016-11-01

Full Text Available Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase and replicating cells (the intracellular-growth phase. The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box (5’-NN(A/TTCCACA-3’. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus. We compared the architecture of the DnaA–oriC complexes (orisomes in homologous (oriC and DnaA from B. bacteriovorus and heterologous (BdoriC and DnaA from prey, E. coli or P. aeruginosa systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium.

Development of a rapid method for direct detection of tet(M) genes in soil from Danish farmland

DEFF Research Database (Denmark)

Agersø, Yvonne; Sengeløv, Gitte; Jensen, Lars Bogø

2004-01-01

. The tet(M) gene was directly detected in 10-80% of the samples from the various farmland soils and could be detected in all samples tested after selective enrichment. To validate the obtained results, the method was applied to garden soil samples where lower prevalence of resistance was found. Result......A method for direct detection of antibiotic resistance genes in soil samples has been developed. The tetracycline resistance gene, tet(M), was used as a model. The method was validated on Danish farmland soil that had repeatedly been treated with pig manure slurry containing resistant bacteria......: A detection limit of 10(2)-10(3) copies of the tet(M) gene per gram of soil (in a Bacillus cereus group bacterium) was achieved. tet(M) gene was detected in soil samples with the highest prevalence on farmland treated with pig manure slurry....

Stenotrophomonas sp. RZS 7, a novel PHB degrader isolated from plastic contaminated soil in Shahada, Maharashtra, Western India.

Science.gov (United States)

Wani, S J; Shaikh, S S; Tabassum, B; Thakur, R; Gulati, A; Sayyed, R Z

2016-12-01

This paper reports an isolation and identification of novel poly-β-hydroxybutyrate (PHB) degrading bacterium Stenotrophomonas sp. RZS 7 and studies on its extracellular PHB degrading depolymerase enzyme. The bacterium isolated from soil samples of plastic contaminated sites of municipal area in Shahada, Maharashtra, Western India. It was identified as Stenotrophomonas sp. RZS 7 based on polyphasic approach. The bacterium grew well in minimal salt medium (MSM) and produced a zone (4.2 mm) of PHB hydrolysis on MSM containing PHB as the only source of nutrient. An optimum yield of enzyme was obtained on the fifth day of incubation at 37 °C and at pH 6.0. Further increase in enzyme production was recorded with Ca 2+ ions, while other metal ions like Fe 2+ (1 mM) and chemical viz. mercaptoethanol severally affected the production of enzyme.

Burkholderia jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil.

Science.gov (United States)

Liu, Xu-Yun; Li, Chun-Xiu; Luo, Xiao-Jing; Lai, Qi-Liang; Xu, Jian-He

2014-09-01

A methyl parathion (MP) degrading bacterial strain, designated MP-1(T), was isolated from a waste land where pesticides were formerly manufactured in Jiangsu province, China. Polyphasic taxonomic studies showed that MP-1(T) is a Gram-stain-negative, non-spore-forming, rod-shaped and motile bacterium. The bacterium could grow at salinities of 0-1 % (w/v) and temperatures of 15-40 °C. Strain MP-1(T) could reduce nitrate to nitrite, utilize d-glucose and l-arabinose, but not produce indole, or hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that MP-1(T) belongs to the genus Burkholderia, showing highest sequence similarity to Burkholderia grimmiae DSM 25160(T) (98.5 %), and similar strains including Burkholderia zhejiangensis OP-1(T) (98.2 %), Burkholderia choica LMG 22940(T) (97.5 %), Burkholderia glathei DSM 50014(T) (97.4 %), Burkholderia terrestris LMG 22937(T) (97.2 %) and Burkholderia telluris LMG 22936(T) (97.0 %). In addition, the gyrB and recA gene segments of strain MP-1(T) exhibited less than 89.0 % and 95.1 % similarities with the most highly-related type strains indicated above. The G+C content of strain MP-1(T) was 62.6 mol%. The major isoprenoid quinone was ubiquinone Q-8. The predominant polar lipids comprised phosphatidyl ethanolamine, phosphatidyl glycerol, aminolipid and phospholipid. The principal fatty acids in strain MP-1(T) were C18 : 1ω7c/C18 : 1ω6c (23.3 %), C16 : 0 (16.8 %), cyclo-C17 : 0 (15.0 %), C16 : 1ω7c/C16 : 1ω6 (8.5 %), cyclo-C19 : 0ω8c (8.1 %), C16 : 1 iso I/C14 : 0 3-OH (5.7 %), C16 : 0 3-OH (5.6 %) and C16 : 02-OH (5.1 %). The DNA-DNA relatedness values between strain MP-1(T) and the three type strains (B. grimmiae DSM 25160(T), B. zhejiangensis OP-1(T) and B. glathei DSM 50014(T)) ranged from 24.6 % to 37.4 %. In accordance with phenotypic and genotypic characteristics, strain MP-1(T) represents a novel

Executive strategy plan for beneficial uses program: cesium-137 sewage sludge irradiation

International Nuclear Information System (INIS)

1981-07-01

Energy-efficient disinfection of sewage sludge, permitting its use as a fertilizer and soil conditioner in areas open to public access or on certain food chain crops, is possible using the process technology developed by Sandia National Laboratories under DOE and EPA joint support. This process accomplishes disinfection by gamma ray irradiation with cesium-137, a by-product isotope recovered from reprocessing of defense production waste. Disinfection with cesium-137 gamma irradiation provides an energy-efficient option for the Nation's cities to beneficially utilize sewage sludge, while at the same time conserving energy by utilizing a radioisotope, traditionally considered waste, in a beneficial manner. While the Sandia sludge irradiation technology has successfully completed its research and development phase, a major consideration remains: the introduction of a new technology into a marketplace which traditionally is skeptical of new products or process technologies until their performance is well proven. This document analyzes the factors important to market introduction of this new technology, develops options, and recommends a program strategy for transfer of the Sandia sludge irradiation technology to the marketplace by developing public awareness and acceptance, and by stimulating private sector commercialization interest

Diversity and Abundance of Soil Animals as Influenced by Long-Term Fertilization in Grey Desert Soil, China

Directory of Open Access Journals (Sweden)

Maibo Jiang

2015-08-01

Full Text Available The relationship between soil fauna and different fertilizer management practices is of growing concern. The aim of this research was to investigate the response of soil fauna to fertilization regimes, to explore the relationships among the community of soil animals, soil moisture and crop yields. The application of organic fertilizers (i.e., sheep manure or crop residues increased crop yields and promoted the number of individuals and species of soil fauna owing to the exogenous organic matter that fertilizers provided for the survival and development of soil fauna. Furthermore, the treatments that applied sheep manure (i.e., sheep manure only or nitrogen, phosphorus, potassium and sheep manure plus were significantly beneficial for increasing crop yields and diversity of soil fauna compared to treatments with crop residues returned (i.e., crop residues returned only or nitrogen, phosphorus, potassium and crop residues returned to the field (p < 0.05 due to the response of soil fauna to diverse exogenous nutrients and the effect of soil fertility. Therefore, the finding that soil fauna abundance is significantly positively correlated with soil moisture and crop yield may mean the effects of fertilizer applications on soil animals were partly masked by the soil moisture and crop yield.

Impact of cover crops and tillage on porosity of podzolic soil

Science.gov (United States)

Błażewicz-Woźniak, M.; Konopiñski, M.

2013-09-01

The aim of the study was to determine the influence of cover crops biomass, mixed with the soil on different dates and with the use of different tools in field conditions. The cover crop biomass had a beneficial influence on the total porosity of the 0-20 cm layer of the soil after winter. The highest porosity was achievedwith cover crops of buckwheat, phacelia and mustard, the lowest with rye. During the vegetation period the highest porosity of soil was observed in the ridges. Among the remaining non-ploughing cultivations, pre-winter use of stubble cultivator proved to have a beneficial influence on the soil porosity, providing results comparable to those achieved in conventional tillage. The differential porosity of the soil was modified not only by the catch crops and the cultivation methods applied, but also by the sample collection dates, and it did change during the vegetation period. The highest content of macropores after winter was observed for the phacelia cover crop, and the lowest in the case of cultivation without any cover crops. Pre-winter tillage with the use of a stubble cultivator increased the amount of macropores in soil in spring, and caused the biggest participation of mesopores as compared with other non-ploughing cultivation treatments of the soil. The smallest amount of mesopores was found in the ridges.

Biofilm treatment of soil for waste containment and remediation

International Nuclear Information System (INIS)

Turner, J.P.; Dennis, M.L.; Osman, Y.A.; Chase, J.; Bulla, L.A.

1997-01-01

This paper examines the potential for creating low-permeability reactive barriers for waste treatment and containment by treating soils with Beijerinckia indica, a bacterium which produces an exopolysaccharide film. The biofilm adheres to soil particles and causes a decrease in soil hydraulic conductivity. In addition, B. Indica biodegrades a variety of polycyclic aromatic hydrocarbons and chemical carcinogens. The combination of low soil hydraulic conductivity and biodegradation capabilities creates the potential for constructing reactive biofilm barriers from soil and bacteria. A laboratory study was conducted to evaluate the effects of B. Indica on the hydraulic conductivity of a silty sand. Soil specimens were molded with a bacterial and nutrient solution, compacted at optimum moisture content, permeated with a nutrient solution, and tested for k sat using a flexible-wall permeameter. Saturated hydraulic conductivity (k sat ) was reduced from 1 x 10 -5 cm/sec to 2 x 10 -8 cm/sec: by biofilm treatment. Permeation with saline, acidic, and basic solutions following formation of a biofilm was found to have negligible effect on the reduced k sat , for up to three pore volumes of flow. Applications of biofilm treatment for creating low-permeability reactive barriers are discussed, including compacted liners for bottom barriers and caps and creation of vertical barriers by in situ treatment

Short-Term Effect of Feedstock and Pyrolysis Temperature on Biochar Characteristics, Soil and Crop Response in Temperate Soils

DEFF Research Database (Denmark)

Nelissen, Victoria; Ruysschaert, Greet; Müller-Stöver, Dorette Sophie

2014-01-01

At present, there is limited understanding of how biochar application to soil could be beneficial to crop growth in temperate regions and which biochar types are most suitable. Biochar’s (two feedstocks: willow, pine; three pyrolysis temperatures: 450 °C, 550 °C, 650 °C) effect on nitrogen (N......) availability, N use efficiency and crop yield was studied in northwestern European soils using a combined approach of process-based and agronomic experiments. Biochar labile carbon (C) fractions were determined and a phytotoxicity test, sorption experiment, N incubation experiment and two pot trials were...... conducted. Generally, biochar caused decreased soil NO3−availability and N use efficiency, and reduced biomass yields compared to a control soil. Soil NO3−concentrations were more reduced in the willow compared to the pine biochar treatments and the reduction increased with increasing pyrolysis temperatures...

Studies on the pathogenic bacterium of ulcer disease in Epinephelus awoara

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

Studies were conducted to determine the cause of the acute mortality of cage-cultured Epinephelus awoara in the Tong'an Bay of Xiamen, China during the summer of 2002. Predominant bacteria strain TS-628 was isolated from the diseased grouper. The virulence test confirmed that TS-628 was the pathogenic bacterium. Biochemical characteristics of the isolates were determined using the automatic bacterial identification system and standard tube tests. To further confirm the identification, a 1 121 bp 16S rRNA gene sequence of the isolate was amplified by PCR, which had been deposited into Genbank (accession number: AY747308). According to the biochemical characteristics and by comparing the 16S rRNA gene homology of the isolate, the pathogenic bacterium was identified as Vibrio harveyi. Drug sensitivity tests showed that this pathogenic bacterium was sensitive to 16 antibacterials, especially to chloramphenicol and actinospectacin, but completely resistant to antibacterials likes vancomycin, penicillin, lincomycin, and so on.

Role of Earthworms in Soil Fertility Maintenance through the Production of Biogenic Structures

International Nuclear Information System (INIS)

Bhadauria, T.; Saxena, K.G.

2010-01-01

The soil biota benefits soil productivity and contributes to the sustainable function of all ecosystems. The cycling of nutrients is a critical function that is essential to life on earth. Earthworms (EWs) are a major component of soil fauna communities in most ecosystems and comprise a large proportion of macro fauna biomass. Their activity is beneficial because it can enhance soil nutrient cycling through the rapid incorporation of detritus into mineral soils. In addition to this mixing effect, mucus production associated with water excretion in earthworm guts also enhances the activity of other beneficial soil microorganisms. This is followed by the production of organic matter. So, in the short term, a more significant effect is the concentration of large quantities of nutrients (N, P, K, and Ca) that are easily assimilable by plants in fresh cast depositions. In addition, earthworms seem to accelerate the mineralization as well as the turnover of soil organic matter. Earthworms are known also to increase nitrogen mineralization, through direct and indirect effects on the microbial community. The increased transfer of organic C and N into soil aggregates indicates the potential for earthworms to facilitate soil organic matter stabilization and accumulation in agricultural systems, and that their influence depends greatly on differences in land management practices. This paper summarises information on published data on the described subjects.

Role of Earthworms in Soil Fertility Maintenance through the Production of Biogenic Structures

Directory of Open Access Journals (Sweden)

Tunira Bhadauria

2010-01-01

Full Text Available The soil biota benefits soil productivity and contributes to the sustainable function of all ecosystems. The cycling of nutrients is a critical function that is essential to life on earth. Earthworms (EWs are a major component of soil fauna communities in most ecosystems and comprise a large proportion of macrofauna biomass. Their activity is beneficial because it can enhance soil nutrient cycling through the rapid incorporation of detritus into mineral soils. In addition to this mixing effect, mucus production associated with water excretion in earthworm guts also enhances the activity of other beneficial soil microorganisms. This is followed by the production of organic matter. So, in the short term, a more significant effect is the concentration of large quantities of nutrients (N, P, K, and Ca that are easily assimilable by plants in fresh cast depositions. In addition, earthworms seem to accelerate the mineralization as well as the turnover of soil organic matter. Earthworms are known also to increase nitrogen mineralization, through direct and indirect effects on the microbial community. The increased transfer of organic C and N into soil aggregates indicates the potential for earthworms to facilitate soil organic matter stabilization and accumulation in agricultural systems, and that their influence depends greatly on differences in land management practices. This paper summarises information on published data on the described subjects.

Study on the effect of organic fertilizers on soil organic matter and enzyme activities of soil in forest nursery

Directory of Open Access Journals (Sweden)

Piaszczyk Wojciech

2017-09-01

Full Text Available The aim of the study was to assess the effects of organic fertilization on selected chemical properties of the soil and the activity of dehydrogenase and β-glucosidase in the soil of forest nursery. The main goal was to evaluate the role of organic fertilizers in carbon storage in the forest nursery soil. Sample plots were located in northern Poland in the Polanów Forest District on a forest nursery. Soil samples were collected from horizon 0–20 cm for laboratory analyzes. In soil samples pH, soil texture, and organic carbon, nitrogen, base cation contents, dehydrogenase activity and β-glucosidase activity were determined. The obtained results were used to evaluate the carbon storage. The results confirm the beneficial effect of the applied organic fertilizer on chemical properties of the soils under study and their biological activity. The applied organic fertilizers had an impact on increased accumulation of soil organic matter. In the soils investigated, there was an increase in the activity of such enzymes as dehydrogenases and β-glucosidase.

Soil management practices under organic farming

Science.gov (United States)

Aly, Adel; Chami Ziad, Al; Hamdy, Atef

2015-04-01

Organic farming methods combine scientific knowledge of ecology and modern technology with traditional farming practices based on naturally occurring biological processes. Soil building practices such as crop rotations, intercropping, symbiotic associations, cover crops, organic fertilizers and minimum tillage are central to organic practices. Those practices encourage soil formation and structure and creating more stable systems. In farm nutrient and energy cycling is increased and the retentive abilities of the soil for nutrients and water are enhanced. Such management techniques also play an important role in soil erosion control. The length of time that the soil is exposed to erosive forces is decreased, soil biodiversity is increased, and nutrient losses are reduced, helping to maintain and enhance soil productivity. Organic farming as systematized and certifiable approach for agriculture, there is no surprise that it faces some challenges among both farmers and public sector. This can be clearly demonstrated particularly in the absence of the essential conditions needed to implement successfully the soil management practices like green manure and composting to improve soil fertility including crop rotation, cover cropping and reduced tillage. Those issues beside others will be fully discussed highlighting their beneficial impact on the environmental soil characteristics. Keywords: soil fertility, organic matter, plant nutrition

Molecular Characterization of the Plant Growth Promoting Bacterium Enterobacter sp. SA187 upon Contact with Arabidopsis thaliana

KAUST Repository

Alsharif, Wiam

2018-05-01

Salt stress is a severe environmental challenge in agriculture, limiting the quality and productivity of the crops around the globe. Plant growth promoting rhizobacteria (PGPR) is proposed as a friendly solution to overcome those challenges. The desert plant endophytic bacterium, Enterobacter sp. SA187 has shown plant growth promotion and salt stress tolerance beneficial effect on the model plant Arabidopsis thaliana in vitro as well as under the field conditions on different crops. SA187 has a distinguished morphology of yellow colonies (SA187Y) that could be due to carotenoid biosynthesis. However, the bacteria tend to lose the yellow color upon incubation with the plants and the colonies turn to white (SA187W). In comparison to SA187Y, SA187W shows 50% reduction on the beneficial impact on A. thaliana fresh and dry weight of root and shoot system. By counting the CFU/plant, we showed that SA187Y and SA187W both have similar colonization rate in both shoots and roots. Under non-salt conditions, optimal bacterial colonization was observed on day 8 after inocubation, however, under the salt stress condition, the optimal colonization was observed at day 4. Moreover, during the time period of the incubation of the SA187Y with the plants, there was a consistent noticeable loss of the yellow color of the colonies. This change in color is only observed eight days after transfer and the number of white colonies increases with the increase of the incubation time. In addition, SA187W was GFP-tagged by Tn7 transposon system and visualized by confocal laser scanning microscopy. The SA187W-GFP colonies have shown a similar colonization pattern as SA187Y-GFP, bacteria were colonizing the differentiation zone and cell elongation zone in the roots. Finally, the gene expression of the carotenoid biosynthesis pathways genes in SA187Y showed an overall higher gene expression compared to SA187W. In conclusion, the color loss seems to affect the beneficial impact of the bacteria on

Decaying organic materials and soil quality in the Inland Northwest: A management opportunity

Science.gov (United States)

Alan E. Harvey; Martin F. Jurgensen; Michael J. Larsen; Russell T. Graham

1987-01-01

Organic debris, including wood residue, is important to the development and function of. forest soil. Organic matter stores nutrients and moisture plus it provides important habitats for microbes beneficial to tree growth. To protect long-term forest soil productivity, organic horizons and their parent materials should be maintained.

Effects of inoculation of biosurfactant-producing Bacillus sp. J119 on plant growth and cadmium uptake in a cadmium-amended soil

International Nuclear Information System (INIS)

Sheng Xiafang; He Linyan; Wang Qingya; Ye Hesong; Jiang Chunyu

2008-01-01

A biosurfactant-producing Bacillus sp. J119 isolated from heavy metal contaminated soils was investigated for its effects on the plant growth-promoting characteristics and heavy metal and antibiotic resistance. A pot experiment was conducted for investigating the capability of the biosurfactant-producing bacterial strain Bacillus sp. J119 to promote the plant growth and cadmium uptake of rape, maize, sudangrass and tomato in soil artificially contaminated with different levels of cadmium (Cd) (0 and 50 mg kg -1 ). The strain was found to exhibit different multiple heavy metal (Pb, Cd, Cu, Ni and Zn) and antibiotic (kanamycin, streptomycin, ampicillin, tetracycline and rifampin) resistance characteristics. The strain had the capacity to produce indole acetic acid (IAA) and siderophores. Cd treatment did not significantly decreased growth of tomato, maize and rape plants, but Cd treatment significantly decreased growth of sudangrass (p -1 , increase in above-ground tissue Cd content varied from 39 to 70% in live bacterium-inoculated plants compared to dead bacterium-inoculated control. In addition, among the inoculated plants, tomato was the greatest Cd accumulator. The bacterial strain was also able to colonize and develop in the rhizosphere soils after root inoculation

Moist Soil Management of Wetland Impoundments for Plants and Invertebrates

Data.gov (United States)

Department of the Interior — In year’s past an impoundment was drained (a drawdown) when floating-leaved plants covered more than 50% of the water area. Drawdowns encourage beneficial moist soil...

The physiology of the filamentous bacterium Microthrix parvicella

NARCIS (Netherlands)

Slijkhuis, H.

1983-01-01

A study has been made of the physiology of Microthrix parvicella. This filamentous bacterium often causes poor settleability of activated sludge in oxidation ditches supplied with domestic sewage. The organism was found to utilize only long chain fatty acids (preferably in

Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri.

Directory of Open Access Journals (Sweden)

Tyler R Schleicher

Full Text Available The beneficial symbiosis between the Hawaiian bobtail squid, Euprymna scolopes, and the bioluminescent bacterium, Vibrio fischeri, provides a unique opportunity to study host/microbe interactions within a natural microenvironment. Colonization of the squid light organ by V. fischeri begins a lifelong association with a regulated daily rhythm. Each morning the host expels an exudate from the light organ consisting of 95% of the symbiont population in addition to host hemocytes and shed epithelial cells. We analyzed the host and symbiont proteomes of adult squid exudate and surrounding light organ epithelial tissue using 1D- and 2D-polyacrylamide gel electrophoresis and multidimensional protein identification technology (MudPIT in an effort to understand the contribution of both partners to the maintenance of this association. These proteomic analyses putatively identified 1581 unique proteins, 870 proteins originating from the symbiont and 711 from the host. Identified host proteins indicate a role of the innate immune system and reactive oxygen species (ROS in regulating the symbiosis. Symbiont proteins detected enhance our understanding of the role of quorum sensing, two-component signaling, motility, and detoxification of ROS and reactive nitrogen species (RNS inside the light organ. This study offers the first proteomic analysis of the symbiotic microenvironment of the adult light organ and provides the identification of proteins important to the regulation of this beneficial association.

Stripping away the soil

OpenAIRE

Bartelme, Ryan P.; Oyserman, Ben O.; Blom, Jesse E.; Sepulveda-Villet, Osvaldo J.; Newton, Ryan J.

2018-01-01

As the processes facilitated by plant growth promoting microorganisms (PGPMs) become better characterized, it is evident that PGPMs may be critical for successful sustainable agricultural practices. Microbes enrich plant growth through various mechanisms, such as enhancing resistance to disease and drought, producing beneficial molecules, and supplying nutrients and trace metals to the plant rhizosphere. Previous studies of PGPMs have focused primarily on soil-based crops. In contrast, aquapo...

Caenorhabditis elegans Predation on Bacillus anthracis: Decontamination of Spore Contaminated Soil with Germinants and Nematodes.

Science.gov (United States)

Schelkle, Bettina; Choi, Young; Baillie, Leslie W; Richter, William; Buyuk, Fatih; Celik, Elif; Wendling, Morgan; Sahin, Mitat; Gallagher, Theresa

2017-01-01

Remediation of Bacillus anthracis -contaminated soil is challenging and approaches to reduce overall spore levels in environmentally contaminated soil or after intentional release of the infectious disease agent in a safe, low-cost manner are needed. B. anthracis spores are highly resistant to biocides, but once germinated they become susceptible to traditional biocides or potentially even natural predators such as nematodes in the soil environment. Here, we describe a two-step approach to reducing B. anthracis spore load in soil during laboratory trials, whereby germinants and Caenorhabditis elegans nematodes are applied concurrently. While the application of germinants reduced B. anthracis spore load by up to four logs depending on soil type, the addition of nematodes achieved a further log reduction in spore count. These laboratory based results suggest that the combined use of nematodes and germinants could represent a promising approach for the remediation of B. anthracis spore contaminated soil. Originality-Significance Statement: This study demonstrates for the first time the successful use of environmentally friendly decontamination methods to inactivate Bacillus anthracis spores in soil using natural predators of the bacterium, nematode worms.

Isolation and characterization of Caldicellulosiruptor lactoaceticus sp. nov., an extremely thermophilic, cellulolytic, anaerobic bacterium

DEFF Research Database (Denmark)

Mladenovska, Zuzana; Mathrani, Indra M.; Ahring, Birgitte Kiær

1995-01-01

An anaerobic, extremely thermophilic, cellulolytic, non-spore-forming bacterium, strain 6A, was isolated from an alkaline hot spring in Hverageroi, Iceland. The bacterium was non-motile, rod-shaped (1.5-3.5 x 0.7 mu m) and occurred singly, in pairs or in chains and stained gram-negative. The growth...

Isolation, identification, and biocontrol of antagonistic bacterium against Botrytis cinerea after tomato harvest

Directory of Open Access Journals (Sweden)

Jun-Feng Shi

Full Text Available ABSTRACT Tomato is one of the most important vegetables in the world. Decay after harvest is a major issue in the development of tomato industry. Currently, the most effective method for controlling decay after harvest is storage of tomato at low temperature combined with usage of chemical bactericide; however, long-term usage of chemical bactericide not only causes pathogen resistance but also is harmful for human health and environment. Biocontrol method for the management of disease after tomato harvest has great practical significance. In this study, antagonistic bacterium B-6-1 strain was isolated from the surface of tomato and identified as Enterobacter cowanii based on morphological characteristics and physiological and biochemical features combined with sequence analysis of 16SrDNA and ropB gene and construction of dendrogram. Effects of different concentrations of antagonistic bacterium E. cowanii suspension on antifungal activity after tomato harvest were analyzed by mycelium growth rate method. Results revealed that antifungal activity was also enhanced with increasing concentrations of antagonistic bacterium; inhibitory rates of 1 × 105 colony-forming units (cfu/mL antagonistic bacterial solution on Fusarium verticillioides, Alternaria tenuissima, and Botrytis cinerea were 46.31%, 67.48%, and 75.67%, respectively. By using in vivo inoculation method, it was further confirmed that antagonistic bacterium could effectively inhibit the occurrence of B. cinerae after tomato harvest, biocontrol effect of 1 × 109 cfu/mL zymotic fluid reached up to 95.24%, and antagonistic bacterium E. cowanii has biocontrol potential against B. cinerea after harvest of fruits and vegetables.

Intercropped Silviculture Systems, a Key to Achieving Soil Fungal Community Management in Eucalyptus Plantations

OpenAIRE

Rachid, Caio T. C. C.; Balieiro, Fabiano C.; Fonseca, Eduardo S.; Peixoto, Raquel Silva; Chaer, Guilherme M.; Tiedje, James M.; Rosado, Alexandre S.

2015-01-01

Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed...

Mineralisation of 2,6-dichlorobenzamide (BAM) in dichlobenil-exposed soils and isolation of a BAM-mineralising Aminobacter sp

DEFF Research Database (Denmark)

Simonsen, A.; Holtze, M.S.; Sørensen, S.R.

2006-01-01

dichlobenil being mineralised within 50 days. By inoculating soil showing the fastest mineralisation of BAM into a mineral medium with BAM as the only carbon and nitrogen source an enrichment culture was established. Community analysis based on extracted DNA revealed a change of the bacterial community...... but without any clear indication of key members within the BAM-mineralising culture. Parallel cultivation resulted for the first time in the isolation of a BAM-mineralising bacterium, identified as an Aminobacter sp. Rapid bacterial mineralisation of BAM in dichlobenil-exposed soils....

Monitoring of a novel bacterium, Lactobacillus thermotolerans , in ...

African Journals Online (AJOL)

Abstract. We successfully established fluorescence in situ hybridization (FISH) method for specific detection and enumeration of a novel bacterium, Lactobacillus thermotolerans, in chicken feces. The specific FISH probes were designed based on the L. thermotolerans 16S rRNA gene sequences, and these sequences were ...

Effect of long-term farming strategies on soil microbiota and soil health

Science.gov (United States)

Sommermann, Loreen; Babin, Doreen; Sandmann, Martin; Smalla, Kornelia; Schellenberg, Ingo; Grosch, Rita; Geistlinger, Joerg

2017-04-01

Increasing food and energy demands have resulted in considerable intensification of farming practices, which brought about severe consequences for agricultural soils, e.g. loss of fertility, erosion and enrichment of soil-borne plant diseases. In order to maintain soil quality and health for the future, the development of more extensive and sustainable farming strategies is urgently needed. The soil microbiome is regarded as a key player in soil ecosystem functions, particularly the natural ability of soils to suppress plant pathogens (suppressiveness). Recent studies showed that soil microbial communities are influenced by agricultural management. To further analyze the effects of farming strategies on soil suppressiveness and plant performance, agricultural soils from three long-term field trials in Thyrow, Bernburg (both in Germany) and Therwil (Switzerland) were sampled and subjected to molecular profiling of soil bacteria and fungi using marker genes and high-throughput amplicon sequencing. Significant effects on bacterial as well as fungal community composition, including plant pathogenic and beneficial taxa, were observed among variants of tillage and crop rotation. The least effect on both communities had fertilization, with no significance between variants. Subsequently, the same soils were subjected to growth chamber pot experiments with lettuce as a model (Lactuca sativa). After a growth period of six weeks significant differences in lettuce shoot and soil microbial biomass were observed among soil samples of the different long-term trials. Furthermore, the lettuce rhizosphere exhibited diverse bacterial community compositions as observed by DGGE (denaturing gradient gel electrophoresis). Using group-specific PCR-DGGE fingerprints, bacterial responders to fertilization, soil management and crop rotation were identified among different taxonomic groups. Currently, bacterial and fungal amplicon sequencing of rhizosphere and bulk soil from these pot

Assessing Soil Nutrient Additions through Different Composting ...

African Journals Online (AJOL)

Bheema

is potentially better growth medium amendment when compared with traditional compost types. The use of vermi-compost is, therefore, very helpful in terms of providing beneficial soil nutrients as compared to other compost types. In contrast to the other chemical and biological properties, the highest pH was recorded in the.

Hydrogen production by co-cultures of Lactobacillus and a photosynthetic bacterium, Rhodobacter sphaeroides RV

Energy Technology Data Exchange (ETDEWEB)

Asada, Yasuo; Ishimi, Katsuhiro [Department of General Education, College of Science and Technology, Nihon University, Narashinodai, Chiba 274-8501 (Japan); Tokumoto, Masaru; Aihara, Yasuyuki; Oku, Masayo; Kohno, Hideki [Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Izumi-cho, Chiba 275-8575 (Japan); Wakayama, Tatsuki; Miyake, Jun [Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology, Nakoji, Amagasaki, Hyogo 661-0974 (Japan); Tomiyama, Masamitsu [Genetic Diversity Department, National Institute of Agrobiological Science, Tsukuba, Ibaraki 305-8602 (Japan)

2006-09-15

Hydrogen production with glucose by using co-immobilized cultures of a lactic acid bacterium, Lactobacillus delbrueckii NBRC13953, and a photosynthetic bacterium, Rhodobacter sphaeroides RV, in agar gels was studied. Glucose was converted to hydrogen gas in a yield of 7.1mol of hydrogen per mole of glucose at a maximum under illuminated conditions. (author)

Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

Science.gov (United States)

Taghavi, Safiyh; van der Lelie, Daniel; Hoffman, Adam; Zhang, Yian-Biao; Walla, Michael D.; Vangronsveld, Jaco; Newman, Lee; Monchy, Sébastien

2010-01-01

Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa×deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT–PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

Dielectrophoretic sample preparation for environmental monitoring of microorganisms: Soil particle removal.

Science.gov (United States)

Fatoyinbo, Henry O; McDonnell, Martin C; Hughes, Michael P

2014-07-01

Detection of pathogens from environmental samples is often hampered by sensors interacting with environmental particles such as soot, pollen, or environmental dust such as soil or clay. These particles may be of similar size to the target bacterium, preventing removal by filtration, but may non-specifically bind to sensor surfaces, fouling them and causing artefactual results. In this paper, we report the selective manipulation of soil particles using an AC electrokinetic microfluidic system. Four heterogeneous soil samples (smectic clay, kaolinitic clay, peaty loam, and sandy loam) were characterised using dielectrophoresis to identify the electrical difference to a target organism. A flow-cell device was then constructed to evaluate dielectrophoretic separation of bacteria and clay in a continous flow through mode. The average separation efficiency of the system across all soil types was found to be 68.7% with a maximal separation efficiency for kaolinitic clay at 87.6%. This represents the first attempt to separate soil particles from bacteria using dielectrophoresis and indicate that the technique shows significant promise; with appropriate system optimisation, we believe that this preliminary study represents an opportunity to develop a simple yet highly effective sample processing system.

Inoculum pretreatment affects bacterial survival, activity and catabolic gene expression during phytoremediation of diesel contaminated soil.

Science.gov (United States)

Khan, Sumia; Afzal, Muhammad; Iqbal, Samina; Mirza, Muhammad Sajjad; Khan, Qaiser M

2013-04-01

Plant-bacteria partnership is a promising approach for remediating soil contaminated with organic pollutants. The colonization and metabolic activity of an inoculated microorganism depend not only on environmental conditions but also on the physiological condition of the applied microorganisms. This study assessed the influence of different inoculum pretreatments on survival, gene abundance and catabolic gene expression of an applied strain (Pantoea sp. strain BTRH79) in the rhizosphere of ryegrass vegetated in diesel contaminated soil. Maximum bacterium survival, gene abundance and expression were observed in the soil inoculated with bacterial cells that had been pregrown on complex medium, and hydrocarbon degradation and genotoxicity reduction were also high in this soil. These findings propose that use of complex media for growing plant inocula may enhance bacterial survival and colonization and subsequently the efficiency of pollutant degradation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study)

OpenAIRE

OCKY KARNA RADJASA; TORBEN MARTENS; HANS-PETER GROSSART; AGUS SABDONO; MEINHARD SIMON; TONNY BACHTIAR

2005-01-01

A coral-associated bacterium was successfully screened for secondary metabolites production based on PCR amplification of the nonribosomal peptide synthetase gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA. The bacterium was found to inhibit the growth of shrimp pathogenic bacterium tested, Vibrio harveyi. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved s...

Volatile-mediated interactions between phylogenetically different soil bacteria

Directory of Open Access Journals (Sweden)

Paolina eGarbeva

2014-06-01

Full Text Available There is increasing evidence that organic volatiles play an important role in interactions between micro-organisms in the porous soil matrix. Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0-1. We applied a novel cultivation approach that mimics the natural nutritional heterogeneity in soil in which P. fluorescens grown on nutrient-limited agar was exposed to volatiles produced by 4 phylogenetically different bacterial isolates (Collimonas pratensis, Serratia plymuthica, Paenibacillus sp. and Pedobacter sp. growing in sand containing artificial root exudates. Contrary to our expectation, the produced volatiles stimulated rather than inhibited the growth of P. fluorescens. A genome-wide, microarray-based analysis revealed that volatiles of all 4 bacterial strains affected gene expression of P. fluorescens, but with a different pattern of gene expression for each strain. Based on the annotation of the differently expressed genes, bacterial volatiles appear to induce a chemotactic motility response in P. fluorescens, but also an oxidative stress response. A more detailed study revealed that volatiles produced by C. pratensis triggered, antimicrobial secondary metabolite production in P. fluorescens. Our results indicate that bacterial volatiles can have an important role in communication, trophic - and antagonistic interactions within the soil bacterial community.

Effect of different levels of magnesium saturation on the extractability of native and applied zinc in red and alluvial soils

International Nuclear Information System (INIS)

Deb, D.L.; Das, S.K.; Sachdev, Pamila

1978-01-01

The investigation showed that Mg saturation of soil has a beneficial effect on the extractibility of native and applied zinc in soil. The soils used in the investigation were alluvial soil from Delhi and red soil from Karnataka under upland and waterlogged conditions. Zinc was applied in the form of ZnSO 4 solution labelled with 65 Zn. (M.G.B.)

Combination of microbial oxidation and biogenic schwertmannite immobilization: A potential remediation for highly arsenic-contaminated soil.

Science.gov (United States)

Yang, Zhihui; Wu, Zijian; Liao, Yingping; Liao, Qi; Yang, Weichun; Chai, Liyuan

2017-08-01

Here, a novel strategy that combines microbial oxidation by As(III)-oxidizing bacterium and biogenic schwertmannite (Bio-SCH) immobilization was first proposed and applied for treating the highly arsenic-contaminated soil. Brevibacterium sp. YZ-1 isolated from a highly As-contaminated soil was used to oxidize As(III) in contaminated soils. Under optimum culture condition for microbial oxidation, 92.3% of water-soluble As(III) and 84.4% of NaHCO 3 -extractable As(III) in soils were removed. Bio-SCH synthesized through the oxidation of ferrous sulfate by Acidithiobacillus ferrooxidans immobilize As(V) in the contaminated soil effectively. Consequently, the combination of microbial oxidation and Bio-SCH immobilization performed better in treating the highly As-contaminated soil with immobilization efficiencies of 99.3% and 82.6% for water-soluble and NaHCO 3 -extractable total As, respectively. Thus, the combination can be considered as a green remediation strategy for developing a novel and valuable solution for As-contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Green roof soil system affected by soil structural changes: A project initiation

Science.gov (United States)

Jelínková, Vladimíra; Dohnal, Michal; Šácha, Jan; Šebestová, Jana; Sněhota, Michal

2014-05-01

Anthropogenic soil systems and structures such as green roofs, permeable or grassed pavements comprise appreciable part of the urban watersheds and are considered to be beneficial regarding to numerous aspects (e.g. carbon dioxide cycle, microclimate, reducing solar absorbance and storm water). Expected performance of these systems is significantly affected by water and heat regimes that are primarily defined by technology and materials used for system construction, local climate condition, amount of precipitation, the orientation and type of the vegetation cover. The benefits and potencies of anthropogenic soil systems could be considerably threatened in case when exposed to structural changes of thin top soil layer in time. Extensive green roof together with experimental green roof segment was established and advanced automated monitoring system of micrometeorological variables was set-up at the experimental site of University Centre for Energy Efficient Buildings as an interdisciplinary research facility of the Czech Technical University in Prague. The key objectives of the project are (i) to characterize hydraulic and thermal properties of soil substrate studied, (ii) to establish seasonal dynamics of water and heat in selected soil systems from continuous monitoring of relevant variables, (iii) to detect structural changes with the use of X-ray Computed Tomography, (iv) to identify with the help of numerical modeling and acquired datasets how water and heat dynamics in anthropogenic soil systems are affected by soil structural changes. Achievements of the objectives will advance understanding of the anthropogenic soil systems behavior in conurbations with the temperate climate.

Can Tomato Inoculation with Trichoderma Compensate Yield and Soil Health Deficiency due to Soil Salinity?

Science.gov (United States)

Wagner, Karl; Apostolakis, Antonios; Daliakopoulos, Ioannis; Tsanis, Ioannis

2016-04-01

Soil salinity is a major soil degradation threat, especially for arid coastal environments where it hinders agricultural production and soil health. Protected horticultural crops in the Mediterranean region, typically under deficit irrigation and intensive cultivation practices, have to cope with increasing irrigation water and soil salinization. This study quantifies the beneficial effects of the Trichoderma harzianum (TH) on the sustainable production of Solanum lycopersicum (tomato), a major greenhouse crop of the RECARE project Case Study in Greece, the semi-arid coastal Timpaki basin in south-central Crete. 20 vigorous 20-day-old Solanum lycopersicum L. cv Elpida seedlings are treated with TH fungi (T) or without (N) and transplanted into 35 L pots under greenhouse conditions. Use of local planting soil with initial Electrical Conductivity (ECe) 1.8 dS m-1 and local cultivation practices aim to simulate the prevailing conditions at the Case Study. In order to simulate seawater intrusion affected irrigation, plants are drip irrigated with two NaCl treatments: slightly (S) saline (ECw = 1.1 dS m-1) and moderately (M) saline water (ECw = 3.5 dS m-1), resulting to very high and excessively high ECe, respectively. Preliminary analysis of below and aboveground biomass, soil quality, salinity, and biodiversity indicators, suggest that TH pre-inoculation of tomato plants at both S and M treatments improve yield, soil biodiversity and overall soil health.

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

Science.gov (United States)

Yang, Hongwu; Li, Juan; Xiao, Yunhua; Gu, Yabing; Liu, Hongwei; Liang, Yili; Liu, Xueduan; Hu, Jin; Meng, Delong; Yin, Huaqun

2017-01-01

The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into ‘healthy’ and ‘infected’ samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health. PMID:29163453

Impact of Ag and Al2O3 nanoparticles on soil organisms: In vitro and soil experiments

International Nuclear Information System (INIS)

Fajardo, C.; Saccà, M.L.; Costa, G.; Nande, M.; Martin, M.

