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Soil microbes

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https://www.readbyqxmd.com/read/28629972/characterization-of-dioxygenases-and-biosurfactants-produced-by-crude-oil-degrading-soil-bacteria
#1
Santhakumar Muthukamalam, Sivalingam Sivagangavathi, Dharmapal Dhrishya, Sadras Sudha Rani
Role of microbes in bioremediation of oil spills has become inevitable owing to their eco friendly nature. This study focused on the isolation and characterization of bacterial strains with superior oil degrading potential from crude-oil contaminated soil. Three such bacterial strains were selected and subsequently identified by 16S rRNA gene sequence analysis as Corynebacterium aurimucosum, Acinetobacter baumannii and Microbacterium hydrocarbonoxydans respectively. The specific activity of catechol 1,2 dioxygenase (C12O) and catechol 2,3 dioxygenase (C23O) was determined in these three strains wherein the activity of C12O was more than that of C23O...
June 3, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/28616451/dataset-on-potential-large-scale-production-of-biosurfactant-using-bacillus-sp
#2
Hesty Heryani, Meilana Dharma Putra
Surfactants are very important in industry. The cost of commercial surfactant production is still high and the surfactant demand is constantly increasing. Microbial production of surfactant known as biosurfactant shows commercial potency. Utilization of Bacillus sp. strain on glucose fermentation for biosurfactant production was then studied. This type of microbe was isolated from soil contaminated with palm oil. The selection of the strain was based on its ability to form emulsifying zone around the colony and its capability to grow compared with those for commercial bacteria of Bacillus pumilus JCM 2508...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28614351/newtonian-boreal-forest-ecology-the-scots-pine-ecosystem-as-an-example
#3
Pertti Hari, Tuomas Aakala, Juho Aalto, Jaana Bäck, Jaakko Hollmén, Kalev Jõgiste, Kourosh Kabiri Koupaei, Mika A Kähkönen, Mikko Korpela, Liisa Kulmala, Eero Nikinmaa, Jukka Pumpanen, Mirja Salkinoja-Salonen, Pauliina Schiestl-Aalto, Asko Simojoki, Mikko Havimo
Isaac Newton's approach to developing theories in his book Principia Mathematica proceeds in four steps. First, he defines various concepts, second, he formulates axioms utilising the concepts, third, he mathematically analyses the behaviour of the system defined by the concepts and axioms obtaining predictions and fourth, he tests the predictions with measurements. In this study, we formulated our theory of boreal forest ecosystems, called NewtonForest, following the four steps introduced by Newton. The forest ecosystem is a complicated entity and hence we needed altogether 27 concepts to describe the material and energy flows in the metabolism of trees, ground vegetation and microbes in the soil, and to describe the regularities in tree structure...
2017: PloS One
https://www.readbyqxmd.com/read/28606355/analysis-of-multiple-components-involved-in-the-interaction-between-cryptococcus-neoformans-and-acanthamoeba-castellanii
#4
Juliana Rizzo, Priscila C Albuquerque, Julie M Wolf, Renata Nascimento, Marcos D Pereira, Joshua D Nosanchuk, Marcio L Rodrigues
Cryptococcus neoformans is an environmental fungus that can cause lethal meningoencephalitis in immunocompromised individuals. The mechanisms by which environmental microbes become pathogenic to mammals are still obscure, but different studies suggest that fungal virulence evolved from selection imposed by environmental predators. The soil-living Acanthamoeba castellanii is a well-known predator of C. neoformans. In this work, we evaluated the participation of C. neoformans virulence-associated structures in the interaction of fungal cells with A...
June 2017: Fungal Biology
https://www.readbyqxmd.com/read/28605646/imidacloprid-application-changes-microbial-dynamics-and-enzymes-in-rice-soil
#5
Bibhab Mahapatra, Totan Adak, Naveen K B Patil, Guru P Pandi G, G Basana Gowda, N N Jambhulkar, Manoj Kumar Yadav, P Panneerselvam, Upendra Kumar, Sushmita Munda, Mayabini Jena
Extensive use of imidacloprid in rice ecosystem may alter dynamics of microorganisms and can change soil biochemical properties. The objective of this study was to assess the effect of imidacloprid on growth and activities of microbes in tropical rice soil ecosystem. Four treatments, namely, recommended dose (at 25g a.i. ha(-1), RD), double the recommended dose (at 50g a.i. ha(-1), 2RD), five times the recommended dose (at 125g a.i. ha(-1), 5RD) & ten times the recommended dose (at 250g a.i. ha(-1), 10RD) along with control were imposed under controlled condition...
June 9, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28601419/how-plant-root-exudates-shape-the-nitrogen-cycle
#6
REVIEW
Devrim Coskun, Dev T Britto, Weiming Shi, Herbert J Kronzucker
Although the global nitrogen (N) cycle is largely driven by soil microbes, plant root exudates can profoundly modify soil microbial communities and influence their N transformations. A detailed understanding is now beginning to emerge regarding the control that root exudates exert over two major soil N processes - nitrification and N2 fixation. We discuss recent breakthroughs in this area, including the identification of root exudates as nitrification inhibitors and as signaling compounds facilitating N-acquisition symbioses...
