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https://www.readbyqxmd.com/read/28444594/bio-transformation-and-stabilization-of-arsenic-as-in-contaminated-soil-using-arsenic-oxidizing-bacteria-and-fecl3-amendment
#1
Santosh Kumar Karn, Xiangliang Pan, Ian R Jenkinson
A combination of biological and chemical methods was applied in the present study to evaluate the removal of arsenic (As) from contaminated soil. The treatment involved As-oxidizing microbes aimed of transforming the more toxic As (III) to less toxic As (V) in the soil. FeCl3 was added at three different concentrations (1, 2, and 3%) to stabilize the As (V). Leaching of the treated soil was investigated by making a soil column and passing tap water through it to determine solubility. Experimental results indicated that the bacterial activity had a pronounced positive effect on the transformation of As, and decreased the soluble exchangeable fraction from 50 to 0...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28442658/predominant-but-previously-overlooked-prokaryotic-drivers-of-reductive-nitrogen-transformation-in-paddy-soils-revealed-by-metatranscriptomics
#2
Yoko Masuda, Hideomi Itoh, Yutaka Shiratori, Kazuo Isobe, Shigeto Otsuka, Keishi Senoo
Waterlogged paddy soils possess anoxic zones in which microbes actively induce reductive nitrogen transformation (RNT). In the present study, a shotgun RNA sequencing analysis (metatranscriptomics) of paddy soil samples revealed that most RNT gene transcripts in paddy soils were derived from Deltaproteobacteria, particularly the genera Anaeromyxobacter and Geobacter. Despite the frequent detection of the rRNA of these microbes in paddy soils, their RNT-associated genes have rarely been identified in previous PCR-based studies...
April 22, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28441597/differences-in-nitrate-and-phosphorus-export-between-wooded-and-grassed-riparian-zones-from-farmland-to-receiving-waterways-under-varying-rainfall-conditions
#3
Amanda D Neilen, Chengrong R Chen, Brett M Parker, Stephen J Faggotter, Michele A Burford
Agricultural activities in catchments can cause excessive nutrient loads in waterways. Catchment nitrogen (N) and phosphorus (P) flows may be intercepted and assimilated by riparian vegetation. While prior studies suggest that woody vegetation is preferable for reducing P loads, the question remains: is woody vegetation or grass cover more effective at reducing catchment N and P exports to waterways. To address this we investigated the relative importance of vegetation type, hydrologic and soil microbial processes on N and P losses from soil to a stream...
April 22, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28439854/user-guide-for-the-lore1-insertion-mutant-resource
#4
Terry Mun, Anna Małolepszy, Niels Sandal, Jens Stougaard, Stig U Andersen
Lotus japonicus is a model legume used in the study of plant-microbe interactions, especially in the field of biological nitrogen fixation due to its ability to enter into a symbiotic relationship with a soil bacterium, Mesorhizobium loti. The LORE1 mutant population is a valuable resource for reverse genetics in L. japonicus due to its non-transgenic nature, high tagging efficiency, and low copy count. Here, we outline a workflow for identifying, ordering, and establishing homozygous LORE1 mutant lines for a gene of interest, LjFls2, including protocols for growth and genotyping of a segregating LORE1 population...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28437663/microbial-communities-associated-with-plants-learning-from-nature-to-apply-it-in-agriculture
#5
REVIEW
Fernando Dini Andreote, Michele de Cássia Pereira E Silva
It is a new consensus that any living organism depends on its partners to strive under environmental conditions along their living period. Plants are also highly dependent on their associated microbes, which can support its development and proper protection under stressors. Along their evolution, plants learned to interact to soil microbiota, extracting their utmost capacity to provide resources for plant development and successful colonization of terrestrial systems, where the great soil biodiversity is keen on properly exert this role...
April 21, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28437662/life-in-earth-the-root-microbiome-to-the-rescue
#6
REVIEW
Tim H Mauchline, Jacob G Malone
Manipulation of the soil microbiome holds great promise for contributing to more environmentally benign agriculture, with soil microbes such as Pseudomonas promoting plant growth and effectively suppressing pathogenic microorganisms. Next-generation sequencing has enabled a new generation of research into soil microbiomes, presenting the opportunity to better understand and exploit these valuable resources. Soil bacterial communities are both highly complex and variable, and contain vast interspecies and intraspecies diversity, both of which respond to environmental variation...