2014-01-01

In vitro analyses were conducted to assess the impact of Al 2 O 3 and Ag nanoparticles on two common soil bacteria, Bacillus cereus and Pseudomonas stutzeri. Al 2 O 3 nanoparticles did not show significant toxicity at any dose or time assayed, whereas exposure to 5 mg L −1 Ag nanoparticles for 48 h caused bactericidal effects. Moreover, alterations at the morphological level were observed by transmission electron microscopy (TEM); Ag but not Al 2 O 3 nanoparticles evoked the entrance of B. cereus cells in an early sporulation stage and both nanoparticles penetrated P. stutzeri cells. At the molecular level, a dramatic increase (8.2-fold) in katB gene expression was found in P. stutzeri following Al 2 O 3 nanoparticles exposure, indicative of an oxidative stress-defence system enhancement in this bacterium. In the microcosm experiment, using two different natural soils, Al 2 O 3 or Ag nanoparticles did not affect the Caenorhabditis elegans toxicity endpoints growth, survival, or reproduction. However, differences in microbial phylogenetic compositions were detected by fluorescence in situ hybridization (FISH). The use of katB- and pykA-based sequences showed that the microbial transcriptional response to nanoparticle exposure decreased, suggesting a decrease in cellular activity. These changes were attributable to both the nanoparticles treatment and soil characteristics, highlighting the importance of considering the soil matrix on a case by case basis. - Highlights: • Al 2 O 3 or Ag NPs impact on bacteria was assessed at phenotypic and molecular level. • katB gene involved in oxidative-stress response was overexpressed in P. stutzeri following Al 2 O 3 NPs exposure. • A decrease in bacterial transcriptional response was detected in NPs-treated soils. • A soil-dependent response to specific NP treatment was observed. • In NPs-treated soils no acute toxic effects on C. elegans were found

Biodegradation of Benzene, Toluene, Ethylbenzene, and o-, m-, and p-Xylenes by the Newly Isolated Bacterium Comamonas sp. JB.

Science.gov (United States)

Jiang, Bei; Zhou, Zunchun; Dong, Ying; Tao, Wei; Wang, Bai; Jiang, Jingwei; Guan, Xiaoyan

2015-07-01

A bacterium designated strain JB, able to degrade six benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) compounds, was isolated from petroleum-contaminated soil. Taxonomic analyses showed that the isolate belonged to Comamonas, and until now, the genus Comamonas has not included any known BTEX degraders. The BTEX biodegradation rate was slightly low on the mineral salt medium (MSM), but adding a small amount of yeast extract greatly enhanced the biodegradation. The relationship between specific degradation rate and individual BTEX was described well by Michaelis-Menten kinetics. The treatment of petrochemical wastewater containing BTEX mixture and phenol was shown to be highly efficient by BTEX-grown JB. In addition, toxicity assessment indicated the treatment of the petrochemical wastewater by BTEX-grown JB led to less toxicity than untreated wastewater.

New recombinant bacterium comprises a heterologous gene encoding glycerol dehydrogenase and/or an up-regulated native gene encoding glycerol dehydrogenase, useful for producing ethanol

DEFF Research Database (Denmark)

2010-01-01

dehydrogenase encoding region of the bacterium, or is inserted into a phosphotransacetylase encoding region of the bacterium, or is inserted into an acetate kinase encoding region of the bacterium. It is operably linked to an inducible, a regulated or a constitutive promoter. The up-regulated glycerol......TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preparation (claimed): Producing recombinant bacterium having enhanced ethanol production characteristics when cultivated in growth medium comprising glycerol comprises: (a) transforming a parental bacterium by (i) the insertion of a heterologous gene encoding...... glycerol dehydrogenase; and/or (ii) up-regulating a native gene encoding glycerol dehydrogenase; and (b) obtaining the recombinant bacterium. Preferred Bacterium: In the recombinant bacterium above, the inserted heterologous gene and/or the up-regulated native gene is encoding a glycerol dehydrogenase...

An investigation of inorganic antimony species and antimony associated with soil humic acid molar mass fractions in contaminated soils

International Nuclear Information System (INIS)

Steely, Sarah; Amarasiriwardena, Dulasiri; Xing Baoshan

2007-01-01

The presence of antimony compounds is often suspected in the soil of apple orchards contaminated with lead arsenate pesticide and in the soil of shooting ranges. Nitric acid (1 M) extractable Sb from the shooting range (8300 μg kg -1 ) and the apple orchard (69 μg kg -1 ) had considerably higher surface Sb levels than the control site ( -1 ), and Sb was confined to the top ∼30 cm soil layer. Sb(V) was the principal species in the shooting range and the apple orchard surface soils. Size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS) analysis of humic acids isolated from the two contaminated soils demonstrated that Sb has complexed to humic acid molar mass fractions. The results also indicate that humic acids have the ability to arrest the mobility of Sb through soils and would be beneficial in converting Sb(III) to a less toxic species, Sb(V), in contaminated areas. - The soil surface and depth distribution Sb(V) and Sb(III) species in a contaminated apple orchard and a shooting range, and the effect soil humic acids on inorganic antimony species is reported

Antagonistic bioactivity of an endophytic bacterium isolated from ...

African Journals Online (AJOL)

Antagonistic bioactivity of an endophytic bacterium isolated from Epimedium brevicornu Maxim. R He, G Wang, X Liu, C Zhang, F Lin. Abstract. Endophytic bacteria are one of the most potential biological control agents in plant disease protection. The aim of this work was to evaluate the antimicrobial activities of a strain of ...

Comparative study of soil erodibility and critical shear stress between loess and purple soils

Science.gov (United States)

Xing, Hang; Huang, Yu-han; Chen, Xiao-yan; Luo, Bang-lin; Mi, Hong-xing

2018-03-01

Loess and purple soils are two very important cultivated soils, with the former in the loess region and the latter in southern sub-tropical region of China, featured with high-risks of erosion, considerable differences of soil structures due to differences in mineral and nutrient compositions. Study on soil erodibility (Kr) and critical shear stress (τc) of these two soils is beneficial to predict soil erosion with such models as WEPP. In this study, rill erosion experimental data sets of the two soils are used for estimating their Kr and τc before they are compared to understand their differences of rill erosion behaviors. The maximum detachment rates of the loess and purple soils are calculated under different hydrodynamic conditions (flow rates: 2, 4, 8 L/min; slope gradients: 5°, 10°, 15°, 20°, 25°) through analytical and numerical methods respectively. Analytical method used the derivative of the function between sediment concentration and rill length to estimate potential detachment rates, at the rill beginning. Numerical method estimated potential detachment rates with the experimental data, at the rill beginning and 0.5 m location. The Kr and τc of these two soils are determined by the linear equation based on experimental data. Results show that the methods could well estimate the Kr and τc of these two soils as they remain basically unchanged under different hydrodynamic conditions. The Kr value of loess soil is about twice of the purple soil, whereas the τc is about half of that. The numerical results have good correlations with the analytical values. These results can be useful in modeling rill erosion processes of loess and purple soils.

Interactions of calcium sulfite with soils and plants

International Nuclear Information System (INIS)

Ritchey, K.D.; Kinraide, T.B.; Wendell, R.R.

1995-01-01

CaSO 3 is a by-product formed by several of the processes used for scrubbing SO 2 from flue gas produced by coal-burning power generators. Using CaSO 3 to improve the calcium status of acid soils would be a beneficial alternative to disposal in landfills. CaSO 3 has biocidal properties and is used as disinfectant and food and drink preservative. It is important to evaluate under what conditions application to soils would not harm plant growth. Laboratory experiments confirmed that two transformations of CaSO 3 occurred in soil systems: (1) decomposition to produce SO 2 gas, and (2) oxidation to calcium suflate. Conversion to SO 2 occurred in solution and soil at low pH, and acid soils treated with CaSO 3 were initially toxic to seedling root growth. The degree of toxicity was time-dependent, with reduction in toxicity occurring as CaSO 3 oxidized to calcium sulfate. Soil reaction also influenced toxicity, and at soil pH levels above 6, little seeding toxicity was evident

Degradation of /sup 14/C-parathion 'in vitro' by microorganisms isolated from a gley humic soil

Energy Technology Data Exchange (ETDEWEB)

Andrea, M.M. de; Ruegg, E.F. (Instituto Biologico, Sao Paulo (Brazil). Centro de Radioisotopos)

It was determined 'in vitro' the degradation of Parathion by a bacterium and a fungus isolated from a sample of Gley Humic soil previously treated with repeated applications of the insecticide. In a qualitative colorimetric assay hydrolysis of parathion to p-nitrophenol just the bacterium gave a positive answer. In quantitative assays of /sup 14/C-parathion degradation in culture media containing both microorganisms, organic solvents extractions resulted in organic and aqueous phases, which were analysed by liquid scintillation counting and thin-layer chromatography. In a mineral salts medium plus buffer, the bacterium and the fungus behaved differently from the control, because part of the /sup 14/C-insecticide was metabolized to, at least, one metabolite and besides, the microorganisms presented smaller percentages of total recovery. The largest percentage of the radio carbon recovery from the extracts of the medium containing the fungus plus extract of yeast, was obtained from the aqueous phase and the existence of other metabolite was demonstrated by chromatograms of the organic phase.

Fertilizer N application rate impacts plant-soil feedback in a sanqi production system.

Science.gov (United States)

Wei, Wei; Yang, Min; Liu, Yixiang; Huang, Huichuan; Ye, Chen; Zheng, Jianfen; Guo, Cunwu; Hao, Minwen; He, Xiahong; Zhu, Shusheng

2018-08-15

Replant failure caused by negative plant-soil feedback (NPFS) in agricultural ecosystems is a critical factor restricting the development of sustainable agriculture. Soil nutrient availability has the capacity to affect plant-soil feedback. Here, we used sanqi (Panax notoginseng), which is severely threatened by NPSF, as a model plant to decipher the overall effects of nitrogen (N) rates on NPSF and the underlying mechanism. We found that a high rate of N at 450kgNha -1 (450N) aggravated the NPSF through the accumulation of pathogens in the soil compared with the optimal 250N. The increased N rates resulted in a significant increase in the soil electrical conductivity and available nitrogen but a decrease in the soil pH and C/N ratio. GeoChip 5.0 data demonstrated that these changed soil properties caused the soil to undergo stress (acidification, salinization and carbon starvation), as indicated by the enriched soil microbial gene abundances related to stress response and nutrition cycling (N, C and S). Accordingly, increased N rates reduced the richness and diversity of soil fungi and bacteria and eventually caused a shift in soil microbes from a bacterial-dominant community to a fungal-dominant community. In particular, the high 450N treatment significantly suppressed the abundance of copiotrophic bacteria, including beneficial genera Bacillus and Pseudomonas, thus weakening the antagonistic activity of these bacteria against fungal pathogens. Moreover, 450N application significantly enriched the abundance of pathogen pathogenicity-related genes. Once sanqi plants were grown in this N-stressed soil, their host-specific fungal pathogen Fusarium oxysporum significantly accumulated, which aggravated the process of NPSF. This study suggested that over-application of nitrogen is not beneficial for disease management or the reduction of fungicide application in agricultural production. Copyright © 2018 Elsevier B.V. All rights reserved.

Beneficiation-hydroretort processing of US oil shales: Volume 2

Energy Technology Data Exchange (ETDEWEB)

None

1989-01-01

This report has been divided into three volumes. Volume I describes the MRI beneficiation work. In addition, Volume I presents the results of joint beneficiation-hydroretorting studies and provides an economic analysis of the combined beneficiation-hydroretorting approach for processing Eastern oil shales. Volume II presents detailed results of hydroretorting tests made by HYCRUDE/IGT on raw and beneficiated oil shales prepared by MRI. Volume III comprises detailed engineering design drawings and supporting data developed by the Roberts and Schaefer Company, Engineers and Contractors, Salt Lake City, Utah, in support of the capital and operating costs for a conceptual beneficiation plant processing an Alabama oil shale.

Influence of triethyl phosphate on phosphatase activity in shooting range soil: Isolation of a zinc-resistant bacterium with an acid phosphatase.

Science.gov (United States)

Story, Sandra; Brigmon, Robin L

2017-03-01

Phosphatase-mediated hydrolysis of organic phosphate may be a viable means of stabilizing heavy metals via precipitation as a metal phosphate in bioremediation applications. We investigated the effect of triethyl phosphate (TEP) on soil microbial-phosphatase activity in a heavy-metal contaminated soil. Gaseous TEP has been used at subsurface sites for bioremediation of organic contaminants but not applied in heavy-metal contaminated areas. Little is known about how TEP affects microbial activity in soils and it is postulated that TEP can serve as a phosphate source in nutrient-poor groundwater and soil/sediments. Over a 3-week period, TEP amendment to microcosms containing heavy-metal contaminated soil resulted in increased activity of soil acid-phosphatase and repression of alkaline phosphatase, indicating a stimulatory effect on the microbial population. A soil-free enrichment of microorganisms adapted to heavy-metal and acidic conditions was derived from the TEP-amended soil microcosms using TEP as the sole phosphate source and the selected microbial consortium maintained a high acid-phosphatase activity with repression of alkaline phosphatase. Addition of 5mM zinc to soil-free microcosms had little effect on acid phosphatase but inhibited alkaline phosphatase. One bacterial member from the consortium, identified as Burkholderia cepacia sp., expressed an acid-phosphatase activity uninhibited by high concentrations of zinc and produced a soluble, indigo pigment under phosphate limitation. The pigment was produced in a phosphate-free medium and was not produced in the presence of TEP or phosphate ion, indicative of purple acid-phosphatase types that are pressed by bioavailable phosphate. These results demonstrate that TEP amendment was bioavailable and increased overall phosphatase activity in both soil and soil-free microcosms supporting the possibility of positive outcomes in bioremediation applications. Copyright © 2016. Published by Elsevier Inc.

Is shade beneficial for mediterranean shrubs experiencing periods of extreme drought and late-winter frosts?

Science.gov (United States)

Valladares, Fernando; Zaragoza-Castells, Joana; Sánchez-Gómez, David; Matesanz, Silvia; Alonso, Beatriz; Portsmuth, Angelika; Delgado, Antonio; Atkin, Owen K

2008-12-01

Plants are naturally exposed to multiple, frequently interactive stress factors, most of which are becoming more severe due to global change. Established plants have been reported to facilitate the establishment of juvenile plants, but net effects of plant-plant interactions are difficult to assess due to complex interactions among environmental factors. An investigation was carried out in order to determine how two dominant evergreen shrubs (Quercus ilex and Arctostaphylos uva-ursi) co-occurring in continental, Mediterranean habitats respond to multiple abiotic stresses and whether the shaded understorey conditions ameliorate the negative effects of drought and winter frosts on the physiology of leaves. Microclimate and ecophysiology of sun and shade plants were studied at a continental plateau in central Spain during 2004-2005, with 2005 being one of the driest and hottest years on record; several late-winter frosts also occurred in 2005. Daytime air temperature and vapour pressure deficit were lower in the shade than in the sun, but soil moisture was also lower in the shade during the spring and summer of 2005, and night-time temperatures were higher in the shade. Water potential, photochemical efficiency, light-saturated photosynthesis, stomatal conductance and leaf 13C composition differed between sun and shade individuals throughout the seasons, but differences were species specific. Shade was beneficial for leaf-level physiology in Q. ilex during winter, detrimental during spring for both species, and of little consequence in summer. The results suggest that beneficial effects of shade can be eclipsed by reduced soil moisture during dry years, which are expected to be more frequent in the most likely climate change scenarios for the Mediterranean region.

Bioaugmentation-assisted phytoextraction of Co, Pb and Zn: an assessment with a phosphate-solubilizing bacterium isolated from metal-contaminated mines of Boryeong Area in South Korea

Directory of Open Access Journals (Sweden)

Arunakumara, KKIU.

2015-01-01

Full Text Available Description of the subject. Make use of microbes having remarkable metal tolerance and plant growth-promoting abilities to remediate metal-contaminated soils. Objectives. The objectives were to isolate phosphate solubilizing bacterial strain, assess metal (Co, Pb and Zn mobilization potential of the strain and to evaluate the effects of the strain on growth and uptake of metals by Helianthus annuus. Method. A phosphate solubilizing bacterium was isolated from metal-contaminated soils. Heavy metal (Co, Pb and Zn tolerance of the strain was assessed using the agar dilution method. Bacterial-assisted growth promotion and metal uptake by H. annuus was evaluated in a pot experiment. The impact of bacterial inoculation on the mobility of metals in soil was investigated in a batch experiment. Results. The strain showed close proximity with Klebsiella oxytoca JCM1665, according to 16S rRNA sequence analysis. The strain was efficient in solubilizing phosphate, both in the presence and absence of metals. Inoculation of the strain enhanced the growth of H. annuus (49, 22 and 39% respectively in Co, Pb and Zn contaminated soils compared to non-inoculated plants. Accumulation and translocation of Co, Pb and Zn from roots to shoots were also enhanced by the strain. Water soluble fraction of Co, Pb and Zn in soil was increased by 51, 24 and 76% respectively in inoculated soils with regard to those of non-inoculated soils. Conclusions. Taking the plant growth promotion and metal mobilizing potential of the strain into account, practical application of the strain in enhancing phytoextraction of Co, Pb and Zn from contaminated soils could be recommended.

Enhanced abiotic and biotic contributions to dechlorination of pentachlorophenol during Fe(III) reduction by an iron-reducing bacterium Clostridium beijerinckii Z

Energy Technology Data Exchange (ETDEWEB)

Xu, Yan [College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058 (China); He, Yan, E-mail: yhe2006@zju.edu.cn [College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058 (China); Feng, Xiaoli [College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058 (China); Liang, Luyi [Experiment Teaching Center for Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058 (China); Xu, Jianming, E-mail: jmxu@zju.edu.cn [College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058 (China); Brookes, Philip C.; Wu, Jianjun [College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058 (China)

2014-03-01

A novel Fe(III) reducing bacterium, Clostridium beijerinckii Z, was isolated from glucose amended paddy slurries, and shown to dechlorinate pentachlorophenol (PCP). Fifty percent of added PCP was removed by C. beijerinckii Z alone, which increased to 83% in the presence of both C. beijerinckii Z and ferrihydrite after 11 days of incubation. Without C. beijerinckii Z, the surface-bound Fe(II) also abiotically dechlorinated more than 40% of the added PCP. This indicated that the biotic dechlorination by C. beijerinckii Z is a dominant process causing PCP transformation through anaerobic dechlorination, and that the dechlorination rates can be accelerated by simultaneous reduction of Fe(III). A biochemical electron transfer coupling process between sorbed Fe(II) produced by C. beijerinckii Z and reductive dehalogenation is a possible mechanism. This finding increases our knowledge of the role of Fe(III) reducing genera of Clostridium in dechlorinating halogenated organic pollutants, such as PCP, in anaerobic paddy soils. - Highlights: • A novel Fe(III) reducing bacterium Clostridium beijerinckii Z was isolated and could dechlorinate pentachlorophenol. • Anaerobic transformation of PCP by C. beijerinckii Z could be accelerated by simultaneous reduction of Fe(III). • Biochemical electron transfer coupling between Fe redox cycling and reductive dechlorination was the mechanism involved. • The finding increases our knowledge of Clostridium sp. regarding their multiple functions for dechlorinating pollutants.

Enhanced abiotic and biotic contributions to dechlorination of pentachlorophenol during Fe(III) reduction by an iron-reducing bacterium Clostridium beijerinckii Z

International Nuclear Information System (INIS)

Xu, Yan; He, Yan; Feng, Xiaoli; Liang, Luyi; Xu, Jianming; Brookes, Philip C.; Wu, Jianjun

2014-01-01

A novel Fe(III) reducing bacterium, Clostridium beijerinckii Z, was isolated from glucose amended paddy slurries, and shown to dechlorinate pentachlorophenol (PCP). Fifty percent of added PCP was removed by C. beijerinckii Z alone, which increased to 83% in the presence of both C. beijerinckii Z and ferrihydrite after 11 days of incubation. Without C. beijerinckii Z, the surface-bound Fe(II) also abiotically dechlorinated more than 40% of the added PCP. This indicated that the biotic dechlorination by C. beijerinckii Z is a dominant process causing PCP transformation through anaerobic dechlorination, and that the dechlorination rates can be accelerated by simultaneous reduction of Fe(III). A biochemical electron transfer coupling process between sorbed Fe(II) produced by C. beijerinckii Z and reductive dehalogenation is a possible mechanism. This finding increases our knowledge of the role of Fe(III) reducing genera of Clostridium in dechlorinating halogenated organic pollutants, such as PCP, in anaerobic paddy soils. - Highlights: • A novel Fe(III) reducing bacterium Clostridium beijerinckii Z was isolated and could dechlorinate pentachlorophenol. • Anaerobic transformation of PCP by C. beijerinckii Z could be accelerated by simultaneous reduction of Fe(III). • Biochemical electron transfer coupling between Fe redox cycling and reductive dechlorination was the mechanism involved. • The finding increases our knowledge of Clostridium sp. regarding their multiple functions for dechlorinating pollutants

methoxyethanol by a new bacterium isolate Pseudomonas sp. Strain

African Journals Online (AJOL)

Michael Horsfall

A 2-methoxyethanol degrading bacterium was isolated from anaerobic sludge of a municipal sewage from ... Stoichiometrically, the strain utilized one mole of oxygen per one mole of 2-methoxyethanol instead of ... physiological and biochemical characterization of the .... observed with acetate and the intact resting cells.

Mechanical properties of tree roots for soil reinforcement models

NARCIS (Netherlands)

Cofie, P.

2001-01-01

Evidence from forestry has shown that part of the forest floor bearing capacity is delivered by tree roots. The beneficial effect however varies and diminishes with increasing number of vehicle passes. Roots potential for reinforcing the soil is known to depend among others on root

Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress.

Science.gov (United States)

Chen, Yanmei; Chao, Yuanqing; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong; Qiu, Rongliang

2016-01-04

Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd(2+) MIC, >250 mg liter(-1)) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Antibacterial activity of antagonistic bacterium Bacillus subtilis DJM-51 against phytopathogenic Clavibacter michiganense subsp. michiganense ATCC 7429 in vitro.

Science.gov (United States)

Jung, W J; Mabood, F; Souleimanov, A; Whyte, L G; Niederberger, T D; Smith, D L

2014-12-01

To investigate antibacterial activity against the tomato pathogen Clavibacter michiganense subsp. michiganense ATCC 7429 (Cmm ATCC 7429), Bacillus subtilis DJM-51 was isolated from rhizosphere soil. For isolation of bacteria, samples were taken from rhizosphere soil. The isolate, DJA-51, had strong antagonistic ability against Tomato pathogen Cmm ATCC 7429 on nutrient-broth yeast extract agar (NBYA) as indicated by inhibition zones around colonies. On the basis of the nucleotide sequence of a conserved segment of the 16S rRNA gene, the bacterium has been identified as B. subtilis DJM-51. The growth of Cmm ATCC 7429 on NBYA plates was inhibited by culture broth of B. subtilis DJM-51 including cells, by the supernatant of culture broth of B. subtilis DJM-51, and by the liquid material resulting from butanol extract of bacterial cultures. The OD value in co-culture mixture was lower than the control throughout the entire incubation period. Antibiotics obtained from B. subtilis DJM-51 inhibited the growth of Tomato pathogen Cmm ATCC 7429. These results provide potentially information about the protection of tomato from pathogen Cmm ATCC 7429 under greenhouse conditions in Quebec. Copyright © 2014 Elsevier Ltd. All rights reserved.

Isolation and evaluation of potent Pseudomonas species for bioremediation of phorate in amended soil.

Science.gov (United States)

Jariyal, Monu; Gupta, V K; Jindal, Vikas; Mandal, Kousik

2015-12-01

Use of phorate as a broad spectrum pesticide in agricultural crops is finding disfavor due to persistence of both the principal compound as well as its toxic residues in soil. Three phorate utilizing bacterial species (Pseudomonas sp. strain Imbl 4.3, Pseudomonas sp. strain Imbl 5.1, Pseudomonas sp. strain Imbl 5.2) were isolated from field soils. Comparative phorate degradation analysis of these species in liquid cultures identified Pseudomonas sp. strain Imbl 5.1 to cause complete metabolization of phorate during seven days as compared to the other two species in 13 days. In soils amended with phorate at different levels (100, 200, 300 mg kg(-1) soil), Pseudomonas sp. strain Imbl 5.1 resulted in active metabolization of phorate by between 94.66% and 95.62% establishing the same to be a potent bacterium for significantly relieving soil from phorate residues. Metabolization of phorate to these phorate residues did not follow the first order kinetics. This study proves that Pseudomonas sp. strain Imbl 5.1 has huge potential for active bioremediation of phorate both in liquid cultures and agricultural soils. Copyright © 2015 Elsevier Inc. All rights reserved.

Halomonas maura is a physiologically versatile bacterium of both ecological and biotechnological interest.

Science.gov (United States)

Llamas, Inmaculada; del Moral, Ana; Martínez-Checa, Fernando; Arco, Yolanda; Arias, Soledad; Quesada, Emilia

2006-01-01

Halomonas maura is a bacterium of great metabolic versatility. We summarise in this work some of the properties that make it a very interesting microorganism both from an ecological and biotechnological point of view. It plays an active role in the nitrogen cycle, is capable of anaerobic respiration in the presence of nitrate and has recently been identified as a diazotrophic bacterium. Of equal interest is mauran, the exopolysaccharide produced by H. maura, which contributes to the formation of biofilms and thus affords the bacterium advantages in the colonisation of its saline niches. Mauran is highly viscous, shows thixotropic and pseudoplastic behaviour, has the capacity to capture heavy metals and exerts a certain immunomodulator effect in medicine. All these attributes have prompted us to make further investigations into its molecular characteristics. To date we have described 15 open reading frames (ORF's) related to exopolysaccharide production, nitrogen fixation and nitrate reductase activity among others.

THE USE OF gusA REPORTER GENE TO MONITOR THE SURVIVAL OF INTRODUCED BACTERIA IN THE SOIL

Directory of Open Access Journals (Sweden)

Edi Husen

2013-07-01

Full Text Available An effective marker to monitor the survival of introduced bacteria in the soil is required for further evaluation of their beneficial effects on plant growth. This study tested the use of gusA gene as a marker to trace the fate of three Gram negative bacteria in the root, rhizosphere, and soil. The study was conducted at the laboratory and greenhouse of the National Institute of Molecular Biology and Biotechnology, Philippines from January to December 2001. Isolates TCaR 61 and TCeRe 60, and Azotobacter vinelandii Mac 259 were selected as test bacteria based on their ability to produce indole-3acetic acid and solubilize precipitated phosphate, which may promote plant growth in the field. These bacteria were marked with gusA reporter gene from Escherichia coli strain S17-1(λ-pir containing mTn5SSgusA21. The gusA (β-glucuronidase gene from the donor (E. coli was transferred to each bacterium (recipient through bacterial conjugation in mating procedures using tryptone-yeast agar followed by the selection of the transconjugants (bacteria receiving gusA in tryptone-yeast agar supplemented with double antibiotics and X-GlcA (5bromo-4chloro- 3indoxyl-β-D-glucuronic acid. The antibiotics used were rifampicin and either streptomycin or spectinomycin based on antibiotic profiles of the donor and recipients. The results showed that the insertion of gusA gene into bacterial genomes of the recipient did not impair its phenotypic traits; the growth rates of the transconjugants as well as their ability to produce indole-3acetic acid and solubilize precipitated phosphate in pure culture were similar to their wild types. All transconjugants colonized the roots of hot pepper (Capsicum annuum L. and survived in the rhizosphere and soil until the late of vegetative growth stage. The distinct blue staining of transconjugants as the expression of gusA gene in media containing X-GlcA coupled with their resistance to rifampicin and streptomycin or spectinomycin

Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

KAUST Repository

Narita, Yuko; Zhang, Lei; Kimura, Zen-ichiro; Ali, Muhammad; Fujii, Takao; Okabe, Satoshi

2017-01-01

Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

KAUST Repository

Narita, Yuko

2017-08-18

Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

Stabilization of Pb and Cd contaminated soils and soil quality improvements using waste oyster shells.

Science.gov (United States)

Ok, Yong Sik; Lim, Jung Eun; Moon, Deok Hyun

2011-02-01

Large amounts of oyster shells are produced as a by-product of shellfish farming in coastal regions without beneficial use options. Accordingly, this study was conducted to evaluate the potential for the use of waste oyster shells (WOS) containing a high amount of CaCO₃ to improve soil quality and to stabilize heavy metals in soil. To accomplish this, an incubation experiment was conducted to evaluate the ability of the addition of 1-5 wt% WOS to stabilize the Pb (total 1,246 mg/kg) and Cd (total 17 mg/kg) in a contaminated soil. The effectiveness of the WOS treatments was evaluated using various single extraction techniques. Soil amended with WOS was cured for 30 days complied with the Korean Standard Test method (0.1 M·HCl extraction). The Pb and Cd concentrations were less than the Korean warning and countermeasure standards following treatment with 5 wt% WOS. Moreover, the concentrations of Cd were greatly reduced in response to WOS treatment following extraction using 0.01 M·CaCl₂, which is strongly associated with phytoavailability. Furthermore, the soil pH and exchangeable Ca increased significantly in response to WOS treatment. Taken together, the results of this study indicated that WOS amendments improved soil quality and stabilized Pb and Cd in contaminated soil. However, extraction with 0.43 M·CH₃ COOH revealed that remobilization of heavy metals can occur when the soil reaches an acidic condition.

Development of a Low Input and sustainable Switchgrass Feedstock Production System Utilizing Beneficial Bacterial Endophytes

Energy Technology Data Exchange (ETDEWEB)

Mei, Chuansheng [IALR; Nowak, Jerzy [VPISU; Seiler, John [VPISU

2014-10-24

Switchgrass represents a promising feedstock crop for US energy sustainability. However, its broad utilization for bioenergy requires improvements of biomass yields and stress tolerance. In this DOE funded project, we have been working on harnessing beneficial bacterial endophytes to enhance switchgrass performance and to develop a low input feedstock production system for marginal lands that do not compete with the production of food crops. We have demonstrated that one of most promising plant growth-promoting bacterial endophytes, Burkholderia phytofirmans strain PsJN, is able to colonize roots and significantly promote growth of switchgrass cv. Alamo under in vitro, growth chamber, greenhouse, as well as field conditions. Furthermore, PsJN bacterization improved growth and development of switchgrass seedlings, significantly stimulated plant root and shoot growth, and tiller number in the field, and enhanced biomass accumulation on both poor (p<0.001) and rich (p<0.05) soils, with more effective stimulation of plant growth in low fertility soil. Plant physiology measurements showed that PsJN inoculated Alamo had consistently lower transpiration, lower stomatal conductance, and higher water use efficiency in greenhouse conditions. These physiological changes may significantly contribute to the recorded growth enhancement. PsJN inoculation rapidly results in an increase in photosynthetic rates which contributes to the advanced growth and development. Some evidence suggests that this initial growth advantage decreases with time when resources are not limited such as in greenhouse studies. Additionally, better drought resistance and drought hardening were observed in PsJN inoculated switchgrass. Using the DOE-funded switchgrass EST microarray, in a collaboration with the Genomics Core Facility at the Noble Foundation, we have determined gene expression profile changes in both responsive switchgrass cv. Alamo and non-responsive cv. Cave-in-Rock (CR) following Ps

Microbial community dynamics during the bioremediation process of chlorimuron-ethyl-contaminated soil by Hansschlegelia sp. strain CHL1.

Directory of Open Access Journals (Sweden)

Liqiang Yang

Full Text Available Long-term and excessive application of chlorimuron-ethyl has led to a series of environmental problems. Strain Hansschlegelia sp. CHL1, a highly efficient chlorimuron-ethyl degrading bacterium isolated in our previous study, was employed in the current soil bioremediation study. The residues of chlorimuron-ethyl in soils were detected, and the changes of soil microbial communities were investigated by phospholipid fatty acid (PLFA analysis. The results showed that strain CHL1 exhibited significant chlorimuron-ethyl degradation ability at wide range of concentrations between 10μg kg-1 and 1000μg kg-1. High concentrations of chlorimuron-ethyl significantly decreased the total concentration of PLFAs and the Shannon-Wiener indices and increased the stress level of microbes in soils. The inoculation with strain CHL1, however, reduced the inhibition on soil microbes caused by chlorimuron-ethyl. The results demonstrated that strain CHL1 is effective in the remediation of chlorimuron-ethyl-contaminated soil, and has the potential to remediate chlorimuron-ethyl contaminated soils in situ.

Microbial Community Dynamics during the Bioremediation Process of Chlorimuron-Ethyl-Contaminated Soil by Hansschlegelia sp. Strain CHL1

Science.gov (United States)

Yang, Liqiang; Li, Xinyu; Li, Xu; Su, Zhencheng; Zhang, Chenggang; Zhang, Huiwen

2015-01-01

Long-term and excessive application of chlorimuron-ethyl has led to a series of environmental problems. Strain Hansschlegelia sp. CHL1, a highly efficient chlorimuron-ethyl degrading bacterium isolated in our previous study, was employed in the current soil bioremediation study. The residues of chlorimuron-ethyl in soils were detected, and the changes of soil microbial communities were investigated by phospholipid fatty acid (PLFA) analysis. The results showed that strain CHL1 exhibited significant chlorimuron-ethyl degradation ability at wide range of concentrations between 10μg kg-1 and 1000μg kg-1. High concentrations of chlorimuron-ethyl significantly decreased the total concentration of PLFAs and the Shannon-Wiener indices and increased the stress level of microbes in soils. The inoculation with strain CHL1, however, reduced the inhibition on soil microbes caused by chlorimuron-ethyl. The results demonstrated that strain CHL1 is effective in the remediation of chlorimuron-ethyl-contaminated soil, and has the potential to remediate chlorimuron-ethyl contaminated soils in situ. PMID:25689050

Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria.

Science.gov (United States)

Wolf, Alexandra B; Vos, Michiel; de Boer, Wietse; Kowalchuk, George A

2013-01-01

The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.

Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria.

Directory of Open Access Journals (Sweden)

Alexandra B Wolf

Full Text Available The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus and a motile rod-shaped bacterium (Bacillus weihenstephanensis to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions. These data, combined with information on bacterial motility (expansion potential across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.

Ethanologenic potential of the bacterium Bacillus cereus NB-19 in ...

African Journals Online (AJOL)

STORAGESEVER

2009-12-01

Dec 1, 2009 ... Ethanologenic bacterium was cultivated in a suspension of sugarcane ... bagasse is very useful for obtaining yields of the different products including cell mass and ethanol as ... the resources for the green fuel generation.

Mineralization of PCBs by the genetically modified strain Cupriavidus necator JMS34 and its application for bioremediation of PCBs in soil

Energy Technology Data Exchange (ETDEWEB)

Saavedra, Juan Matias; Acevedo, Francisca; Gonzalez, Myriam; Seeger, Michael [Universidad Tecnica Federico Santa Maria, Valparaiso (Chile). Lab. de Microbiologia Molecular y Biotecnologia

2010-07-15

Polychlorobiphenyls (PCBs) are classified as ''high-priority pollutants''. Diverse microorganisms are able to degrade PCBs. However, bacterial degradation of PCBs is generally incomplete, leading to the accumulation of chlorobenzoates (CBAs) as dead-end metabolites. To obtain a microorganism able to mineralize PCB congeners, the bph locus of Burkholderia xenovorans LB400, which encodes one of the most effective PCB degradation pathways, was incorporated into the genome of the CBA-degrading bacterium Cupriavidus necator JMP134-X3. The bph genes were transferred into strain JMP134-X3, using the mini-Tn5 transposon system and biparental mating. The genetically modified derivative, C. necator strain JMS34, had only one chromosomal insertion of bph locus, which was stable under nonselective conditions. This modified bacterium was able to grow on biphenyl, 3-CBA and 4-CBA, and degraded 3,5-CBA in the presence of m-toluate. The strain JMS34 mineralized 3-CB, 4-CB, 2,4{sup '}-CB, and 3,5-CB, without accumulation of CBAs. Bioaugmentation of PCB-polluted soils with C. necator strain JMS34 and with the native B. xenovorans LB400 was monitored. It is noteworthy that strain JMS34 degraded, in 1 week, 99% of 3-CB and 4-CB and approximately 80% of 2,4{sup '}-CB in nonsterile soil, as well as in sterile soil. Additionally, the bacterial count of strain JMS34 increased by almost two orders of magnitude in PCB-polluted nonsterile soil. In contrast, the presence of native microflora reduced the degradation of these PCBs by strain LB400 from 73% (sterile soil) to approximately 50% (nonsterile soil). This study contributes to the development of improved biocatalysts for remediation of PCB-contaminated environments. (orig.)

Biotransformation of As (III to As (V and their stabilization in soil with Bacillus sp. XS2 isolated from gold mine tailing of Xinjiang, China

Directory of Open Access Journals (Sweden)

Santosh Kumar Karn

2016-09-01

Full Text Available Xinjiang province is one of the most polluted region in China, this region affected by multi-metal problem, especially arsenic (As affect very badly. Two major forms of As present in the environment As (III and As (V as compared to As (V, As (III is much more toxic. Our aim is to remediate As (III contaminated soil by using As (III resistant microbe, having the high transforming ability for As (III to As (V. An As (III oxidizing bacterium Bacillus sp. XS2, isolated and selected from gold mine tailing which have shown high resistance up to 6400 mg L−1 and efficiently transformed up to 4000 mg L−1 in sucrose low phosphate medium (SLP, higher than any of the previous reported Bacillus sp.. In soil, we found that XS2 successfully transformed up to 81% of soluble exchangeable fraction within 10 d in contaminated soil (with 500 mg kg−1, which makes it potential microbe for the removal of contaminated site with arsenic in the environment. Further XS2 was characterized for their molecular basis of resistance and we establish that XS2 having arsenic oxidase enzyme activity which is accountable for the detoxification of arsenic at high concentration and provide resistance to the bacterium. Gene encoding arsenic oxidase (aioA-gene was also amplified from this bacterium using polymerase chain reaction (PCR with degenerate primer. The aioA-gene is specific for the arsenite-oxidizing bacteria. The deduced amino acid sequence had shown 42% similarity with pseudomonas sp. arsenic oxidase. Further, the strain was characterized by 16s rRNA gene sequence analysis and shown maximum similarity with Bacillus sp.

Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response.

Science.gov (United States)

Van Puyvelde, Sandra; Cloots, Lore; Engelen, Kristof; Das, Frederik; Marchal, Kathleen; Vanderleyden, Jos; Spaepen, Stijn

2011-05-01

The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.

Understanding the interaction between an obligate hyperparasitic bacterium, Pasteuria penetrans and its obligate plant-parasitic nematode host, Meloidogyne spp.

Science.gov (United States)

Davies, Keith G

2009-01-01

Pasteuria penetrans is an endospore-forming bacterium, which is a hyperparasite of root-knot nematodes Meloidogyne spp. that are economically important pests of a wide range of crops. The life cycle of the bacterium and nematode are described with emphasis on the bacterium's potential as a biocontrol agent. Two aspects that currently prohibit the commercial development of the bacterium as a biocontrol agent are the inability to culture it outside its host and its host specificity. Vegetative growth of the bacterium is possible in vitro; however, getting the vegetative stages of the bacterium to enter sporogenesis has been problematic. Insights from genomic survey sequences regarding the role of cation concentration and the phosphorylation of Spo0F have proved useful in inducing vegetative bacteria to sporulate. Similarly, genomic data have also proved useful in understanding the attachment of endospores to the cuticle of infective nematode juveniles, and a Velcro-like model of spore attachment is proposed that involves collagen-like fibres on the surface of the endospore interacting with mucins on the nematode cuticle. Ecological studies of the interactions between Daphnia and Pasteuria ramosa are examined and similarities are drawn between the co-evolution of virulence in the Daphnia system and that of plant-parasitic nematodes.

Description of a bacterium associated with redmouth disease of rainbow trout (Salmo gairdneri)

Science.gov (United States)

Ross, A.J.; Rucker, R.R.; Ewing, W.H.

1966-01-01

A description was given of a gram-negative, peritrichously flagellated, fermentative bacterium that was isolated on numerous occasions from kidney tissues of rainbow trout (Salmo gairdneri) afflicted with redmouth disease. Although the bacteria apparently were members of the family Enterobacteriaceae, it was impossible to determine their taxonomic position within the family with certainty. Hence it was recommended that their taxonomic position remain sub judice for the present. As a temporary designation RM bacterium was used. Redmouth disease was transmitted from infected to normal fish through the medium of water.