June 7, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28598721/iron-and-immunity
#7
Eline H Verbon, Pauline L Trapet, Ioannis A Stringlis, Sophie Kruijs, Peter A H M Bakker, Corné M J Pieterse
Iron is an essential nutrient for most life on Earth because it functions as a crucial redox catalyst in many cellular processes. However, when present in excess iron can lead to the formation of harmful hydroxyl radicals. Hence, the cellular iron balance must be tightly controlled. Perturbation of iron homeostasis is a major strategy in host-pathogen interactions. Plants use iron-withholding strategies to reduce pathogen virulence or to locally increase iron levels to activate a toxic oxidative burst. Some plant pathogens counteract such defenses by secreting iron-scavenging siderophores that promote iron uptake and alleviate iron-regulated host immune responses...
June 9, 2017: Annual Review of Phytopathology
https://www.readbyqxmd.com/read/28597417/elevation-gradient-of-soil-bacterial-communities-in-bamboo-plantations
#8
Yu-Te Lin, Chih-Yu Chiu
BACKGROUND: Elevation trends of macro organisms have long been well studied. However, whether microbes also exhibit such patterns of elevation change is unknown. Here, we investigated the changes in bamboo forest soil bacterial communities along six elevation gradients, from 600 to 1800 m a.s.l. in Mt. Da-an, a subtropical montane area in Nantou county at central Taiwan. RESULTS: Data from 16S rRNA gene clone libraries revealed that more than 70 % of the six communities contained Acidobacteria and Proteobacteria, although the relative abundance differed...
December 2016: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28585939/linking-rhizosphere-microbiome-composition-of-wild-and-domesticated-phaseolus-vulgaris-to-genotypic-and-root-phenotypic-traits
#9
Juan E Pérez-Jaramillo, Víctor J Carrión, Mirte Bosse, Luiz F V Ferrão, Mattias de Hollander, Antonio A F Garcia, Camilo A Ramírez, Rodrigo Mendes, Jos M Raaijmakers
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585935/shifts-in-rhizosphere-fungal-community-during-secondary-succession-following-abandonment-from-agriculture
#10
S Emilia Hannula, Elly Morriën, Mattias de Hollander, Wim H van der Putten, Johannes A van Veen, Wietse de Boer
Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585781/interspecies-cross-talk-between-co-cultured-pseudomonas-putida-and-escherichia-coli
#11
Carlos Molina-Santiago, Zulema Udaondo, Baldo F Cordero, Juan L Ramos
Pseudomonas putida and Escherichia coli are ubiquitous microorganisms that can be isolated from soil rhizosphere, the surface of vegetables, fresh waters and wastewaters-environments in which they likely co-exist. Despite this, the potential interactions between these microbes have not been studied in detail. To analyze these interactions, we carried out RNA-seq transcriptomic analysis of these microbes as monocultures and as co-cultures. Our results show that co-culture of these microbes significantly alters transcriptional profiles...
June 6, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28585372/widespread-production-of-nonmicrobial-greenhouse-gases-in-soils
#12
Bin Wang, Manuel Lerdau, Yongli He
Carbon dioxide (CO2 ), methane (CH4 ), and nitrous oxide (N2 O) are the three most important greenhouse gases (GHGs), and all show large uncertainties in their atmospheric budgets. Soils of natural and managed ecosystems play an extremely important role in modulating their atmospheric abundance. Mechanisms underlying the exchange of these GHGs at the soil-atmosphere interface are often assumed to be exclusively microbe-mediated (M-GHGs). We argue that it is a widespread phenomenon for soil systems to produce GHGs through nonmicrobial pathways (NM-GHGs) based on a review of the available evidence accumulated over the past half century...
June 6, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28584447/analysis-of-eawag-bbd-pathway-prediction-system-for-the-identification-of-malathion-degrading-microbes
#13
Subramaniam Sivakumar, Palanivel Anitha, Balsubramanian Ramesh, Gopal Suresh
Insecticides are the toxic substances that are used to kill insects. The use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the 20th century. The organophosphates are now the largest and most versatile class of insecticide used and Malathion is the predominant type utilized. The accumulation of Malathion in environment is the biggest threat to the environment because of its toxicity. Malathion is lethal to beneficial insects, snails, micro crustaceans, fish, birds, amphibians, and soil microorganisms...
