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Soil microbial dna extraction

Stacie Tardif, Étienne Yergeau, Julien Tremblay, Pierre Legendre, Lyle G Whyte, Charles W Greer
The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv...
2016: Frontiers in Microbiology
Hongling Qin, Xiangbi Chen, Yafang Tang, Haijun Hou, Rong Sheng, Jinlin Shen
OBJECTIVE: Paddy soils contain relatively greater organic matter and water contents than other soils thereby limiting effective mRNA extraction. A modification of the conventional mRNA soil extraction method specific to paddy soils is described. RESULTS: Two main modifications for co-extraction of DNA and RNA are: (1) addition of 20 % (w/v) sodium dodecyl sulphate to 10 % (w/v) hexadecyltrimethylammonium bromide extraction buffer, and (2) fresh soil, initially frozen at -80 °C, is immediately immersed in extraction buffer...
September 15, 2016: Biotechnology Letters
Sarah M Allard, Christopher S Walsh, Anna E Wallis, Andrea R Ottesen, Eric W Brown, Shirley A Micallef
Due to the intimate association between plants and their microbial symbionts, an examination of the influence of agricultural practices on phytobiome structure and diversity could foster a more comprehensive understanding of plant health and produce safety. Indeed, the impact of upstream crop producti006Fn practices cannot be overstated in their role in assuring an abundant and safe food supply. To assess whether fertilizer type impacted rhizosphere and phyllosphere bacterial communities associating with tomato plants, the bacterial microbiome of tomato cv...
August 28, 2016: Science of the Total Environment
Fei Cheng, Lin Hou, Keith Woeste, Zhengchun Shang, Xiaobang Peng, Peng Zhao, Shuoxin Zhang
Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants...
October 2016: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
Fabiana Roberta Segura, Emilene Arusievicz Nunes, Fernanda Pollo Paniz, Ana Carolina Cavalheiro Paulelli, Gabriela Braga Rodrigues, Gilberto Úbida Leite Braga, Walter Dos Reis Pedreira Filho, Fernando Barbosa, Giselle Cerchiaro, Fábio Ferreira Silva, Bruno Lemos Batista
On November 5th, 2015, Samarco's iron mine dam - called Fundão - spilled 50-60 million m(3) of mud into Gualaxo do Norte, a river that belongs to Rio Doce Basin. Approximately 15 km(2) were flooded along the rivers Gualaxo do Norte, Carmo and Doce, reaching the Atlantic Ocean on November 22nd, 2015. Six days after, our group collected mud, soil and water samples in Bento Rodrigues (Minas Gerais, Brazil), which was the first impacted area. Overall, the results, water samples - potable and surface water from river - presented chemical elements concentration according to Brazilian environmental legislations, except silver concentration in surface water that ranged from 1...
November 2016: Environmental Pollution
Luciano Cavani, Luisa M Manici, Francesco Caputo, Elisabetta Peruzzi, Claudio Ciavatta
This study aimed at investigating the degree of interference of high soil copper (Cu) contamination when an old vineyard is converted into a protected area. This study was performed within an intensive agricultural system; it was organized into a two-factorial nested design to analyze the impact of management (conventional vs re-naturalized orchard) and position within each orchard (tree-rows and strips). Chemical and biochemical properties along with bacterial and fungal communities, evaluated with PCR-DGGE starting from total soil DNA, were analyzed...
November 1, 2016: Journal of Environmental Management
Varsik Martirosyan, Adrian Unc, Gad Miller, Tirza Doniger, Chaim Wachtel, Yosef Steinberger
Microbial function, composition, and distribution play a fundamental role in ecosystem ecology. The interaction between desert plants and their associated microbes is expected to greatly affect their response to changes in this harsh environment. Using comparative analyses, we studied the impact of three desert shrubs, Atriplex halimus (A), Artemisia herba-alba (AHA), and Hammada scoparia (HS), on soil- and leaf-associated microbial communities. DNA extracted from the leaf surface and soil samples collected beneath the shrubs were used to study associated microbial diversity using a sequencing survey of variable regions of bacterial 16S rRNA and fungal ribosomal internal transcribed spacer (ITS1)...
October 2016: Microbial Ecology
Robyn A Barbato, Natàlia Garcia-Reyero, Karen Foley, Robert Jones, Zoe Courville, Thomas Douglas, Edward Perkins, Charles M Reynolds
The cryosphere offers access to preserved organisms that persisted under past environmental conditions. In fact, these frozen materials could reflect conditions over vast time periods and investigation of biological materials harbored inside could provide insight of ancient environments. To appropriately analyze these ecosystems and extract meaningful biological information from frozen soils and ice, proper collection and processing of the frozen samples is necessary. This is especially critical for microbial and DNA analyses since the communities present may be so uniquely different from modern ones...