Tenax TA extraction to understand the rate-limiting factors in methyl-β-cyclodextrin-enhanced bioremediation of PAH-contaminated soil.

Science.gov (United States)

Sun, Mingming; Luo, Yongming; Teng, Ying; Christie, Peter; Jia, Zhongjun; Li, Zhengao

2013-06-01

The effectiveness of many bioremediation systems for PAH-contaminated soil may be constrained by low contaminant bioaccessibility due to limited aqueous solubility or large sorption capacity. Information on the extent to which PAHs can be readily biodegraded is of vital importance in the decision whether or not to remediate a contaminated soil. In the present study the rate-limiting factors in methyl-β-cyclodextrin (MCD)-enhanced bioremediation of PAH-contaminated soil were evaluated. MCD amendment at 10 % (w/w) combined with inoculation with the PAH-degrading bacterium Paracoccus sp. strain HPD-2 produced maximum removal of total PAHs of up to 35 %. The desorption of PAHs from contaminated soil was determined before and after 32 weeks of bioremediation. 10 % (w/w) MCD amendment (M2) increased the Tenax extraction of total PAHs from 12 to 30 % and promoted degradation by up to 26 % compared to 6 % in the control. However, the percentage of Tenax extraction for total PAHs was much larger than that of degradation. Thus, in the control and M2 treatment it is likely that during the initial phase the bioaccessibility of PAHs is high and biodegradation rates may be limited by microbial processes. On the other hand, when the soil was inoculated with the PAH-degrading bacterium (CKB and MB2), the slowly and very slowly desorbing fractions (F sl and F vl ) became larger and the rate constants of slow and very slow desorption (k sl and k vl ) became extremely small after bioremediation, suggesting that desorption is likely rate limiting during the second, slow phase of biotransformation. These results have practical implications for site risk assessment and cleanup strategies.

Degradation and utilization of polycyclic aromatic hydrocarbons by indigenous soil bacteria

International Nuclear Information System (INIS)

Stetzenbach, L.D.A.

1986-01-01

The persistence of industrially derived polycyclic aromatic hydrocarbons in the subsurface may be significantly affected by the metabolism of soil bacteria. This study was conducted to determine the ability of indigenous soil bacteria to decrease the concentration of four polycyclic aromatic hydrocarbons (naphthalene, fluorene, anthracene, and pyrene) and to utilize the compounds as a substrate for growth. Soil cores from petroleum contaminated and noncontaminated sites contained 10 5 -10 7 viable microorganisms per gram dryweight of soil. Gram negative rod-shaped bacteria predominated. Decreases in the concentration of the four polycyclic aromatic hydrocarbons were observed during incubation with bacterial isolates in aqueous suspension by the use of high performance liquid chromatography. Corresponding increases in bacterial numbers indicated utilization of the compounds as a carbon source. Soil samples from the contaminated sites contained greater numbers of bacteria utilizing anthracene and pyrene than soil samples from uncontaminated sites. Degradation rates of the four polycyclic aromatic hydrocarbons were related to the compound, its concentration, and the bacterium. Biodegradation of pyrene was positively correlated with the presence of oxygen. Pyrene was biodegraded by an Acinetobacter sp. under aerobic conditions but not under anaerobic or microaerophilic conditions. Studies with radiolabeled 14 C-anthracene demonstrated utilization of the labeled carbon as a source of carbon by viable bacterial cells in aqueous suspension. Incorporation of 14 C into cellular biomass however was not observed during incubation of 14 C-anthracene in soil

Feasibility study of a soil-based rubberized CLSM.

Science.gov (United States)

Wu, Jason Y; Tsai, Mufan

2009-02-01

The development of beneficial uses of recycled scrap tires is always in great demand around the world. The disposal of on-site surplus excavated soil and the production of standard engineering aggregates have also been facing increasing environmental and ecological challenges in congested islands, such as Taiwan. This paper presents an experimental study using recycled crumb rubber and native silty sand to produce a lightweight, soil-based, rubberized controlled low strength material (CLSM) for a bridge approach repair. To assess the technical feasibility of this material, the effects of weight ratios of cement-to-water (C/W) and water-to-solid (W/S), and of rubber content on the engineering properties for different mixtures were investigated. The presented test results include flowability, unit weight, strength, settlement potential, and bearing capacity. Based on the findings, we conclude that a soil-based rubberized CLSM with 40% sand by weight and an optimal design ratio of 0.7 for C/W and 0.35 for W/S can be used for the proposed bridge approach repair. Such a mixture has demonstrated acceptable flowability, strength, and bearing capacity. Its lower unit weight, negligible compressibility, and hydrocollapse potential also help ensure that detrimental settlement is unlikely to occur. The results illustrate a novel scheme of CLSM production, and suggest a beneficial alternative for the reduction of scrap tires as well as conservation of resources and environment.

Complete genome sequence of the photoautotrophic and bacteriochlorophyll e-synthesizing green sulfur bacterium Chlorobaculum limnaeum DSM 1677T

DEFF Research Database (Denmark)

Tank, Marcus; Liu, Zhenfeng; Frigaard, Niels-Ulrik

2017-01-01

Chlorobaculum limnaeum DSM 1677T is a mesophilic, brown-colored, chlorophototrophic green sulfur bacterium that produces bacteriochlorophyll e and the carotenoid isorenieratene as major pigments. This bacterium serves as a model organism in molecular research on photosynthesis, sulfur metabolism...

Non-obligate predatory bacterium burkholderia casidaeand uses thereof

OpenAIRE

1998-01-01

A novel predator bacterium Burkholderia casidae is disclosed. The invention is directed to the isolation and use of Burkholderia casidae to control microbial diseases of plants. The genetic, biochemical and physiological characteristics of Burkholderia casidae are described. Biocontrol compositions comprising Burkholderia casidae, and antimicrobial compounds and antimicrobial preparations prepared from Burkholderia casidae are also disclosed, as are methods for accomplishing all of the forego...

[Prebiotics: concept, properties and beneficial effects].

Science.gov (United States)

Corzo, N; Alonso, J L; Azpiroz, F; Calvo, M A; Cirici, M; Leis, R; Lombó, F; Mateos-Aparicio, I; Plou, F J; Ruas-Madiedo, P; Rúperez, P; Redondo-Cuenca, A; Sanz, M L; Clemente, A

2015-02-07

Prebiotics are non-digestible food ingredients (oligosaccharides) that reach the colon and are used as substrate by microorganisms producing energy, metabolites and micronutrients used for the host; in addition they also stimulate the selective growth of certain beneficial species (mainly bifidobacteria and lactobacilli) in the intestinal microbiota. In this article, a multidisciplinary approach to understand the concept of prebiotic carbohydrates, their properties and beneficial effects in humans has been carried out. Definitions of prebiotics, reported by relevant international organizations and researchers, are described. A comprehensive description of accepted prebiotics having strong scientific evidence of their beneficial properties in humans (inulin-type fructans, FOS, GOS, lactulose and human milk oligosaccharides) is reported. Emerging prebiotics and those which are in the early stages of study have also included in this study. Taken into account that the chemical structure greatly influences carbohydrates prebiotic properties, the analytical techniques used for their analysis and characterization are discussed. In vitro and in vivo models used to evaluate the gastrointestinal digestion, absorption resistance and fermentability in the colon of prebiotics as well as major criteria to design robust intervention trials in humans are described. Finally, a comprehensive summary of the beneficial effects of prebiotics for health at systemic and intestinal levels is reported. The research effort on prebiotics has been intensive in last decades and has demonstrated that a multidisciplinary approach is necessary in order to claim their health benefits. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Structural changes in latosols of the cerrado region: II - soil compressive behavior and modeling of additional compaction

Directory of Open Access Journals (Sweden)

Eduardo da Costa Severiano

2011-06-01

Full Text Available Currently in Brazil, as in other parts of the world, the concern is great with the increase of degraded agricultural soil, which is mostly related to the occurrence of soil compaction. Although soil texture is recognized as a very important component in the soil compressive behaviors, there are few studies that quantify its influence on the structural changes of Latosols in the Brazilian Cerrado region. This study aimed to evaluate structural changes and the compressive behavior of Latosols in Rio Verde, Goiás, through the modeling of additional soil compaction. The study was carried out using five Latosols with very different textures, under different soil compaction levels. Water retention and soil compression curves, and bearing capacity models were determined from undisturbed samples collected on the B horizons. Results indicated that clayey and very clayey Latosols were more susceptible to compression than medium-textured soils. Soil compression curves at density values associate with edaphic functions were used to determine the beneficial pressure (σ b , i.e., pressure with optimal water retention, and critical pressure (σcrMAC, i.e., pressure with macroporosity below critical levels. These pressure values were higher than the preconsolidation pressure (σp, and therefore characterized as additional compaction. Based on the compressive behavior of these Latosols, it can be concluded that the combined preconsolidation pressure, beneficial pressure and critical pressure allow a better understanding of compression processes of Latosols.

A novel radio-tolerant astaxanthin-producing bacterium reveals a new astaxanthin derivative: astaxanthin dirhamnoside.

Science.gov (United States)

Asker, Dalal; Awad, Tarek S; Beppu, Teruhiko; Ueda, Kenji

2012-01-01

Astaxanthin is a red ketocarotenoid that exhibits extraordinary health-promoting activities such as antioxidant, anti-inflammatory, antitumor, and immune booster. The recent discovery of the beneficial roles of astaxanthin against many degenerative diseases such as cancers, heart diseases, and exercise-induced fatigue has raised its market demand as a nutraceutical and medicinal ingredient in aquaculture, food, and pharmaceutical industries. To satisfy the growing demand for this high-value nutraceuticals ingredient and consumer interest in natural products, many research efforts are being made to discover novel microbial producers with effective biotechnological production of astaxanthin. Using a rapid screening method based on 16S rRNA gene, and effective HPLC-Diodearray-MS methods for carotenoids analysis, we succeeded to isolate a unique astaxanthin-producing bacterium (strain TDMA-17(T)) that belongs to the family Sphingomonadaceae (Asker et al., Appl Microbiol Biotechnol 77: 383-392, 2007). In this chapter, we provide a detailed description of effective HPLC-Diodearray-MS methods for rapid analysis and identification of the carotenoids produced by strain TDMA-17(T). We also describe the methods of isolation and identification for a novel bacterial carotenoid (astaxanthin derivative), a major carotenoid that is produced by strain TDMA-17(T). Finally, we describe the polyphasic taxonomic analysis of strain TDMA-17(T) and the description of a novel species belonging to genus Sphingomonas.

DNA damage response in a radiation resistant bacterium Deinococcus radiodurans: a paradigm shift

International Nuclear Information System (INIS)

Misra, H.S.

2015-01-01

Deinococcusradiodurans is best known for its extraordinary resistance to gamma radiation with its D 10 12kGy, and several other DNA damaging agents including desiccation to less than 5% humidity and chemical xenotoxicants. An efficient DNA double strand break (DSB) repair and its ability to protect biomolecules from oxidative damage are a few mechanisms attributed to these phenotypes in this bacterium. Although it regulates its proteome and transcriptome in response to DNA damage for its growth and survival, it lacks LexA mediated classical SOS response mechanism. Since LexA mediated damages response mechanism is highly and perhaps only, characterized DNA damage response processes in prokaryotes, this bacterium keeps us guessing how it responds to extreme doses of DNA damage. Interestingly, this bacterium encodes a large number of eukaryotic type serine threonine/tyrosine protein kinases (eST/YPK), phosphatases and response regulators and roles of eST/YPKs in cellular response to DNA damage and cell cycle regulations are well established in eukaryotes. Here, we characterized an antioxidant and DNA damage inducible eST/YPK (RqkA) and established its role in extraordinary radioresistance and DSB repair in this bacterium. We identified native phosphoprotein substrates for this kinase and demonstrated the involvement of some of these proteins phosphorylation in the regulation of DSB repair and growth under radiation stress. Findings suggesting the possible existence of eST/YPK mediated DNA damage response mechanism as an alternate to classical SOS response in this prokaryote would be discussed. (author)

Rare beneficial mutations can halt Muller's ratchet

Science.gov (United States)

Balick, Daniel; Goyal, Sidhartha; Jerison, Elizabeth; Neher, Richard; Shraiman, Boris; Desai, Michael

2012-02-01

In viral, bacterial, and other asexual populations, the vast majority of non-neutral mutations are deleterious. This motivates the application of models without beneficial mutations. Here we show that the presence of surprisingly few compensatory mutations halts fitness decay in these models. Production of deleterious mutations is balanced by purifying selection, stabilizing the fitness distribution. However, stochastic vanishing of fitness classes can lead to slow fitness decay (i.e. Muller's ratchet). For weakly deleterious mutations, production overwhelms purification, rapidly decreasing population fitness. We show that when beneficial mutations are introduced, a stable steady state emerges in the form of a dynamic mutation-selection balance. We argue this state is generic for all mutation rates and population sizes, and is reached as an end state as genomes become saturated by either beneficial or deleterious mutations. Assuming all mutations have the same magnitude selective effect, we calculate the fraction of beneficial mutations necessary to maintain the dynamic balance. This may explain the unexpected maintenance of asexual genomes, as in mitochondria, in the presence of selection. This will affect in the statistics of genetic diversity in these populations.

Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

KAUST Repository

Wang, Yong

2016-07-01

Aerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.

Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties.

Science.gov (United States)

El Kafsi, Hela; Binesse, Johan; Loux, Valentin; Buratti, Julien; Boudebbouze, Samira; Dervyn, Rozenn; Hammani, Amal; Maguin, Emmanuelle; van de Guchte, Maarten

2014-07-17

Lactobacillus delbrueckii subsp. lactis CNRZ327 is a dairy bacterium with anti-inflammatory properties both in vitro and in vivo. Here, we report the genome sequence of this bacterium, which appears to contain no less than 215 insertion sequence (IS) elements, an exceptionally high number regarding the small genome size of the strain. Copyright © 2014 El Kafsi et al.

Chitin utilization by the insect-transmitted bacterium Xylella fastidiosa.

Science.gov (United States)

Killiny, Nabil; Prado, Simone S; Almeida, Rodrigo P P

2010-09-01

Xylella fastidiosa is an insect-borne bacterium that colonizes xylem vessels of a large number of host plants, including several crops of economic importance. Chitin is a polysaccharide present in the cuticle of leafhopper vectors of X. fastidiosa and may serve as a carbon source for this bacterium. Biological assays showed that X. fastidiosa reached larger populations in the presence of chitin. Additionally, chitin induced phenotypic changes in this bacterium, notably increasing adhesiveness. Quantitative PCR assays indicated transcriptional changes in the presence of chitin, and an enzymatic assay demonstrated chitinolytic activity by X. fastidiosa. An ortholog of the chitinase A gene (chiA) was identified in the X. fastidiosa genome. The in silico analysis revealed that the open reading frame of chiA encodes a protein of 351 amino acids with an estimated molecular mass of 40 kDa. chiA is in a locus that consists of genes implicated in polysaccharide degradation. Moreover, this locus was also found in the genomes of closely related bacteria in the genus Xanthomonas, which are plant but not insect associated. X. fastidiosa degraded chitin when grown on a solid chitin-yeast extract-agar medium and grew in liquid medium with chitin as the sole carbon source; ChiA was also determined to be secreted. The gene encoding ChiA was cloned into Escherichia coli, and endochitinase activity was detected in the transformant, showing that the gene is functional and involved in chitin degradation. The results suggest that X. fastidiosa may use its vectors' foregut surface as a carbon source. In addition, chitin may trigger X. fastidiosa's gene regulation and biofilm formation within vectors. Further work is necessary to characterize the role of chitin and its utilization in X. fastidiosa.

Infection with Soil-Transmitted Helminths Is Associated with Increased Insulin Sensitivity

NARCIS (Netherlands)

Wiria, A.E.; Hamid, F.; Wammes, L.J.; Prasetyani, M.A.; Dekkers, O.M.; May, L.; Kaisar, M.M.; Verweij, J.J.; Guigas, B.; Partono, F.; Sartono, E.; Supali, T.; Yazdanbakhsh, M.; Smit, J.W.A.

2015-01-01

OBJECTIVE: Given that helminth infections have been shown to improve insulin sensitivity in animal studies, which may be explained by beneficial effects on energy balance or by a shift in the immune system to an anti-inflammatory profile, we investigated whether soil-transmitted helminth

Toxicity of perfluorooctanoic acid towards earthworm and enzymatic activities in soil.

Science.gov (United States)

He, Wenxiang; Megharaj, Mallavarapu; Naidu, Ravi

2016-07-01

Perfluorooctanoic acid (PFOA) is a widespread persistent organic contaminant in the environment that has recently raised much of regulatory and public concern. Therefore, assessment of its ecological risk is a top priority research. Hence, this study investigated the toxicity of PFOA to beneficial microbial processes in the soil such as activities of dehydrogenase, urease and potential nitrification in addition to earthworm survival, weight loss and PFOA bioaccumulation in two contrasting soils. In general, PFOA caused inhibition of all the measured microbial processes in a dose-dependent manner and the inhibition was higher in Williamtown (WT) soil than Edinburgh (EB) soil. Thus, WT soil being sandy in nature with low clay content showed higher PFOA bioavailability and hence showed higher toxicity. There was no mortality in earthworms exposed up to 100 mg PFOA/kilogram soil in both the soils; however, there was a significant weight loss from 25 mg/kg onwards. This study clearly demonstrates that soil contamination of PFOA can lead to adverse effects on soil health.

Single-bacterium nanomechanics in biomedicine: unravelling the dynamics of bacterial cells

International Nuclear Information System (INIS)

Aguayo, S; Bozec, L; Donos, N; Spratt, D

2015-01-01

The use of the atomic force microscope (AFM) in microbiology has progressed significantly throughout the years since its first application as a high-resolution imaging instrument. Modern AFM setups are capable of characterizing the nanomechanical behaviour of bacterial cells at both the cellular and molecular levels, where elastic properties and adhesion forces of single bacterium cells can be examined under different experimental conditions. Considering that bacterial and biofilm-mediated infections continue to challenge the biomedical field, it is important to understand the biophysical events leading towards bacterial adhesion and colonization on both biological and non-biological substrates. The purpose of this review is to present the latest findings concerning the field of single-bacterium nanomechanics, and discuss future trends and applications of nanoindentation and single-cell force spectroscopy techniques in biomedicine. (topical review)

The Bacterium That Got Infected by a Cow! - Horizontal Gene

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 1. The Bacterium That Got Infected by a Cow! - Horizontal Gene Transfer and Evolution. Saurabh Dhawan Tomás John Ryan. General Article Volume 12 Issue 1 January 2007 pp 49-59 ...

Earthworms as vectors of Escherichia coli O157:H7 in soil and vermicomposts.

Science.gov (United States)

Williams, A Prysor; Roberts, Paula; Avery, Lisa M; Killham, Ken; Jones, David L

2006-10-01

Survival and movement of Escherichia coli O157:H7 in both soil and vermicompost is of concern with regards to human health. Whilst it is accepted that E. coli O157:H7 can persist for considerable periods in soils, it is not expected to survive thermophilic composting processes. However, the natural behavior of earthworms is increasingly utilized for composting (vermicomposting), and the extent to which earthworms promote the survival and dispersal of the bacterium within such systems is unknown. The faecal material produced by earthworms provides a ready supply of labile organic substrates to surrounding microbes within soil and compost, thus promoting microbial activity. Earthworms can also cause significant movement of organisms through the channels they form. Survival and dispersal of E. coli O157:H7 were monitored in contaminated soil and farmyard manure subjected to earthworm digestion over 21 days. Our findings lead to the conclusion that anecic earthworms such as Lumbricus terrestris may significantly aid vertical movement of E. coli O157 in soil, whereas epigeic earthworms such as Dendrobaena veneta significantly aid lateral movement within compost. Although the presence of earthworms in soil and compost may aid proliferation of E. coli O157 in early stages of contamination, long-term persistence of the pathogen appears to be unaffected.

No apparent costs for facultative antibiotic production by the soil bacterium Pseudomonas fluorescens Pf0-1

NARCIS (Netherlands)

Garbeva, P.V.; Tyc, O.; Remus-Emsermann, M.N.P.; Van der Wal, A.; Vos, M.; Silby, M.W.; De Boer, W.

2011-01-01

Background: Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the

Nice to meet you: genetic, epigenetic and metabolic controls of plant perception of beneficial associative and endophytic diazotrophic bacteria in non-leguminous plants.

Science.gov (United States)

Carvalho, T L G; Ballesteros, H G F; Thiebaut, F; Ferreira, P C G; Hemerly, A S

2016-04-01

A wide range of rhizosphere diazotrophic bacteria are able to establish beneficial associations with plants, being able to associate to root surfaces or even endophytically colonize plant tissues. In common, both associative and endophytic types of colonization can result in beneficial outcomes to the plant leading to plant growth promotion, as well as increase in tolerance against biotic and abiotic stresses. An intriguing question in such associations is how plant cell surface perceives signals from other living organisms, thus sorting pathogens from beneficial ones, to transduce this information and activate proper responses that will finally culminate in plant adaptations to optimize their growth rates. This review focuses on the recent advances in the understanding of genetic and epigenetic controls of plant-bacteria signaling and recognition during beneficial associations with associative and endophytic diazotrophic bacteria. Finally, we propose that "soil-rhizosphere-rhizoplane-endophytes-plant" could be considered as a single coordinated unit with dynamic components that integrate the plant with the environment to generate adaptive responses in plants to improve growth. The homeostasis of the whole system should recruit different levels of regulation, and recognition between the parties in a given environment might be one of the crucial factors coordinating these adaptive plant responses.

Biosorption of heavy metals by a marine bacterium

Energy Technology Data Exchange (ETDEWEB)

Iyer, Anita [Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat (India); Mody, Kalpana [Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat (India)]. E-mail: khmody@csmcri.org; Jha, Bhavanath [Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat (India)

2005-03-01

Heavy metal chelation property of exopolysaccharide produced by Enterobacter cloaceae, a marine bacterium, isolated from the West Coast of India, is reported in this paper. The exopolysaccharide demonstrated excellent chelating properties with respect to cadmium (65%) followed by copper (20%) and cobalt (8%) at 100 mg/l heavy metal concentration. However, it could not chelate mercury. A comparative study of the percentage biosorption of the above mentioned metals is presented here.

Biosorption of heavy metals by a marine bacterium

International Nuclear Information System (INIS)

Iyer, Anita; Mody, Kalpana; Jha, Bhavanath

2005-01-01

Heavy metal chelation property of exopolysaccharide produced by Enterobacter cloaceae, a marine bacterium, isolated from the West Coast of India, is reported in this paper. The exopolysaccharide demonstrated excellent chelating properties with respect to cadmium (65%) followed by copper (20%) and cobalt (8%) at 100 mg/l heavy metal concentration. However, it could not chelate mercury. A comparative study of the percentage biosorption of the above mentioned metals is presented here

Antimicrobial polyketide furanoterpenoids from seaweed-associated heterotrophic bacterium Bacillus subtilis MTCC 10403.

Science.gov (United States)

Chakraborty, Kajal; Thilakan, Bini; Raola, Vamshi Krishna

2017-10-01

Brown seaweed Anthophycus longifolius (Turner) Kützing (family Sargassaceae) associated heterotrophic bacterium Bacillus subtilis MTCC 10403 was found to be a potent isolate with broad range of antibacterial activity against important perceptive food pathogens Vibrio parahaemolyticus, V. vulnificus, and Aeromonas hydrophila. This bacterium was positive for polyketide synthetase gene (KC589397), and therefore, was selected to bioprospect specialized metabolites bearing polyketide backbone. Bioactivity-guided chromatographic fractionation of the ethyl acetate extract of the seaweed-associated bacterium segregated four homologous polyketide furanoterpenoids with potential antibacterial activities against clinically important pathogens. The minimum inhibitory concentration (MIC) assay showed that the referral antibiotics tetracycline and ampicillin were active at 25 μg/mL against the test pathogens, whereas the previously undescribed (4E)-methyl 13-((16-(furan-2-yl) ethyl)-octahydro-7-hydroxy-4-((E)-23-methylbut-21-enyl)-2H-chromen-6-yl)-4-methylpent-4-enoate (compound 1) and methyl 3-(hexahydro-9-((E)-3-methylpent-1-enyl)-4H-furo[3,2-g]isochromen-6-yl) propanoate (compound 3) displayed antibacterial activities against the test pathogens at a lesser concentration (MIC subtilis MTCC 10403 demonstrated to represent a potential source of antimicrobial polyketides for pharmaceutical applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Beneficial rhizobacteria

DEFF Research Database (Denmark)

Michelsen, Charlotte Frydenlund

Potatoes are cultivated in Southwest Greenland without the use of pesticides and with limited crop rotation. However, despite the fact that plant-pathogenic fungi are present in the Greenlandic potato soils, no severe disease outbreaks, such as late blight, have been observed. In this PhD project...

Aerobic degradation of N-methyl-4-nitroaniline (MNA by Pseudomonas sp. strain FK357 isolated from soil.

Directory of Open Access Journals (Sweden)

Fazlurrahman Khan

Full Text Available N-Methyl-4-nitroaniline (MNA is used as an additive to lower the melting temperature of energetic materials in the synthesis of insensitive explosives. Although the biotransformation of MNA under anaerobic condition has been reported, its aerobic microbial degradation has not been documented yet. A soil microcosms study showed the efficient aerobic degradation of MNA by the inhabitant soil microorganisms. An aerobic bacterium, Pseudomonas sp. strain FK357, able to utilize MNA as the sole carbon, nitrogen, and energy source, was isolated from soil microcosms. HPLC and GC-MS analysis of the samples obtained from growth and resting cell studies showed the formation of 4-nitroaniline (4-NA, 4-aminophenol (4-AP, and 1, 2, 4-benzenetriol (BT as major metabolic intermediates in the MNA degradation pathway. Enzymatic assay carried out on cell-free lysates of MNA grown cells confirmed N-demethylation reaction is the first step of MNA degradation with the formation of 4-NA and formaldehyde products. Flavin-dependent transformation of 4-NA to 4-AP in cell extracts demonstrated that the second step of MNA degradation is a monooxygenation. Furthermore, conversion of 4-AP to BT by MNA grown cells indicates the involvement of oxidative deamination (release of NH2 substituent reaction in third step of MNA degradation. Subsequent degradation of BT occurs by the action of benzenetriol 1, 2-dioxygenase as reported for the degradation of 4-nitrophenol. This is the first report on aerobic degradation of MNA by a single bacterium along with elucidation of metabolic pathway.

Assessment of the biostimulation against bioaugmentation and natural attenuation on contaminated soil with diesel-gasoline mixing

International Nuclear Information System (INIS)

Gomez, Wilmar; Gaviria, Jair; Cardona, Santiago

2009-01-01

In this study carried out the bioremediation of a contaminated soil with a gasoline-diesel fuel mixture in a laboratory scale, to evaluate biostimulation against natural attenuation and bioaugmentation. The reduction of Total Petroleum Hydrocarbons (TPH) concentration during three months was 52.79 % for natural attenuation, 60.45 % for biostimulation and 64.92 % for bioaugmentation. For the inoculation in the bioaugmentation treatment, was isolated a bacterium with the capacity of degrade hydrocarbons which was identified as Bacillus sp.

Take advantage of mycorrhizal fungi for improved soil fertility and plant health

Science.gov (United States)

Arbuscular mycorrhizal [AM] fungi are naturally-occurring soil fungi that form a beneficial symbiosis with the roots of most crops. The plants benefit because the symbiosis increases mineral nutrient uptake, drought resistance, and disease resistance. These characteristics make utilization of AM f...

Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study

Directory of Open Access Journals (Sweden)

OCKY KARNA RADJASA

2005-06-01

Full Text Available A coral-associated bacterium was successfully screened for secondary metabolites production based on PCR amplification of the nonribosomal peptide synthetase gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA.The bacterium was found to inhibit the growth of shrimp pathogenic bacterium tested, Vibrio harveyi. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved signature regions for peptide synthetases and revealed a high similarity to NosD (40% identity, a multifunctional peptide synthetase from Nostoc sp. GSV224, and NdaB (44% identity, a peptide synthetase module of Nodularia spumigena.

Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study

Directory of Open Access Journals (Sweden)

OCKY KARNA RADJASA

2005-06-01

Full Text Available A coral-associated bacterium was successfully screened for secondary metabolites production based on PCR amplification of the nonribosomal peptide synthetase gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA. The bacterium was found to inhibit the growth of shrimp pathogenic bacterium tested, Vibrio harveyi. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved signature regions for peptide synthetases and revealed a high similarity to NosD (40% identity, a multifunctional peptide synthetase from Nostoc sp. GSV224, and NdaB (44% identity, a peptide synthetase module of Nodularia spumigena

Beneficial use of isotopes

International Nuclear Information System (INIS)

Bertel, E.; Stevens, G.H.

1998-01-01

The paper gives an outlook on the main isotopes currently used for beneficial applications, provides an overview on geographic distribution of isotope production capabilities and identifies the main suppliers world-wide. It analyses trends in different countries and regions, including the refurbishment and/or replacement of ageing facilities and the implementation of new capabilities. Issues related to adequate supply of isotopes and potential under or over capacity of production for some key products are discussed. The evolution of the isotope production sector is analysed. Issues such as lowering of governmental support to production facilities, emergence of international co-operation and agreements on production capabilities, and developments in non-OECD/NEA countries are addressed. The paper offers some concluding remarks on the importance of maintaining and enhancing beneficial uses of isotopes, the role of government policies, the need for co-operation between countries and between the private and public sectors. The paper addresses the role of international cooperation in making efficient use of existing isotope production capacity and investigates ways for reducing the need for investment in additional capacity. (author)

Combustion characterization of beneficiated coal-based fuels

Energy Technology Data Exchange (ETDEWEB)

Chow, O.K.; Levasseur, A.A.

1995-11-01

The Pittsburgh Energy Technology Center (PETC) of the U.S. Department of Energy is sponsoring the development of advanced coal-cleaning technologies aimed at expanding the use of the nation`s vast coal reserves in an environmentally and economically acceptable manner. Because of the lack of practical experience with deeply beneficiated coal-based fuels, PETC has contracted Combustion Engineering, Inc. to perform a multi-year project on `Combustion Characterization of Beneficiated Coal-Based Fuels.` The objectives of this project include: (1) the development of an engineering data base which will provide detailed information on the properties of Beneficiated Coal-Based Fuels (BCs) influencing combustion, ash deposition, ash erosion, particulate collection, and emissions; and (2) the application of this technical data base to predict the performance and economic impacts of firing the BCFs in various commercial boiler designs.

The Agr communication system provides a benefit to the populations of Listeria monocytogenes in soil.

Science.gov (United States)

Vivant, Anne-Laure; Garmyn, Dominique; Gal, Laurent; Piveteau, Pascal

2014-01-01

In this study, we investigated whether the Agr communication system of the pathogenic bacterium Listeria monocytogenes was involved in adaptation and competitiveness in soil. Alteration of the ability to communicate, either by deletion of the gene coding the response regulator AgrA (response-negative mutant) or the signal pro-peptide AgrD (signal-negative mutant), did not affect population dynamics in soil that had been sterilized but survival was altered in biotic soil suggesting that the Agr system of L. monocytogenes was involved to face the complex soil biotic environment. This was confirmed by a set of co-incubation experiments. The fitness of the response-negative mutant was lower either in the presence or absence of the parental strain but the fitness of the signal-negative mutant depended on the strain with which it was co-incubated. The survival of the signal-negative mutant was higher when co-cultured with the parental strain than when co-cultured with the response-negative mutant. These results showed that the ability to respond to Agr communication provided a benefit to listerial cells to compete. These results might also indicate that in soil, the Agr system controls private goods rather than public goods.

Rapid and sensitive Nitrosomonas europaea biosensor assay for quantification of bioavailable ammonium sensu strictu in soil.

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Nguyen, Minh Dong; Risgaard-Petersen, Nils; Sørensen, Jan; Brandt, Kristian K

2011-02-01

Knowledge on bioavailable ammonium sensu strictu (i.e., immediately available for cellular uptake) in soil is required to understand nutrient uptake processes in microorganisms and thus of vital importance for plant production. We here present a novel ammonium biosensor approach based on the lithoautotrophic ammonia-oxidizing bacterium Nitrosomonas europaea transformed with a luxAB sensor plasmid. Bioluminescence-based ammonium detection was achieved within 10 min with a quantification limit in liquid samples of ∼20 μM and a linear response range up to 400 μM. Biosensor and conventional chemical quantification of ammonium in soil solutions agreed well across a range of sample and assay conditions. The biosensor was subsequently applied for a solid phase-contact assay allowing for direct interaction of biosensor cells with soil particle-associated (i.e., exchangeable plus fixed) ammonium. The assay successfully quantified bioavailable ammonium even in unfertilized soil and demonstrated markedly higher ratios of bioavailable ammonium to water- or 2 M KCl-exchangeable ammonium in anoxic soil than in corresponding oxic soil. Particle-associated ammonium contributed by at least 74% and 93% of the total bioavailable pool in oxic and anoxic soil, respectively. The N. europaea biosensor should have broad relevance for environmental monitoring of bioavailable ammonium and processes depending on ammonium bioavailability.

Beneficial Use of Dredged Material

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An important goal of managing dredged material is to ensure that the material is used or disposed of in an environmentally sound manner.Most of this dredged material could be used in a beneficial manner instead.

Use of organic amendments as a bioremediation strategy to reduce the bioavailability of chlorpyrifos insecticide in soils. Effects on soil biology.

Science.gov (United States)

Tejada, Manuel; Gómez, Isidoro; Del Toro, Marina

2011-10-01

The sorption capacity of both an organic municipal solid waste by-product (MSW) and a cow manure (CM) in a soil polluted with chlorpyrifos, as well as its effect on soil microbial activity, and weight, reproductive parameters and glutathione-S-transferase activity of two earthworm species (Eisenia fetida and Lumbricus terrestris) were studied. Chlorpyrifos was added at the recommended application rate (5 L ha(-1); 768 mg chlorpyrifos kg(-1)) and treated with MSW at a rate of 10% and CM at a rate of 5.8% in order to apply the same amount of organic matter to the soil. An unamended polluted soil was used as control. Earthworm cocoon number, average weight of cocoon, and number of juveniles per cocoon were measured after 30 days of incubation, whereas soil enzymatic activities, earthworm weight, and glutathione-S-transferase activity of earthworms were measured after 3, 45 and 90 days. Soil enzymatic activities, reproductive and glutathione-S-transferase activity in both worms decreased in polluted soil. The inhibition percentage of soil enzymatic activities, reproductive and glutathione-S-transferase activity in both worms was lower in MSW-amended soil than for CM-amended soil. The toxic effect of chlorpyrifos on E. fetida was lowest compared to L. terrestris. This suggested that the addition of organic wastes with higher humic than fulvic acid concentration is more beneficial for remediation of soils polluted with chlorpyrifos. Copyright © 2011 Elsevier Inc. All rights reserved.

Agrobacterium tumefaciens is a diazotrophic bacterium

International Nuclear Information System (INIS)

Kanvinde, L.; Sastry, G.R.K.

1990-01-01

This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate 15 N supplied as 15 N 2 . As with most other well-characterized diazotrophic bacteria, the presence of NH 4 + in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship

Determining water and nitrogen balances for beneficial management practices using lysimeters at Wagna test site (Austria).

Science.gov (United States)

Klammler, Gernot; Fank, Johann

2014-11-15

The shallow Murtal aquifer south of Graz, Austria, provides easily withdrawable groundwater, which is supplied as drinking water without any chemical treatment. The aquifer is also used intensively by agriculture. Common agricultural management practices are the main source for diffuse nitrogen leaching and high groundwater nitrate concentrations. To safeguard the coexisting use of these two important resources, lysimeters are operated at the agricultural test site Wagna, Austria, and the influence of two beneficial management practices--low nitrogen input and organic farming--on nitrogen leaching towards groundwater is investigated. The technical lysimeter design as presented here consists of: (1) high-resolution weighing cells, (2) a suction controlled lower boundary condition for sucking off seepage water, thus emulating undisturbed field conditions, (3) comparative soil temperature, water content and matrix potential measurements inside and outside the lysimeter at different depths, (4) an installation of the lysimeters directly into test plots and (5) a removable upper lysimeter ring enabling machinery soil tillage. Our results indicate that oasis effects or fringe effects of the lysimeter cylinder on unsaturated water flow did not occur. Another lysimeter cultivated with lawn is operated for observing grass-reference evapotranspiration, which resulted in good agreement with calculated grass-reference evapotranspiration according to the FAO-Penman-Monteith method. We conclude that lysimeters installed at Wagna test site did not show any fringe effects and, thus, are appropriate tools for measuring water balance elements and nitrogen leaching of arable and grass land at point scale. Furthermore, our results for the period of 2005 to 2011 show that beneficial management practices reduced nitrate leaching and, hence, may allow for a sustainable coexistence of drinking water supply and agriculture in the Murtal aquifer. Copyright © 2014 Elsevier B.V. All rights

Pseudomonas fluorescens JH 70-4 promotes pb stabilization and early seedling growth of sudan grass in contaminated mining site soil.

Science.gov (United States)

Shim, Jaehong; Babu, A Giridhar; Velmurugan, Palanivel; Shea, Patrick J; Oh, Byung-Taek

2014-01-01

A bacterial strain (JH 70-4) exhibiting plant growth promoting characteristics (indoleacetic acid production and 1-aminocyclopropane-1-carboxylate deaminase activity), as well as heavy metal(loid) (HM) tolerance and Pb precipitation, was isolated from HM-contaminated soil at an abandoned mine site. The bacterium was identified as Pseudomonas fluorescens based on 16S rDNA sequencing. The JH 70-4 strain induced precipitation of Pb as PbS nanoparticles, confirmed by X-ray diffraction. Solution pH, incubation time, and Pb concentration influenced removal and PbS formation. Inoculating contaminated soil with JH 70-4 decreased Pb availability; exchangeable Pb decreased while organic- and sulphide-bound Pb increased. The toxicity characteristic leaching procedure showed a 65% decrease in Pb in leachate 60 d after inoculating soil with JH 70-4. Shoot and root lengths of Sudan grass grown in the inoculated soil were greater than in the uninoculated soil. Findings suggest that microbial Pb fixation is a viable strategy for remediating soil and promoting plant growth for phytostabilization of contaminated sites.

Improvement of red pepper yield and soil environment by summer catch aquatic crops in greenhouses

Science.gov (United States)

Du, X. F.; Wang, L. Z.; Peng, J.; Wang, G. L.; Guo, X. S.; Wen, T. G.; Gu, D. L.; Wang, W. Z.; Wu, C. W.

2016-08-01

To investigate effects of the rotation of summer catch crops on remediation retrogressed soils in continuous cropping, a field experiment was conducted. Rice, water spinach, or cress were selected as summer catch crops; bare fallow during summer fallow was used as the control group. Results showed that aquatic crops grown in summer fallow period could effectively reduce soil bulk density and pH, facilitate soil nutrient release, and improve soil physical and chemical properties compared with those grown in fallow period. Paddy-upland rotation could improve soil microbial members and increase bacterial and actinomycete populations; by contrast, paddy-upland rotation could reduce fungal populations and enhance bacterium-to-fungus ratio. Paddy-upland rotation could also actively promote activities of soil enzymes, such as urease, phosphatase, invertase, and catalase. The proposed paddy-upland rotation significantly affected the growth of red pepper; the yield and quality of the grown red pepper were enhanced. Summer catch crops, such as rice, water spinach, and cress significantly increased pepper yield in the following growing season by 15.4%, 10.2% and 14.0%, respectively, compared with those grown in fallow treatment. Therefore, the proposed paddy-upland crop rotation could be a useful method to alleviate continuous cropping problems involved in cultivating red pepper in greenhouses.

FtsEX-CwlO regulates biofilm formation by a plant-beneficial rhizobacterium Bacillus velezensis SQR9.