2017: Bioinformation
https://www.readbyqxmd.com/read/28578806/bio-mining-the-forest-ecosystem-of-north-east-india-for-identification-of-antimicrobial-metabolites-from-fungi-through-submerged-fermentation
#14
Sarangthem Indira Devi, H Lotjem, Elangbam Julia Devi, Momota Potshangbam, Ng Ngashangva, Jagat Bora, Dinabandhu Sahoo, Chandradev Sharma
In this study, fungi isolated from less explored forest soil ecosystem of Northeast India were studied for the production of potential antimicrobial metabolites (AMM). Out of the 68 fungi isolated from forest soil of Manipur, 7 of them showed AMA against the test pathogens. Among them, Aspergillus terreus (IBSD-F4) showed the most significant activity against Staphylococcus aureus (ATCC-25923), Bacillus anthracis (IBSD-C370), Pseudomonas fluorescens (ATCC-13525), Salmonella typhimurium (ATCC-14028), Escherichia coli (ATCC-25922) and Candida albicans (ATCC-10231)...
May 21, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28577402/comparative-effects-of-sulfuric-and-nitric-acid-rain-on-litter-decomposition-and-soil-microbial-community-in-subtropical-plantation-of-yangtze-river-delta-region
#15
Xin Liu, Bo Zhang, Wenrui Zhao, Ling Wang, Dejin Xie, Wentong Huo, Yanwen Wu, Jinchi Zhang
Acid rain is mainly caused by dissolution of sulfur dioxide and nitrogen oxides in the atmosphere, and has a significant negative effect on ecosystems. The relative composition of acid rain is changing gradually from sulfuric acid rain (SAR) to nitric acid rain (NAR) with the rapidly growing amount of nitrogen deposition. In this study, we investigated the impact of simulated SAR and NAR on litter decomposition and the soil microbial community over four seasons since March 2015. Results first showed that the effects of acid rain on litter decomposition and soil microbial were positive in the early period of the experiment, except for SAR on soil microbes...
May 31, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28571847/impact-of-microbial-communities-from-tropical-soils-on-the-mobilization-of-trace-metals-during-dissolution-of-cinnabar-ore
#16
Clarisse Balland-Bolou-Bi, Benjamin Turc, Vanessa Alphonse, Noureddine Bousserrhine
Biodissolution experiments on cinnabar ore (mercury sulphide and other sulphide minerals, such as pyrite) were performed with microorganisms extracted directly from soil. These experiments were carried out in closed systems under aerobic and anaerobic conditions with 2 different soils sampled in French Guyana. The two main objectives of this study were (1) to quantify the ability of microorganisms to mobilize metals (Fe, Al, Hg) during the dissolution of cinnabar ore, and (2) to identify the links between the type and chemical properties of soils, environmental parameters such as season and the strategies developed by indigenous microorganisms extracted from tropical natural soils to mobilize metals...
June 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/28567447/comparative-genomic-analysis-reveals-habitat-specific-genes-and-regulatory-hubs-within-the-genus-novosphingobium
#17
Roshan Kumar, Helianthous Verma, Shazia Haider, Abhay Bajaj, Utkarsh Sood, Kalaiarasan Ponnusamy, Shekhar Nagar, Mallikarjun N Shakarad, Ram Krishan Negi, Yogendra Singh, J P Khurana, Jack A Gilbert, Rup Lal
Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats...
May 2017: MSystems
https://www.readbyqxmd.com/read/28556511/host-specific-effects-of-soil-microbial-filtrates-prevail-over-those-of-arbuscular-mycorrhizae-in-a-fragmented-landscape
#18
Camila Pizano, Scott A Mangan, James H Graham, Kaoru Kitajima
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 9 native species)...
May 28, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28555427/optimization-of-high-yielding-protocol-for-dna-extraction-from-the-forest-rhizosphere-microbes
#19
Sadam D V Satyanarayana, M S R Krishna, Pindi Pavan Kumar
Soil is major reservoir for microbes and harbors a vast microbial diversity. Soil microbiota plays a pivotal role in biogeochemical cycles, bioremediation, and in health and disease states of humans, animals, and plants. It is imperative to understand the microbial signatures which are specific in such an ecosystem to unravel their potential role and impact on environment. During the recent years, exploration of soil microbial communities has been geared up with the advent of advanced sequencing technologies...
June 2017: 3 Biotech
https://www.readbyqxmd.com/read/28555132/stimulation-of-fengycin-type-antifungal-lipopeptides-in-bacillus-amyloliquefaciens-in-the-presence-of-the-maize-fungal-pathogen-rhizomucor-variabilis
#20
Parent Zihalirwa Kulimushi, Anthony Argüelles Arias, Laurent Franzil, Sébastien Steels, Marc Ongena
Most isolates belonging to the Bacillus amyloliquefaciens subsp. plantarum clade retain the potential to produce a vast array of structurally diverse antimicrobial compounds that largely contribute to their efficacy as biocontrol agents against numerous plant fungal pathogens. In that context, the role of cyclic lipopeptides (CLPs) has been well-documented but still little is known about the impact of interactions with other soil-inhabiting microbes on the expression of these molecules. In this work, we wanted to investigate the antagonistic activity developed by this bacterium against Rhizomucor variabilis, a pathogen isolated from diseased maize cobs in Democratic Republic of Congo...
2017: Frontiers in Microbiology
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