April 21, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28433932/the-unseen-rhizosphere-root-soil-microbe-interactions-for-crop-production
#7
REVIEW
Ruifu Zhang, Jorge M Vivanco, Qirong Shen
The underground root-soil-microbe interactions are extremely complex, but vitally important for aboveground plant growth, health and fitness. The pressure to reduce our reliance on agrochemicals, and sustainable efforts to develop agriculture makes rhizosphere interactions' research a hotspot. Recent advances provide new insights about the signals, pathways, functions and mechanisms of these interactions. In this review, we provide an overview about recent progress in rhizosphere interaction networks in crops...
April 20, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28421325/plant-microbial-competition-for-nitrogen-increases-microbial-activities-and-carbon-loss-in-invaded-soils
#8
Matthew E Craig, Jennifer M Fraterrigo
Many invasive plant species show high rates of nutrient acquisition relative to their competitors. Yet the mechanisms underlying this phenomenon, and its implications for ecosystem functioning, are poorly understood, particularly in nutrient-limited systems. Here, we test the hypothesis that an invasive plant species (Microstegium vimineum) enhances its rate of nitrogen (N) acquisition by outcompeting soil organic matter-degrading microbes for N, which in turn accelerates soil N and carbon (C) cycling. We estimated plant cover as an indicator of plant N acquisition rate and quantified plant tissue N, soil C and N content and transformations, and extracellular enzyme activities in invaded and uninvaded plots...
April 18, 2017: Oecologia
https://www.readbyqxmd.com/read/28421249/co-effects-of-pyrene-and-nitrate-on-the-activity-and-abundance-of-soil-denitrifiers-under-anaerobic-condition
#9
Zhi-Feng Zhou, Yan-Hong Yao, Ming-Xia Wang, Xiao-Hu Zuo
It has previously been confirmed that polycyclic aromatic hydrocarbons (PAHs) could be degraded by soil microbes coupling with denitrification, but the relationships among soil denitrifiers, PAHs, and nitrate under obligate anaerobic condition are still unclear. Here, co-effects of pyrene and nitrate on the activity and abundance of soil denitrifiers were investigated through a 45-day incubation experiment. Two groups of soil treatments with (N30) and without (N0) nitrate (30 mg kg(-1) dry soil) amendment were conducted, and each group contained three treatments with different pyrene concentrations (0, 30, and 60 mg kg(-1) dry soil denoted as P0, P30, and P60, respectively)...
April 18, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28421053/elevated-air-humidity-changes-soil-bacterial-community-structure-in-the-silver-birch-stand
#10
Marika Truu, Ivika Ostonen, Jens-Konrad Preem, Krista Lõhmus, Hiie Nõlvak, Teele Ligi, Katrin Rosenvald, Kaarin Parts, Priit Kupper, Jaak Truu
Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch (Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28419436/ammonia-oxidizer-populations-vary-with-nitrogen-cycling-across-a-tropical-montane-mean-annual-temperature-gradient
#11
S Pierre, I Hewson, J P Sparks, C M Litton, C Giardina, P M Groffman, T J Fahey
Functional gene approaches have been used to better understand the roles of microbes in driving forest soil nitrogen (N) cycling rates and bioavailability. Ammonia oxidation is a rate limiting step in nitrification, and is a key area for understanding environmental constraints on N availability in forests. We studied how increasing temperature affects the role of ammonia oxidizing archaea (AOA) and bacteria (AOB) in soil N cycling and availability by using a highly constrained natural mean annual temperature (MAT) elevation gradient in a tropical montane wet forest...
April 18, 2017: Ecology
https://www.readbyqxmd.com/read/28409237/prevalence-of-sucretolerant-bacteria-in-common-soils-and-their-isolation-and-characterization
#12
Casper Fredsgaard, Donald B Moore, Fei Chen, Benton C Clark, Mark A Schneegurt
Sucretolerant microbes grow in the presence of sugar concentrations high enough to substantially lower water activities. Natural habitats high in sugars are mainly limited to dried fruit, floral nectar, honey, sugarcane, and associated soils. Organisms that tolerate extremes of solute concentration, high enough to lower water activities, might not be expected in common oligoosmotic soils. We report on the isolation of sucretolerant bacteria from common soils using media supplemented with 50% sucrose (a w 0...
April 13, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28405627/bacterial-community-composition-associated-with-pyrogenic-organic-matter-biochar-varies-with-pyrolysis-temperature-and-colonization-environment
#13
Zhongmin Dai, Albert Barberán, Yong Li, Philip C Brookes, Jianming Xu
Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization...
March 2017: MSphere
https://www.readbyqxmd.com/read/28401921/distinct-soil-microbial-communities-in-habitats-of-differing-soil-water-balance-on-the-tibetan-plateau
#14
Yuntao Li, Jonathan Adams, Yu Shi, Hao Wang, Jin-Sheng He, Haiyan Chu
Global change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community...