Science.gov (United States)

Li, Qing; Li, Zunfeng; Li, Xingxing; Xia, Liming; Zhou, Xuan; Xu, Zhihui; Shao, Jiahui; Shen, Qirong; Zhang, Ruifu

2018-04-01

Bacillus velezensis strain SQR9 is a well-investigated rhizobacterium with an outstanding ability to colonize roots, enhance plant growth and suppress soil-borne diseases. The recognition that biofilm formation by plant-beneficial bacteria is crucial for their root colonization and function has resulted in increased interest in understanding molecular mechanisms related to biofilm formation. Here, we report that the gene ftsE, encoding the ATP-binding protein of an FtsEX ABC transporter, is required for efficient SQR9 biofilm formation. FtsEX has been reported to regulate the atolysin CwlO. We provided evidence that FtsEX-CwlO was involved in the regulation of SQR9 biofilm formation; however, this effect has little to do with CwlO autolysin activity. We propose that regulation of biofilm formation by CwlO was exerted through the spo0A pathway, since transcription of spo0A cascade genes was altered and their downstream extracellular matrix genes were downregulated in SQR9 ftsE/cwlO deletion mutants. CwlO was also shown to interact physically with KinB/KinD. CwlO may therefore interact with KinB/KinD to interfere with the spo0A pathway. This study revealed that FtsEX-CwlO plays a previously undiscovered regulatory role in biofilm formation by SQR9 that may enhance root colonization and plant-beneficial functions of SQR9 and other beneficial rhizobacteria as well. Copyright © 2018 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Bioremediation of copper-contaminated soils by bacteria.

Science.gov (United States)

Cornu, Jean-Yves; Huguenot, David; Jézéquel, Karine; Lollier, Marc; Lebeau, Thierry

2017-02-01

Although copper (Cu) is an essential micronutrient for all living organisms, it can be toxic at low concentrations. Its beneficial effects are therefore only observed for a narrow range of concentrations. Anthropogenic activities such as fungicide spraying and mining have resulted in the Cu contamination of environmental compartments (soil, water and sediment) at levels sometimes exceeding the toxicity threshold. This review focuses on the bioremediation of copper-contaminated soils. The mechanisms by which microorganisms, and in particular bacteria, can mobilize or immobilize Cu in soils are described and the corresponding bioremediation strategies-of varying levels of maturity-are addressed: (i) bioleaching as a process for the ex situ recovery of Cu from Cu-bearing solids, (ii) bioimmobilization to limit the in situ leaching of Cu into groundwater and (iii) bioaugmentation-assisted phytoextraction as an innovative process for in situ enhancement of Cu removal from soil. For each application, the specific conditions required to achieve the desired effect and the practical methods for control of the microbial processes were specified.

Extractability of added lead in soils and its concentration in plants

Energy Technology Data Exchange (ETDEWEB)

MacLean, A J; Halstead, R L; Finn, B J

1969-01-01

The concentrations of Pb in five species of plants were found to increase with proximity of the sampling sites to a well-travelled highway. The Pb content of oats and alfalfa grown in four soils pretreated with PbCl/sub 2/ in pot tests varied inversely with the organic matter content and pH of the soils. The amounts of Pb taken up by the plants were reduced upon addition of phosphate or of lime to the acid soils. Furthermore, the beneficial effects of organic matter, phosphate and lime in reducing Pb in the plants were usually in accord with corresponding reductions in extractable Pb in the soils as measured in 1 N neutral ammonium acetate and 0.1 M CaCl/sub 2/. 11 references, 6 tables.

Plant-Microbe Communication Enhances Auxin Biosynthesis by a Root-Associated Bacterium, Bacillus amyloliquefaciens SQR9.

Science.gov (United States)

Liu, Yunpeng; Chen, Lin; Zhang, Nan; Li, Zunfeng; Zhang, Guishan; Xu, Yu; Shen, Qirong; Zhang, Ruifu

2016-04-01

Mechanisms by which beneficial rhizobacteria promote plant growth include tryptophan-dependent indole-3-acetic acid (IAA) synthesis. The abundance of tryptophan in the rhizosphere, however, may influence the level of benefit provided by IAA-producing rhizobacteria. This study examined the cucumber-Bacillus amyloliquefaciens SQR9 system and found that SQR9, a bacterium previously shown to enhance the growth of cucumber, increased root secretion of tryptophan by three- to fourfold. Using a split-root system, SQR9 colonization of roots in one chamber not only increased tryptophan secretion from the noninoculated roots but also increased the expression of the cucumber tryptophan transport gene but not the anthranilate synthesis gene in those roots. The increased tryptophan in isolated rhizosphere exudates was sufficient to support increased IAA production by SQR9. Moreover, SQR9 colonization of roots in one chamber in the split-root system resulted in sufficient tryptophan production by the other roots to upregulate SQR9 IAA biosynthesis genes, including a 27-fold increase in the indole-3-acetonitrilase gene yhcX during subsequent colonization of those roots. Deletion of yhcX eliminated SQR9-mediated increases in root surface area, likely by reducing IAA-stimulated lateral root growth. This study demonstrates a chemical dialogue between B. amyloliquefaciens and cucumber in which this communication contributes to bacteria-mediated plant-growth enhancement.

[Effects of biochar on microbial ecology in agriculture soil: a review].

Science.gov (United States)

Ding, Yan-Li; Liu, Jie; Wang, Ying-Ying

2013-11-01

Biochar, as a new type of soil amendment, has been obtained considerable attention in the research field of environmental sciences worldwide. The studies on the effects of biochar in improving soil physical and chemical properties started quite earlier, and already covered the field of soil microbial ecology. However, most of the studies considered the soil physical and chemical properties and the microbial ecology separately, with less consideration of their interactions. This paper summarized and analyzed the interrelationships between the changes of soil physical and chemical properties and of soil microbial community after the addition of biochar. Biochar can not only improve soil pH value, strengthen soil water-holding capacity, increase soil organic matter content, but also affect soil microbial community structure, and alter the abundance of soil bacteria and fungi. After the addition of biochar, the soil environment and soil microorganisms are interacted each other, and promote the improvement of soil microbial ecological system together. This review was to provide a novel perspective for the in-depth studies of the effects of biochar on soil microbial ecology, and to promote the researches on the beneficial effects of biochar to the environment from ecological aspect. The methods to improve the effectiveness of biochar application were discussed, and the potential applications of biochar in soil bioremediation were further analyzed.

Impact of Ag and Al{sub 2}O{sub 3} nanoparticles on soil organisms: In vitro and soil experiments

Energy Technology Data Exchange (ETDEWEB)

Fajardo, C., E-mail: carmen.fajardo@vet.ucm.es [Facultad de Veterinaria, Universidad Complutense, 28040 Madrid (Spain); Saccà, M.L., E-mail: marialudovicasacca@pdi.ucm.es [Facultad de Veterinaria, Universidad Complutense, 28040 Madrid (Spain); Campus de Excelencia Internacional de Moncloa, 28040 Madrid (Spain); Costa, G., E-mail: costag@vet.ucm.es [Facultad de Veterinaria, Universidad Complutense, 28040 Madrid (Spain); Nande, M., E-mail: mnande@vet.ucm.es [Facultad de Veterinaria, Universidad Complutense, 28040 Madrid (Spain); Martin, M., E-mail: margamar@vet.ucm.es [Facultad de Veterinaria, Universidad Complutense, 28040 Madrid (Spain)

2014-03-01

In vitro analyses were conducted to assess the impact of Al{sub 2}O{sub 3} and Ag nanoparticles on two common soil bacteria, Bacillus cereus and Pseudomonas stutzeri. Al{sub 2}O{sub 3} nanoparticles did not show significant toxicity at any dose or time assayed, whereas exposure to 5 mg L{sup −1} Ag nanoparticles for 48 h caused bactericidal effects. Moreover, alterations at the morphological level were observed by transmission electron microscopy (TEM); Ag but not Al{sub 2}O{sub 3} nanoparticles evoked the entrance of B. cereus cells in an early sporulation stage and both nanoparticles penetrated P. stutzeri cells. At the molecular level, a dramatic increase (8.2-fold) in katB gene expression was found in P. stutzeri following Al{sub 2}O{sub 3} nanoparticles exposure, indicative of an oxidative stress-defence system enhancement in this bacterium. In the microcosm experiment, using two different natural soils, Al{sub 2}O{sub 3} or Ag nanoparticles did not affect the Caenorhabditis elegans toxicity endpoints growth, survival, or reproduction. However, differences in microbial phylogenetic compositions were detected by fluorescence in situ hybridization (FISH). The use of katB- and pykA-based sequences showed that the microbial transcriptional response to nanoparticle exposure decreased, suggesting a decrease in cellular activity. These changes were attributable to both the nanoparticles treatment and soil characteristics, highlighting the importance of considering the soil matrix on a case by case basis. - Highlights: • Al{sub 2}O{sub 3} or Ag NPs impact on bacteria was assessed at phenotypic and molecular level. • katB gene involved in oxidative-stress response was overexpressed in P. stutzeri following Al{sub 2}O{sub 3} NPs exposure. • A decrease in bacterial transcriptional response was detected in NPs-treated soils. • A soil-dependent response to specific NP treatment was observed. • In NPs-treated soils no acute toxic effects on C. elegans were found.

Effects of Biochar and Lime on Soil Physicochemical Properties and Tobacco Seedling Growth in Red Soil

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ZHU Pan

2015-12-01

Full Text Available Red soil, mainly found in the southern China, is developed in a warm, moist climate. The main property of the soils is strong acidity, aluminum toxicity, and low available nutrients. In this study, different effects of biochar and lime on soil physicochemical properties and tobacco growth were determined in red soil, so as to provide a scientific foundation for soil improvement tobacco field. A pot experiment was designed and conducted at four biochar levels(0, 0.5%, 1%, 2% and normal lime level (0.3% to study effects of two different soil amendments on red soil pH, exchangeable aluminum(Exc-Al and exchangeable manganese(Exc-Mn, available nutrients and organic carbon (SOC. Meanwhile, agronomic traits, biomass and leaves elements of tobacco were also tested. Results showed that the agronomic characters and biomass of tobacco seedling had changed effectively after biochar or lime was added. Under 0.5%, 1% biochar treatment, the content of nitrogen(N, phosphorus(P, potassium(K, calcium(Ca and magnesium(Mg in tobacco leaves substantially raised. However, when 2% biochar was applied, leaves N content declined by 9.3%. Compared with the control, leaves N, P and Ca content increased observably in the lime treatment. However, its K and Mg content decreased by 9.0% and 13.3% respectively. Alkaline nitrogen(SAN, available phosphorus (SAP, available potassium (SAK, and exchangeable calcium (Exc-Ca and exchangeable magnesium (Exc-Mg were improved obviously in soil applied with biochar. Only the content of Exc-Ca was significantly increased in lime treatment. In addition, it was beneficial to improve soil pH and reduce soil Exc-Al when biochar or lime had been used. Thus, both biochar and lime are propitious to increase soil pH value, lessen soil Exc-Al content, and improve the growth of tobacco seedling. Furthermore, biochar application also can raise the content of available nutrient and SOC in red soil.

Formulation of humic-based soil conditioners

Science.gov (United States)

Amanova, M. A.; Mamytova, G. A.; Mamytova, B. A.; Kydralieva, K. A.; Jorobekova, Sh. J.

2009-04-01

: Chemical composition of (i) ash: 53-54% SiO2; 26-27% Al2O3; 3-5% Fe2O3; 1.7-2.9% CaO; 1.3-2.3% MgO; 0.5-0.8% Na2O; 1.0-1.5% K2O and; (ii), slag: 17-20% SiO2; 15-20% Al2O3; 30-40% CaO; 1-6% Fe2O3; 4-11% MgO. Of all samples assessed, per 5 samples from various regions with various compositions (high, average and low content of metal oxides) were selected and tested as component of SC in vegetative pot and field experiments, i.e., to study the immobilization processes including microorganisms and inorganic ingredients. This study helped to elucidate the influence of ash and slag composition on microbial development. The next stage was (i) to evaluate microbial activity of selected soils from Kyrgyzstan, (ii) to isolate microorganisms exhibiting antagonistic activity against pathogenic microorganisms present in the soil and, (iii) to utilize microbes as nutrient sources. Candidate microbial cultures were isolated from soils/crops and assessed as plant growth promoting microorganisms. The characteristics of the physiological groups of microorganisms were also investigated. Of different physiological groups of microorganisms selected, ca, 3 consortia of agronomical-valued microbial groups from undisturbed soils was selected as component of soil conditioners. Microorganisms, namely oligonitrophils, ammonifiers, nitrifiers, were tested based on beneficial bioactivity including plant biomass and stem length on commercial onion and lettuce crops. Our results demonstrate that all the combinations ash/slag, humic acids and consortium of beneficial agronomical-valued microbial groups into one environmentally friendly soil conditioner possessed equal or higher growth-promoting potential in relation to lettuce. However, our results demonstrated clearly that among studied scope of soil conditioners only one of them could be recommended for further study in terms of practical applications. Namely, it was mixture consisting of humic acids, ash and oligonitrophils as soil conditioning agent

Soil, Food Security and Human Health

Science.gov (United States)

Oliver, Margaret

2017-04-01

"Upon this handful of soil our survival depends. Husband it and it will grow food, our fuel, and our shelter and surround us with beauty. Abuse it and the soil will collapse and die, taking humanity with it" Vedas Sanskrit Scripture, 1500 BC. As the world's population increases issues of food security become more pressing as does the need to sustain soil fertility and to minimize soil degradation. Soil and land are finite resources, and agricultural land is under severe competition from many other uses. Lack of adequate food and food of poor nutritional quality lead to under-nutrition of different degrees, all of which can cause ill- or suboptimal-health. The soil can affect human health directly and indirectly. Direct effects of soil or its constituents result from its ingestion, inhalation or absorption. For example, hook worms enter the body through the skin and cause anaemia, and fungi and dust can be inhaled resulting in respiratory problems. The soil is the source of actinomycetes on which our earliest antibiotics are based (actinomycin, neomycin and streptomycin). Furthermore, it is a potential reservoir of new antibiotics with methods such as functional metagenomics to identify antibiotic resistant genes. Indirect effects of soil arise from the quantity and quality of food that humans consume. Trace elements can have both beneficial and toxic effects on humans, especially where the range for optimal intake is narrow as for selenium. Deficiencies of four trace elements, iodine, iron, selenium and zinc, will be considered because of their substantial effects on human health. Relations between soil and human health are often difficult to extricate because of the many confounding factors present such as the source of food, social factors and so on. Nevertheless, recent scientific understanding of soil processes and factors that affect human health are enabling greater insight into the effects of soil on our health. Multidisciplinary research that includes soil

Ecotoxicological standard tests confirm beneficial effects of nitrate capture in organically coated grapewood biochar

Science.gov (United States)

Haller, Andreas; Kammann, Claudia; Löhnertz, Otmar

2017-04-01

Due to the rising use of mineral N fertilizers and legume use in agriculture, the input of reactive N into the global N cycle has dramatically increased. Therefore new agricultural techniques that increase N use efficiency and reduce the loss of soil mineral N to surface and ground waters are urgently required. Pyrogenic carbon (biochar) produced from biomass may be used as a beneficial soil amendment to sequester carbon (C) in soils, increase soil fertility in the long term, and reduce environmental pollution such as nitrate leaching or N2O emissions. However, reduced nitrate leaching is not a constant finding when using biochar as a soil amendment and the mechanisms are poorly understood. To investigate if biochar is able to reduce nitrate pollution and its subsequent effects on soil and aquatic fauna, we conducted a series of experiments using standard ecotoxicological test methods: (1) the collembolan reproduction test (ISO 11267 (1999)), (2) the earthworm reproduction test (ISO 11268-2 (1998)), (3) the aquatic Daphnia acute test (ISO 6341 (1996)) and (4) a seedling emergence and growth test (ISO 11269-2 (2006)) also involving leaching events. For the tests grapewood biochar produced with a Kon-Tiki kiln (600-700°C) was used which had previously demonstrated nitrate capture; terrestrial tests were carried out with loamy sand standard soil 2.2 (LUFA-Speyer, Germany). The tests included the factors: (A) nitrate addition (using critical values for the test organisms) or no nitrate addition, (B) control (no biochar), pure biochar and organically-coated biochar. In the aquatic test (3), a nitrate amount which caused 50% of the Daphnia-immobilizing toxic nitrate concentration in leachates was applied to the soil or soil-biochar mixtures. Subsequently, soils were incubated overnight and leached on the next day, producing (in the control) the calculated nitrate concentrations. Daphnids were incubated for 48 hours. Test results without nitrate confirmed that soil

Non-obligate predatory bacterium Burkholderia casidae and uses thereof

OpenAIRE

2001-01-01

A novel predator bacterium Burkholderia casidae is disclosed. The invention is directed to the isolation and use of Burkholderia casidae to control microbial diseases of plants. The genetic, biochemical and physiological characteristics of Burkholderia casidae are described. Biocontrol compositions comprising Burkholderia casidae, and antimicrobial compounds and antimicrobial preparations prepared from Burkholderia casidae are also disclosed, as are methods for accomplishing all of the forego...

Thermophilic Anaerobic Degradation of Butyrate by a Butyrate-Utilizing Bacterium in Coculture and Triculture with Methanogenic Bacteria

OpenAIRE

Ahring, Birgitte K.; Westermann, Peter

1987-01-01

We studied syntrophic butyrate degradation in thermophilic mixed cultures containing a butyrate-degrading bacterium isolated in coculture with Methanobacterium thermoautotrophicum or in triculture with M. thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic bacterium. Butyrate was β-oxidized to acetate with protons as the electron acceptors. Acetate was used concurrently with its production in the triculture. We found a higher butyrate degradation rate in th...

Uranium speciation in Fernald soils

International Nuclear Information System (INIS)

Morris, D.E.; Conradson, S.D.; Tait, C.D.; Chisholm-Brause, C.J.; Berg, J.; Musgrave, J.

1992-01-01

This report details progress made from January 1 to May 31, 1992 in this analytical support task to determine the speciation of uranium in contaminated soil samples from the Fernald Environmental Management Project site under the auspices of the Uranium in Soils Integrated Demonstration funded through the US DOE's Office of Technology Development. The authors' efforts have focused on characterization of soil samples collected by S.Y. Lee (Oak Ridge National Laboratory) from five locales at the Fernald site. These were chosen to sample a broad range of uranium source terms. On the basis of x-ray absorption spectroscopy data, they have determined that the majority of uranium (> 80--90%) exists in the hexavalent oxidation state for all samples examined. This is a beneficial finding from the perspective of remediation, because U(VI) species are more soluble in general than uranium species in other oxidation states. Optical luminescence data from many of the samples show the characteristic structured yellow-green emission from the uranyl (UO 2 2+ ) moiety. The luminescence data also suggest that much of the uranium in these soils is present as well-crystallized UO 2 2+ species. Some clear spectroscopic distinctions have been noted for several samples that illustrate significant differences in the speciation (1) from site to site, (2) within different horizons at the same site, and (3) within different size fractions of the soils in the same horizon at the same site. This marked heterogeneity in uranyl speciation suggests that several soil washing strategies may be necessary to reduce the total uranium concentrations within these soils to regulatory limits

Aerobic and anaerobic biosynthesis of nano-selenium for remediation of mercury contaminated soil.

Science.gov (United States)

Wang, Xiaonan; Zhang, Daoyong; Pan, Xiangliang; Lee, Duu-Jong; Al-Misned, Fahad A; Mortuza, M Golam; Gadd, Geoffrey Michael

2017-03-01

Selenium (Se) nanoparticles are often synthesized by anaerobes. However, anaerobic bacteria cannot be directly applied for bioremediation of contaminated top soil which is generally aerobic. In this study, a selenite-reducing bacterium, Citrobacter freundii Y9, demonstrated high selenite reducing power and produced elemental nano-selenium nanoparticles (nano-Se 0 ) under both aerobic and anaerobic conditions. The biogenic nano-Se 0 converted 45.8-57.1% and 39.1-48.6% of elemental mercury (Hg 0 ) in the contaminated soil to insoluble mercuric selenide (HgSe) under anaerobic and aerobic conditions, respectively. Addition of sodium dodecyl sulfonate enhanced Hg 0 remediation, probably owing to the release of intracellular nano-Se 0 from the bacterial cells for Hg fixation. The reaction product after remediation was identified as non-reactive HgSe that was formed by amalgamation of nano-Se 0 and Hg 0 . Biosynthesis of nano-Se 0 both aerobically and anaerobically therefore provides a versatile and cost-effective remediation approach for Hg 0 -contaminated surface and subsurface soils, where the redox potential often changes dramatically. Copyright © 2016. Published by Elsevier Ltd.

Microbiomes associated with infective stages of root-knot and lesion nematodes in soil.

Directory of Open Access Journals (Sweden)

Ahmed Elhady

Full Text Available Endoparasitic root-knot (Meloidogyne spp. and lesion (Pratylenchus spp. nematodes cause considerable damage in agriculture. Before they invade roots to complete their life cycle, soil microbes can attach to their cuticle or surface coat and antagonize the nematode directly or by induction of host plant defenses. We investigated whether the nematode-associated microbiome in soil differs between infective stages of Meloidogyne incognita and Pratylenchus penetrans, and whether it is affected by variation in the composition of microbial communities among soils. Nematodes were incubated in suspensions of five organically and two integrated horticultural production soils, recovered by sieving and analyzed for attached bacteria and fungi after washing off loosely adhering microbes. Significant effects of the soil type and nematode species on nematode-associated fungi and bacteria were revealed as analyzed by community profiling using denaturing gradient gel electrophoresis. Attached microbes represented a small specific subset of the soil microbiome. Two organic soils had very similar bacterial and fungal community profiles, but one of them was strongly suppressive towards root-knot nematodes. They were selected for deep amplicon sequencing of bacterial 16S rRNA genes and fungal ITS. Significant differences among the microbiomes associated with the two species in both soils suggested specific surface epitopes. Among the 28 detected bacterial classes, Betaproteobacteria, Bacilli and Actinobacteria were the most abundant. The most frequently detected fungal genera were Malassezia, Aspergillus and Cladosporium. Attached microbiomes did not statistically differ between these two soils. However, Malassezia globosa and four fungal species of the family Plectosphaerellaceae, and the bacterium Neorhizobium galegae were strongly enriched on M. incognita in the suppressive soil. In conclusion, the highly specific attachment of microbes to infective stages of

The atherogenic bacterium Porphyromonas gingivalis evades circulating phagocytes by adhering to erythrocytes

DEFF Research Database (Denmark)

Belstrøm, Daniel; Holmstrup, Palle; Damgaard, Christian

2011-01-01

A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows...... the bacterium to adhere to human red blood cells (RBCs) and thereby evade attack by circulating phagocytes. On incubation with normal human serum, the P. gingivalis strain efficiently fixed complement component 3 (C3). Incubation of bacteria with washed whole blood cells suspended in autologous serum resulted...... in a dose- and time-dependent adherence to RBCs. The adherence required functionally intact complement receptor 1 (CR1; also called CD35) on the RBCs and significantly inhibited the uptake of P. gingivalis by neutrophils and B cells within 1 min of incubation (by 64% and 51%, respectively...

Mitigation of membrane biofouling by a quorum quenching bacterium for membrane bioreactors.

Science.gov (United States)

Ham, So-Young; Kim, Han-Shin; Cha, Eunji; Park, Jeong-Hoon; Park, Hee-Deung

2018-06-01

In this study, a quorum-quenching (QQ) bacterium named HEMM-1 was isolated at a membrane bioreactor (MBR) plant. HEMM-1 has diplococcal morphology and 99% sequence identity to Enterococcus species. The HEMM-1 cell-free supernatant (CFS) showed higher QQ activities than the CFS of other QQ bacteria, mostly by degrading N-acyl homoserine lactones (AHLs) with short acyl chains. Instrumental analyses revealed that HEMM-1 CFS degraded AHLs via lactonase activity. Under static, flow, and shear conditions, the HEMM-1 CFS was effective in reducing bacterial and activated-sludge biofilms formed on membrane surfaces. In conclusion, the HEMM-1 isolate is a QQ bacterium applicable to the control of biofouling in MBRs via inhibition of biofilm formation on membrane surfaces. Copyright © 2018 Elsevier Ltd. All rights reserved.

Low occurrence of Pseudomonas aeruginosa in agricultural soils with and without organic amendment

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Sylvie eNazaret

2014-04-01

Full Text Available The occurrence of Pseudomonas aeruginosa was monitored at a broad spatial scale in French agricultural soils, from various soil types and under various land uses to evaluate the ability of soil to be a natural habitat for that species. To appreciate the impact of agricultural practices on the potential dispersion of P. aeruginosa, we further investigated the impact of organic amendment at experimental sites in France and Burkina Faso. A real-time quantitative PCR (qPCR approach was used to analyze a set of 380 samples selected within the French RMQS (‘Réseau de Mesures de la Qualité des Sols’ soil library. In parallel, a culture-dependent approach was tested on a subset of samples. The results showed that P. aeruginosa was very rarely detected suggesting a sporadic presence of this bacterium in soils from France and Burkina Faso, whatever the structural and physico-chemical characteristics or climate. When we analyzed the impact of organic amendment on the prevalence of P. aeruginosa, we found that even if it was detectable in various manures (at levels from 103 to 105 CFU or DNA targets (g drywt-1 of sample, it was hardly ever detected in the corresponding soils, which raises questions about its survival. The only case reports were from a vineyard soil amended with a compost of mushroom manure in Burgundy, and a few samples from two fields amended with raw urban wastes in the sub-urban area of Ouagadougou, Burkina Faso. In these soils the levels of culturable cells were below 10 CFU (g drywt-1.

Agrobacterium tumefaciens is a diazotrophic bacterium

Energy Technology Data Exchange (ETDEWEB)

Kanvinde, L.; Sastry, G.R.K. (Univ. of Leeds (England))

1990-07-01

This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate {sup 15}N supplied as {sup 15}N{sub 2}. As with most other well-characterized diazotrophic bacteria, the presence of NH{sub 4}{sup +} in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship.

Development of clean coal and clean soil technologies using advanced agglomeration techniques

International Nuclear Information System (INIS)

Ignasiak, B.; Ignasiak, T.; Szymocha, K.

1990-01-01

Three major topics are discussed in this report: (1) Upgrading of Low Rank Coals by the Agflotherm Process. Test data, procedures, equipment, etc., are described for co-upgrading of subbituminous coals and heavy oil; (2) Upgrading of Bituminous Coals by the Agflotherm Process. Experimental procedures and data, bench and pilot scale equipments, etc., for beneficiating bituminous coals are described; (3) Soil Clean-up and Hydrocarbon Waste Treatment Process. Batch and pilot plant tests are described for soil contaminated by tar refuse from manufactured gas plant sites. (VC)

Beneficial use of industrial by-products for phytoremediation of an arsenic-rich soil from a gold mining area.

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Lopes, G; Ferreira, P A A; Pereira, F G; Curi, N; Rangel, W M; Guilherme, L R G

2016-08-02

This study investigated two industrial by-products - red mud (RM) and its mixture with phosphogypsum (RMG), as amendments in an As((5+))-contaminated soil from a gold mining area in Brazil in order to grow three plant species: Brachiaria decumbens, Crotalaria spectabilis, and Stylosanthes cv. Campo Grande. These amendments were applied to reach a soil pH of 6.0. Using RM and RMG increased shoot dry matter (SDM) and root dry matter (RDM) of most plants, with RMG being more effective. Adding RMG increased the SDM of Brachiaria and Crotalaria by 18 and 25% and the RDM by 25 and 12%, respectively. Stylosanthes was sensitive to As toxicity and grew poorly in all treatments. Arsenic concentration in shoots of Brachiaria and Crotalaria decreased by 26% with the use of RMG while As in roots reduced by 11 and 30%, respectively. Also, the activities of the plant oxidative stress enzymes varied following treatments with the by-products. The plants grew in the As-contaminated soil from the gold mining area. Thus, they might be employed for phytoremediation purposes, especially with the use of RMG due to its potential advantage in terms of nutrient supply (Ca(2+) and SO4(2-) from phosphogypsum).

Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

DEFF Research Database (Denmark)

Bang-Andreasen, Toke; Nielsen, Jeppe T.; Voriskova, Jana

2017-01-01

Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid......-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse...... and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha(-1). We used culture-based enumerations of general bacteria, Pseudomonas...

Chelating capture and magnetic removal of non-magnetic heavy metal substances from soil

OpenAIRE

Liren Fan; Jiqing Song; Wenbo Bai; Shengping Wang; Ming Zeng; Xiaoming Li; Yang Zhou; Haifeng Li; Haiwei Lu

2016-01-01

A soil remediation method based on magnetic beneficiation is reported. A new magnetic solid chelator powder, FS@IDA (core-shell Fe3O4@SiO2 nanoparticles coated with iminodiacetic acid chelators), was used as a reactive magnetic carrier to selectively capture non-magnetic heavy metals in soil by chelation and removal by magnetic separation. FS@IDA was prepared via inorganic-organic and organic synthesis reactions that generated chelating groups on the surface of magnetic, multi-core, core-shel...

Taxonomic characterisation of Proteus terrae sp. nov., a N2O-producing, nitrate-ammonifying soil bacterium.

Science.gov (United States)

Behrendt, Undine; Augustin, Jürgen; Spröer, Cathrin; Gelbrecht, Jörg; Schumann, Peter; Ulrich, Andreas

2015-12-01

In the context of studying the influence of N-fertilization on N2 and N2O flux rates in relation to the soil bacterial community composition in fen peat grassland, a group of bacterial strains was isolated that performed dissimilatory nitrate reduction to ammonium and concomitantly produced N2O. The amount of nitrous oxide produced was influenced by the C/N ratio of the medium. The potential to generate nitrous oxide was increased by higher availability of nitrate-N. Phylogenetic analysis based on the 16S rRNA and the rpoB gene sequences demonstrated that the investigated isolates belong to the genus Proteus, showing high similarity with the respective type strains of Proteus vulgaris and Proteus penneri. DNA-DNA hybridization studies revealed differences at the species level. These differences were substantiated by MALDI-TOF MS analysis and several distinct physiological characteristics. On the basis of these results, it was concluded that the soil isolates represent a novel species for which the name Proteus terrae sp. nov. (type strain N5/687(T) =DSM 29910(T) =LMG 28659(T)) is proposed.

Biochar reduces copper toxicity in Chenopodium quinoa Willd. In a sandy soil.

Science.gov (United States)

Buss, Wolfram; Kammann, Claudia; Koyro, Hans-Werner

2012-01-01

Mining, smelting, land applications of sewage sludge, the use of fungicides containing copper (Cu), and other human activities have led to widespread soil enrichment and contamination with Cu and potentially toxic conditions. Biochar (BC) can adsorb several substances, ranging from herbicides to plant-inhibiting allelochemicals. However, the range of potential beneficial effects on early-stage plant growth with regard to heavy metal toxicity is largely unexplored. We investigated the ameliorating properties of a forestry-residue BC under Cu toxicity conditions on early plant growth. Young quinoa plants () were grown in the greenhouse in the presence of 0, 2, and 4% BC application (w/w) added to a sandy soil with 0, 50, or 200 μg g Cu supplied. The plants without BC showed severe stress symptoms and reduced growth shortly after Cu application of 50 μg g and died at 200 μg Cu g. Increasing BC concentrations in the growth medium significantly increased the plant performance without Cu toxicity or under Cu stress. At the 4% BC application rate, the plants with 200 μg g Cu almost reached the same biomass as in the control treatment. In the presence of BC, less Cu entered the plant tissues, which had reduced Cu concentrations in the order roots, shoots, leaves. The amelioration effect also was reflected in the plant-soil system CO gas exchange, which showed clear signs of improvement with BC presence. The most likely ameliorating mechanisms were adsorption of Cu to negatively charged BC surfaces and an improvement of the water supply. Overall, BC seems to be a beneficial amendment with the potential to ameliorate Cu toxicity in sandy soils. Further research with a broad spectrum of different soil types, BCs, and crop plants is required. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Antibacterial marine bacterium deter luminous vibriosis in shrimp larvae

OpenAIRE

Abraham, T.J.

2004-01-01

Inhibitory activity of a marine pigmented bacterium - Alteromonas sp. - isolated from Penaeus monodon Fabricius larva against pathogenic and environmental isolates of Vibrio harveyi was studied. All the isolates were inhibited to varying degrees by Alteromonas sp. in vitro. The antibacterial substance produced by the Alteromonas sp. was soluble in organic solvent and closely bound to the external surface of bacterial cells. The antibacterial Alteromonas sp., when allowed to colonize on shrimp...

Application of agglomerative clustering for analyzing phylogenetically on bacterium of saliva

Science.gov (United States)

Bustamam, A.; Fitria, I.; Umam, K.

2017-07-01

Analyzing population of Streptococcus bacteria is important since these species can cause dental caries, periodontal, halitosis (bad breath) and more problems. This paper will discuss the phylogenetically relation between the bacterium Streptococcus in saliva using a phylogenetic tree of agglomerative clustering methods. Starting with the bacterium Streptococcus DNA sequence obtained from the GenBank, then performed characteristic extraction of DNA sequences. The characteristic extraction result is matrix form, then performed normalization using min-max normalization and calculate genetic distance using Manhattan distance. Agglomerative clustering technique consisting of single linkage, complete linkage and average linkage. In this agglomerative algorithm number of group is started with the number of individual species. The most similar species is grouped until the similarity decreases and then formed a single group. Results of grouping is a phylogenetic tree and branches that join an established level of distance, that the smaller the distance the more the similarity of the larger species implementation is using R, an open source program.

Melanin from the nitrogen-fixing bacterium Azotobacter chroococcum: a spectroscopic characterization.

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Aulie Banerjee

Full Text Available Melanins, the ubiquitous hetero-polymer pigments found widely dispersed among various life forms, are usually dark brown/black in colour. Although melanins have variety of biological functions, including protection against ultraviolet radiation of sunlight and are used in medicine, cosmetics, extraction of melanin from the animal and plant kingdoms is not an easy task. Using complementary physicochemical techniques (i.e. MALDI-TOF, FTIR absorption and cross-polarization magic angle spinning solid-state (13C NMR, we report here the characterization of melanins extracted from the nitrogen-fixing non-virulent bacterium Azotobacter chroococcum, a safe viable source. Moreover, considering dihydroxyindole moiety as the main constituent, an effort is made to propose the putative molecular structure of the melanin hetero-polymer extracted from the bacterium. Characterization of the melanin obtained from Azotobacter chroococcum would provide an inspiration in extending research activities on these hetero-polymers and their use as protective agent against UV radiation.

Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis.

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Zhiping Wang

Full Text Available Autotrophic CO2 fixation is the most important biotransformation process in the biosphere. Research focusing on the diversity and distribution of relevant autotrophs is significant to our comprehension of the biosphere. In this study, a draft genome of a bacterium from candidate phylum SBR1093 was reconstructed with the metagenome of an industrial activated sludge. Based on comparative genomics, this autotrophy may occur via a newly discovered carbon fixation path, the hydroxypropionate-hydroxybutyrate (HPHB cycle, which was demonstrated in a previous work to be uniquely possessed by some genera from Archaea. This bacterium possesses all of the thirteen enzymes required for the HPHB cycle; these enzymes share 30∼50% identity with those in the autotrophic species of Archaea that undergo the HPHB cycle and 30∼80% identity with the corresponding enzymes of the mixotrophic species within Bradyrhizobiaceae. Thus, this bacterium might have an autotrophic growth mode in certain conditions. A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. This bacterium is clustered with phylotypes from organically contaminated environments, implying a demand for organics in heterotrophic metabolism. Considering the types of regulators, such as FnR, Fur, and ArsR, this bacterium might be a facultative aerobic mixotroph with potential multi-antibiotic and heavy metal resistances. This is the first report on Bacteria that may perform potential carbon fixation via the HPHB cycle, thus may expand our knowledge of the distribution and importance of the HPHB cycle in the biosphere.

Laccase from a non-melanogenic, alkalotolerant gamma-proteobacterium JB isolated from industrial wastewater drained soil.

Science.gov (United States)

Bains, Jasleen; Capalash, Neena; Sharma, Prince

2003-07-01

A gram-negative, alkalotolerant bacterium, isolated from the soil continually drained with industrial wastewater and identified as gamma-proteobacterium by partial 16S rRNA sequence analysis, produced a polyphenol oxidase, which showed laccase but not tyrosinase activity. The organism grew well from pH 6 to 10 and produced laccase maximally at pH 10. The enzyme was stable from pH 3 to 10.6 for at least 24 h and was optimally active at 55 degrees C and pH 6.5 in a 5 min assay.

Host-specific effects of soil microbial filtrates prevail over those of arbuscular mycorrhizae in a fragmented landscape.

Science.gov (United States)

Pizano, Camila; Mangan, Scott A; Graham, James H; Kitajima, Kaoru

2017-09-01

Plant-soil interactions have been shown to determine plant community composition in a wide range of environments. However, how plants distinctly interact with beneficial and detrimental organisms across mosaic landscapes containing fragmented habitats is still poorly understood. We experimentally tested feedback responses between plants and soil microbial communities from adjacent habitats across a disturbance gradient within a human-modified tropical montane landscape. In a greenhouse experiment, two components of soil microbial communities were amplified; arbuscular mycorrhizal fungi (AMF) and a filtrate excluding AMF spores from the soils of pastures (high disturbance), coffee plantations (intermediate disturbance), and forest fragments (low disturbance), using potted seedlings of 11 plant species common in these habitats (pasture grass, coffee, and nine native species). We then examined their effects on growth of these same 11 host species with reciprocal habitat inoculation. Most plant species received a similar benefit from AMF, but differed in their response to the filtrates from the three habitats. Soil filtrate from pastures had a net negative effect on plant growth, while filtrates from coffee plantations and forests had a net positive effect on plant growth. Pasture grass, coffee, and five pioneer tree species performed better with the filtrate from "away" (where these species rarely occur) compared to "home" (where these species typically occur) habitat soils, while four shade-tolerant tree species grew similarly with filtrates from different habitats. These results suggest that pastures accumulate species-specific soil enemies, while coffee plantations and forests accumulate beneficial soil microbes that benefit pioneer native plants and coffee, respectively. Thus, compared to AMF, soil filtrates exerted stronger habitat and host-specific effects on plants, being more important mediators of plant-soil feedbacks across contrasting habitats. © 2017 by

Combined effects of biocontrol agents and soil amendments on soil microbial populations, plant growth and incidence of charcoal rot of cowpea and wilt of cumin

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Vijeta SINGH

2012-09-01

Full Text Available Field experiments were conducted for 2 years to determine the effectiveness of combined use of two biocontrol agents, Bacillus firmus and Aspergillus versicolor for control of Macrophomina phaseolina induced charcoal rot of cowpea and Fusarium oxysporum f. sp. cumini induced wilt of cumin. The lowest level of plant mortality (3‒4% due to charcoal rot of cowpea was recorded when bacterium coated seeds were sown in radish compost amended soil compared to the non-amended soil (13.8‒20.5%, but this was not significantly better than some other treatments. Cowpea roots from B. firmus coated seeds had better nodulation than any of the individual A. versicolor treatments. Although B. firmus coated seeds + A. versicolor + farmyard manure resulted in maximum nodulation this was not significantly different to B. firmus seed coating. Root colonization by the combined biocontrol agent treatments was better than the individual biocontrol agent treatments. Combining A. versicolor with farmyard manure supported the maximum populations of total fungi and actinomycetes. In both winter seasons, the lowest incidence of wilt (1.0‒5.2% on cumin was recorded when A. versicolor was amended with neem compost compared to the non-amended soil (5.7‒10.5%. Maximum colonization of A. versicolor on roots was observed in B. firmus + A. versicolor + farmyard manure amended plots. During both years, the treatment combination of A. versicolor in neem compost amended plots resulted in maximum populations of fungi, bacteria and A. versicolor in the soil, which was greater than in the non-amended soil. Significant increases in disease control were not recorded after single or repeated delivery of A. versicolor. These results suggest that combining B. firmus as seed coatings with A. versicolor as soil applications gives improved control of M. phaseolina and Fusarium induced diseases on legume and seed spice crops in arid soils.

Biodegradation of buprofezin by Rhodococcus sp. strain YL-1 isolated from rice field soil.