2016: Journal of Visualized Experiments: JoVE
Karl J Romanowicz, Zachary B Freedman, Rima A Upchurch, William A Argiroff, Donald R Zak
Predicting the impact of environmental change on soil microbial functions requires an understanding of how environmental factors shape microbial composition. Here, we investigated the influence of environmental factors on bacterial and fungal communities across an expanse of northern hardwood forest in Michigan, USA, which spans a 500-km regional climate gradient. We quantified soil microbial community composition using high-throughput DNA sequencing on coextracted rDNA (i.e. total community) and rRNA (i.e...
October 2016: FEMS Microbiology Ecology
C Ryan Penton, Vadakattu V S R Gupta, Julian Yu, James M Tiedje
We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms...
2016: Frontiers in Microbiology
Amy Kenwell, Alexis Navarre-Sitchler, Rodrigo Prugue, John R Spear, Amanda S Hering, Reed M Maxwell, Rosemary W H Carroll, Kenneth H Williams
A better understanding of how microbial communities interact with their surroundings in physically and chemically heterogeneous subsurface environments will lead to improved quantification of biogeochemical reactions and associated nutrient cycling. This study develops a methodology to predict potential elevated rates of biogeochemical activity (microbial "hotspots") in subsurface environments by correlating microbial DNA and aspects of the community structure with the spatial distribution of geochemical indicators in subsurface sediments...
September 1, 2016: Science of the Total Environment
Qiang Wang, Hongxun Zhang, Xiu Liu
The solid-state fermentation state of Chinese Maotai liquor involves the interaction of several complex microbial communities leading to the generation of the most complex liquor fermentation system in the world and contributes to the unique flavor and aroma of the liquor. In this study, total DNA was extracted from 3 fermented grain samples (FG1, FG2, and FG3) and 12 environmental samples, including Daqu (DA1, DA2, DA3, and DA4), cellar mud (CS1, CS2, and CS3), soil (SL1 and SL2), air (A1 and A2), and sorghum (SH), and the 16S and 18S rRNA genes were amplified...
June 2016: Journal of Food Science
Zhen-jiang Jin, Hong-hu Zeng, Qiang Li, Ya-ping Cheng, Hua-feng Tang, Min Li, Bing-fu Huang
The purpose of this study is to compare microbial number, microbial biomass as well as soil enzyme activity between paddy field and dryland originated karst wetland ecosystems. The soil samples (0-20 cm) of uncultivated wetland, paddy field and dryland were collected in Huixian karst cave wetland, Guilin, China. Microbial numbers and biomass were detected using dilute plate incubation counting and chloroform fumigation-extraction, respectively. Microbial DNA was extracted according to the manufacturer's instructions of the kit...
January 15, 2016: Huan Jing Ke Xue= Huanjing Kexue
Caitlin P Youngquist, Shannon M Mitchell, Craig G Cogger
Antibiotics and antibiotic-resistant bacteria (ARB) enter the environment through municipal and agricultural waste streams and pose a potential risk to human and livestock health through either direct exposure to antibiotic-resistant pathogens or selective pressure on the soil microbial community. This review summarizes current literature on the fate of antibiotics, ARB, and antibiotic resistance genes (ARGs) during anaerobic digestion and composting of manure and wastewater residuals. Studies have shown that removal of antibiotics varies widely during mesophilic anaerobic digestion, even within the same class of antibiotics...
March 2016: Journal of Environmental Quality
Naama Lang-Yona, Yinon Mazar, Michal Pardo, Yinon Rudich
Outdoor aerosol research commonly uses particulate matter sampled on filters. This procedure enables various characterizations of the collected particles to be performed in parallel. The purpose of the method presented here is to obtain a highly accurate and reliable analysis of the endotoxin and DNA content of bio-aerosols extracted from filters. The extraction of high molecular weight organic molecules, such as lipopolysaccharides, from sampled filters involves shaking the sample in a pyrogen-free water-based medium...
2016: Journal of Visualized Experiments: JoVE
M Kuś, A Ossowski, G Zielińska
The identification of unknown victims is one of the most challenging tasks faced by forensic medicine. This is due to the rapid decomposition of tissues, beginning at the moment of death and caused by released enzymes and microbial activity. Decay is directly associated with the decomposition of soft tissues and also the degradation of genetic material inside cells. Decomposition rates vary depending on a number of environmental factors, including temperature, humidity, season, and soil properties. Decomposition also differs between bodies left in the open air or buried...
May 2016: Journal of Forensic and Legal Medicine
Vrutika Patel, Anukriti Sharma, Rup Lal, Naif Abdullah Al-Dhabi, Datta Madamwar
BACKGROUND: Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. RESULTS: Taxonomic profiling was carried out by two different complementary approaches i...
2016: BMC Microbiology
C T C C Rachid, C A Pires, D C A Leite, H L C Coutinho, R S Peixoto, A S Rosado, J Salton, J A Zanatta, F M Mercante, G A R Angelini, