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https://www.readbyqxmd.com/read/28075523/extreme-rainfall-and-snowfall-alter-responses-of-soil-respiration-to-nitrogen-fertilization-a-3-year-field-experiment
#1
Zengming Chen, Yehong Xu, Xuhui Zhou, Jianwu Tang, Yakov Kuzyakov, Hongyan Yu, Jianling Fan, Weixin Ding
Extreme precipitation is predicted to be more frequent and intense accompanying global warming, and may have profound impacts on soil respiration (Rs) and its components, i.e., autotrophic (Ra) and heterotrophic (Rh) respiration. However, how natural extreme rainfall or snowfall events affect these fluxes are still lacking, especially under nitrogen (N) fertilization. In this study, extreme rainfall and snowfall events occurred during a 3-year field experiment, allowing us to examine their effects on the response of Rs, Rh and Ra to N supply...
January 11, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28071697/diel-scale-temporal-dynamics-recorded-for-bacterial-groups-in-namib-desert-soil
#2
Eoin Gunnigle, Aline Frossard, Jean-Baptiste Ramond, Leandro Guerrero, Mary Seely, Don A Cowan
Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28066816/from-genomes-to-phenotypes-traitar-the-microbial-trait-analyzer
#3
Aaron Weimann, Kyra Mooren, Jeremy Frank, Phillip B Pope, Andreas Bremges, Alice C McHardy
The number of sequenced genomes is growing exponentially, profoundly shifting the bottleneck from data generation to genome interpretation. Traits are often used to characterize and distinguish bacteria and are likely a driving factor in microbial community composition, yet little is known about the traits of most microbes. We describe Traitar, the microbial trait analyzer, which is a fully automated software package for deriving phenotypes from a genome sequence. Traitar provides phenotype classifiers to predict 67 traits related to the use of various substrates as carbon and energy sources, oxygen requirement, morphology, antibiotic susceptibility, proteolysis, and enzymatic activities...
November 2016: MSystems
https://www.readbyqxmd.com/read/28063185/soil-microbial-communities-are-shaped-by-vegetation-type-and-park-age-in-cities-under-cold-climate
#4
Nan Hui, Ari Jumpponen, Gaia Francini, D Johan Kotze, Xinxin Liu, Martin Romantschuk, Rauni Strömmer, Heikki Setälä
Soil microbes play a key role in controlling ecosystem functions and providing ecosystem services. Yet, microbial communities in urban green space soils remain poorly characterized. Here we compared soil microbial communities in 41 urban parks of (i) divergent plant functional types (evergreen trees, deciduous trees, lawn) and (ii) different ages (constructed 10, ∼50, and >100 years ago). These microbial communities were also compared to those in 5 control forests in southern Finland. Our results indicate that, despite frequent disturbances in urban parks, urban soil microbes still followed the classic patterns typical of plant-microbe associations in natural environments: both bacterial and fungal communities in urban parks responded to plant functional groups, but fungi were under tighter control of plants than bacteria...
January 7, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28054231/regulation-of-root-development-in-arabidopsis-thaliana-by-phytohormone-secreting-epiphytic-methylobacteria
#5
Jana Klikno, Ulrich Kutschera
In numerous experimental studies, seedlings of the model dicot Arabidopsis thaliana have been raised on sterile mineral salt agar. However, under natural conditions, no plant has ever grown in an environment without bacteria. Here, we document that germ-free (gnotobiotic) seedlings, raised on mineral salt agar without sucrose, develop very short root hairs. In the presence of a soil extract that contains naturally occurring microbes, root hair elongation is promoted; this effect can be mimicked by the addition of methylobacteria to germ-free seedlings...
January 4, 2017: Protoplasma
https://www.readbyqxmd.com/read/28042183/integrated-anaerobic-aerobic-biodegradation-of-multiple-contaminants-including-chlorinated-ethylenes-benzene-toluene-and-dichloromethane
#6
Miho Yoshikawa, Ming Zhang, Koki Toyota
Complete bioremediation of soils containing multiple volatile organic compounds (VOCs) remains a challenge. To explore the possibility of complete bioremediation through integrated anaerobic-aerobic biodegradation, laboratory feasibility tests followed by alternate anaerobic-aerobic and aerobic-anaerobic biodegradation tests were performed. Chlorinated ethylenes, including tetrachloroethylene (PCE), trichloroethylene (TCE), cis-dichloroethylene (cis-DCE), and vinyl chloride (VC), and dichloromethane (DCM) were used for anaerobic biodegradation, whereas benzene, toluene, and DCM were used for aerobic biodegradation tests...
2017: Water, Air, and Soil Pollution
https://www.readbyqxmd.com/read/28034543/using-soil-microbial-inoculations-to-enhance-substrate-performance-on-extensive-green-roofs
#7
Chloe J Molineux, Alan C Gange, Darryl J Newport
Green roofs are increasing in popularity in the urban environment for their contribution to green infrastructure; but their role for biodiversity is not often a design priority. Maximising biodiversity will impact positively on ecosystem services and is therefore fundamental for achieving the greatest benefits from green roofs. Extensive green roofs are lightweight systems generally constructed with a specialised growing medium that tends to be biologically limited and as such can be a harsh habitat for plants to thrive in...
December 26, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/28031806/intensified-plant-n-and-c-pool-with-more-available-nitrogen-under-experimental-warming-in-an-alpine-meadow-ecosystem
#8
Fei Peng, Xian Xue, Quangang You, Manhou Xu, Xiang Chen, Jian Guo, Tao Wang
Nitrogen (N) availability is projected to increase in a warming climate. But whether the more available N is immobilized by microbes (thus stimulates soil carbon (C) decomposition), or is absorbed by plants (thus intensifies C uptake) remains unknown in the alpine meadow ecosystem. Infrared heaters were used to simulate climate warming with a paired experimental design. Soil ammonification, nitrification, and net mineralization were obtained by in situ incubation in a permafrost region of the Qinghai-Tibet Plateau (QTP)...
December 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28028877/indole-associated-predator-prey-interactions-between-the-nematode-caenorhabditis-elegans-and-bacteria
#9
Jin-Hyung Lee, Yong-Guy Kim, Minsu Kim, Eonmi Kim, Hyukjae Choi, Younghoon Kim, Jintae Lee
Indole is an intercellular and interkingdom signaling molecule found in diverse ecological niches. Caenorhabditis elegans is a bacterivorous nematode that lives in soil and compost environments and a useful model host for studies of host-microbe interactions. Although various bacteria and some plants produce large quantities of extracellular indole, little is known about the effects of indole, its derivatives, or of indole-producing bacteria on the behaviors of C. elegans or other animals. Here, we show C. elegans senses and moves toward indole and several indole-producing bacteria, but avoids non-indole producing pathogenic bacteria...
December 28, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/28025789/nutrient-leaching-soil-ph-and-changes-in-microbial-community-increase-with-time-in-lead-contaminated-boreal-forest-soil-at-a-shooting-range-area
#10
Salla Selonen, Heikki Setälä
Despite the known toxicity of lead (Pb), Pb pellets are widely used at shotgun shooting ranges over the world. However, the impacts of Pb on soil nutrients and soil microbes, playing a crucial role in nutrient cycling, are poorly understood. Furthermore, it is unknown whether these impacts change with time after the cessation of shooting. To shed light on these issues, three study sites in the same coniferous forest in a shooting range area were studied: an uncontaminated control site and an active and an abandoned shooting range, both sharing a similar Pb pellet load in the soil, but the latter with a 20-year longer contamination history...
December 26, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28018306/the-plant-as-metaorganism-and-research-on-next-generation-systemic-pesticides-prospects-and-challenges
#11
Zisis Vryzas
Systemic pesticides (SPs) are usually recommended for soil treatments and as seed coating agents and are taken up from the soil by involving various plant-mediated processes, physiological, and morphological attributes of the root systems. Microscopic insights and next-generation sequencing combined with bioinformatics allow us now to identify new functions and interactions of plant-associated bacteria and perceive plants as meta-organisms. Host symbiotic, rhizo-epiphytic, endophytic microorganisms and their functions on plants have not been studied yet in accordance with uptake, tanslocation and action of pesticides...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28008835/-microbiotes-and-metabolic-diseases-the-bases-for-therapeutic-strategies
#12
Rémy Burcelin, Simon Nicolas, Vincent Blasco-Baque
After more than one and a half century, i.e. since Louis Pasteur work on microbes, fermentation, and diseases, biological science has made a giant step in bacteria knowledge. Thanks to an ultra-powerful "microscope", i.e. ultra-fast DNA sequencing, scientists have been able to read and group within a catalog over the last decade, the gene code of bacteria, i.e. the metagenome at the surface of our epithelia. More recently, live bacteria within adipose tissue, defining a tissue microbiota, as well as bacterial fragments such as DNA within the liver, the brain and the blood have been identified...