Science.gov (United States)

Li, Chao; Zhang, Ji; Wu, Zhi-Guo; Cao, Li; Yan, Xin; Li, Shun-Peng

2012-03-14

A buprofezin-degrading bacterium, YL-1, was isolated from rice field soil. YL-1 was identified as Rhodococcus sp. on the basis of the comparative analysis of 16S rDNA sequences. The strain could use buprofezin as the sole source of carbon and nitrogen for growth and was able to degrade 92.4% of 50 mg L(-1) buprofezin within 48 h in liquid culture. During the degradation of buprofezin, four possible metabolites, 2-tert-butylimino-3-isopropyl-1,3,5-thiadiazinan-4-one, N-tert-butyl-thioformimidic acid formylaminomethyl ester, 2-isothiocyanato-2-methyl-propane, and 2-isothiocyanato-propane, were identified using gas chromatography-mass spectrometry (GC-MS) analysis. The catechol 2,3-dioxygenase activity was strongly induced during the degradation of buprofezin. A novel microbial biodegradation pathway for buprofezin was proposed on the basis of these metabolites. The inoculation of soils treated with buprofezin with strain YL-1 resulted in a higher degradation rate than that observed in noninoculated soils, indicating that strain YL-1 has the potential to be used in the bioremediation of buprofezin-contaminated environments.

Keratinase production and biodegradation of polluted secondary chicken feather wastes by a newly isolated multi heavy metal tolerant bacterium-Alcaligenes sp. AQ05-001.

Science.gov (United States)

Yusuf, Ibrahim; Ahmad, Siti Aqlima; Phang, Lai Yee; Syed, Mohd Arif; Shamaan, Nor Aripin; Abdul Khalil, Khalilah; Dahalan, Farrah Aini; Shukor, Mohd Yunus

2016-12-01

Biodegradation of agricultural wastes, generated annually from poultry farms and slaughterhouses, can solve the pollution problem and at the same time yield valuable degradation products. But these wastes also constitute environmental nuisance, especially in Malaysia where their illegal disposal on heavy metal contaminated soils poses a serious biodegradation issue as feather tends to accumulate heavy metals from the surrounding environment. Further, continuous use of feather wastes as cheap biosorbent material for the removal of heavy metals from effluents has contributed to the rising amount of polluted feathers, which has necessitated the search for heavy metal-tolerant feather degrading strains. Isolation, characterization and application of a novel heavy metal-tolerant feather-degrading bacterium, identified by 16S RNA sequencing as Alcaligenes sp. AQ05-001 in degradation of heavy metal polluted recalcitrant agricultural wastes, have been reported. Physico-cultural conditions influencing its activities were studied using one-factor-at-a-time and a statistical optimisation approach. Complete degradation of 5 g/L feather was achieved with pH 8, 2% inoculum at 27 °C and incubation period of 36 h. The medium optimisation after the response surface methodology (RSM) resulted in a 10-fold increase in keratinase production (88.4 U/mL) over the initial 8.85 U/mL when supplemented with 0.5% (w/v) sucrose, 0.15% (w/v) ammonium bicarbonate, 0.3% (w/v) skim milk, and 0.01% (w/v) urea. Under optimum conditions, the bacterium was able to degrade heavy metal polluted feathers completely and produced valuable keratinase and protein-rich hydrolysates. About 83% of the feathers polluted with a mixture of highly toxic metals were degraded with high keratinase activities. The heavy metal tolerance ability of this bacterium can be harnessed not only in keratinase production but also in the bioremediation of heavy metal-polluted feather wastes. Copyright © 2016. Published by

Photoproduction of hydrogen by a non-sulphur bacterium isolated from root zones of water fern Azolla pinnata

Energy Technology Data Exchange (ETDEWEB)

Singh, S.P.; Srivastava, S.C.; Pandey, K.D. (Banaras Hindu Univ., Varanasi (IN). Centre of Advanced Study in Botany)

1990-01-01

A photosynthetic bacterium Rhodopseudomonas sp. BHU strain 1 was isolated from the root zone of water fern Azolla pinnata. The bacterium was found to produce hydrogen with potato starch under phototrophic conditions. The immobilized bacterial cells showed sustained hydrogen production with a more than 4-fold difference over free cell suspensions. The data have been discussed in the light of possible utilization of relatively cheaper raw materials by non-sulphur bacteria to evolve hydrogen. (author).

["Candidatus contubernalis alkalaceticum," an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum].

Science.gov (United States)

Zhilina, T N; Zavarzina, D G; Kolganova, T V; Turova, T P; Zavarzin, G A

2005-01-01

From the silty sediments of the Khadyn soda lake (Tuva), a binary sulfidogenic bacterial association capable of syntrophic acetate oxidation at pH 10.0 was isolated. An obligately syntrophic, gram-positive, spore-forming alkaliphilic rod-shaped bacterium performs acetate oxidation in a syntrophic association with a hydrogenotrophic, alkaliphilic sulfate-reducing bacterium; the latter organism was previously isolated and characterized as the new species Desulfonatronum cooperativum. Other sulfate-reducing bacteria of the genera Desulfonatronum and Desulfonatronovibrio can also act as the hydrogenotrophic partner. Apart from acetate, the syntrophic culture can oxidize ethanol, propanol, isopropanol, serine, fructose, and isobutyric acid. Selective amplification of 16S rRNA gene fragments of the acetate-utilizing syntrophic component of the binary culture was performed; it was found to cluster with clones of uncultured gram-positive bacteria within the family Syntrophomonadaceae. The acetate-oxidizing bacterium is thus the first representative of this cluster obtained in a laboratory culture. Based on its phylogenetic position, the new acetate-oxidizing syntrophic bacterium is proposed to be assigned, in a Candidate status, to a new genus and species: "Candidatus Contubernalis alkalaceticum."

Aliidiomarina haloalkalitolerans sp. nov., a marine bacterium isolated from coastal surface seawater

Digital Repository Service at National Institute of Oceanography (India)

Srinivas, T.N.R.; Nupur; AnilKumar, P.

A novel Gram-negative, rod shaped, motile, non-sporing strictly aerobic bacterium, designated strain AK5 sup(T), was isolated from a sea water sample collected near Visakhapatnam coast, Bay of Bengal, India. Colonies on marine agar were circular, 3...

Microbacterium horti sp. nov., a bacterium isolated from Cucurbita maxima cultivating soil.

Science.gov (United States)

Akter, Shahina; Park, Jae Hee; Yin, Chang Shik

2016-04-01

A novel bacterial strain THG-SL1(T) was isolated from a soil sample of Cucurbita maxima garden and was characterized by using a polyphasic approach. Cells were Gram-reaction-positive, non-motile and rod-shaped. The strain was aerobic, catalase positive and weakly positive for oxidase. Phylogenetic analysis based on 16S rRNA gene sequence analysis but it shared highest similarity with Microbacterium ginsengisoli KCTC 19189(T) (96.6 %), indicating that strain THG-SL1(T) belongs to the genus Microbacterium. The DNA G + C content of the isolate was 68.9 mol %. The major fatty acids were anteiso-C15: 0 (39.7 %), anteiso-C17: 0 (24.4 %) and iso-C16: 0 (18.5 %). The major polar lipids of strain THG-SL1(T) were phosphatidylglycerol (PG) and an unidentified glycolipid (GL). The predominant respiratory isoprenoid quinones were menaquinone-11 and menaquinone-12. The diamino acid in the cell-wall peptidoglycan was ornithine. Based on the results of polyphasic characterization, strain THG-SL1(T) represented a novel species within the genus Microbacterium, for which the name Microbacterium horti sp. nov. is proposed. The type strain is THG-SL1(T) (=KACC 18286(T)=CCTCC AB 2015117(T)).

[Effect of soil phenolic acids on soil microbe of coal-mining depressed land after afforestation restoration by different tree species].

Science.gov (United States)

Ji, Li; Yang, Li Xue

2017-12-01

Phenolic acids are one of the most important factors that influence microbial community structure. Investigating the dynamic changes of phenolic acids and their relationship with the microbial community structure in plantation soils with different tree species could contribute to better understanding and revealing the mechanisms of microbial community changes under afforestation restoration in coal-mining subsidence areas. In this study, plantations of three conifer and one deciduous species (Pinus koraiensis, Larix gmelinii, Pinus sylvestris var. mongolica, and Populus ussuriensis) were established on abandoned coal-mining subsidence areas in Baoshan District, Shuangyashan City. The contents of soil phenols, 11 types of phenolic acids, and microbial communities in all plots were determined. The results showed that the contents of soil complex phenol in plantations were significantly higher than that of abandoned land overall. Specifically, soils in larch and poplar plantations had higher contents of complex phenol, while soils in larch and Korean pine plantations had greater contents of total phenol. Moreover, soil in the P. koraiensis plantation had a higher content of water-soluble phenol compared with abandoned lands. The determination of 11 phenolic acids indicated that the contents of ferulic acid, abietic acid, β-sitosterol, oleanolic acid, shikimic acid, linoleic acid, and stearic acid were higher in plantation soils. Although soil phenol contents were not related with soil microbial biomass, the individual phenolic acids showed a significant relationship with soil microbes. Ferulic acid, abietic acid, and β-sitosterol showed significant promoting effects on soil microbial biomass, and they showed positive correlations with fungi and fungi/bacteria ratio. These three phenolic acids had higher contents in the poplar plantation, suggesting that poplar affo-restation had a beneficial effect on soil quality in coal-mining subsidence areas.

Novel Glucose-1-Phosphatase with High Phytase Activity and Unusual Metal Ion Activation from Soil Bacterium Pantoea sp. Strain 3.5.1.

Science.gov (United States)

Suleimanova, Aliya D; Beinhauer, Astrid; Valeeva, Liia R; Chastukhina, Inna B; Balaban, Nelly P; Shakirov, Eugene V; Greiner, Ralf; Sharipova, Margarita R

2015-10-01

Phosphorus is an important macronutrient, but its availability in soil is limited. Many soil microorganisms improve the bioavailability of phosphate by releasing it from various organic compounds, including phytate. To investigate the diversity of phytate-hydrolyzing bacteria in soil, we sampled soils of various ecological habitats, including forest, private homesteads, large agricultural complexes, and urban landscapes. Bacterial isolate Pantoea sp. strain 3.5.1 with the highest level of phytase activity was isolated from forest soil and investigated further. The Pantoea sp. 3.5.1 agpP gene encoding a novel glucose-1-phosphatase with high phytase activity was identified, and the corresponding protein was purified to apparent homogeneity, sequenced by mass spectroscopy, and biochemically characterized. The AgpP enzyme exhibits maximum activity and stability at pH 4.5 and at 37°C. The enzyme belongs to a group of histidine acid phosphatases and has the lowest Km values toward phytate, glucose-6-phosphate, and glucose-1-phosphate. Unexpectedly, stimulation of enzymatic activity by several divalent metal ions was observed for the AgpP enzyme. High-performance liquid chromatography (HPLC) and high-performance ion chromatography (HPIC) analyses of phytate hydrolysis products identify dl-myo-inositol 1,2,4,5,6-pentakisphosphate as the final product of the reaction, indicating that the Pantoea sp. AgpP glucose-1-phosphatase can be classified as a 3-phytase. The identification of the Pantoea sp. AgpP phytase and its unusual regulation by metal ions highlight the remarkable diversity of phosphorus metabolism regulation in soil bacteria. Furthermore, our data indicate that natural forest soils harbor rich reservoirs of novel phytate-hydrolyzing enzymes with unique biochemical features. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Enhanced bioremediation of PAH-contaminated soil by immobilized bacteria with plant residue and biochar as carriers

Energy Technology Data Exchange (ETDEWEB)

Chen, Baoliang; Yuan, Miaoxin; Qian, Linbo [Zhejiang Univ., Hangzhou (China). Dept. of Environmental Science; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou (China)

2012-10-15

Polycyclic aromatic hydrocarbons (PAHs) are largely accumulated in soils in China. The immobilized-microorganism technique (IMT) is a potential approach for abating soil contamination with PAHs. However, few studies about the application of IMT to contaminated soil remediation were reported. Due to recalcitrance to decomposition, biochar application to soil may enhance soil carbon sequestration, but few studies on the application of biochars to remediation of contaminated soil were reported. In this study, we illustrated enhanced bioremediation of soil having a long history of PAH contamination by IMT using plant residues and biochars as carriers. Two PAH-degrading bacteria, Pseudomonas putida and an unidentified indigenous bacterium, were selected for IMT. The extractability and biodegradation of 15 PAHs in solution and an actual PAH-contaminated soil amended with immobilized-bacteria materials were investigated under different incubation periods. The effects of carriers and the molecular weight of PAHs on bioremediation efficiency were determined to illustrate their different bio-dissipation mechanisms of PAHs in soil. The IMT can considerably enhance the removal of PAHs. Carriers impose different effects on PAH bio-dissipation by amended soil with immobilized-bacteria, which can directly degrade the carrier-associated PAHs. The removal of PAHs from soil depended on PAH molecular weight and carrier types. Enhanced bio-dissipation by IMT was much stronger for 4- and 5-ring PAHs than for 3- and 6-ring ones in soil. Only P400 biochar-immobilized bacteria enhanced bio-dissipation of all PAHs in contaminated soil after a 90-day incubation. Biochar can promote bioremediation of contaminated soil as microbial carriers of IMT. It is vital to select an appropriate biochar as an immobilized carrier to stimulate biodegradation. It is feasible to use adsorption carriers with high sorptive capabilities to concentrate PAHs as well as microorganisms and thereby enhance

Beneficial bread without preservatives

OpenAIRE

Denkova, Zapryana; Denkova, Rositsa

2014-01-01

Besides their inherent nutritional value functional foods contain substances that have beneficial impact on the functioning of organs and systems in the human body and reduce the risk of disease. Bread and bakery goods are basic foods in the diet of contemporary people. Preservatives are added to the composition of foods in order to ensure their microbiological safety, but these substances affect directly the balance of microflora in the tract. A great problem is mold and bacterial spoilage (...

Comparative evaluation of extracellular β-D-fructofuranosidase in submerged and solid-state fermentation produced by newly identified Bacillus subtilis strain.

Science.gov (United States)

Lincoln, Lynette; More, Sunil S

2018-04-17

To screen and identify a potential extracellular β-D-fructofuranosidase or invertase producing bacterium from soil, and comparatively evaluate the enzyme biosynthesis under submerged and solid-state fermentation. Extracellular invertase producing bacteria were screened from soil. Identification of the potent bacterium was performed based on microscopic examinations and 16S rDNA molecular sequencing. Bacillus subtilis LYN12 invertase secretion was surplus with wheat bran humidified with molasses medium (70%), with elevated activity at 48 h and 37 °C under solid-state fermentation, whereas under submerged conditions increased activity was observed at 24 h and 45 °C in the molasses medium. The study revealed a simple fermentative medium for elevated production of extracellular invertase from a fast growing Bacillus strain. Bacterial invertases are scarce and limited reports are available. By far, this is the first report on the comparative analysis of optimization of extracellular invertase synthesis from Bacillus subtilis strain by submerged and solid-state fermentation. The use of agricultural residues increased yields resulting in development of a cost-effective and stable approach. Bacillus subtilis LYN12 invertase possesses excellent fermenting capability to utilize agro-industrial residues under submerged and solid-state conditions. This could be a beneficial candidate in food and beverage processing industries. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Use of Flue Gas Desulfurization (FGD) Gypsum as a Heavy Metal Stabilizer in Contaminated Soils

Science.gov (United States)

Flue Gas Desulfurization (FGD) gypsum is a synthetic by-product generated from the flue gas desulfurization process in coal power plants. It has several beneficial applications such as an ingredient in cement production, wallboard production and in agricultural practice as a soil...

Beneficial reuse of US DOE Radioactive scrap metal

Energy Technology Data Exchange (ETDEWEB)

Motl, G.P.

1995-01-19

The US Department of Energy (DOE) has more than 2.5 million tons of radioactive scrap metal (RSM) that is either in inventory or expected to be generated over the next 25 years as major facilities within the weapons complex are decommissioned. Since much of this metal cannot be decontaminated easily, past practice has been to either retain this material in inventory or ship it to DOE disposal sites for burial. In an attempt to conserve natural resources and to avoid burial of this material at DOE disposal sites, options are now being explored to ``beneficially reuse`` this material. Under the beneficial reuse concept, RSM that cannot be decontaminated and free released is used in applications where the inherent contamination is not a detriment to its end use. This paper describes initiatives currently in progress in the United States that support the DOE beneficial reuse concept.

Beneficial reuse of US DOE Radioactive scrap metal

International Nuclear Information System (INIS)

Motl, G.P.

1995-01-01

The US Department of Energy (DOE) has more than 2.5 million tons of radioactive scrap metal (RSM) that is either in inventory or expected to be generated over the next 25 years as major facilities within the weapons complex are decommissioned. Since much of this metal cannot be decontaminated easily, past practice has been to either retain this material in inventory or ship it to DOE disposal sites for burial. In an attempt to conserve natural resources and to avoid burial of this material at DOE disposal sites, options are now being explored to ''beneficially reuse'' this material. Under the beneficial reuse concept, RSM that cannot be decontaminated and free released is used in applications where the inherent contamination is not a detriment to its end use. This paper describes initiatives currently in progress in the United States that support the DOE beneficial reuse concept

Adhesive properties of a symbolic bacterium from a wood-boreing marine shipworm

International Nuclear Information System (INIS)

Imam, S.H.; Greene, R.V.; Griffin, H.L.

1990-01-01

Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. 35 S-labeled cells of the shipworm bacterium bound preferentially Whatman no.1 cellulose filter paper, compared with its binding to other cellulose substrata or substrata lacking cellulose. The ability of the bacteria to bind to Whatman no. 1 filter paper was significantly reduced by glutaraldehyde or heat treatment of cells. Pretreatment of cells with azide, valinomycin, gramicidin-D, bis-hexafluoroacetylacetone (1799), or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone inhibited adhesion activity. Cells pretreated with pronase or trypsin also exhibited reduced binding activity, but chymotrypsin and peptidase had no effect on adhesion activity. Cellodextrins and methyl cellulose 15 inhibited the adhesion of the shipworm bacteria to filter paper, whereas glucose, cellobiose, and soluble carboxymethyl cellulose had no significant effect. The divalent cation chelators EDTA and EGTA [ethylene hlycol-bis(β-aminoethyl ether)-N,N,N'N'-tetraacetic acid] had little or no effect on adhesive properties of shipworm bacteria. Also, preabsorbing the substratum with extracellular endoglucanase isolated from the ship worm bacterium or 1% bovine serum albumin had no apparent effect on bacterial binding. Low concentration (0.01%) of sodium dodecyl sulfate solubilized a fraction from whole cells, which appeared to be involved in cellular binding activity. After removal of sodium dodecyl, sulfate, several proteins in this fraction associated with intact cells. These cells exhibited up to 50% enhanced binding to filter paper in comparison to cells which had not been exposed to the sodium dodecyl sulfate-solubilized fraction

THE EFFECT OF HIGH DIFENOCONAZOLE CONCENTRATION ON SOIL MICROBIOTA ASSESSED BY MICROBIOLOGICAL ANALYSIS

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Marioara Nicoleta FILIMON

2016-12-01

Full Text Available In order to improve crop quality and production efficiency, are widely used pesticides. Although they are beneficial in this respect it acts as a stressor on the soil, changing its microbiological balance. The study took into account the determination of physico-chemical parameters (temperature, pH, humidity and content of organic matter, biochemical (enzymatic activities of dehydrogenase, urease, phosphatase and protease and microbiological (determining the total plate count aerobic mesophilic that develops at 37 ° C, determining the number of colonies of fungi and identifying genres. The determinations were made in a dynamic period of 21 days. Elevated difenoconazole had a deleterious effect on communities affecting soil microorganisms and soil quality.

Genotypic Diversity of Escherichia coli in the Water and Soil of Tropical Watersheds in Hawaii ▿

Science.gov (United States)

Goto, Dustin K.; Yan, Tao

2011-01-01

High levels of Escherichia coli were frequently detected in tropical soils in Hawaii, which present important environmental sources of E. coli to water bodies. This study systematically examined E. coli isolates from water and soil of several watersheds in Hawaii and observed high overall genotypic diversity (35.5% unique genotypes). In the Manoa watershed, fewer than 9.3% of the observed E. coli genotypes in water and 6.6% in soil were shared between different sampling sites, suggesting the lack of dominant fecal sources in the watershed. High temporal variability of E. coli genotypes in soil was also observed, which suggests a dynamic E. coli population corresponding with the frequently observed high concentrations in tropical soils. When E. coli genotypes detected from the same sampling events were compared, limited sharing between the soil and water samples was observed in the majority of comparisons (73.5%). However, several comparisons reported up to 33.3% overlap of E. coli genotypes between soil and water, illustrating the potential for soil-water interactions under favorable environmental conditions. In addition, genotype accumulation curves for E. coli from water and soil indicated that the sampling efforts in the Manoa watershed could not exhaust the overall genotypic diversity. Comparisons of E. coli genotypes from other watersheds on Oahu, Hawaii, identified no apparent grouping according to sampling locations. The results of the present study demonstrate the complexity of using E. coli as a fecal indicator bacterium in tropical watersheds and highlight the need to differentiate environmental sources of E. coli from fecal sources in water quality monitoring. PMID:21515724

Dicty_cDB: Contig-U10497-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ce 9 from Patent WO0234921. ... 79 2e-13 AF511570_1( AF511570 |pid:none) Uncultured soil bacterium clone 57....000542_2092( CP000542 |pid:none) Verminephrobacter eiseniae EF01... 58 4e-07 AF511571_1( AF511571 |pid:none) Uncultured soil... Pseudomonas fluorescens Pf0-1, ... 51 7e-05 AF511572_1( AF511572 |pid:none) Uncultured soil bacterium clone

[Effects of controlled release blend bulk urea on soil nitrogen and soil enzyme activity in wheat and rice fields].

Science.gov (United States)

Zhang, Jing Sheng; Wang, Chang Quan; Li, Bing; Liang, Jing Yue; He, Jie; Xiang, Hao; Yin, Bin; Luo, Jing

2017-06-18

A field experiment was conducted to investigate the effect of controlled-release fertilizer (CRF) combined with urea (UR) on the soil fertility and environment in wheat-rice rotation system. Changes in four forms of nitrogen (total nitrogen, ammonium nitrogen, nitrate nitrogen, and microbial biomass nitrogen) and in activities of three soil enzymes participating in nitrogen transformation (urease, protease, and nitrate reductase) were measured in seven fertilization treatments (no fertilization, routine fertilization, 10%CRF+90%UR, 20%CRF+80%UR, 40%CRF+60%UR, 80%CRF+20%UR, and 100%CRF). The results showed that soil total nitrogen was stable in the whole growth period of wheat and rice. There was no significant difference among the treatments of over 20% CRF in soil total nitrogen content of wheat and rice. The soil inorganic nitrogen content was increased dramatically in treatments of 40% or above CRF during the mid-late growing stages of wheat and rice. With the advance of the growth period, conventional fertilization significantly decreased soil microbial biomass nitrogen, but the treatments of 40% and above CRF increased the soil microbial biomass nitrogen significantly. The soil enzyme activities were increased with over 40% of CRF in the mid-late growing stage of wheat and rice. By increasing the CRF ratio, the soil protease activity and nitrate reductase activity were improved gradually, and peaked in 100% CRF. The treatments of above 20% CRF could decrease the urease activity in tillering stage of rice and delay the peak of ammonium nitrogen, which would benefit nitrogen loss reduction. The treatments of 40% and above CRF were beneficial to improving soil nitrogen supply and enhancing soil urease and protease activities, which could promote the effectiveness of nitrogen during the later growth stages of wheat and rice. The 100% CRF treatment improved the nitrate reductase activity significantly during the later stage of wheat and rice. Compared with the

Bioavailability and mobility of organic contaminants in soil: new three-step ecotoxicological evaluation.

Science.gov (United States)

Prokop, Zbyněk; Nečasová, Anežka; Klánová, Jana; Čupr, Pavel

2016-03-01

A novel approach was developed for rapid assessment of bioavailability and potential mobility of contaminants in soil. The response of the same test organism to the organic extract, water extract and solid phase of soil was recorded and compared. This approach was designed to give an initial estimate of the total organic toxicity (response to organic extractable fraction), as well as the mobile (response to water extract) and bioavailable fraction (response to solid phase) of soil samples. Eighteen soil samples with different levels of pollution and content of organic carbon were selected to validate the novel three-step ecotoxicological evaluation approach. All samples were chemically analysed for priority contaminants, including aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), hexachlorocyclohexane (HCH) and dichlordiphenyltrichloroethane (DDT). The ecotoxicological evaluation involved determination of toxicity of the organic, mobile and bioavailable fractions of soil to the test organism, bacterium Bacillus cereus. We found a good correlation between the chemical analysis and the toxicity of organic extract. The low toxicity of water extracts indicated low water solubility, and thus, low potential mobility of toxic contaminants present in the soil samples. The toxicity of the bioavailable fraction was significantly greater than the toxicity of water-soluble (mobile) fraction of the contaminants as deduced from comparing untreated samples and water extracts. The bioavailability of the contaminants decreased with increasing concentrations of organic carbon in evaluated soil samples. In conclusion, the three-step ecotoxicological evaluation utilised in this study can give a quick insight into soil contamination in context with bioavailability and mobility of the contaminants present. This information can be useful for hazard identification and risk assessment of soil-associated contaminants. Graphical Abstract New three-step ecotoxicological

Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil.

Science.gov (United States)

Röttig, Annika; Atasayar, Ewelina; Meier-Kolthoff, Jan Philipp; Spröer, Cathrin; Schumann, Peter; Schauer, Jennifer; Steinbüchel, Alexander

2017-06-01

A novel strain, G25T, was isolated from desert soil collected near Jeddah in Saudi Arabia. The strain could accumulate nearly 65 % of its cell dry weight as fatty acids, grow on a broad range of carbon sources and tolerate temperatures of up to 50 °C. With respect to to its 16S rRNA gene sequence, G25T is most closely related to Streptomyces massasporeus DSM 40035T, Streptomyces hawaiiensis DSM 40042T, Streptomyces indiaensis DSM 43803T, Streptomyces luteogriseus DSM 40483T and Streptomyces purpurascens DSM 40310T. Conventional DNA-DNA hybridization (DDH) values ranged from 18.7 to 46.9 % when G25T was compared with these reference strains. Furthermore, digital DDH values between the draft genome sequence of G25T and the genome sequences of other species of the genus Streptomyces were also significantly below the threshold of 70 %. The DNA G+C content of the draft genome sequence, consisting of 8.46 Mbp, was 70.3 %. The prevalent cellular fatty acids of G25T comprised anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The polar lipids profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannosides as well as unidentified phospholipids and phosphoaminolipids. The cell wall contained ll-diaminopimelic acid. Whole-cell sugars were predominantly glucose with small traces of ribose and mannose. The results of the polyphasic approach confirmed that this isolate represents a novel species of the genus Streptomyces, for which the name Streptomyces jeddahensis sp. nov. is proposed. The type strain of this species is G25T (=DSM 101878T =LMG 29545T =NCCB 100603T).

Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences

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Bhagwan N. Rekadwad

2016-01-01

Full Text Available A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713. Genome-to-Genome Distance (GGDC showed high similarity to Pseudoalteromonas haloplanktis (X67024. The generated unique Quick Response (QR codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates using MEGA6 software. Principal Component Analysis (PCA was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.

ENVIRONMENTAL EVALUATION FOR UTILIZATION OF ASH IN SOIL STABILIZATION

Energy Technology Data Exchange (ETDEWEB)

David J. Hassett; Loreal V. Heebink

2001-08-01

The Minnesota Pollution Control Agency (MPCA) approved the use of coal ash in soil stabilization, indicating that environmental data needed to be generated. The overall project goal is to evaluate the potential for release of constituents into the environment from ash used in soil stabilization projects. Supporting objectives are: (1) To ensure sample integrity through implementation of a sample collection, preservation, and storage protocol to avoid analyte concentration or loss. (2) To evaluate the potential of each component (ash, soil, water) of the stabilized soil to contribute to environmental release of analytes of interest. (3) To use laboratory leaching methods to evaluate the potential for release of constituents to the environment. (4) To facilitate collection of and to evaluate samples from a field runoff demonstration effort. The results of this study indicated limited mobility of the coal combustion fly ash constituents in laboratory tests and the field runoff samples. The results presented support previous work showing little to negligible impact on water quality. This and past work indicates that soil stabilization is an environmentally beneficial CCB utilization application as encouraged by the U.S. Environmental Protection Agency. This project addressed the regulatory-driven environmental aspect of fly ash use for soil stabilization, but the demonstrated engineering performance and economic advantages also indicate that the use of CCBs in soil stabilization can and should become an accepted engineering option.

Tolerance and Reduction of Chromium(VI by Bacillus sp. MNU16 Isolated from Contaminated Coal Mining Soil

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Neha Upadhyay

2017-05-01

Full Text Available The bacterium MNU16 was isolated from contaminated soils of coal mine and subsequently screened for different plant growth promoting (PGP activities. The isolate was further identified by 16S rRNA sequencing as Bacillus subtilis MNU16 with IAA concentration (56.95 ± 0.43 6μg/ml, siderophore unit (9.73 ± 2.05%, phosphate solubilization (285.13 ± 1.05 μg/ml and ACC deaminase activity (116.79 ± 0.019 μmoles α-ketobutyrate/mg/24 h. Further, to evaluate the metal resistance profile of bacterium, the isolate was screened for multi-metal resistance (viz. 900 mg/L for Cr, 600 mg/L for As, 700 mg/L for Ni and 300 mg/L for Hg. Additionally, the resistance pattern of B. subtilis MNU16 against Cr(VI (from 50 to 300 mg/L treatments were evaluated. An enriched population was observed at 0–200 mg/L Cr(VI concentration while slight reductions were observed at 250 and 300 mg/L Cr(VI. Further, the chromium reduction ability at 50 mg/L of Cr(VI highlighted that the bacterium B. subtilis MNU16 reduced 75% of Cr(VI to 13.23 mg/L within 72 h. The localization of electron dense precipitates was observed in the TEM images of B. subtilis MNU16 which is might be due to the reduction of Cr(VI to Cr(III. The data of fluorescence microscopy and flow cytometry with respect to Cr(VI treatments (50–300 mg/L showed a similar pattern and clearly revealed the less toxic effect of hexavalent chromium upto 200 mg/L Cr(VI concentration. However, toxicity effects were more pronounced at 300 mg/L Cr(VI. Therefore, the present study suggests that the plant growth promoting potential and resistance efficacy of B. subtilis MNU16 will go a long way in developing an effective bioremediation approach for Cr(VI contaminated soils.

Enhanced phytoremediation of soils contaminated with PAHs by arbuscular mycorrhiza and rhizobium.

Science.gov (United States)

Ren, Cheng-Gang; Kong, Cun-Cui; Bian, Bian; Liu, Wei; Li, Yan; Luo, Yong-Ming; Xie, Zhi-Hong

2017-09-02

Greenhouse experiment was conducted to evaluate the potential effectiveness of a legume (Sesbania cannabina), arbuscular mycorrhizal fungi (AMF) (Glomus mosseae), and rhizobia (Ensifer sp.) symbiosis for remediation of Polycyclic aromatic hydrocarbons (PAHs) in spiked soil. AMF and rhizobia had a beneficial impact on each other in the triple symbiosis. AMF and/or rhizobia significantly increased plant biomass and PAHs accumulation in plants. The highest PAHs dissipation was observed in plant + AMF + rhizobia treated soil, in which >97 and 85-87% of phenanthrene and pyrene, respectively, had been degraded, whereas 81-85 and 72-75% had been degraded in plant-treated soil. During the experiment, a relatively large amount of water-soluble phenolic compounds was detected in soils of AMF and/or rhizobia treatment. It matches well with the high microbial activity and soil enzymes activity. These results suggest that the mutual interactions in the triple symbiosis enhanced PAHs degradation via stimulating both microbial development and soil enzyme activity. The mutual interactions between rhizobia and AMF help to improve phytoremediation efficiency of PAHs by S. cannabina.

Earthworm (Eisenia andrei Avoidance of Soils Treated with Cypermethrin

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Mara M. de Andréa

2011-11-01

Full Text Available The pyrethroid insecticide cypermethrin is used for agricultural and public health campaigns. Its residues may contaminate soils and the beneficial soil organisms, like the earthworms, that may ingest the contaminated soil particles. Due to its ecological relevance, earthworms Eisenia andrei/fetida have been used in different ecotoxicological tests. The avoidance of soils treated with cypermethrin by compost worms Eisenia andrei was studied here as a bioindicator of the influence of treatment dosage and the pesticide formulation in three different agricultural soils indicated by the Brazilian environmental authorities for ecotoxicological tests. This earthworms’ behavior was studied here as a first attempt to propose the test for regulation purposes. The two-compartment test systems, where the earthworms were placed for a two-day exposure period, contained samples of untreated soil alone or together with soil treated with technical grade or wettable powder formulation of cypermethrin. After 48 h, there was no mortality, but the avoidance was clear because all earthworms were found in the untreated section of each type of soil (p < 0.05. No differences were found by the Fisher’s exact test (p ≤ 1.000 for each soil and treatment, demonstrating that the different soil characteristics, the cypermethrin concentrations and formulation, as well as the smaller amounts of soil and earthworms did not influence the avoidance behavior of the earthworms to cypermethrin. The number and range of treatments used in this study do not allow a detailed recommendation of the conditions applied here, but to the best of our knowledge, this is the first reported attempt to identify the avoidance of pesticide treated tropical soils by earthworms.

Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin.

Science.gov (United States)

Svitil, A L; Chadhain, S; Moore, J A; Kirchman, D L

1997-02-01

Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), probably because of the more open structure of (beta)-chitin. When exposed to different types of chitin, V. harveyi excreted several chitin-degrading proteins into the culture media. Some chitinases were present with all of the tested chitins, while others were unique to a particular chitin. We cloned and identified six separate chitinase genes from V. harveyi. These chitinases appear to be unique based on DNA restriction patterns, immunological data, and enzyme activity. This marine bacterium and probably others appear to synthesize separate chitinases for efficient utilization of different forms of chitin and chitin by-products.

Sexual transmission of a plant pathogenic bacterium, Candidatus Liberibacter asiaticus, between conspecific insect vectors during mating.

Directory of Open Access Journals (Sweden)

Rajinder S Mann

Full Text Available Candidatus Liberibacter asiaticus is a fastidious, phloem-inhabiting, gram-negative bacterium transmitted by Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae. The bacterium is the presumed causal agent of huanglongbing (HLB, one of the most destructive and economically important diseases of citrus. We investigated whether Las is transmitted between infected and uninfected D. citri adults during courtship. Our results indicate that Las was sexually transmitted from Las-infected male D. citri to uninfected females at a low rate (<4% during mating. Sexual transmission was not observed following mating of infected females and uninfected males or among adult pairs of the same sex. Las was detected in genitalia of both sexes and also in eggs of infected females. A latent period of 7 days or more was required to detect the bacterium in recipient females. Rod shaped as well as spherical structures resembling Las were observed in ovaries of Las-infected females with transmission electron microscopy, but were absent in ovaries from uninfected D. citri females. The size of the rod shaped structures varied from 0.39 to 0.67 µm in length and 0.19 to 0.39 µm in width. The spherical structures measured from 0.61 to 0.80 µm in diameter. This investigation provides convincing evidence that a plant pathogenic bacterium is sexually transmitted from male to female insects during courtship and established evidence that bacteria persist in reproductive organs. Moreover, these findings provide an alternative sexually horizontal mechanism for the spread of Las within populations of D. citri, even in the absence of infected host trees.

The chemical formula of a magnetotactic bacterium.

Science.gov (United States)

Naresh, Mohit; Das, Sayoni; Mishra, Prashant; Mittal, Aditya

2012-05-01

Elucidation of the chemical logic of life is one of the grand challenges in biology, and essential to the progress of the upcoming field of synthetic biology. Treatment of microbial cells explicitly as a "chemical" species in controlled reaction (growth) environments has allowed fascinating discoveries of elemental formulae of a few species that have guided the modern views on compositions of a living cell. Application of mass and energy balances on living cells has proved to be useful in modeling of bioengineering systems, particularly in deriving optimized media compositions for growing microorganisms to maximize yields of desired bio-derived products by regulating intra-cellular metabolic networks. In this work, application of elemental mass balance during growth of Magnetospirillum gryphiswaldense in bioreactors has resulted in the discovery of the chemical formula of the magnetotactic bacterium. By developing a stoichiometric equation characterizing the formation of a magnetotactic bacterial cell, coupled with rigorous experimental measurements and robust calculations, we report the elemental formula of M. gryphiswaldense cell as CH(2.06)O(0.13)N(0.28)Fe(1.74×10(-3)). Remarkably, we find that iron metabolism during growth of this magnetotactic bacterium is much more correlated individually with carbon and nitrogen, compared to carbon and nitrogen with each other, indicating that iron serves more as a nutrient during bacterial growth rather than just a mineral. Magnetotactic bacteria have not only invoked some interest in the field of astrobiology for the last two decades, but are also prokaryotes having the unique ability of synthesizing membrane bound intracellular organelles. Our findings on these unique prokaryotes are a strong addition to the limited repertoire, of elemental compositions of living cells, aimed at exploring the chemical logic of life. Copyright © 2011 Wiley Periodicals, Inc.

Beneficial Effects of Temperate Forage Legumes that Contain Condensed Tannins

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Jennifer W. MacAdam

2015-07-01

Full Text Available The two temperate forage legumes containing condensed tannins (CT that promote ruminant production are birdsfoot trefoil (Lotus corniculatus L.; BFT and sainfoin (Onobrychis viciifolia Scop.; SF. Both are well-adapted to the cool-temperate climate and alkaline soils of the Mountain West USA. Condensed tannins comprise a diverse family of bioactive chemicals with multiple beneficial functions for ruminants, including suppression of internal parasites and enteric methane. Birdsfoot trefoil contains 10 to 40 g·CT·kg−1 dry matter (DM, while SF contains 30 to 80 g·CT·kg−1 DM. Our studies have focused on these two plant species and have demonstrated consistently elevated rates of gain for beef calves grazing both BFT and SF. Novel results from our BFT research include carcass dressing percentages and consumer sensory evaluations equivalent to feedlot-finished steers and significantly greater than grass-finished steers, but with omega-3 fatty acid concentrations equal to grass-finished beef. We have further demonstrated that ruminants fed BFT or SF will consume more endophyte-infected tall fescue (Schedonorus arundinaceus (Schreb. Dumort. forage or seed than ruminants fed a non-CT forage legume. There is great potential value for sustainable livestock production in the use of highly digestible, nitrogen-fixing legumes containing tannins demonstrated to improve ruminant productivity.

Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

Science.gov (United States)

Xiong, Wu; Zhao, Qingyun; Zhao, Jun; Xun, Weibing; Li, Rong; Zhang, Ruifu; Wu, Huasong; Shen, Qirong

2015-07-01

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

Do dorsal raphe 5-HT neurons encode "beneficialness"?

Science.gov (United States)

Luo, Minmin; Li, Yi; Zhong, Weixin

2016-11-01

The neurotransmitter serotonin (5-hydroxytryptamine; 5-HT) affects numerous behavioral and physiological processes. Drugs that alter 5-HT signaling treat several major psychiatric disorders and may lead to widespread abuse. The dorsal raphe nucleus (DRN) in the midbrain provides a majority of 5-HT for the forebrain. The importance of 5-HT signaling propels the search for a general theoretical framework under which the diverse functions of the DRN 5-HT neurons can be interpreted and additional therapeutic solutions may be developed. However, experimental data so far support several seeming irreconcilable theories, suggesting that 5-HT neurons mediate behavioral inhibition, aversive processing, or reward signaling. Here, we review recent progresses and propose that DRN 5-HT neurons encode "beneficialness" - how beneficial the current environmental context represents for an individual. Specifically, we speculate that the activity of these neurons reflects the possible net benefit of the current context as determined by p·R-C, in which p indicates reward probability, R the reward value, and C the cost. Through the widespread projections of these neurons to the forebrain, the beneficialness signal may reconfigure neural circuits to bias perception, boost positive emotions, and switch behavioral choices. The "beneficialness" hypothesis can explain many conflicting observations, and at the same time raises new questions. We suggest additional experiments that will help elucidate the exact computational functions of the DRN 5-HT neurons. Copyright © 2016 Elsevier Inc. All rights reserved.

Plant-soil interactions promote co-occurrence of three nonnative woody shrubs.