April 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28397264/population-densities-of-indigenous-acidobacteria-change-in-the-presence-of-plant-growth-promoting-rhizobacteria-pgpr-in-rhizosphere
#15
Sadaf Kalam, Subha Narayan Das, Anirban Basu, Appa Rao Podile
Rhizosphere microbial community has diverse metabolic capabilities and plays a crucial role in maintaining plant health. Oligotrophic plant growth promoting rhizobacteria (PGPR), along with difficult-to-culture microbial fractions, might be involved synergistically in microbe-microbe and plant-microbe interactions in the rhizosphere. Among the difficult-to-culture microbial fractions, Acidobacteria constitutes the most dominant phylum thriving in rhizospheric soils. We selected effective PGPR for tomato and black gram and studied their effect on population densities of acidobacterial members...
April 11, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28395259/effects-of-18-pharmaceuticals-on-the-physiological-diversity-of-edaphic-microorganisms
#16
Mª Rosa Pino-Otín, Selene Muñiz, Jonatan Val, Enrique Navarro
Pharmaceutical residues can enter the terrestrial environment through the application of recycled water and contaminated biosolids to agricultural soils, were edaphic microfauna can would be threatened. This study thus assessed the effect of 18 widely consumed pharmaceuticals, belonging to four groups: antibiotics, non-steroidal anti-inflammatory drugs (NSAIDs), blood lipid-lowering agents (BLLA) and β-blockers, on the physiology of soil microbial communities from a ecological crop field. Biolog EcoPlates, containing 31 of the most common carbon sources found in forest and crop soils, were used to calculate both the averaged well colour development (AWCD), as an indicator of the entire capacity of degrading carbon sources, and the diversity of carbon source utilization, as an indicator of the physiological diversity...
April 7, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28393846/an-algorithm-of-association-rule-mining-for-microbial-energy-prospection
#17
Muhammad Shaheen, Muhammad Shahbaz
The presence of hydrocarbons beneath earth's surface produces some microbiological anomalies in soils and sediments. The detection of such microbial populations involves pure bio chemical processes which are specialized, expensive and time consuming. This paper proposes a new algorithm of context based association rule mining on non spatial data. The algorithm is a modified form of already developed algorithm which was for spatial database only. The algorithm is applied to mine context based association rules on microbial database to extract interesting and useful associations of microbial attributes with existence of hydrocarbon reserve...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28389537/airborne-pathogens-inside-automobiles-for-domestic-use-assessing-in-car-air-decontamination-devices-using-staphylococcus-aureus-as-the-challenge
#18
Syed A Sattar, Bahram Zargar, Kathryn E Wright, Joseph R Rubino, M Khalid Ijaz
Family cars represent ∼74% of the yearly global output of motorized vehicles. With the life-expectancy of ∼8 decades in many countries, one spends >100 minutes daily inside the confined and often shared space of the car with exposure to a mix of potentially harmful microbes. Can commercial in-car air microbial decontamination devices mitigate the risk? Three such devices (designated as Device #s1-3) with HEPA filters were tested in the modified passenger cabin (3.25 m3) of a four-door sedan housed within a biosafety level 3 containment facility...
April 7, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28386252/caenorhabditis-elegans-as-a-model-for-microbiome-research
#19
Fan Zhang, Maureen Berg, Katja Dierking, Marie-Anne Félix, Michael Shapira, Buck S Samuel, Hinrich Schulenburg
The nematode Caenorhabditis elegans is used as a central model system across biological disciplines. Surprisingly, almost all research with this worm is performed in the absence of its native microbiome, possibly affecting generality of the obtained results. In fact, the C. elegans microbiome had been unknown until recently. This review brings together results from the first three studies on C. elegans microbiomes, all published in 2016. Meta-analysis of the data demonstrates a considerable conservation in the composition of the microbial communities, despite the distinct geographical sample origins, study approaches, labs involved and perturbations during worm processing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28384186/75-years-of-dryland-science-trends-and-gaps-in-arid-ecology-literature
#20
Aaron C Greenville, Chris R Dickman, Glenda M Wardle
Growth in the publication of scientific articles is occurring at an exponential rate, prompting a growing need to synthesise information in a timely manner to combat urgent environmental problems and guide future research. Here, we undertake a topic analysis of dryland literature over the last 75 years (8218 articles) to identify areas in arid ecology that are well studied and topics that are emerging. Four topics-wetlands, mammal ecology, litter decomposition and spatial modelling, were identified as 'hot topics' that showed higher than average growth in publications from 1940 to 2015...
2017: PloS One
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