November 2016: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/28008686/a-new-theory-of-plant-microbe-nutrient-competition-resolves-inconsistencies-between-observations-and-model-predictions
#13
Qing Zhu, William J Riley, Jinyun Tang
Terrestrial plants assimilate anthropogenic CO2 through photosynthesis and synthesizing new tissues. However, sustaining these processes requires plants to compete with microbes for soil nutrients, which therefore calls for an appropriate understanding and modeling of nutrient competition mechanisms in Earth System Models (ESMs). Here, we survey existing plant-microbe competition theories and their implementations in Earth System Models (ESMs). We found no consensus regarding the representation of nutrient competition and that observational and theoretical support for current implementations are weak...
December 23, 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28007984/microbial-competition-in-porous-environments-can-select-against-rapid-biofilm-growth
#14
Katharine Z Coyte, Hervé Tabuteau, Eamonn A Gaffney, Kevin R Foster, William M Durham
Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors...
December 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27990026/assessment-of-bioavailable-organic-phosphorus-in-tropical-forest-soils-by-organic-acid-extraction-and-phosphatase-hydrolysis
#15
Tegan Darch, Martin S A Blackwell, David Chadwick, Philip M Haygarth, Jane M B Hawkins, Benjamin L Turner
Soil organic phosphorus contributes to the nutrition of tropical trees, but is not accounted for in standard soil phosphorus tests. Plants and microbes can release organic anions to solubilize organic phosphorus from soil surfaces, and synthesize phosphatases to release inorganic phosphate from the solubilized compounds. We developed a procedure to estimate bioavailable organic phosphorus in tropical forest soils by simulating the secretion processes of organic acids and phosphatases. Five lowland tropical forest soils with contrasting properties (pH 4...
December 15, 2016: Geoderma
https://www.readbyqxmd.com/read/27979623/soil-microbial-community-composition-and-its-role-in-carbon-mineralization-in-long-term-fertilization-paddy-soils
#16
Xiaoqin Dai, Huimin Wang, Xiaoli Fu
Microbial communities are critical in mediating soil biological processes, including C mineralization; yet, the mechanism of microbial mediation for soil C mineralization remains poorly understood under the long-term fertilization. To identify the relative roles of microbes in C mineralization in the soil of rice paddies, we investigated the long-term (11years) effects of repeated N, P, and K fertilization on crop yield, soil properties and microbial communities and their relationships with C mineralization...
December 12, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27976685/disentangling-the-influence-of-earthworms-in-sugarcane-rhizosphere
#17
Lucas P P Braga, Caio A Yoshiura, Clovis D Borges, Marcus A Horn, George G Brown, Harold L Drake, Siu M Tsai
For the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, we performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW-, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane...
December 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27973567/utility-of-a-lateral-flow-immunoassay-lfi-to-detect-burkholderia-pseudomallei-in-soil-samples
#18
Patpong Rongkard, Viriya Hantrakun, Sabine Dittrich, Prapaporn Srilohasin, Premjit Amornchai, Sayan Langla, Cherry Lim, Nicholas P J Day, David AuCoin, Vanaporn Wuthiekanun, Direk Limmathurotsakul
BACKGROUND: Culture is the gold standard for the detection of environmental B. pseudomallei. In general, soil specimens are cultured in enrichment broth for 2 days, and then the culture broth is streaked on an agar plate and incubated further for 7 days. However, identifying B. pseudomallei on the agar plates among other soil microbes requires expertise and experience. Here, we evaluate a lateral flow immunoassay (LFI) developed to detect B. pseudomallei capsular polysaccharide (CPS) in clinical samples as a tool to detect B...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27965639/antibacterial-compounds-macrolactin-alters-the-soil-bacterial-community-and-abundance-of-the-gene-encoding-pks
#19
Jun Yuan, Mengli Zhao, Rong Li, Qiwei Huang, Christopher Rensing, Waseem Raza, Qirong Shen
Macrolactin produced by many soil microbes has been shown to be an efficient antibacterial agent against many bacterial pathogens. However, studies examining the effect of macrolactin on both the soil bacterial community and the intrinsic bacterial species that harbor genes responsible for the production of this antibiotic have not been conducted so far. In this study, a mixture of macrolactin was isolated from the liquid culture of Bacillus amyloliquefaciens NJN-6, and applied to the soil once a week for four weeks...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27965632/primer-sets-developed-for-functional-genes-reveal-shifts-in-functionality-of-fungal-community-in-soils
#20
S Emilia Hannula, Johannes A van Veen
Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional...
2016: Frontiers in Microbiology
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