Science.gov (United States)

Kuebbing, Sara E; Classen, Aimée T; Call, Jaime J; Henning, Jeremiah A; Simberloff, Daniel

2015-08-01

Ecosystems containing multiple nonnative plant species are common, but mechanisms promoting their co-occurrence are understudied. Plant-soil interactions contribute to the dominance of singleton species in nonnative ranges because many nonnatives experience stronger positive feedbacks relative to co-occurring natives. Plant-soil interactions could impede other nonnatives if an individual nonnative benefits from its soil community to a greater extent than its neighboring nonnatives, as is seen with natives. However, plant-soil interactions could promote nonnative co-occurrence if a nonnative accumulates beneficial soil mutualists that also assist other nonnatives. Here, we use greenhouse and field experiments to ask whether plant-soil interactions (1) promote the codominance of two common nonnative shrubs (Ligustrum sinense and Lonicera maackii) and (2) facilitate the invasion of a less-common nonnative shrub (Rhamnus davurica) in deciduous forests of the southeastern United States. In the greenhouse, we found that two of the nonnatives, L. maackii and R. davurica, performed better in soils conditioned by nonnative shrubs compared to uninvaded forest soils, which. suggests that positive feedbacks among co-occurring nonnative shrubs can promote continued invasion of a site. In both greenhouse and field experiments, we found consistent signals that the codominance of the nonnatives L. sinense and L. maackii may be at least partially explained by the increased growth of L. sinense in L. maackii soils. Overall, significant effects of plant-soil interactions on shrub performance indicate that plant-soil interactions can potentially structure the co-occurrence patterns of these nonnatives.

A pathway closely related to the (D)-tagatose pathway of gram-negative enterobacteria identified in the gram-positive bacterium Bacillus licheniformis.

Science.gov (United States)

Van der Heiden, Edwige; Delmarcelle, Michaël; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M; Galleni, Moreno; Joris, Bernard

2013-06-01

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus.

A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

OpenAIRE

Van der Heiden, Edwige; Delmarcelle, Michaël; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

2013-01-01

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus.

Gracilibacillus aidingensis sp. nov., a novel moderately halophilic bacterium isolated from Aiding salt lake.

Science.gov (United States)

Guan, Tong-Wei; Tian, Lei; Li, En-Yuan; Tang, Shu-Kun; Zhang, Xiao-Ping

2017-11-01

A novel Gram-positive, aerobe, moderately halophilic bacterium was isolated from saline soil of Aiding lake in Xinjiang, north-west of China, designated strain YIM 98001 T . Cells were rod-shaped, motile and grew at 5-20% (w/v) NaCl (optimum 10%), pH 6-10 (optimum pH 7.0) and 4-45 °C (optimum 37 °C). The major cellular fatty acids were anteiso C 15:0 , anteiso C 17:0 , iso C 15:0 . The predominant respiratory quinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid were the major polar lipids. Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan. The G+C content was 36.46 mol%. 16S rRNA gene sequence analysis showed that the strain belongs to the family Bacillaceae, with the highest sequence similarity to the type strain Gracilibacillus thailandensis TP2-8 T (96.84%), followed by Gracilibacillus saliphilus YIM 91119 T (96.78%) and Gracilibacillus ureilyticus MF38 T (96.57%), thus confirming the affiliation of strain YIM 98001 T to the genus Gracilibacillus. The polyphasic approach indicates that strain YIM 98001 T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus aidingensis is proposed. The type strain is YIM 98001 T (=KCTC 42683 T  = DSMZ 104330 T ).

GEMAS - Soil geochemistry and health implications

Science.gov (United States)

Ernstsen, Vibeke; Ladenberger, Anna; Wragg, Joanna; Gulan, Aleksandra

2014-05-01

The GEMAS Project resulted in a large coherent data set displaying baseline levels of elements in agricultural and grazing land soil, which has a wide variety of applications. Medical geology is an emerging new discipline providing a link between geoscience and medicine by interpreting natural geological factors in relation to human and animal health and their geographical distribution. Medical geology shows not only problems related to harmful health effects of natural geological materials and processes, but also deals with their beneficial aspects. Since the GEMAS project demonstrates the importance of geological factors in geochemical patterns in European soil, this data set can be used in improving our understanding of how the geological processes may affect human health in Europe. The main potential health problems are related to deficiency of nutrients in soil and toxic effects of potentially harmful elements. Deficiency in macro- (e.g., K, Fe, Mg, P) and micro-nutrients (e.g., Se, Zn, Cl) can be responsible for a reduction in crop productivity and certain health issues for livestock and humans. On the other hand, bioavailability of crucial elements depends on soil parameters, e.g., pH; namely, low pH in soil (in northern Europe) makes more micronutrients bioavailable, with the exception of Mo, P and Ca. Rocks underlying the soil layer have a major impact on soil composition, and soil parent material can be a main source of toxic metals, for instance, soil developed on black shale (e.g., Oslo region) shows potentially toxic levels of metals, such as As, Cd, U, Zn and Pb. High content of organic matter is another factor amplifying the toxic levels of metals in soil. Several important topics with health implications can be then addressed using the GEMAS data set, namely, soil properties and element bioavailability, arsenic toxicity, selenium deficiency, potential health effects of liming, uranium in European soil, influence of recent and historical volcanic

Magnetic guidance of the magnetotactic bacterium Magnetospirillum gryphiswaldense.

Science.gov (United States)

Loehr, Johannes; Pfeiffer, Daniel; Schüler, Dirk; Fischer, Thomas M

2016-04-21

Magnetospirillum gryphiswaldense is a magnetotactic bacterium with a permanent magnetic moment capable of swimming using two bipolarly located flagella. In their natural environment these bacteria swim along the field lines of the homogeneous geomagnetic field in a typical run and reversal pattern and thereby create non-differentiable trajectories with sharp edges. In the current work we nevertheless achieve stable guidance along curved lines of mechanical instability by using a heterogeneous magnetic field of a garnet film. The successful guidance of the bacteria depends on the right balance between motility and the magnetic moment of the magnetosome chain.

Monitoring bacterial population dynamics using real-time PCR during the bioremediation of crude-oil-contaminated soil.

Science.gov (United States)

Baek, Kyung-Hwa; Yoon, Byung-Dae; Cho, Dae-Hyun; Kim, Byung-Hyuk; Oh, Hee-Mock; Kim, Hee-Sik

2009-04-01

We evaluated the activity and abundance of the crude oil- degrading bacterium Nocardia sp. H17-1 during bioremediation of oil-contaminated soil, using real-time PCR. The total petroleum hydrocarbon (TPH) degradation rate constants (k) of the soils treated with and without H17-1 were 0.103 d-1 and 0.028 d-1, respectively. The degradation rate constant was 3.6 times higher in the soil with H17-1 than in the soil without H17-1. In order to detect and quantify the Nocardia sp. H17-1 in soil samples, we quantified the genes encoding 16S ribosomal RNA (16S rRNA), alkane monooxygenase (alkB4), and catechol 2,3-dioxygenase (23CAT) with real-time PCR using SYBR green. The amounts of H17-1 16S rRNA and alkB4 detected increased rapidly up to 1,000-folds for the first 10 days, and then continued to increase only slightly or leveled off. However, the abundance of the 23CAT gene detected in H17-1-treated soil, where H17-1 had neither the 23CAT gene for the degradation of aromatic hydrocarbons nor the catechol 2,3-dioxygenase activity, did not differ significantly from that of the untreated soil (alpha=0.05, p>0.22). These results indicated that H17-1 is a potential candidate for the bioaugmentation of alkane-contaminated soil. Overall, we evaluated the abundance and metabolic activity of the bioremediation strain H17-1 using real-time PCR, independent of cultivation.

Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes. Final Report

International Nuclear Information System (INIS)

Lidstrom, Mary E.

2003-01-01

Aqueous mixed low level wastes (MLLW) containing radionuclides, solvents, and/or heavy metals represent a serious current and future problem for DOE environmental management and cleanup. In order to provide low-cost treatment alternatives under mild conditions for such contained wastes, we have proposed to use the radiation-resistant bacterium, Deinococcus radiodurans. This project has focused on developing D. radiodurans strains for dual purpose processes: cometabolic treatment of haloorganics and other solvents and removal of heavy metals from waste streams in an above-ground reactor system. The characteristics of effective treatment strains that must be attained are: (a) high biodegradative and metal binding activity; (b) stable treatment characteristics in the absence of selection and in the presence of physiological stress; (c) survival and activity under harsh chemical conditions, including radiation. The result of this project has been a suite of strains with high biodegradative capabilities that are candidates for pilot stage treatment systems. In addition, we have determined how to create conditions to precipitate heavy metals on the surface of the bacterium, as the first step towards creating dual-use treatment strains for contained mixed wastes of importance to the DOE. Finally, we have analyzed stress response in this bacterium, to create the foundation for developing treatment processes that maximize degradation while optimizing survival under high stress conditions

Bioremediation of uranium contaminated soils and wastes

International Nuclear Information System (INIS)

Francis, A.J.

1998-01-01

Contamination of soils, water, and sediments by radionuclides and toxic metals from uranium mill tailings, nuclear fuel manufacturing and nuclear weapons production is a major concern. Studies of the mechanisms of biotransformation of uranium and toxic metals under various microbial process conditions has resulted in the development of two treatment processes: (1) stabilization of uranium and toxic metals with reduction in waste volume and (2) removal and recovery of uranium and toxic metals from wastes and contaminated soils. Stabilization of uranium and toxic metals in wastes is accomplished by exploiting the unique metabolic capabilities of the anaerobic bacterium, Clostridium sp. The radionuclides and toxic metals are solubilized by the bacteria directly by enzymatic reductive dissolution, or indirectly due to the production of organic acid metabolites. The radionuclides and toxic metals released into solution are immobilized by enzymatic reductive precipitation, biosorption and redistribution with stable mineral phases in the waste. Non-hazardous bulk components of the waste volume. In the second process uranium and toxic metals are removed from wastes or contaminated soils by extracting with the complexing agent citric acid. The citric-acid extract is subjected to biodegradation to recover the toxic metals, followed by photochemical degradation of the uranium citrate complex which is recalcitrant to biodegradation. The toxic metals and uranium are recovered in separate fractions for recycling or for disposal. The use of combined chemical and microbiological treatment process is more efficient than present methods and should result in considerable savings in clean-up and disposal costs

Reclassification of Clostridium proteoclasticum as Butyrivibrio proteoclasticus comb. nov., a butyrate-producing ruminal bacterium

Czech Academy of Sciences Publication Activity Database

Moon, C. D.; Pacheco, D. M.; Kelly, W. J.; Leahy, S. C.; Li, D.; Kopečný, Jan; Attwood, G. T.

2008-01-01

Roč. 58, - (2008), s. 2041-2045 ISSN 1466-5026 Institutional research plan: CEZ:AV0Z50450515 Keywords : Butyrivibrio * ruminal bacterium Subject RIV: EE - Microbiology, Virology Impact factor: 2.222, year: 2008

Biochar effects on wet and dry regions of the soil water retention curve of a sandy loam

DEFF Research Database (Denmark)

Arthur, Emmanuel; Moldrup, Per; Sun, Zhencai

2014-01-01

Reported beneficial effects of biochar on soil physical properties and processes include decreased soil density, and increased soil water transport, water holding capacity and retention (mainly for the wet region). Research is limited on biochar effects on the full soil water retention curve (wet...... and dry regions) for a given soil and biochar amendment scenarios. This study evaluates how biochar applied to a sandy loam field at rates from 0 to 50 Mg ha−1 yr–1 in 2011, 2012, or both years (2011+2012) influences the full water retention curve. Inorganic fertilizer and pig slurry were added to all...... treatments. Six months after the last biochar application, intact and disturbed soil samples were collected for analyses. Soil water retention was measured from −1 kPa to −100 kPa using tension tables and ceramic plates and from −10 MPa to −480 MPa using a Vapor Sorption Analyzer. Soil specific area...

A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

Science.gov (United States)

Van der Heiden, Edwige; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

2013-01-01

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. PMID:23524682

[Identification and function test of an alkali-tolerant denitrifying bacterium].

Science.gov (United States)

Wang, Ru; Zheng, Ping; Li, Wei; Chen, Hui; Chen, Tingting; Ghulam, Abbas

2013-04-04

We obtained an alkali-tolerant denitrifying bacterium, and determined its denitrifying activity and alkali-tolerance. An alkali-tolerant denitrifying bacterial strain was obtained by isolation and purification. We identified the bacterial strain by morphological observation, physiological test and 16S rRNA analysis. We determined the denitrifying activity and alkali-tolerance by effects of initial nitrate concentration and initial pH on denitrification. An alkali-tolerant denitrifier strain R9 was isolated from the lab-scale high-rate denitrifying reactor, and it was identified as Diaphorobater nitroreducens. The strain R9 grew heterotrophically with methanol as the electron donor and nitrate as the electron acceptor. The nitrate conversion was 93.25% when strain R9 was cultivated for 288 h with initial nitrate concentration 50 mg/L and initial pH 9.0. The denitrification activity could be inhibited at high nitrate concentration with a half inhibition constant of 202.73 mg N/L. Strain R9 showed a good alkali tolerance with the nitrate removal rate at pH 11.0 remained 86% of that at pH 9.0. Strain R9 was identified as Diaphorobater nitroreducens, and it was an alkali-tolerant denitrifying bacterium with optimum pH value of 9.0.

Design of semi industrial radium separator by a new bacterium MGF-48

International Nuclear Information System (INIS)

Ghafourian, H.; Emami, M.R.; Farazmand, A.

1998-01-01

Following of a research work which has been recently published in AEOI scientific Bulletin no. 14, a semi industrial bioreactor has been designed for separation of radium using a new bacterium MGF-48. This bioreactor could be utilized for a high rate separation of radium in semi industrial scale. (author)

Five new amicoumacins isolated from a marine-derived Bacterium bacillus subtilis

KAUST Repository

Li, Yongxin; Xu, Ying; Liu, Lingli; Han, Zhuang; Lai, Pok Yui; Guo, Xiangrong; Zhang, Xixiang; Lin, Wenhan; Qian, Pei-Yuan

2012-01-01

Four novel amicoumacins, namely lipoamicoumacins A-D (1-4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. 2012 by the authors; licensee MDPI.

Five new amicoumacins isolated from a marine-derived Bacterium bacillus subtilis

KAUST Repository

Li, Yongxin

2012-02-03

Four novel amicoumacins, namely lipoamicoumacins A-D (1-4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. 2012 by the authors; licensee MDPI.

Recycling of organic wastes in burnt soils: combined application of poultry manure and plant cultivation.

Science.gov (United States)

Villar, M C; Petrikova, V; Díaz-Raviña, M; Carballas, T

2004-01-01

A pot experiment was conducted to investigate the efficacy of a post-fire land management practice, including plant cultivation (Lolium perenne) combined with poultry manure addition, for restoring the protective vegetation cover in soils degraded by high intensity wildfires. The greenhouse experiment was performed with three burnt pine forest soils with added poultry manure at two doses of application and comparing the data with those obtained using NPK fertilizer. A significant effect of the amendment, soil properties and the interaction between amendment and soil properties on vegetation cover (phytomass production, nutrient content) was detected, but often the amendment treatment explained most of the variance. Changes induced by the organic amendment were more marked than those induced by inorganic fertilization. The increase of phytomass and nutrient uptake with poultry manure addition indicated the beneficial effects of this soil management practice. These findings can serve to develop field experiments and burnt soils reclamation technology.

Beneficial and Deleterious Bacterial - Host Interactions in Chronic Wound Pathophysiology

Science.gov (United States)

2015-04-02

treatment with P. acnes that had been incubated in PBS.70 This study suggests that glycerol fermentation and the production of compounds, like...SE, Wolcott RD, Zischkau AM. Identification of yeast in chronic wounds using new pathogen-detection technologies. J Wound Care. 2009;18(3):103–104...University. 2008;11(3):111–116. 70. Shu M, Wang Y, Yu J, et al. Fermentation of Propionibacterium acnes, a commensal bacterium in the human skin

Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4

OpenAIRE

Masuda, Shinji; Hori, Koichi; Maruyama, Fumito; Ren, Shukun; Sugimoto, Saori; Yamamoto, Nozomi; Mori, Hiroshi; Yamada, Takuji; Sato, Shusei; Tabata, Satoshi; Ohta, Hiroyuki; Kurokawa, Ken

2013-01-01

We report the draft genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum. The photosynthesis gene cluster comprises two segments?a unique feature among photosynthesis gene clusters of purple bacteria. The genome information will be useful for further analysis of bacterial photosynthesis.

Diversity of microorganisms isolated from the soil sample surround Chroogomphus rutilus in the Beijing region

DEFF Research Database (Denmark)

Wang, P; Liu, Y; Yin, Y

2011-01-01

to isolate and classify beneficial microorganisms that could affect its growth, which could be used in future research on artificial cultivation. In total, 342 isolates were isolated from soil samples collected around a C. rutilus colony in the Beijing region. Of these, 22 bacterial and 14 fungal isolates...

Growth of a Strictly Anaerobic Bacterium on Furfural (2-Furaldehyde)

OpenAIRE

Brune, Gerhard; Schoberth, Siegfried M.; Sahm, Hermann

1983-01-01

A strictly anaerobic bacterium was isolated from a continuous fermentor culture which converted the organic constituents of sulfite evaporator condensate to methane and carbon dioxide. Furfural is one of the major components of this condensate. This furfural isolate could degrade furfural as the sole source of carbon and energy in a defined mineral-vitamin-sulfate medium. Acetic acid was the major fermentation product. This organism could also use ethanol, lactate, pyruvate, or fumarate and c...

Persistence of detectable insecticidal proteins from Bacillus thuringiensis (Cry) and toxicity after adsorption on contrasting soils

International Nuclear Information System (INIS)

Hung, T.P.; Truong, L.V.; Binh, N.D.; Frutos, R.; Quiquampoix, H.; Staunton, S.

2016-01-01

Insecticidal Cry, or Bt, proteins are produced by the soil-endemic bacterium, Bacillus thuringiensis and some genetically modified crops. Their environmental fate depends on interactions with soil. Little is known about the toxicity of adsorbed proteins and the change in toxicity over time. We incubated Cry1Ac and Cry2A in contrasting soils subjected to different treatments to inhibit microbial activity. The toxin was chemically extracted and immunoassayed. Manduca sexta was the target insect for biotests. Extractable toxin decreased during incubation for up to four weeks. Toxicity of Cry1Ac was maintained in the adsorbed state, but lost after 2 weeks incubation at 25 °C. The decline in extractable protein and toxicity were much slower at 4 °C with no significant effect of soil sterilization. The major driving force for decline may be time-dependent fixation of adsorbed protein, leading to a decrease in the extraction yield in vitro, paralleled by decreasing solubilisation in the larval gut. - Graphical abstract: Biotest, presenting Cry-contaminated feed to Manduca sexta larvae in individual Perspex boxes. Display Omitted - Highlights: • Toxicity of Cry protein is initially conserved after adsorption on soil. • Toxicity and extractability decline with time, more rapidly at 25 °C than 4 °C. • Similar dynamics of Cry1AC and Cry2A on soil with varying texture and organic C. • Sterilization of soil does not change Cry dynamics or temperature effect in soil. • Cry decline is determined by progressive fixation on soil not microbial breakdown. - Toxicity was initially maintained after adsorption on soil and both extractable Cry and toxicity declined rapidly, more slowly at low temperature, due to different fixation dynamics. Toxicity of Cry protein is initially conserved after adsorption on soil.

Effects of Soil Quality Enhancement on Pollinator-Plant Interactions

Directory of Open Access Journals (Sweden)

Yasmin J. Cardoza

2012-01-01

Full Text Available Both biotic and abiotic factors can affect soil quality, which can significantly impact plant growth, productivity, and resistance to pests. However, the effects of soil quality on the interactions of plants with beneficial arthropods, such as pollinators, have not been extensively examined. We studied the effects of vermicompost (earthworm compost, VC soil amendment on behavioral and physiological responses of pollinators to flowers and floral resources, using cucumbers, Cucumis sativus, as our model system. Results from experiments conducted over three field seasons demonstrated that, in at least two out of three years, VC amendment significantly increased visit length, while reducing the time to first discovery. Bumblebee (Bombus impatiens workers that fed on flowers from VC-amended plants had significantly larger and more active ovaries, a measure of nutritional quality. Pollen fractions of flowers from VC-grown plants had higher protein compared to those of plants grown in chemically fertilized potting soil. Nectar sugar content also tended to be higher in flowers from VC-grown plants, but differences were not statistically significant. In conclusion, soil quality enhancement, as achieved with VC amendment in this study, can significantly affect plant-pollinator interactions and directly influences pollinator nutrition and overall performance.

The effect of Pseudoxanthomonas sp. as manganese oxidizing bacterium on the corrosion behavior of carbon steel

Energy Technology Data Exchange (ETDEWEB)

Ashassi-Sorkhabi, H., E-mail: habib_ashassi@yahoo.com [Electrochemistry Research Laboratory, Physical Chemistry Department, Faculty of Chemistry, University of Tabriz, Tabriz (Iran, Islamic Republic of); Moradi-Haghighi, M. [Electrochemistry Research Laboratory, Physical Chemistry Department, Faculty of Chemistry, University of Tabriz, Tabriz (Iran, Islamic Republic of); Zarrini, G. [Microbiology laboratory, Biology Department, Science Faculty, University of Tabriz, Tabriz (Iran, Islamic Republic of)

2012-02-01

The present study investigated the role of manganese oxidizing bacterium (MOB), namely Pseudoxanthomonas sp. on the corrosion behavior of carbon steel. This bacterium was isolated from sewage treatment plants and identified by biochemical and molecular methods. The electrochemical techniques such as open circuit potentiometry, electrochemical impedance spectroscopy, potentiodynamic and cyclic polarization were used to measure the corrosion rate and observe the corrosion mechanism. Also, scanning electron microscopy and X-ray diffraction studies were applied to surface analysis. This study revealed the strong adhesion of the biofilm on the metal surface in the presence of Pseudoxanthomonas sp. that enhanced the corrosion of carbon steel. X-ray diffraction patterns identified a high content of MnO{sub 2} deposition within these biofilms. This is the first report that discloses the involvement of Pseudoxanthomonas sp. as manganese oxidizing bacteria on the corrosion of carbon steel. - Highlights: Black-Right-Pointing-Pointer A new type of manganese oxidizing bacteria, namely Pseudoxanthomonas sp. was indicated. Black-Right-Pointing-Pointer This bacterium can create a biofilm on the part of metal surface and affect localized corrosion. Black-Right-Pointing-Pointer In the presence of biofilm, the diffusion of oxygen vacancies and manganese ions has occurred.

The effect of Pseudoxanthomonas sp. as manganese oxidizing bacterium on the corrosion behavior of carbon steel

International Nuclear Information System (INIS)

Ashassi-Sorkhabi, H.; Moradi-Haghighi, M.; Zarrini, G.

2012-01-01

The present study investigated the role of manganese oxidizing bacterium (MOB), namely Pseudoxanthomonas sp. on the corrosion behavior of carbon steel. This bacterium was isolated from sewage treatment plants and identified by biochemical and molecular methods. The electrochemical techniques such as open circuit potentiometry, electrochemical impedance spectroscopy, potentiodynamic and cyclic polarization were used to measure the corrosion rate and observe the corrosion mechanism. Also, scanning electron microscopy and X-ray diffraction studies were applied to surface analysis. This study revealed the strong adhesion of the biofilm on the metal surface in the presence of Pseudoxanthomonas sp. that enhanced the corrosion of carbon steel. X-ray diffraction patterns identified a high content of MnO 2 deposition within these biofilms. This is the first report that discloses the involvement of Pseudoxanthomonas sp. as manganese oxidizing bacteria on the corrosion of carbon steel. - Highlights: ► A new type of manganese oxidizing bacteria, namely Pseudoxanthomonas sp. was indicated. ► This bacterium can create a biofilm on the part of metal surface and affect localized corrosion. ► In the presence of biofilm, the diffusion of oxygen vacancies and manganese ions has occurred.

The use of bacteria for detecting toxic effects of pollutants in soil and water

Science.gov (United States)

Obiakor, Maximilian; Wilson, Susan; Tighe, Matthew; Pereg, Lily

2017-04-01

Microbial abundance and diversity are essential for sustaining soil structure and function and have been strongly linked to human health and wellbeing. Antimony (Sb) in the environment can present an ecological hazard and depending on concentration can be lethal. The toxic effects of Sb(III) and Sb(V) on the model soil bacterium Azospirillum brasilense Sp7 were assessed in exposure-dose-response assays and water samples from an Sb contaminated creek were analyzed for bacterial mortality. In both cases, Sb(III) and Sb(V) greatly affected the survival of A. brasilense Sp7 cells. The Sb(III) had a greater toxic effect than Sb(V) at all concentrations tested. Critical concentrations of Sb also caused variant colonies to appear, indicating both acute and sub-lethal effects, which were dose and time dependent. This work demonstrates the usefulness of A. brasilense as an indicator species to detect harmful effects of an environmental pollutant of emerging concern.

New strains of oil-degrading microorganisms for treating contaminated soils and wastes

Science.gov (United States)

Muratova, A. Yu; Panchenko, L. V.; Semina, D. V.; Golubev, S. N.; Turkovskaya, O. V.

2018-01-01

Two new strains Achromobacter marplatensis101n and Acinetobacter sp. S-33, capable of degrading 49 and 46% of oil within 7 days were isolated, identified, and characterized. The application of A. marplatensis 101n in combination with ammonium nitrate (100 mg·kg-1) for 30 days of cultivation resulted in the degradation of 49% of the initial total petroleum hydrocarbon content (274 g·kg-1) in the original highly acid (pH 4.9) oil-contaminated waste. Up to 30% of oil sludge added to a liquid mineral medium at a concentration of 15% was degraded after 10 days of cultivation of A. marplatensis 101n. Application of yellow alfalfa (Medicago falcata L.) plants with Acinetobacter sp. S-33 for bioremediation of oil-sludge-contaminated soil improved the quality of cleanup in comparison with the bacterium- or plant-only treatment. Inoculation of Acinetobacter sp. S-33 increased the growth of both roots and shoots by more than 40%, and positively influenced the soil microflora. We conclude that the new oil-degrading strains, Acinetobacter sp. S-33 and A. marplatensis 101n, can serve as the basis for new bioremediation agents for the treatment of oil contaminated soils and waste.

Ratiometric Gas Reporting: A Nondisruptive Approach To Monitor Gene Expression in Soils.

Science.gov (United States)

Cheng, Hsiao-Ying; Masiello, Caroline A; Del Valle, Ilenne; Gao, Xiaodong; Bennett, George N; Silberg, Jonathan J

2018-03-16

Fluorescent proteins are ubiquitous tools that are used to monitor the dynamic functions of natural and synthetic genetic circuits. However, these visual reporters can only be used in transparent settings, a limitation that complicates nondisruptive measurements of gene expression within many matrices, such as soils and sediments. We describe a new ratiometric gas reporting method for nondisruptively monitoring gene expression within hard-to-image environmental matrices. With this approach, C 2 H 4 is continuously synthesized by ethylene forming enzyme to provide information on viable cell number, and CH 3 Br is conditionally synthesized by placing a methyl halide transferase gene under the control of a conditional promoter. We show that ratiometric gas reporting enables the creation of Escherichia coli biosensors that report on acylhomoserine lactone (AHL) autoinducers used for quorum sensing by Gram-negative bacteria. Using these biosensors, we find that an agricultural soil decreases the bioavailable concentration of a long-chain AHL up to 100-fold. We also demonstrate that these biosensors can be used in soil to nondisruptively monitor AHLs synthesized by Rhizobium leguminosarum and degraded by Bacillus thuringiensis. Finally, we show that this new reporting approach can be used in Shewanella oneidensis, a bacterium that lives in sediments.

Soil geochemical parameters influencing the spatial distribution of anthrax in Northwest Minnesota, USA

International Nuclear Information System (INIS)

Nath, Samuel; Dere, Ashlee

2016-01-01

Bacillus anthracis is the pathogenic bacterium that causes anthrax, which dwells in soils as highly resilient endospores. B. anthracis spore viability in soil is dependent upon environmental conditions, but the soil properties necessary for spore survival are unclear. In this study we used a range of soil geochemical and physical parameters to predict the spatial distribution of B. anthracis in northwest Minnesota, where 64 cases of anthrax in livestock were reported from 2000 to 2013. Two modeling approaches at different spatial scales were used to identify the soil conditions most correlated to known anthrax cases using both statewide and locally collected soil data. Ecological niche models were constructed using the Maximum Entropy (Maxent) approach and included 11 soil parameters as environmental inputs and recorded anthrax cases as known presences. One ecological niche model used soil data and anthrax presences for the entire state while a second model used locally sampled soil data (n = 125) and a subset of anthrax presences, providing a test of spatial scale. In addition, simple logistic regression models using the localized soil data served as an independent measure of variable importance. Maxent model results indicate that at a statewide level, soil calcium and magnesium concentrations, soil pH, and sand content are the most important properties for predicting soil suitability for B. anthracis while at the local level, clay and sand content along with phosphorous and strontium concentrations are most important. These results also show that the spatial scale of analysis is important when considering soil parameters most important for B. anthracis spores. For example, at a broad scale, B. anthracis spores may require Ca-rich soils and an alkaline pH, but may also concentrate in microenvironments with high Sr concentrations. The study is also one of the first ecological niche models that demonstrates the major importance of soil texture for defining

Constitutive modelling of the undrained shear strength of fine grained soils containing gas

Energy Technology Data Exchange (ETDEWEB)

Grozic, J.L.H. [Calgary Univ., AB (Canada); Nadim, F.; Kvalstad, T.J. [Norwegian Geotechnical Inst., Oslo (Norway)

2002-07-01

The behaviour of fine grained gassy soils was studied in order to develop a technique to quantitatively evaluate geohazards. Gas can occur in seabeds either in solution in pore water, undissolved in the form of gas filled voids, or as gas hydrates. In offshore soils, the degree of saturation is generally greater than 90 per cent, resulting in a soil structure with a continuous water phase and a discontinuous gas phase. The presence of methane gas will impact the strength of the soil, which alters its resistance to submarine sliding. This paper presents a constitutive model for determining the undrained shear strength of fine-grained gassy soils to assess the stability of deep water marine slopes for offshore developments. Methane gas is shown to have a beneficial effect on the soil strength in compressive loading, but the peak strength is achieved at larger deformations. The increased strength is a result of compression and solution gas which cause partial drainage and reduced pore pressures. The undrained shear strength of gassy soils was shown to increase with increasing initial consolidation stress, increasing volumetric coefficient of solubility, and increasing initial void ratio. 9 refs., 3 tabs., 6 figs.

Autochthonous bioaugmentation with environmental samples rich in hydrocarbonoclastic bacteria for bench-scale bioremediation of oily seawater and desert soil.

Science.gov (United States)

Ali, Nedaa; Dashti, Narjes; Salamah, Samar; Al-Awadhi, Husain; Sorkhoh, Naser; Radwan, Samir

2016-05-01

Oil-contaminated seawater and desert soil batches were bioaugmented with suspensions of pea (Pisum sativum) rhizosphere and soil with long history of oil pollution. Oil consumption was measured by gas-liquid chromatography. Hydrocarbonoclastic bacteria in the bioremediation batches were counted using a mineral medium with oil vapor as a sole carbon source and characterized by their 16S ribosomal RNA (rRNA)-gene sequences. Most of the oil was consumed during the first 2-4 months, and the oil-removal rate decreased or ceased thereafter due to nutrient and oxygen depletion. Supplying the batches with NaNO3 (nitrogen fertilization) at a late phase of bioremediation resulted in reenhanced oil consumption and bacterial growth. In the seawater batches bioaugmented with rhizospheric suspension, the autochthonous rhizospheric bacterial species Microbacterium oxidans and Rhodococcus spp. were established and contributed to oil-removal. The rhizosphere-bioaugmented soil batches selectively favored Arthrobacter nitroguajacolicus, Caulobacter segnis, and Ensifer adherens. In seawater batches bioaugmented with long-contaminated soil, the predominant oil-removing bacterium was the marine species Marinobacter hydrocarbonoclasticus. In soil batches on the other hand, the autochthonous inhabitants of the long-contaminated soil, Pseudomonas and Massilia species were established and contributed to oil removal. It was concluded that the use of rhizospheric bacteria for inoculating seawater and desert soil and of bacteria in long-contaminated soil for inoculating desert soil follows the concept of "autochthonous bioaugmentation." Inoculating seawater with bacteria in long-contaminated soil, on the other hand, merits the designation "allochthonous bioaugmentation."

Bacillus subtilis biofilm induction by plant polysaccharides.

Science.gov (United States)

Beauregard, Pascale B; Chai, Yunrong; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

2013-04-23

Bacillus subtilis is a plant-beneficial Gram-positive bacterium widely used as a biofertilizer. However, relatively little is known regarding the molecular processes underlying this bacterium's ability to colonize roots. In contrast, much is known about how this bacterium forms matrix-enclosed multicellular communities (biofilms) in vitro. Here, we show that, when B. subtilis colonizes Arabidopsis thaliana roots it forms biofilms that depend on the same matrix genes required in vitro. B. subtilis biofilm formation was triggered by certain plant polysaccharides. These polysaccharides served as a signal for biofilm formation transduced via the kinases controlling the phosphorylation state of the master regulator Spo0A. In addition, plant polysaccharides are used as a source of sugars for the synthesis of the matrix exopolysaccharide. The bacterium's response to plant polysaccharides was observed across several different strains of the species, some of which are known to have beneficial effects on plants. These observations provide evidence that biofilm genes are crucial for Arabidopsis root colonization by B. subtilis and provide insights into how matrix synthesis may be triggered by this plant.

Soil types effect on grape and wine composition in Helan Mountain area of Ningxia.

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Rui Wang

Full Text Available Different soil types can significantly affect the composition of wine grapes and the final wine product. In this study, the effects of soil types on the composition of Cabernet Sauvignon grapes and wine produced in the Helan Mountains were evaluated. Three different representative soil types--aeolian, sierozem and irrigation silting soil were studied. The compositions of grapes and wines were measured, and in addition, the weights of 100-berry samples were determined. The grapes that grown on the aeolian and sierozem soils matured sooner than those grown on the irrigation silting soil. The highest sugar content, total soluble solids content, sugar to acid ratio and anthocyanin content were found in the grapes that grown on the aeolian soil. The wine produced from this soil had improved chroma and tone and higher-quality phenols. The grapes grown on the sierozem soil had the highest total phenol and tannin contents, which affected the wine composition. The grapes grown on the irrigation silting soil had higher acidities, but the remaining indices were lower. In addition, the grapes grown on the aeolian soil resulted in wines with better chroma and aroma. The sierozem soil was beneficial for the formation of wine tannins and phenols and significantly affected the wine composition. The quality of the grapes from the irrigation silting soil was relatively low, resulting in lower-quality wine.

Soil types effect on grape and wine composition in Helan Mountain area of Ningxia.

Science.gov (United States)

Wang, Rui; Sun, Quan; Chang, Qingrui

2015-01-01

Different soil types can significantly affect the composition of wine grapes and the final wine product. In this study, the effects of soil types on the composition of Cabernet Sauvignon grapes and wine produced in the Helan Mountains were evaluated. Three different representative soil types--aeolian, sierozem and irrigation silting soil were studied. The compositions of grapes and wines were measured, and in addition, the weights of 100-berry samples were determined. The grapes that grown on the aeolian and sierozem soils matured sooner than those grown on the irrigation silting soil. The highest sugar content, total soluble solids content, sugar to acid ratio and anthocyanin content were found in the grapes that grown on the aeolian soil. The wine produced from this soil had improved chroma and tone and higher-quality phenols. The grapes grown on the sierozem soil had the highest total phenol and tannin contents, which affected the wine composition. The grapes grown on the irrigation silting soil had higher acidities, but the remaining indices were lower. In addition, the grapes grown on the aeolian soil resulted in wines with better chroma and aroma. The sierozem soil was beneficial for the formation of wine tannins and phenols and significantly affected the wine composition. The quality of the grapes from the irrigation silting soil was relatively low, resulting in lower-quality wine.

Soil Types Effect on Grape and Wine Composition in Helan Mountain Area of Ningxia

Science.gov (United States)

Wang, Rui; Sun, Quan; Chang, Qingrui

2015-01-01

Different soil types can significantly affect the composition of wine grapes and the final wine product. In this study, the effects of soil types on the composition of Cabernet Sauvignon grapes and wine produced in the Helan Mountains were evaluated. Three different representative soil types—aeolian, sierozem and irrigation silting soil were studied. The compositions of grapes and wines were measured, and in addition, the weights of 100-berry samples were determined. The grapes that grown on the aeolian and sierozem soils matured sooner than those grown on the irrigation silting soil. The highest sugar content, total soluble solids content, sugar to acid ratio and anthocyanin content were found in the grapes that grown on the aeolian soil. The wine produced from this soil had improved chroma and tone and higher-quality phenols. The grapes grown on the sierozem soil had the highest total phenol and tannin contents, which affected the wine composition. The grapes grown on the irrigation silting soil had higher acidities, but the remaining indices were lower. In addition, the grapes grown on the aeolian soil resulted in wines with better chroma and aroma. The sierozem soil was beneficial for the formation of wine tannins and phenols and significantly affected the wine composition. The quality of the grapes from the irrigation silting soil was relatively low, resulting in lower-quality wine. PMID:25706126

Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater

Science.gov (United States)

A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50**T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rDNA sequences revealed that the novel isolate represented...

Ecological enrichment in agroecosystems: Utilizing wildflowers to promote beneficial arthropod communities

Science.gov (United States)

Beneficial arthropods which provide important ecosystems services have come under threat as a result of intensive agricultural practices and landscape simplification. Engineering diverse heterogeneous agricultural landscapes to provide optimal resources for beneficial arthropods may recover and enha...

The Role of Hydrophobicity and Surface Receptors at Hyphae of Lyophyllum sp. Strain Karsten in the Interaction with Burkholderia terrae BS001 – Implications for Interactions in Soil

Science.gov (United States)

Vila, Taissa; Nazir, Rashid; Rozental, Sonia; dos Santos, Giulia M. P.; Calixto, Renata O. R.; Barreto-Bergter, Eliana; Wick, Lukas Y.; van Elsas, Jan Dirk

2016-01-01

The soil bacterium Burkholderia terrae strain BS001 can interact with varying soil fungi, using mechanisms that range from the utilization of carbon/energy sources such as glycerol to the ability to reach novel territories in soil via co-migration with growing fungal mycelia. Here, we investigate the intrinsic properties of the B. terrae BS001 interaction with the basidiomycetous soil fungus Lyophyllum sp. strain Karsten. In some experiments, the ascomycetous Trichoderma asperellum 302 was also used. The hyphae of Lyophyllum sp. strain Karsten were largely hydrophilic on water-containing media versus hydrophobic when aerial, as evidenced by contact angle analyses (CA). Co-migration of B. terrae strain BS001 cells with the hyphae of the two fungi occurred preferentially along the - presumably hydrophilic - soil-dwelling hyphae, whereas aerial hyphae did not allow efficient migration, due to reduced thickness of their surrounding mucous films. Moreover, the cell numbers over the length of the hyphae in soil showed an uneven distribution, i.e., the CFU numbers increased from minima at the inoculation point to maximal numbers in the middle of the extended hyphae, then decreasing toward the terminal side. Microscopic analyses of the strain BS001 associations with the Lyophyllum sp. strain Karsten hyphae in the microcosms confirmed the presence of B. terrae BS001 cells on the mucous matter that was present at the hyphal surfaces of the fungi used. Cell agglomerates were found to accumulate at defined sites on the hyphal surfaces, which were coined ‘fungal-interactive’ hot spots. Evidence was further obtained for the contention that receptors for a physical bacterium-fungus interaction occur at the Lyophyllum sp. strain Karsten hyphal surface, in which the specific glycosphingolipid ceramide monohexoside (CMH) plays an important role. Thus, bacterial adherence may be mediated by heterogeneously distributed fungal-specific receptors, implying the CMH moieties. This

Effect of Polonite used for phosphorus removal from wastewater on soil properties and fertility of a mountain meadow

International Nuclear Information System (INIS)

Cucarella, Victor; Mazurek, Ryszard; Zaleski, Tomasz; Kopec, Michal; Renman, Gunno

2009-01-01

Reactive filter materials used for phosphorus (P) removal from wastewater can be disposed of as soil amendments after treatment, thus recycling P and other macro- and micro-nutrients to plants. In addition, materials with a high pH and Ca content, such as Polonite, are potential soil conditioners, which can be particularly beneficial for acid soils. Polonite previously used for on-site wastewater treatment was applied as a soil amendment to a mountain meadow. The amendment significantly increased soil pH and decreased the hydrolytic acidity, thus reducing Al toxicity risks. The effects were comparable to those of liming. No difference in yield and P uptake by meadow plants was observed. The uptake of metals was lower for amended soils, especially the uptake of Mn. Using Polonite after wastewater treatment as a soil amendment is thus a viable disposal alternative that can replace liming, when necessary, being capable of recycling P and other nutrients to meadow plants. - Filter substrate Polonite can benefit acid soils after wastewater treatment.

Three-year study of fast-growing trees in degraded soils amended with composts: Effects on soil fertility and productivity.

Science.gov (United States)

Madejón, Paula; Alaejos, Joaquin; García-Álbala, José; Fernández, Manuel; Madejón, Engracia

2016-03-15

Currently, worries about the effects of intensive plantations on long-term nutrient supply and a loss of productivity have risen. In this study two composts were added to degraded soils where this type of intensive crops were growing, to avoid the soil fertility decrease and try to increase biomass production. For the experiment, two degraded soils in terms of low organic carbon content and low pH were selected in South-West Spain: La Rábida (RA) and Villablanca (VI) sites. Both study sites were divided into 24 plots. In RA, half of the plots were planted with Populus x canadensis "I-214"; the other half was planted with Eucalyptus globulus. At the VI site, half of the plots were planted with Paulownia fortunei, and the other plots were planted with Eucalyptus globulus. For each tree and site, three treatments were established (two organic composts and a control without compost), with four replications per treatment. The organic amendments were "alperujo" compost, AC, a solid by-product from the extraction of olive oil, and BC, biosolid compost. During the three years of experimentation, samples of soils and plants were analyzed for studying chemical and biochemical properties of soil, plant growth and plant nutritional status and biomass production. The composts increased total organic carbon, water-soluble carbon, nutrients and pH of soil only in the most acidic soil. Soil biochemical quality was calculated with the geometric mean of the enzymatic activities (Dehydrogenase, β-glucosidase, Phosphatase and Urease activities) determined in soils. The results showed a beneficial improvement in comparison with soils without compost. However, the best results were found in the growth and biomass production of the studied trees, especially in Eucalyptus. Nutritional levels of leaves of the trees were, in general, in the normal established range for each species, although no clear effect of the composts was observed. The results of this study justify the addition of

Comment on "A bacterium that degrades and assimilates poly(ethylene terephthalate)".

Science.gov (United States)

Yang, Yu; Yang, Jun; Jiang, Lei

2016-08-19

Yoshida et al (Report, 11 March 2016, p. 1196) reported that the bacterium Ideonella sakaiensis 201-F6 can degrade and assimilate poly(ethylene terephthalate) (PET). However, the authors exaggerated degradation efficiency using a low-crystallinity PET and presented no straightforward experiments to verify depolymerization and assimilation of PET. Thus, the authors' conclusions are rather misleading. Copyright © 2016, American Association for the Advancement of Science.

Mineralogical and particulate morphological characterization of geophagic clayey soils from Botswana

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Georges-Ivo Ekosse

2012-12-01

Full Text Available This study focused on determining the minerals composition and particle morphology of geophagic clayey soils from Botswana in order to infer on how they could influence human health. Six representative geophagic clayey soils from Botswana were mineralogically characterized using X-ray powder diffractometry (XRPD, optical microscopy, and environmental scanning electron microscopy (ESEM. Results of identified mineral phases revealed quartz (SiO2 as the most dominant in all samples constituting close to 70 wt %; followed by goethite (FeO.OH having a mean concentration of 9 wt%, and kaolinite (Al2Si2O5(OH4 with a mean concentration of 8 wt%. Other minerals present were smectite ((Na,Ca(Al,Mg6(Si4O103(OH6-n(H2O, mica (AB2-3(Al,SiSi3O10(F,OH2, feldspar (Na/K(AlSi3O8 and hematite (Fe2O3. The quartz particles were generally coarse; and angular to very angular in morphology. Due to ions present in goethite, kaolinite, and smectite, these minerals impact positively on properties of geophagic clayey soils and could possibly influence human health when consumed. The quartz particles could negatively affect dental enamel as a result of mastication; and cause abrasion of the walls of the gastro-intestinal tract which may lead to rupturing. Although the studied clayey soils could have potential to provide medicinal benefits to the consumer, there is need for beneficiation exercise to be conducted to reduce the coarse angular particles contained in them. It is therefore necessary for constructive efforts to be directed at beneficiating geophagic materials which will render them safe for human consumption.DOI: http://dx.doi.org/10.4314/bcse.v26i3.6

Bacterium-like Particles for efficient immune stimulation of existing vaccines and new subunit vaccines in mucosal applications

Directory of Open Access Journals (Sweden)

Natalija eVan Braeckel-Budimir

2013-09-01

Full Text Available The successful development of a mucosal vaccine critically depends on the use of a safe and effective immunostimulant and/or carrier system. This review describes the effectiveness and mode of action of an immunostimulating particle derived from bacteria in mucosal subunit vaccines. The non-living particles, designated Bacterium-like Particles (BLPs are based on the food-grade bacterium Lactococcus lactis. The focus of the overview is on the development of intranasal BLP-based vaccines to prevent diseases caused by influenza and respiratory syncytial virus, and includes a selection of Phase I clinical data for the intranasal FluGEM vaccine.

Fourier transform infrared spectroscopic characterisation of heavy metal-induced metabolic changes in the plant-associated soil bacterium Azospirillum brasilense Sp7

Science.gov (United States)

Kamnev, A. A.; Antonyuk, L. P.; Tugarova, A. V.; Tarantilis, P. A.; Polissiou, M. G.; Gardiner, P. H. E.

2002-06-01

Structural and compositional features of whole cells of the plant-growth-promoting rhizobacterium Azospirillum brasilense Sp7 under standard and heavy metal-stressed conditions are analysed using Fourier transform infrared (FTIR) spectroscopy and compared with the FT-Raman spectroscopic data obtained previously [J. Mol. Struct. 563-564 (2001) 199]. The structural spectroscopic information is considered together with inductively coupled plasma-mass spectrometric (ICP-MS) analytical data on the content of the heavy metal cations (Co2+, Cu2+ and Zn2+) in the bacterial cells. As a bacterial response to heavy metal stress, all the three metals, being taken up by bacterial cells from the culture medium (0.2 mM) in significant amounts (ca. 0.12, 0.48 and 4.2 mg per gram of dry biomass for Co, Cu and Zn, respectively), are shown to induce essential metabolic changes in the bacterium revealed in the spectra, including the accumulation of polyester compounds in bacterial cells and their enhanced hydration affecting certain IR vibrational modes of functional groups involved.

FtsZ from radiation resistant bacterium Deinococcus radiodurans is different from its characterized homologues

International Nuclear Information System (INIS)

Mehta, Kruti P.; Misra, H.S.

2012-01-01

Polymerization/depolymerization dynamics of FtsZ and its GTPase activity are interdependent and the regulation of these processes determines the growth rate in a bacterium. Deinococcus radiodurans R1 that is best known for its extraordinary radiation resistance and efficient DNA double strand break repair is a comparatively slow growing bacterium and its growth gets arrested in response to gamma radiation. Mechanisms of cell division and its regulation under gamma stressed growth condition would be worth investigating. Genome of this bacterium encodes at least all the known components of divisome. Recombinant FtsZ of D. radiodurans (drFtsZ) preferred Mg 2+ for its GTPase activity. Relatively a very low GTPase activity was observed in presence of Mn 2+ , Co 2+ and Ni 2+ while release of inorganic phosphate could not be detected in presence of other divalent ions including Ca 2+ . GTPase activity of drFtsZ was lower than E. coli but higher than Mycobacterium and it required both Mg 2+ and GTP for its polymerization. Its GTPase activity did not increase with increasing concentration of Mg 2+ and correlates with the bundling of protofilaments. Results obtained from transmission electron microscopy and sedimentation analysis supported the reciprocal correlation of polymerization/depolymerization with the levels of GTPase activity. Dynamic light scattering in presence of 5mM or higher concentration of Mg 2+ and Mn 2 showed a characteristic cyclic change in light scattering without addition of extra metal ion or GTP

Apatite ore mine tailings as an amendment for remediation of a lead-contaminated shooting range soil.

Science.gov (United States)

Venäläinen, Salla H

2011-10-01

This study investigated the use of tailings from apatite ore beneficiation in the remediation of a heavily contaminated shooting range soil. The tailings originating in Siilinjärvi carbonatite complex, Finland, consist of apatite residues accompanied by phlogopite and calcite. In a pot experiment, organic top layer of a boreal forest soil predisposed to pellet-derived lead (Pb) was amended with tailings of various particle-sizes (Ø>0.2mm, Øremediation technique at polluted sites. Copyright © 2011 Elsevier B.V. All rights reserved.

Use of sewage sludge as a fertilizer for increasing soil fertility and crop production

International Nuclear Information System (INIS)

Suess, A.

1997-01-01

The high nutrient and organic-matter contents of sewage sludge make it a useful soil amendment for farmers. In this study at four locations in Bavaria, the application of sewage sludge produced com yields that were similar to or better than those produced by an equal application (in terms of N) of chemical fertilizer. High rates of sludge (800 m 3 /ha) further improved crop yields, although such are impractical for farmers' fields. Residual beneficial effects of sewage-sludge application were seen also in terms of subsequent yields of barley. Application of sludge also improved biological and physical properties of the soils. More long-term studies are needed to better understand how sewage sludge contributes to the improvement of soil fertility and crop yields. (author)

Arbuscular mycorrhizal fungi enhance soil carbon sequestration in the coalfields, northwest China

Science.gov (United States)

Wang, Zhi-Gang; Bi, Yin-Li; Jiang, Bin; Zhakypbek, Yryszhan; Peng, Su-Ping; Liu, Wen-Wen; Liu, Hao

2016-10-01

Carbon storage is affected by photosynthesis (Pn) and soil respiration (Rs), which have been studied extensively in natural and agricultural systems. However, the effects of Pn and Rs on carbon storages in the presence of arbuscular mycorrhizal fungi (AMF) in coalfields remain unclear. A field experiment was established in 2014 in Shendong coal mining subsidence area. The treatments comprised two inoculation levels (inoculated with or without 100 g AMF inoculums per seedlings) and four plant species [wild cherry (Prunus discadenia Koebne L.), cerasus humilis (Prunus dictyneura Diels L.), shiny leaf Yellow horn (Xanthoceras sorbifolium Bunge L.) and apricot (Armeniaca sibirica L.)]. AMF increased Pn of four species ranging from 15.3% to 33.1% and carbon storage, averaged by 17.2% compared to controls. Soil organic carbon (OC), easily extractable glomalin-relation soil protein (EE-GRSP), and total glomalin-relation soil protein (T-GRSP) were significantly increased by AMF treatment. The effect of AMF on the sensitivity of Rs depended on soil temperature. The results highlighted the exponential models to explain the responses of Rs to soil temperature, and for the first time quantified AMF caused carbon sequestration and Rs. Thus, to our knowledge, AMF is beneficial to ecosystems through facilitating carbon conservation in coalfield soils.

(AJST) THE BENEFICIATION OF MUMBWA PHOSPHATE DEPOSIT ...

African Journals Online (AJOL)

minerals, heavy media separation using Bromoform and subsequently flotation were applied in the beneficiation tests. ... of pegmatite bodies with high grade P2O5 were discovered by MINEX ..... presence of negatively charged ions such as.

Plant growth promoting effect of Bacillus amyloliquefaciens H-2-5 on crop plants and influence on physiological changes in soybean under soil salinity.

Science.gov (United States)

Kim, Min-Ji; Radhakrishnan, Ramalingam; Kang, Sang-Mo; You, Young-Hyun; Jeong, Eun-Ju; Kim, Jong-Guk; Lee, In-Jung

2017-07-01

This study was aimed to identify plant growth-promoting bacterial isolates from soil samples and to investigate their ability to improve plant growth and salt tolerance by analysing phytohormones production and phosphate solubilisation. Among the four tested bacterial isolates (I-2-1, H-1-4, H-2-3, and H-2-5), H-2-5 was able to enhance the growth of Chinese cabbage, radish, tomato, and mustard plants. The isolated bacterium H-2-5 was identified as Bacillus amyloliquefaciens H-2-5 based on 16S rDNA sequence and phylogenetic analysis. The secretion of gibberellins (GA 4 , GA 8 , GA 9 , GA 19 , and GA 20 ) from B. amyloliquefaciens H-2-5 and their phosphate solubilisation ability may contribute to enhance plant growth. In addition, the H-2-5-mediated mitigation of short term salt stress was tested on soybean plants that were affected by sodium chloride. Abscisic acid (ABA) produced by the H-2-5 bacterium suppressed the NaCl-induced stress effects in soybean by enhancing plant growth and GA 4 content, and by lowering the concentration of ABA, salicylic acid, jasmonic acid, and proline. These results suggest that GAs, ABA production, and the phosphate solubilisation capacity of B. amyloliquefaciens H-2-5 are important stimulators that promote plant growth through their interaction and also to improve plant growth by physiological changes in soybean at saline soil.

Stripping Away the Soil: Plant Growth Promoting Microbiology Opportunities in Aquaponics

OpenAIRE

Bartelme, Ryan P; Oyserman, Ben O; Blom, Jesse E; Sepulveda-Villet, Osvaldo J; Newton, Ryan J

2018-01-01

As the processes facilitated by plant growth promoting microorganisms (PGPMs) become better characterized, it is evident that PGPMs may be critical for successful sustainable agricultural practices. Microbes enrich plant growth through various mechanisms, such as enhancing resistance to disease and drought, producing beneficial molecules, and supplying nutrients and trace metals to the plant rhizosphere. Previous studies of PGPMs have focused primarily on soil-based crops. In contrast, aquapo...

Engineering Pseudomonas putida KT2440 for simultaneous degradation of organophosphates and pyrethroids and its application in bioremediation of soil.

Science.gov (United States)

Zuo, Zhenqiang; Gong, Ting; Che, You; Liu, Ruihua; Xu, Ping; Jiang, Hong; Qiao, Chuanling; Song, Cunjiang; Yang, Chao

2015-06-01

Agricultural soils are usually co-contaminated with organophosphate (OP) and pyrethroid pesticides. To develop a stable and marker-free Pseudomonas putida for co-expression of two pesticide-degrading enzymes, we constructed a suicide plasmid with expression cassettes containing a constitutive promoter J23119, an OP-degrading gene (mpd), a pyrethroid-hydrolyzing carboxylesterase gene (pytH) that utilizes the upp gene as a counter-selectable marker for upp-deficient P. putida. By introduction of suicide plasmid and two-step homologous recombination, both mpd and pytH genes were integrated into the chromosome of a robust soil bacterium P. putida KT2440 and no selection marker was left on chromosome. Functional expression of mpd and pytH in P. putida KT2440 was demonstrated by Western blot analysis and enzyme activity assays. Degradation experiments with liquid cultures showed that the mixed pesticides including methyl parathion, fenitrothion, chlorpyrifos, permethrin, fenpropathrin, and cypermethrin (0.2 mM each) were degraded completely within 48 h. The inoculation of engineered strain (10(6) cells/g) to soils treated with the above mixed pesticides resulted in a higher degradation rate than in noninoculated soils. All six pesticides could be degraded completely within 15 days in fumigated and nonfumigated soils with inoculation. Theses results highlight the potential of the engineered strain to be used for in situ bioremediation of soils co-contaminated with OP and pyrethroid pesticides.

Federal Standard: Beneficial Use of Dredged Material

Science.gov (United States)

The purpose of this document is to provide national guidance that explains the role of the Federal Standard in implementing beneficial uses of dredged material from U.S. Army Corps of Engineers’ new and maintenance navigation projects.

Bioremediation and reclamation of soil contaminated with petroleum oil hydrocarbons by exogenously seeded bacterial consortium: a pilot-scale study.

Science.gov (United States)

Mukherjee, Ashis K; Bordoloi, Naba K

2011-03-01

Spillage of petroleum hydrocarbons causes significant environmental pollution. Bioremediation is an effective process to remediate petroleum oil contaminant from the ecosystem. The aim of the present study was to reclaim a petroleum oil-contaminated soil which was unsuitable for the cultivation of crop plants by using petroleum oil hydrocarbon-degrading microbial consortium. Bacterial consortium consisting of Bacillus subtilis DM-04 and Pseudomonas aeruginosa M and NM strains were seeded to 20% (v/w) petroleum oil-contaminated soil, and bioremediation experiment was carried out for 180 days under laboratory condition. The kinetics of hydrocarbon degradation was analyzed using biochemical and gas chromatographic (GC) techniques. The ecotoxicity of the elutriates obtained from petroleum oil-contaminated soil before and post-treatment with microbial consortium was tested on germination and growth of Bengal gram (Cicer aretinum) and green gram (Phaseolus mungo) seeds. Bacterial consortium showed a significant reduction in total petroleum hydrocarbon level in contaminated soil (76% degradation) as compared to the control soil (3.6% degradation) 180 days post-inoculation. The GC analysis confirmed that bacterial consortium was more effective in degrading the alkane fraction compared to aromatic fraction of crude petroleum oil hydrocarbons in soil. The nitrogen, sulfur, and oxygen compounds fraction was least degraded. The reclaimed soil supported the germination and growth of crop plants (C. aretinum and P. mungo). In contrast, seeds could not be germinated in petroleum oil-contaminated soil. The present study reinforces the application of bacterial consortium rather than individual bacterium for the effective bioremediation and reclamation of soil contaminated with petroleum oil.

Beneficial utilization of nuclear waste products

International Nuclear Information System (INIS)

Dix, G.P.

1975-01-01

A sufficient supply of isotopes exists to conduct demonstrational experiments in the 1975-1980 time frame to stimulate a market for waste products. A large potential market exists for a number of waste products, measured in terms of billions of dollars. Actinide by-products can become a feed stock for producing other energy producing isotopes by neutron irradiation whose value may exceed that of the fission products. Commercial reprocessors will not invest in the extraction and separation of isotopes from the waste stream until a proven market has evolved. Economic studies must be performed to establish the trade-offs between the beneficial use or disposal of wastes. Fundamental to these studies are process economics, safety analyses applications studies, and market analyses, both domestic and foreign. Regardless of the degree of beneficial utilization of wastes, some residual material from wastes not utilized and spent by-products after utilization will have to undergo ultimate disposal. Isotopic waste products have the potential for solving a number of societal and national security problems and represent a unique source of energy and materials

Enhancing growth performance of chromolaena odorata in two soil samples by using cow manure as amendment

International Nuclear Information System (INIS)

Anyasi, R.

2014-01-01

A greenhouse experiment was conducted to study the effect of cow manure on the growth of Chromolaena odorata propagated for the purpose of phytoremediation of organic contaminant in soil. Cow manure was mixed separately with two soil types: clay soil and sandy-loam soils in a ratio of 9:1 (soil:manure) and put into 2 L PVC pots, the homogenized soil types were measured into 2 L PVC planting pots. Selected sprouting stem cuttings of Chromolaena odorata were transplanted into the pots containing the soil-manure mixture. Nutrient status of the soil was monitored weekly through the period of experimentation and the growth of the plants and biomass accumulation were measured. Control experiment was set up with manure. Survival of plants after transplanting was highest for cuttings transplanting after 3 weeks (95%) and 5 weeks (50%) of sprouting in the nursery. Profuse growth of plants in the both amended soil types were observed when compared with the control. Biomass accumulation was significantly higher in amended soils compared to the control. This study has shown that organic manure amendment to both soil types can enhance the growth and biomass accumulation of Chromolaena odorata. This is a good indication that the amendment could be beneficial in soil phytoremediation studies involving C. odorata. (author)

Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides.

Science.gov (United States)

Devendran, Saravanan; Abdel-Hamid, Ahmed M; Evans, Anton F; Iakiviak, Michael; Kwon, In Hyuk; Mackie, Roderick I; Cann, Isaac

2016-10-17

Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose.

A newly discovered bacterium associated with parthenogenesis and a change in host selection behavior in parasitoid wasps.

Science.gov (United States)

Zchori-Fein, E; Gottlieb, Y; Kelly, S E; Brown, J K; Wilson, J M; Karr, T L; Hunter, M S

2001-10-23

The symbiotic bacterium Wolbachia pipientis has been considered unique in its ability to cause multiple reproductive anomalies in its arthropod hosts. Here we report that an undescribed bacterium is vertically transmitted and associated with thelytokous parthenogenetic reproduction in Encarsia, a genus of parasitoid wasps. Although Wolbachia was found in only one of seven parthenogenetic Encarsia populations examined, the "Encarsia bacterium" (EB) was found in the other six. Among seven sexually reproducing populations screened, EB was present in one, and none harbored Wolbachia. Antibiotic treatment did not induce male production in Encarsia pergandiella but changed the oviposition behavior of females. Cured females accepted one host type at the same rate as control females but parasitized significantly fewer of the other host type. Phylogenetic analysis based on the 16S rDNA gene sequence places the EB in a unique clade within the Cytophaga-Flexibacter-Bacteroid group and shows EB is unrelated to the Proteobacteria, where Wolbachia and most other insect symbionts are found. These results imply evolution of the induction of parthenogenesis in a lineage other than Wolbachia. Importantly, these results also suggest that EB may modify the behavior of its wasp carrier in a way that enhances its transmission.

Framing in the Spanish press about the health crisis because of the E. coli bacterium

Directory of Open Access Journals (Sweden)

Paloma López Villafranca

2013-12-01

Full Text Available This research article analyses  the approach made by press media and other institutional advertising about the E. coli bacterium, most commonly known as cucumber crisis in Spain. While in the rest of Europe this crisis receives the same treatment as A Flu or mad cow disease in this country it is treated as a crisis that affects to the spanish economy and not to the health of the citizen. Economic interests prevail over public health and this is due to official information given. An analysis of contents of the most popular journals in Spain, according to OJD, is made to prove this hypothesis, El Pais, El Mundo and ABC, as well as a study of the main institutional advertising made about E. coli bacterium by official spanish organizations and the media.

Reuse of Winery Wastewater by Application to Vineyard Soils

Science.gov (United States)

Mosse, K. P.; Patti, A. F.; Parikh, S.; Steenwerth, K. L.; Buelow, M. C.; Cavagnaro, T. R.

2010-12-01

The ability to reuse winery wastewater (WWW) has potential benefits both with respect to treatment of a waste stream, as well as providing a beneficial water resource in water limited regions such as south-eastern Australia, California and South Africa. Our study in south-eastern Australia and California has focused on characterizing the physicochemical properties and microbial communities on soils following WWW application. Studies in the Yarra Valley, Victoria, Australia considered the effect of a single WWW application on paired soil sites, one of which was acclimatized to WWW application via 30 years of this practice, and the other of which was not. Soils that had received WWW appear to have a primed microbial population, with soil respiration showing a significantly greater spike following the single WWW application. In addition, the nitrate and ammonium spikes were impacted upon in the acclimatised site. Taken together, this information suggests that long-term WWW application causes an alteration to the microbial community, which may be more readily able to assimilate the carbon and nitrogen sources present in WWW. Studies are currently underway to assess the impacts of the application of a synthetic WWW on vineyard soils in Davis, California. In this study, four different synthetic WWWs are being applied as irrigation water, and soil will be sampled at the time of grape harvest. Results from this ongoing work will be presented with a view to informing long term vineyard management for sustainability.

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti

Science.gov (United States)

Walker, Graham C.; Finan, Turlough M.; Mengoni, Alessio; Griffitts, Joel S.

2018-01-01

Bacterial genome evolution is characterized by gains, losses, and rearrangements of functional genetic segments. The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner. In the symbiotic soil bacterium Sinorhizobium meliloti, the genome is composed of a chromosome and two large extrachromosomal replicons (pSymA and pSymB, which together constitute 45% of the genome). Massively parallel transposon insertion sequencing (Tn-seq) was employed to evaluate the contributions of chromosomal genes to growth fitness in both the presence and absence of these extrachromosomal replicons. Ten percent of chromosomal genes from diverse functional categories are shown to genetically interact with pSymA and pSymB. These results demonstrate the pervasive robustness provided by the extrachromosomal replicons, which is further supported by constraint-based metabolic modeling. A comprehensive picture of core S. meliloti metabolism was generated through a Tn-seq-guided in silico metabolic network reconstruction, producing a core network encompassing 726 genes. This integrated approach facilitated functional assignments for previously uncharacterized genes, while also revealing that Tn-seq alone missed over a quarter of wild-type metabolism. This work highlights the many functional dependencies and epistatic relationships that may arise between bacterial replicons and across a genome, while also demonstrating how Tn-seq and metabolic modeling can be used together to yield insights not obtainable by either method alone. PMID:29672509

Fluidized bed dry dense medium coal beneficiation

CSIR Research Space (South Africa)

North, Brian C

2017-10-01

Full Text Available medium beneficiation using a fluidized bed was investigated. Bed materials of sand, magnetite and ilmenite were used in a laboratory sized cylindrical fluidized bed. The materials were individually tested, as were mixes of sand and heavy minerals. Coal...

The non-target impact of spinosyns on beneficial arthropods.

Science.gov (United States)

Biondi, Antonio; Mommaerts, Veerle; Smagghe, Guy; Viñuela, Elisa; Zappalà, Lucia; Desneux, Nicolas

2012-12-01

Spinosyn-based products, mostly spinosad, have been widely recommended by extension specialists and agribusiness companies; consequently, they have been used to control various pests in many different cropping systems. Following the worldwide adoption of spinosad-based products for integrated and organic farming, an increasing number of ecotoxicological studies have been published in the past 10 years. These studies are primarily related to the risk assessment of spinosad towards beneficial arthropods. This review takes into account recent data with the aim of (i) highlighting potentially adverse effects of spinosyns on beneficial arthropods (and hence on ecosystem services that they provide in agroecosystems), (ii) clarifying the range of methods used to address spinosyn side effects on biocontrol agents and pollinators in order to provide new insights for the development of more accurate bioassays, (iii) identifying pitfalls when analysing laboratory results to assess field risks and (iv) gaining increasing knowledge on side effects when using spinosad for integrated pest management (IPM) programmes and organic farming. For the first time, a thorough review of possible risks of spinosad and novel spinosyns (such as spinetoram) to beneficial arthropods (notably natural enemies and pollinators) is provided. The acute lethal effect and multiple sublethal effects have been identified in almost all arthropod groups studied. This review will help to optimise the future use of spinosad and new spinosyns in IPM programmes and for organic farming, notably by preventing the possible side effects of spinosyns on beneficial arthropods. Copyright © 2012 Society of Chemical Industry.

Approach to study of Cu, Ni and Zn content in soil for ecotoxicological risk assessment

Science.gov (United States)

Boluda, R.; Marimon, L.; Gil, C.; Roca-Pérez, L.

2009-04-01

Current Spanish legislation on contaminated soils defines contaminated soil as "that whose characteristics have been negatively altered by the presence of dangerous human-derived chemical components whose concentration is such that it is an unacceptable risk for human health or the environment and has been expressly declared as such by legal ruling". Regarding heavy metals, the Spanish Autonomous Communities will promote measures to obtain generic reference values to declare a soil to be contaminated. In the Valencian Community, these reference values still do not exist. So if the protection of ecosystems is considered a priority to declare a soil to be contaminated and to assess the level of risk, emergency toxicity tests and seed growth in land plants are resorted to, or tests with aquatic organisms or other experiments with leached soils obtained by standard procedures are carried out. We studied the toxic effects of calcareous contaminated soils by Cu, Ni and Zn on marine bacterium Vibrio fisheri (MicrotoxR test assay) (1) and on barley (Hordeum vulgare L.) in plate (germination index) (2) and pot (UNE 77301) (3) experiments for the purpose of establishing the Cu, Ni and Zn concentrations in soil which may lead to toxicity in order to observe, therefore, whether there is any likelihood of these pollutants coming into contact with any receptor and if adverse effects exist for living beings and the environment. The results showed significant differences among the three types of tests done but, in all cases, the concentrations needed to reflect toxicity effect on organisms were around 20 -70 (Cu and Ni) to 1000 (Zn) times higher than the levels of the control soils. The sensitivity order of the bio-assay was: (1) < (3) < (2). We would like to thank Spanish government-MICINN for partial funding and support (MICINN, project CGL2006-09776).

Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age.

Science.gov (United States)

Murfin, Kristen E; Dillman, Adler R; Foster, Jeremy M; Bulgheresi, Silvia; Slatko, Barton E; Sternberg, Paul W; Goodrich-Blair, Heidi

2012-08-01

Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.

Soil risk assessment of As and Zn contamination in a coal mining region using geostatisretics

International Nuclear Information System (INIS)

Komnitsas, Kostas; Modis, Kostas

2006-01-01

The present paper aims to map As and Zn contamination and assess the risk for agricultural soils in a wider disposal site containing wastes derived from coal beneficiation. Geochemical data related to environmental studies show that the waste characteristics favor solubilisation and mobilization of inorganic contaminants and in some cases the generation of acidic leachates. 135 soil samples were collected from a 34 km 2 area and analysed by using geostatistics under the maximum entropy principle in order to produce risk assessment maps and estimate the probability of soil contamination. In addition, the present paper discusses the main issues related to risk assessment in wider mining and waste disposal sites in order to assist decision makers in selecting feasible rehabilitation schemes

Soil Segregation Methods for Reducing Transportation and Disposal Costs - 13544

Energy Technology Data Exchange (ETDEWEB)

Frothingham, David; Andrews, Shawn; Barker, Michelle; Boyle, James; Buechi, Stephen; Graham, Marc; Houston, Linda; Polek, Michael; Simmington, Robert; Spector, Harold [U.S. Army Corps of Engineers, Buffalo District, 1776 Niagara St., Buffalo, NY 14207 (United States); Elliott, Robert ' Dan' [U.S. Army Reserve, 812A Franklin St.,Worcester, MA 01604 (United States); Durham, Lisa [Argonne National Laboratory, Environmental Science Division, 9700 S. Cass Ave., Argonne, IL 60439 (United States)

2013-07-01

At Formerly Utilized Sites Remedial Action Program (FUSRAP) sites where the selected alternative for contaminated soil is excavation and off-site disposal, the most significant budget items of the remedial action are the costs for transportation and disposal of soil at an off-site facility. At these sites, the objective is to excavate and dispose of only those soils that exceed derived concentration guideline levels. In situ soil segregation using gross gamma detectors to guide the excavation is often challenging at sites where the soil contamination is overlain by clean soil or where the contaminated soil is located in isolated, subsurface pockets. In addition, data gaps are often identified during the alternative evaluation and selection process, resulting in increased uncertainty in the extent of subsurface contamination. In response, the U.S. Army Corps of Engineers, Buffalo District is implementing ex situ soil segregation methods. At the remediated Painesville Site, soils were excavated and fed through a conveyor-belt system, which automatically segregated them into above- and below-cleanup criteria discharge piles utilizing gamma spectroscopy. At the Linde Site and the Shallow Land Disposal Area (SLDA) Site, which are both in the remediation phase, soils are initially segregated during the excavation process using gross gamma detectors and then transported to a pad for confirmatory manual surveying and sampling. At the Linde Site, the ex situ soils are analyzed on the basis of a site-specific method, to establish compliance with beneficial reuse criteria that were developed for the Linde remediation. At the SLDA Site, the ex situ soils are surveyed and sampled based on Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM) final status survey guidance to demonstrate compliance with the derived concentration guideline levels. At all three sites, the ex situ soils that meet the site- specific DCGLs are retained on-site and used as backfill

Soil Segregation Methods for Reducing Transportation and Disposal Costs - 13544

International Nuclear Information System (INIS)

Frothingham, David; Andrews, Shawn; Barker, Michelle; Boyle, James; Buechi, Stephen; Graham, Marc; Houston, Linda; Polek, Michael; Simmington, Robert; Spector, Harold; Elliott, Robert 'Dan'; Durham, Lisa

2013-01-01

At Formerly Utilized Sites Remedial Action Program (FUSRAP) sites where the selected alternative for contaminated soil is excavation and off-site disposal, the most significant budget items of the remedial action are the costs for transportation and disposal of soil at an off-site facility. At these sites, the objective is to excavate and dispose of only those soils that exceed derived concentration guideline levels. In situ soil segregation using gross gamma detectors to guide the excavation is often challenging at sites where the soil contamination is overlain by clean soil or where the contaminated soil is located in isolated, subsurface pockets. In addition, data gaps are often identified during the alternative evaluation and selection process, resulting in increased uncertainty in the extent of subsurface contamination. In response, the U.S. Army Corps of Engineers, Buffalo District is implementing ex situ soil segregation methods. At the remediated Painesville Site, soils were excavated and fed through a conveyor-belt system, which automatically segregated them into above- and below-cleanup criteria discharge piles utilizing gamma spectroscopy. At the Linde Site and the Shallow Land Disposal Area (SLDA) Site, which are both in the remediation phase, soils are initially segregated during the excavation process using gross gamma detectors and then transported to a pad for confirmatory manual surveying and sampling. At the Linde Site, the ex situ soils are analyzed on the basis of a site-specific method, to establish compliance with beneficial reuse criteria that were developed for the Linde remediation. At the SLDA Site, the ex situ soils are surveyed and sampled based on Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM) final status survey guidance to demonstrate compliance with the derived concentration guideline levels. At all three sites, the ex situ soils that meet the site- specific DCGLs are retained on-site and used as backfill

Sustainable agriculture, soil management and erosion from prehistoric times to 2100

Science.gov (United States)

Vanwalleghem, Tom; Gómez, Jose Alfonso; Infante Amate, Juan; González Molina, Manuel; Fernández, David Soto; Guzmán, Gema; Vanderlinden, Karl; Laguna, Ana; Giráldez, Juan Vicente

2015-04-01

The rational use of soil requires the selection of management practices to take profit of the beneficial functions of plant growth, water and nutrient storage, and pollutants removal by filtering and decomposition without altering its properties. However, the first evidence of important and widespread erosion peaks can generally be found with the arrival of the first farmers all over the world. In areas with a long land-use history such as the Mediterranean, clear signs indicating the advanced degradation status of the landscape, such as heavily truncated soils, are visible throughout. Soil conservation practices are then aimed at reducing erosion to geological rates, in equilibrium with long-term soil formation rates, while maximizing agricultural production. The adoption of such practices in most areas of the world are as old as the earliest soil erosion episodes themselves. This work firstly reviews historical evidence linking soil management and soil erosion intensity, with examples from N Europe and the Mediterranean. In particular, work by the authors in olive orchards will be presented that shows how significant variations in soil erosion rates between could be linked to the historical soil management. The potential of historical documents for calibrating a soil erosion model is shown as the model, in this case RUSLE-based and combining tillage and water erosion, adequately represents the measured erosion rate dynamics. Secondly, results from present-day, long-term farm experiments in the EU are reviewed to evaluate the effect of different soil management practices on physical soil properties, such as bulk density, penetration resistance, aggregate stability, runoff coefficient or sediment yield. Finally, we reflect upon model and field data that indicate how future global climate change is expected to affect soil management and erosion and how the examples used above hold clues about sustainable historical management practices that can be used successfully

Physical and water properties of selected Polish heavy soils of various origins

Directory of Open Access Journals (Sweden)

Kaczmarek Zbigniew

2015-12-01

Full Text Available The paper presents the characteristics of selected physical, chemical, and water properties of four mineral arable soils characterized with heavy and very heavy texture. Soil samples from genetic horizons of black earths from areas near Kętrzyn, Gniew and Kujawy, and alluvial soils from Żuławy were used. The following properties were determined in the samples of undisturbed and disturbed structure: texture, particle density, bulk density, porosity, natural and hygroscopic moistures, maximal hygroscopic capacity, saturated hydraulic conductivity, potential of water bonding in soil, total and readily available water, total retention in the horizon of 0–50 cm, drainage porosity, content of organic carbon and total nitrogen Parent rocks of these soils were clays, silts and loams of various origin. High content of clay fraction strongly influenced the values of all the analyzed properties. All the examined soils had high content of organic carbon and total nitrogen and reaction close to neutral or alkaline. High content of mineral and organic colloids and, what follows, beneficial state of top horizons’ structure, determined – apart from heavy texture – low soil bulk density and high porosity. The investigated soils were characterized by high field water capacity and wide scopes of total and readily available water. The saturated hydraulic conductivity was low and characteristic to heavy mineral arable soils. The parameter which influenced the variability of analyzed parameters most was texture.

Chemical and toxicological characterization of slurry reactor biotreatment of explosives-contaminated soils

Energy Technology Data Exchange (ETDEWEB)

Griest, W.H.; Stewart, A.J.; Vass, A.A.; Ho, C.H.

1998-08-01

Treatment of 2,4,6-trinitrotoluene (TNT)-contaminated soil in the Joliet Army Ammunition Plant (JAAP) soil slurry bioreactor (SSBR) eliminated detectable TNT but left trace levels of residual monoamino and diamino metabolites under some reactor operating conditions. The reduction of solvent-extractable bacterial mutagenicity in the TNT-contaminated soil was substantial and was similar to that achieved by static pile composts at the Umatilla Army Depot Activity (UMDA) field demonstration. Aquatic toxicity to Ceriodaphnia dubia from TNT in the leachates of TNT-contaminated soil was eliminated in the leachates of JAAP SSBR product soil. The toxicity of soil product leachates to Ceriodaphnia dubia was reasonably predicted using the specific toxicities of the components detected, weighted by their leachate concentrations. In samples where TNT metabolites were observed in the soil product and its leachates, this method determined that the contribution to predicted toxicity values was dominated by trace amounts of the diamino-metabolites, which are very toxic to ceriodaphnia dubia. When the SSBR operating conditions reduced the concentrations of TNT metabolites in the product soils and their leachates to undetectable concentrations, the main contributors to predicted aquatic toxicity values appeared to be molasses residues, potassium, and bicarbonate. Potassium and bicarbonate are beneficial or benign to the environment, and molasses residues are substantially degraded in the environment. Exotoxins, pathogenic bacteria, inorganic particles, ammonia, and dissolved metals did not appear to be important to soil product toxicity.

Septicemia caused by the gram-negative bacterium CDC IV c-2 in an immunocompromised human.

OpenAIRE

Dan, M; Berger, S A; Aderka, D; Levo, Y

1986-01-01

A 37-year-old man with plasma cell leukemia developed nonfatal septicemia caused by the gram-negative bacterium CDC IV c-2. Recovery followed appropriate treatment with antibiotics. The biochemical features of this organism are reviewed.

Characterization of a Neochlamydia-like Bacterium Associated with Epitheliocystis in Cultured Artic Char Salvelinus alpinus

Science.gov (United States)

Infections of branchial epithelium by intracellular gram-negative bacteria, termed epitheliocystis, have limited culture of Arctic char (Salvelinus alpinus). To characterize a bacterium associated with epitheliocystis in cultured char, gills were sampled for histopathologic examination, conventional...

How phytohormones shape interactions between plants and the soil-borne fungus Fusarium oxysporum

Directory of Open Access Journals (Sweden)

Xiaotang eDi

2016-02-01

Full Text Available Plants interact with a huge variety of soil microbes, ranging from pathogenic to mutualistic. The Fusarium oxysporum (Fo species complex consists of ubiquitous soil inhabiting fungi that can infect and cause disease in over 120 different plant species including tomato, banana, cotton and Arabidopsis. However, in many cases Fo colonization remains symptomless or even has beneficial effects on plant growth and/or stress tolerance. Also in pathogenic interactions a lengthy asymptomatic phase usually precedes disease development. All this indicates a sophisticated and fine-tuned interaction between Fo and its host. The molecular mechanisms underlying this balance are poorly understood. Plant hormone signaling networks emerge as key regulators of plant-microbe interactions in general. In this review we summarize the effects of the major phytohormones on the interaction between Fo and its diverse hosts. Generally, Salicylic Acid (SA signaling reduces plant susceptibility, whereas Jasmonic Acid (JA, Ethylene (ET, Abscisic Acid (ABA and auxin have complex effects, and are potentially hijacked by Fo for host manipulation. Finally, we discuss how plant hormones and Fo effectors balance the interaction from beneficial to pathogenic and vice versa.

Effect of long-term combined application of organic and inorganic fertilizers on soil nematode communities within aggregates.

Science.gov (United States)

Zhang, Zhiyong; Zhang, Xiaoke; Mahamood, Md; Zhang, Shuiqing; Huang, Shaomin; Liang, Wenju

2016-08-09

A long-term fertilization experiment was conducted to examine the effects of different fertilization practices on nematode community composition within aggregates in a wheat-maize rotation system. The study was a randomized complete block design with three replicates. The experiment involved the following four treatments: no fertilizer, inorganic N, P and K fertilizer (NPK), NPK plus manure (NPKM) and NPK plus maize straw (NPKS). Soil samples were taken at 0-20 cm depth during the wheat harvest stage. Based on our results, NPKS contributed to soil aggregation and moisture retention, with a positive effect on soil total nitrogen accumulation, particularly within small macroaggregates (0.25-1 mm) and microaggregates (fertilizer application effectively improved soil physicochemical properties and were also beneficial for nematode survival within small aggregate size fractions.

Application of Fast Pyrolysis Biochar to a Loamy soil - Effects on carbon and nitrogen dynamics and potential for carbon sequestration

DEFF Research Database (Denmark)

Bruun, Esben

-biochar for agronomic use, since field trials are needed in order to verify potential benefits or drawbacks on soil fertility and crop yields. However, this thesis has improved the mechanistic understanding of the effects of applying FP-biochar to soil, and shows that wheat-straw FP-biochar has properties beneficial...... increased it moderately. Moreover, soil amendment of FP-biochar caused immobilization of considerable amounts of soil N, whereas SP-biochar resulted in a net mineralization of N after two months of soil incubation. Nitrogen immobilisation can be detrimental to crop yields, as shown in a Barley pot trial......Thermal decomposition of biomass in an oxygen-free environment (pyrolysis) produces bio-oil, syngas, and char. All three products can be used to generate energy, but an emerging new use of the recalcitrant carbon-rich char (biochar) is to apply it to the soil in order to enhance soil fertility...

Mixed Phenolic Acids Mediated Proliferation of Pathogens Talaromyces helicus and Kosakonia sacchari in Continuously Monocultured Radix pseudostellariae Rhizosphere Soil

Science.gov (United States)

Wu, Hongmiao; Wu, Linkun; Wang, Juanying; Zhu, Quan; Lin, Sheng; Xu, Jiahui; Zheng, Cailiang; Chen, Jun; Qin, Xianjin; Fang, Changxun; Zhang, Zhixing; Azeem, Saadia; Lin, Wenxiong

2016-01-01

Radix pseudostellariae L. is a common and popular Chinese medication. However, continuous monoculture has increased its susceptibility to severe diseases. We identified two pathogenic microorganisms, Talaromyces helicus M. (KU355274) and Kosakonia sacchari W. (KU324465), and their antagonistic bacterium, Bacillus pumilus Z. in rhizosphere soil of continuously monocultured R. pseudostellariae. Nine types of phenolic acids were identified both in the rhizosphere soil and in culture medium under sterile conditions. A syringic acid and phenolic acid mixture significantly promoted the growth of T. helicus and K. sacchari. T. helicus could utilize eight types of phenolic acids, whereas K. sacchari could only use four phenolic acids. K. sacchari produced protocatechuic acid when consuming vanillin. Protocatechuic acid negatively affected the growth of B. pumilus. The 3A-DON toxin produced by T. helicus promoted the growth of K. sacchari and inhibited growth of B. pumilus at low concentrations. These data help explain why phenolic exudates mediate a microflora shift and structure disorder in the rhizosphere soil of continuously monocultured R. pseudostellariae and lead to increased replanting disease incidence. PMID:27014250

A risk assessment approach to identifying constituents in oilfield produced water for treatment prior to beneficial use.

Science.gov (United States)

Horner, Jennifer E; Castle, James W; Rodgers, John H

2011-05-01

A risk assessment approach incorporating exposure pathways and calculated risk quotients was applied to identifying constituents requiring treatment prior to beneficial use of oilfield produced water (OPW). In this study, risk quotients are ratios of constituent concentrations in soil or water to guideline concentrations for no adverse effects to receptors. The risk assessment approach is illustrated by an example of an oilfield water produced from non-marine geologic strata of a rift basin in sub-Saharan Africa. The OPW studied has the following characteristics: 704-1370 mg L(-1) total dissolved solids (TDS), 45-48 mg L(-1) chloride, and 103.8 mg L(-1) oil and grease. Exposure pathways of constituents in OPW used for irrigation include: ingestion of plant tissue, ingestion and direct contact of irrigated soil by livestock, inhalation of aerosols or volatilized constituents, and ingestion of OPW directly by livestock. Applying risk quotient methods for constituents in soil and water, constituents of concern (COCs) identified for irrigation and livestock watering using the OPW studied include: iron (Fe), manganese (Mn), nickel (Ni), zinc (Zn), and oil and grease. Approximately 165,000 barrels d(-1) (26,233 m(3) d(-1)) of OPW from the study site are available for use. Identification of COCs and consideration of water quantity allows for development of reliable treatment design criteria to ensure effective and consistent treatment is achieved to meet guideline levels required for irrigation, livestock watering, or other uses. This study illustrates the utility of risk assessment for identifying the COCs in OPW for treatment, the level of treatment required, and viable options for use of the treated water. Copyright © 2011 Elsevier Inc. All rights reserved.

Removal of zinc from aqueous solution by metal resistant symbiotic bacterium Mesorhizobium amorphae

DEFF Research Database (Denmark)

Hao, Xiuli; Mohamad, Osama Abdalla; Xie, Pin

2014-01-01

Biosorption of zinc by living biomasses of metal resistant symbiotic bacterium Mesorhizobium amorphae CCNWGS0123 was investigated under optimal conditions at pH 5.0, initial metal concentrations of 100 mg L-1, and a dose of 1.0 g L-1. M. amorphae exhibited an efficient removal of Zn2+ from aqueous...

Two-dimensional gel-based alkaline proteome of the probiotic bacterium Lactobacillus acidophilus NCFM

DEFF Research Database (Denmark)

Majumder, Avishek; Cai, Liyang; Ejby, Morten

2012-01-01

Lactobacillus acidophilus NCFM (NCFM) is a well‐documented probiotic bacterium isolated from human gut. Detailed 2D gel‐based NCFM proteomics addressed the so‐called alkaline range, i.e., pH 6–11. Proteins were identified in 150 of the 202 spots picked from the Coomassie Brilliant Blue stained 2D...

Factors Affecting Zebra Mussel Kill by the Bacterium Pseudomonas fluorescens

Energy Technology Data Exchange (ETDEWEB)

Daniel P. Molloy

2004-02-24

The specific purpose of this research project was to identify factors that affect zebra mussel kill by the bacterium Pseudomonas fluorescens. Test results obtained during this three-year project identified the following key variables as affecting mussel kill: treatment concentration, treatment duration, mussel siphoning activity, dissolved oxygen concentration, water temperature, and naturally suspended particle load. Using this latter information, the project culminated in a series of pipe tests which achieved high mussel kill inside power plants under once-through conditions using service water in artificial pipes.

Selenite reduction by the obligate aerobic bacterium Comamonas testosteroni S44 isolated from a metal-contaminated soil

DEFF Research Database (Denmark)

Zheng, Shixue; Su, Jing; Wang, Liang

2014-01-01

impacted cellular growth and subsequent resistance to multiple heavy metal(loid)s. Conclusions: C. testosteroni S44 could be very useful for bioremediation in heavy metal(loid) polluted soils due to the ability to both reduce toxic Se(VI) and Se(IV) to non-toxic Se (0) under aerobic conditions...

Application of carbon nanotubes to immobilize heavy metals in contaminated soils

Energy Technology Data Exchange (ETDEWEB)

Matos, Martim P. S. R.; Correia, António Alberto S., E-mail: aalberto@dec.uc.pt [University of Coimbra, Department of Civil Engineering, CIEPQPF—Chemical Process Engineering and Forest Products Research Centre (Portugal); Rasteiro, Maria G. [University of Coimbra, Department of Chemical Engineering, CIEPQPF (Portugal)

2017-04-15

The contamination of soils with heavy metals is a growing concern in modern societies. To avoid the spread of contamination, soil stabilization techniques can be applied mixing materials with the soil in order to partially immobilize heavy metals. Carbon nanotubes (CNTs) are nanomaterials known for its exceptional properties, like high surface area and adsorption capacity. Due to these unique properties, the potential use of CNTs in heavy metal contaminated water has been studied, with very satisfactory results; however, their application in contaminated soils is practically unexplored. This experimental work is focused on studying the potential of using CNTs in soil remediation, especially to immobilize the heavy metals ions: lead (Pb{sup 2+}), copper (Cu{sup 2+}), nickel (Ni{sup 2+}), and zinc (Zn{sup 2+}), commonly present in contaminated soils. In order to avoid CNT agglomeration, which originates the loss of their beneficial properties, an aqueous suspension of CNTs was prepared using a non-ionic surfactant combined with ultrasonic energy to promote CNTs dispersion. Then, the soil, with and without the addition of CNTs, was subjected to adsorption tests to evaluate the CNT capacity to improve heavy metal immobilization. To validate the adsorption test results, permeability tests were executed, simulating the conditions of a real-case scenario. The results obtained led to the conclusion that the addition of a small amount of dispersed CNTs can successfully increase the adsorption capacity of the soil and consequently improve the immobilization of heavy metals in the soil matrix. The immobilization percentage varies with the different heavy metals under study.

Application of carbon nanotubes to immobilize heavy metals in contaminated soils

International Nuclear Information System (INIS)

Matos, Martim P. S. R.; Correia, António Alberto S.; Rasteiro, Maria G.

2017-01-01

The contamination of soils with heavy metals is a growing concern in modern societies. To avoid the spread of contamination, soil stabilization techniques can be applied mixing materials with the soil in order to partially immobilize heavy metals. Carbon nanotubes (CNTs) are nanomaterials known for its exceptional properties, like high surface area and adsorption capacity. Due to these unique properties, the potential use of CNTs in heavy metal contaminated water has been studied, with very satisfactory results; however, their application in contaminated soils is practically unexplored. This experimental work is focused on studying the potential of using CNTs in soil remediation, especially to immobilize the heavy metals ions: lead (Pb"2"+), copper (Cu"2"+), nickel (Ni"2"+), and zinc (Zn"2"+), commonly present in contaminated soils. In order to avoid CNT agglomeration, which originates the loss of their beneficial properties, an aqueous suspension of CNTs was prepared using a non-ionic surfactant combined with ultrasonic energy to promote CNTs dispersion. Then, the soil, with and without the addition of CNTs, was subjected to adsorption tests to evaluate the CNT capacity to improve heavy metal immobilization. To validate the adsorption test results, permeability tests were executed, simulating the conditions of a real-case scenario. The results obtained led to the conclusion that the addition of a small amount of dispersed CNTs can successfully increase the adsorption capacity of the soil and consequently improve the immobilization of heavy metals in the soil matrix. The immobilization percentage varies with the different heavy metals under study.

Application of carbon nanotubes to immobilize heavy metals in contaminated soils

Science.gov (United States)

Matos, Martim P. S. R.; Correia, António Alberto S.; Rasteiro, Maria G.

2017-04-01

The contamination of soils with heavy metals is a growing concern in modern societies. To avoid the spread of contamination, soil stabilization techniques can be applied mixing materials with the soil in order to partially immobilize heavy metals. Carbon nanotubes (CNTs) are nanomaterials known for its exceptional properties, like high surface area and adsorption capacity. Due to these unique properties, the potential use of CNTs in heavy metal contaminated water has been studied, with very satisfactory results; however, their application in contaminated soils is practically unexplored. This experimental work is focused on studying the potential of using CNTs in soil remediation, especially to immobilize the heavy metals ions: lead (Pb2+), copper (Cu2+), nickel (Ni2+), and zinc (Zn2+), commonly present in contaminated soils. In order to avoid CNT agglomeration, which originates the loss of their beneficial properties, an aqueous suspension of CNTs was prepared using a non-ionic surfactant combined with ultrasonic energy to promote CNTs dispersion. Then, the soil, with and without the addition of CNTs, was subjected to adsorption tests to evaluate the CNT capacity to improve heavy metal immobilization. To validate the adsorption test results, permeability tests were executed, simulating the conditions of a real-case scenario. The results obtained led to the conclusion that the addition of a small amount of dispersed CNTs can successfully increase the adsorption capacity of the soil and consequently improve the immobilization of heavy metals in the soil matrix. The immobilization percentage varies with the different heavy metals under study.

A Comparative biochemical study on two marine endophytes, Bacterium SRCnm and Bacillus sp. JS, Isolated from red sea algae.

Science.gov (United States)

Ahmed, Eman Fadl; Hassan, Hossam Mokhtar; Rateb, Mostafa Ezzat; Abdel-Wahab, Noha; Sameer, Somayah; Aly Taie, Hanan Anwar; Abdel-Hameed, Mohammed Sayed; Hammouda, Ola

2016-01-01

Two marine endophytic bacteria were isolated from the Red Sea algae; a red alga; Acanthophora dendroides and the brown alga Sargassum sabrepandum. The isolates were identified based on their 16SrRNA sequences as Bacterium SRCnm and Bacillus sp. JS. The objective of this study was to investigate the potential anti-microbial and antioxidant activities of the extracts of the isolated bacteria grown in different nutrient conditions. Compared to amoxicillin (25μg/disk) and erythromycin (15μg/disk), the extracts of Bacterium SRCn min media II, III, IV and V were potent inhibitors of the gram-positive bacterium Sarcina maxima even at low concentrations. Also, the multidrug resistant Staphylococcus aureus(MRSA) was more sensitive to the metabolites produced in medium (II) of the same endophyte than erythromycin (15μg/disk). A moderate activity of the Bacillus sp. JS extracts of media I and II was obtained against the same pathogen. The total compounds (500ug/ml) of both isolated endophytes showed moderate antioxidant activities (48.9% and 46.1%, respectively). LC/MS analysis of the bacterial extracts was carried out to investigate the likely natural products produced. Cyclo(D-cis-Hyp-L-Leu), dihydrosphingosine and 2-Amino-1,3-hexadecanediol were identified in the fermentation medium of Bacterium SRCnm, whereas cyclo (D-Pro-L-Tyr) and cyclo (L-Leu-L-Pro) were the suggested compounds of Bacillus sp. JS.

17 CFR 229.403 - (Item 403) Security ownership of certain beneficial owners and management.

Science.gov (United States)

2010-04-01

... of certain beneficial owners and management. 229.403 Section 229.403 Commodity and Securities... Management and Certain Security Holders § 229.403 (Item 403) Security ownership of certain beneficial owners and management. (a) Security ownership of certain beneficial owners. Furnish the following information...

Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water

Digital Repository Service at National Institute of Oceanography (India)

Bhumika, V.; Ravinder, K.; Korpole, S.; Srinivas, T.N.R.; AnilKumar, P.

A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21^T , was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, L-proline arylamidase...

Isolation and Antibiotic Sensitivity of Bacillus thuringinesis Strain From Dump Soil

Directory of Open Access Journals (Sweden)

Sarker, D.

2010-01-01

Full Text Available Bacillus thuringiensis (or Bt is a commonly used as a pesticide. B. thuringiensis is a naturally-occurring soil bacterium, also occurs naturally in the gut of caterpillars of various types of moths and butterflies, as well as on the dark surface of plants. The xylanase producing bacterial strains were isolated from dump soil. The strains were isolated on xylan agar media and screening was carried out by xylanolysis method. To test the sensitivity of the isolates, ten different antibiotics were used. The strains were tested for resistance to doxycyclin, erythromycin, chloramphenical, cephallaxin, kanamycin, ampicillin, steptomycin, vancomycin, amoxycillin and neomycin. The strains showed sensitive to doxycyclin, erythromycin, chloramphenical, cephallaxin, kanamycin, ampicillin, steptomycin and vancomycin and also showed resistance to amoxycillin and neomycin, when tested by disc diffusion method on nutrient agar plate confirmed by antibiotic spread plate method. The inhibitory effect of B. thuringiensis strains against the test bacteria Bacillus subtilis, Sarcina lutca, Shigella dysenteriae, Shigella sonnei and Pseudomonus aeruginosa examined. It was found that, B. thuringiensis S1, B. thuringiensis S2 and B. thuringiensis S3 strains showed an inhibitory effect on all of the test bacteria.

A highly infective plant-associated bacterium influences reproductive rates in pea aphids.

Science.gov (United States)

Hendry, Tory A; Clark, Kelley J; Baltrus, David A

2016-02-01

Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction.

A highly infective plant-associated bacterium influences reproductive rates in pea aphids

Science.gov (United States)

Hendry, Tory A.; Clark, Kelley J.; Baltrus, David A.

2016-01-01

Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction. PMID:26998321

Soil microbial activities beneath Stipa tenacissima L. and in surrounding bare soil

Science.gov (United States)

Novosadová, I.; Ruiz Sinoga, J. D.; Záhora, J.; Fišerová, H.

2010-05-01

Open steppes dominated by Stipa tenacissima L. constitute one of the most representative ecosystems of the semi-arid zones of Eastern Mediterranean Basin (Iberian Peninsula, North of Africa). These steppes show a higher degree of variability in composition and structure. Ecosystem functioning is strongly related to the spatial pattern of grass tussocks. Soils beneath S. tenacissima grass show higher fertility and improved microclimatic conditions, favouring the formation of "resource islands" (Maestre et al., 2007). On the other hand in "resource islands" and in surrounding bare soil exists the belowground zone of influence. The competition for water and resources between plants and microorganisms is strong and mediated trough an enormous variety of exudates and resource depletion intended to regulate soil microbial communities in the rhizosphere, control herbivory, encourage beneficial symbioses, and change chemical and physical properties in soil (Pugnaire et Armas, 2008). Secondary compounds and allelopathy restrict other species growth and contribute to patchy plant distribution. Active root segregation affects not only neighbourś growth but also soil microbial activities. The objective of this study was to assess the effect of Stipa tenacissima on the key soil microbial activities under controlled incubation conditions (basal and potential respiration; net nitrogen mineralization). The experimental plots were located in the province Almería in Sierra de los Filabres Mountains near the village Gérgal (southeast Spain) in the small catchment which is situated between 1090 - 1165 m a.s.l. The area with extent of 82 000 m2 is affected by soil degradation. The climate is semiarid Mediterranean. The mean annual rainfall is of about 240 mm mostly concentrated in autumn and spring. The mean annual temperature is 13.9° C. The studied soil has a loam to sandy clay texture and is classified as Lithosol (FAO-ISRIC and ISSS, 1998). The vegetation of these areas is an

Purification and Characterization of Haloalkaline, Organic Solvent Stable Xylanase from Newly Isolated Halophilic Bacterium-OKH

Science.gov (United States)

Sanghvi, Gaurav; Jivrajani, Mehul; Patel, Nirav; Jivrajani, Heta; Bhaskara, Govinal Badiger; Patel, Shivani

2014-01-01

A novel, alkali-tolerant halophilic bacterium-OKH with an ability to produce extracellular halophilic, alkali-tolerant, organic solvent stable, and moderately thermostable xylanase was isolated from salt salterns of Mithapur region, Gujarat, India. Identification of the bacterium was done based upon biochemical tests and 16S rRNA sequence. Maximum xylanase production was achieved at pH 9.0 and 37°C temperature in the medium containing 15% NaCl and 1% (w/v) corn cobs. Sugarcane bagasse and wheat straw also induce xylanase production when used as carbon source. The enzyme was active over a range of 0–25% sodium chloride examined in culture broth. The optimum xylanase activity was observed at 5% sodium chloride. Xylanase was purified with 25.81%-fold purification and 17.1% yield. Kinetic properties such as Km and Vmax were 4.2 mg/mL and 0.31 μmol/min/mL, respectively. The enzyme was stable at pH 6.0 and 50°C with 60% activity after 8 hours of incubation. Enzyme activity was enhanced by Ca2+, Mn2+, and Mg2+ but strongly inhibited by heavy metals such as Hg2+, Fe3+, Ni2+, and Zn2+. Xylanase was found to be stable in organic solvents like glutaraldehyde and isopropanol. The purified enzyme hydrolysed lignocellulosic substrates. Xylanase, purified from the halophilic bacterium-OKH, has potential biotechnological applications. PMID:27350996

Potassium solubilizing bacteria-assisted phytoextraction of radiocesium on pechay plants grown in cesium contaminated Fukushima Soils

International Nuclear Information System (INIS)

Rallos, R.V.; Yokoyama, T.

2015-01-01

Increasing the efficiency of metal uptake by plants is important to achieve successful phytoremediation of metal-polluted soils. The presence of potassium solubilizing bacteria (KSB) increases the solubilization of K-containing minerals thereby enhancing the availability of potassium (K+) and other cations including radicesium (137Cs+) for plant uptake. In this study, five KSB isolates were obtained from soybean rhizosphere in Fukushima radiocesium contaminated soils. Based on biochemical and 16S rRNA gene sequence analysis, the bacteria were identified as Bacillus megaterium, Pseudomonas putida, P. frederiksbergensis, Burkholderia sabiae, and P. mandelii. The KSB isolates were evaluated for plant growth promotion, potassium (K) uptake and radiocesium phytoextraction of pechay in three different cesium-contaminated Fukushima soils. Inoculation with KSB showed beneficial effects on plant growth and increased the phytoextraction of radiocesium, with much greater magnitude in roots than in shoots. The results indicated that KSB inoculation may be essential in managing radiocesium-contaminated soils and manipulating the transfer from soils to plants.(author)

Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences

NARCIS (Netherlands)

Vanfossen, A.L.; Verhaart, M.R.A.; Kengen, S.W.M.; Kelly, R.M.

2009-01-01

Co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on

Spatial oxygen distribution and nitrous oxide emissions from soil after manure application

DEFF Research Database (Denmark)

Zhu, Kun; Bruun, Sander; Larsen, Morten

2014-01-01

The availability and spatial distribution of oxygen (O2) in agricultural soil are controlling factors in the production and emission of nitrous oxide (N2O) to the atmosphere, but most experiments investigating the effects of various factors on N2O emissions in soil have been conducted without...... to interpret data on N2O emissions following a uniform or layered amendment of manure to agricultural soil. The spatial distribution of O2 and gas emission rates were monitored for 12 h. An anoxic layer formed rapidly around the layered manure, whereas the uniformly distributed manure led to a more widespread...... anoxia. Nitrous oxide emissions increased immediately after depletion of O2 in the manure-amended treatments. Greater understanding and improved knowledge of the spatial distribution of O2 is clearly beneficial and can be used to devise improved application strategies for mitigating N2O emissions from...

[Correlation analysis of nutrients and microorganisms in soils with polyphenols and total flavonoids of Houttuynia cordata].

Science.gov (United States)

Wu, Dan; Luo, Shi-qiong; Yang, Zhan-nan; Ma, Jing; Hong, Liang

2015-04-01

The relationship of nutrients and microorganisms in soils with polyphenols and total flavonoids of Houttuynia cordata were investigated by measuring nutrients, enzyme activity, pH, concentrations of microbe phospholipid fatty acids (PLFAs) in soils, and determining concentrations of polyphenols and total flavonoids of H. cordata. The research is aimed to understand characteristics of the planting soils and improve the quality of cultivated H. cordata. The soils at different sample sites varied greatly in nutrients, enzyme activity, pH, microbic PLFAs and polyphenols and all flavonoids. The content of total PLFAs in sample sites was following: bacteria > fungi > actinomyces > nematode. The content of bacteria PLFAs was 37.5%-65.0% at different sample sites. Activities of polyphenol oxidease, concentrations of available P and content of PLFAs of bacteria, actinomyces and total microorganisms in soils were significantly and positively related to the concentrations of polyphenols and total flavonoids of H. cordata, respectively (P soils was significantly and negatively related to concentrations of polyphenols and total flavonoids of H. cordata, respectively (P soil nutrient, which may be improved due to transformation of soil microorganisms and enzymes to N and P in the soils, was beneficial to adaptation of H. cordata adapted to different soil conditions, and significantly affects metabolic accumulation of polyphenols and flavonoids of H. cordata.

Effect of water treatment residuals on soil phosphorus, copper and aluminium availability and toxicity

Energy Technology Data Exchange (ETDEWEB)

Lombi, E., E-mail: enzo.lombi@unisa.edu.a [CSIRO Land and Water, Centre for Environmental Contaminant Research, PMB 2, Glen Osmond, SA 5064 (Australia); Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes Campus, Mawson Lakes, SA 5095 (Australia); CRC CARE, PO Box 486, Salisbury, SA 5106 (Australia); Stevens, D.P. [CSIRO Land and Water, Centre for Environmental Contaminant Research, PMB 2, Glen Osmond, SA 5064 (Australia); Arris Pty Ltd, PO Box 5143, Burnley, Victoria 3121 (Australia); McLaughlin, M.J. [CSIRO Land and Water, Centre for Environmental Contaminant Research, PMB 2, Glen Osmond, SA 5064 (Australia); Soil and Land Systems, University of Adelaide, PMB 1, Glen Osmond, SA 5064 (Australia)

2010-06-15

Water treatment residuals (WTRs) are produced by the treatment of potable water with coagulating agents. Beneficial recycling in agriculture is hampered by the fact that WTRs contain potentially toxic contaminants (e.g. copper and aluminium) and they bind phosphorus strongly. These issues were investigated using a plant bioassay (Lactuca sativa), chemical extractions and an isotopic dilution technique. Two WTRs were applied to an acidic and a neutral pH soil at six rates. Reductions in plant growth in amended soils were due to WTR-induced P deficiency, rather than Al or Cu toxicity. The release of potentially toxic Al from WTRs was found to be mitigated by their alkaline nature and pH buffering capacity. However, acidification of WTRs was shown to release more soluble Al than soil naturally high in Al. Copper availability was relatively low in all treatments. However, the lability of WTR-Cu increased when the WTR was applied to the soil. - The effect of water treatment residue application to soil was investigated in relation to phosphorus availability, and copper and aluminium phytotoxicity.

Effect of water treatment residuals on soil phosphorus, copper and aluminium availability and toxicity

International Nuclear Information System (INIS)

Lombi, E.; Stevens, D.P.; McLaughlin, M.J.

2010-01-01

Water treatment residuals (WTRs) are produced by the treatment of potable water with coagulating agents. Beneficial recycling in agriculture is hampered by the fact that WTRs contain potentially toxic contaminants (e.g. copper and aluminium) and they bind phosphorus strongly. These issues were investigated using a plant bioassay (Lactuca sativa), chemical extractions and an isotopic dilution technique. Two WTRs were applied to an acidic and a neutral pH soil at six rates. Reductions in plant growth in amended soils were due to WTR-induced P deficiency, rather than Al or Cu toxicity. The release of potentially toxic Al from WTRs was found to be mitigated by their alkaline nature and pH buffering capacity. However, acidification of WTRs was shown to release more soluble Al than soil naturally high in Al. Copper availability was relatively low in all treatments. However, the lability of WTR-Cu increased when the WTR was applied to the soil. - The effect of water treatment residue application to soil was investigated in relation to phosphorus availability, and copper and aluminium phytotoxicity.

Trace element mobility in a contaminated soil two years after field-amendment with a greenwaste compost mulch

Energy Technology Data Exchange (ETDEWEB)

Clemente, Rafael, E-mail: rclemente@cebas.csic.e [Faculty of Sciences, Liverpool John Moores University, Liverpool L3 3AF (United Kingdom); Hartley, William [Faculty of Sciences, Liverpool John Moores University, Liverpool L3 3AF (United Kingdom); Riby, Philip [School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF (United Kingdom); Dickinson, Nicholas M.; Lepp, Nicholas W. [Faculty of Sciences, Liverpool John Moores University, Liverpool L3 3AF (United Kingdom)

2010-05-15

Application of greenwaste compost to brownfield land is increasingly common in soil and landscape restoration. Previous studies have demonstrated both beneficial and detrimental effects of this material on trace element mobility. A pot experiment with homogenised soil/compost investigated distribution and mobility of trace elements, two years after application of greenwaste compost mulch to shallow soils overlying a former alkali-works contaminated with Pb, Cu and As (approx900, 200 and 500 mg kg{sup -1}, respectively). Compost mulch increased organic carbon and Fe in soil pore water, which in turn increased As and Sb mobilization; this enhanced uptake by lettuce and sunflower. A very small proportion of the total soil trace element pool was in readily-exchangeable form (<0.01% As, <0.001% other trace elements), but the effect of compost on behaviour of metals was variable and ambiguous. It is concluded that greenwaste compost should be applied with caution to multi-element contaminated soils. - Arsenic solubility and bioavailability increases in soil two years after application of greenwaste compost mulch.

Trace element mobility in a contaminated soil two years after field-amendment with a greenwaste compost mulch

International Nuclear Information System (INIS)

Clemente, Rafael; Hartley, William; Riby, Philip; Dickinson, Nicholas M.; Lepp, Nicholas W.

2010-01-01

Application of greenwaste compost to brownfield land is increasingly common in soil and landscape restoration. Previous studies have demonstrated both beneficial and detrimental effects of this material on trace element mobility. A pot experiment with homogenised soil/compost investigated distribution and mobility of trace elements, two years after application of greenwaste compost mulch to shallow soils overlying a former alkali-works contaminated with Pb, Cu and As (∼900, 200 and 500 mg kg -1 , respectively). Compost mulch increased organic carbon and Fe in soil pore water, which in turn increased As and Sb mobilization; this enhanced uptake by lettuce and sunflower. A very small proportion of the total soil trace element pool was in readily-exchangeable form (<0.01% As, <0.001% other trace elements), but the effect of compost on behaviour of metals was variable and ambiguous. It is concluded that greenwaste compost should be applied with caution to multi-element contaminated soils. - Arsenic solubility and bioavailability increases in soil two years after application of greenwaste compost mulch.

Exploiting the Adaptation Dynamics to Predict the Distribution of Beneficial Fitness Effects.

Directory of Open Access Journals (Sweden)

Sona John

Full Text Available Adaptation of asexual populations is driven by beneficial mutations and therefore the dynamics of this process, besides other factors, depends on the distribution of beneficial fitness effects. It is known that on uncorrelated fitness landscapes, this distribution can only be of three types: truncated, exponential and power law. We performed extensive stochastic simulations to study the adaptation dynamics on rugged fitness landscapes, and identified two quantities that can be used to distinguish the underlying distribution of beneficial fitness effects. The first quantity studied here is the fitness difference between successive mutations that spread in the population, which is found to decrease in the case of truncated distributions, remains nearly a constant for exponentially decaying distributions and increases when the fitness distribution decays as a power law. The second quantity of interest, namely, the rate of change of fitness with time also shows quantitatively different behaviour for different beneficial fitness distributions. The patterns displayed by the two aforementioned quantities are found to hold good for both low and high mutation rates. We discuss how these patterns can be exploited to determine the distribution of beneficial fitness effects in microbial experiments.

Optimization of liquid media and biosafety assessment for algae-lysing bacterium NP23.

Science.gov (United States)

Liao, Chunli; Liu, Xiaobo; Shan, Linna

2014-09-01

To control algal bloom caused by nutrient pollution, a wild-type algae-lysing bacterium was isolated from the Baiguishan reservoir in Henan province of China and identified as Enterobacter sp. strain NP23. Algal culture medium was optimized by applying a Placket-Burman design to obtain a high cell concentration of NP23. Three minerals (i.e., 0.6% KNO3, 0.001% MnSO4·H2O, and 0.3% K2HPO4) were found to be independent factors critical for obtaining the highest cell concentration of 10(13) CFU/mL, which was 10(4) times that of the control. In the algae-lysing experiment, the strain exhibited a high lysis rate for the 4 algae test species, namely, Chlorella vulgari, Scenedesmus, Microcystis wesenbergii, and Chlorella pyrenoidosa. Acute toxicity and mutagenicity tests showed that the bacterium NP23 had no toxic and mutagenic effects on fish, even in large doses such as 10(7) or 10(9) CFU/mL. Thus, Enterobacter sp. strain NP23 has strong potential application in the microbial algae-lysing project.

Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass.

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Boutard, Magali; Cerisy, Tristan; Nogue, Pierre-Yves; Alberti, Adriana; Weissenbach, Jean; Salanoubat, Marcel; Tolonen, Andrew C

2014-11-01

Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), and anaerobic growth screening. We apply this method to study how the bacterium Clostridium phytofermentans ferments plant biomass components including glucans, mannans, xylans, galactans, pectins, and arabinans. These polysaccharides are fermented with variable efficiencies, and diauxies prioritize metabolism of preferred substrates. Strand-specific RNA-seq reveals how this bacterium responds to polysaccharides by up-regulating specific groups of CAZymes, transporters, and enzymes to metabolize the constituent sugars. Fifty-six up-regulated CAZymes were purified, and their activities show most polysaccharides are degraded by multiple enzymes, often from the same family, but with divergent rates, specificities, and cellular localizations. CAZymes were then tested in combination to identify synergies between enzymes acting on the same substrate with different catalytic mechanisms. We discuss how these results advance our understanding of how microbes degrade and metabolize plant biomass.

Dynamic succession of soil bacterial community during continuous cropping of peanut (Arachis hypogaea L..

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Mingna Chen

Full Text Available Plant health and soil fertility are affected by plant-microbial interactions in soils. Peanut is an important oil crop worldwide and shows considerable adaptability, but growth and yield are negatively affected by continuous cropping. In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation. Six libraries were constructed for peanut over three continuous cropping cycles and during its seedling and pod-maturing growth stages. Cluster analyses indicated that soil bacterial assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. The diversity of bacterial sequences identified in each growth stage library of the three peanut cropping cycles was high and these sequences were affiliated with 21 bacterial groups. Eight phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia were dominant. The related bacterial phylotypes dynamic changed during continuous cropping progress of peanut. This study demonstrated that the bacterial populations especially the beneficial populations were positively selected. The simplification of the beneficial microbial communities such as the phylotypes of Alteromonadales, Burkholderiales, Flavobacteriales, Pseudomonadales, Rhizobiales and Rhodospirillales could be important factors contributing to the decline in peanut yield under continuous cropping. The microbial phylotypes that did not successively changed with continuous cropping, such as populations related to Rhizobiales and Rhodospirillales, could potentially resist stress due to continuous cropping and deserve attention. In addition, some phylotypes, such as Acidobacteriales, Chromatiales and Gemmatimonadales, showed a contrary tendency, their abundance or diversity increased with continuous peanut cropping progress. Some bacterial phylotypes including

Economic Game Theory to Model the Attenuation of Virulence of an Obligate Intracellular Bacterium.

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Tago, Damian; Meyer, Damien F

2016-01-01

Diseases induced by obligate intracellular pathogens have a large burden on global human and animal health. Understanding the factors involved in the virulence and fitness of these pathogens contributes to the development of control strategies against these diseases. Based on biological observations, a theoretical model using game theory is proposed to explain how obligate intracellular bacteria interact with their host. The equilibrium in such a game shows that the virulence and fitness of the bacterium is host-triggered and by changing the host's defense system to which the bacterium is confronted, an evolutionary process leads to an attenuated strain. Although, the attenuation procedure has already been conducted in practice in order to develop an attenuated vaccine (e.g., with Ehrlichia ruminantium), there was a lack of understanding of the theoretical basis behind this process. Our work provides a model to better comprehend the existence of different phenotypes and some underlying evolutionary mechanisms for the virulence of obligate intracellular bacteria.

Beneficial use of off-specification fly ashes to increase the shear strength and stiffness of expansive soil-rubber (ESR) mixtures.

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2011-07-01

The use of off-specification fly ashes to increase the shear strength and stiffness of an expansive soil-rubber (ESR) mixture is investigated systematically in this study. The off-specification fly ashes used include a high-sulfur content and a high-...

The impact of a pathogenic bacterium on a social carnivore population.

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Höner, Oliver P; Wachter, Bettina; Goller, Katja V; Hofer, Heribert; Runyoro, Victor; Thierer, Dagmar; Fyumagwa, Robert D; Müller, Thomas; East, Marion L

2012-01-01

1. The long-term ecological impact of pathogens on group-living, large mammal populations is largely unknown. We evaluated the impact of a pathogenic bacterium, Streptococcus equi ruminatorum, and other key ecological factors on the dynamics of the spotted hyena Crocuta crocuta population in the Ngorongoro Crater, Tanzania. 2. We compared key demographic parameters during two years when external signs of bacterial infection were prevalent ('outbreak') and periods of five years before and after the outbreak when such signs were absent or rare. We also tested for density dependence and calculated the basic reproductive rate R(0) of the bacterium. 3. During the five pre-outbreak years, the mean annual hyena mortality rate was 0.088, and annual population growth was relatively high (13.6%). During the outbreak, mortality increased by 78% to a rate of 0.156, resulting in an annual population decline of 4.3%. After the outbreak, population size increased moderately (5.1%) during the first three post-outbreak years before resuming a growth similar to pre-outbreak levels (13.9%). We found no evidence that these demographic changes were driven by density dependence or other ecological factors. 4. Most hyenas showed signs of infection when prey abundance in their territory was low. During the outbreak, mortality increased among adult males and yearlings, but not among adult females - the socially dominant group members. These results suggest that infection and mortality were modulated by factors linked to low social status and poor nutrition. During the outbreak, we estimated R(0) for the bacterium to be 2.7, indicating relatively fast transmission. 5. Our results suggest that the short-term 'top-down' impact of S. equi ruminatorum during the outbreak was driven by 'bottom-up' effects on nutritionally disadvantaged age-sex classes, whereas the longer-term post-outbreak reduction in population growth was caused by poor survival of juveniles during the outbreak and subsequent

Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants

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Khan, Abdur Rahim; Park, Gun-Seok; Asaf, Sajjad; Hong, Sung-Jun; Jung, Byung Kwon

2017-01-01

Serratia marcescens RSC-14 is a Gram-negative bacterium that was previously isolated from the surface-sterilized roots of the Cd-hyperaccumulator Solanum nigrum. The strain stimulates plant growth and alleviates Cd stress in host plants. To investigate the genetic basis for these traits, the complete genome of RSC-14 was obtained by single-molecule real-time sequencing. The genome of S. marcescens RSC-14 comprised a 5.12-Mbp-long circular chromosome containing 4,593 predicted protein-coding genes, 22 rRNA genes, 88 tRNA genes, and 41 pseudogenes. It contained genes with potential functions in plant growth promotion, including genes involved in indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis, and phosphate solubilization. Moreover, annotation using NCBI and Rapid Annotation using Subsystem Technology identified several genes that encode antioxidant enzymes as well as genes involved in antioxidant production, supporting the observed resistance towards heavy metals, such as Cd. The presence of IAA pathway-related genes and oxidative stress-responsive enzyme genes may explain the plant growth-promoting potential and Cd tolerance, respectively. This is the first report of a complete genome sequence of Cd-tolerant S. marcescens and its plant growth promotion pathway. The whole-genome analysis of this strain clarified the genetic basis underlying its phenotypic and biochemical characteristics, underpinning the beneficial interactions between RSC-14 and plants. PMID:28187139

Diversity of biosurfactant producing microorganisms isolated from soils contaminated with diesel oil.

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Menezes Bento, Fátima; de Oliveira Camargo, Flavio A; Okeke, Benedict C; Frankenberger, William T

2005-01-01

Biosurfactant production is a desirable property of hydrocarbon-degrading microorganisms (HDM). We characterized biosurfactant producing microbial populations from a Long Beach soil, California (USA) and a Hong Kong soil (China), contaminated with diesel oil. A total of 33 hydrocarbon-utilizing microorganisms were isolated from the soils. Twelve isolates and three defined consortia were tested for biosurfactant production and emulsification activity. The highest reduction of surface tension was achieved with a consortium of L1, L2 and L3 isolates from a Long Beach soil (41.4mN m(-1)). Isolate L1 (Acinetobacter junii) displayed the highest reduction of surface tension (46.5 mN m(-1)). The emulsifying capacity evaluated by the E24 emulsification index was highest in the culture of isolate L5 (74%). No substantial emulsification was achieved with the cell-free extracts, indicating that the emulsifying activity was not extracellular. Based on surface tension and the E24 index results, isolates F1, F2, F3, F4, L1, L2, L3 and L4 were identified by 16S rRNA gene sequencing as Bacillus cereus, Bacillus sphaericus, B. fusiformis, Acinetobacter junii, a non-cultured bacterium, Pseudomonas sp. and B. pumilus, respectively. Cluster analyses of 16S rRNA gene sequences of the bacterial isolates revealed 70% similarity amongst hydrocarbon-degrading bacterial community present in both soils. Five isolates (isolates F1, F2, F3, F4 and L4) belong to the Firmicutes order, two isolates (L1 and L3) belong to the Proteobacteria order and one isolate (L2) is an Actinomyces sp. Simpson's index (1 - D) and the Shannon-Weaver index (H) revealed more diversity of HDM in the Hong Kong soil, while evenness (E) and the equitability (J) data indicated that there was not a dominant population. Bacterial isolates displaying substantial potential for production of biosurfactants can be applied in the bioremediation of soils contaminated with petroleum hydrocarbons.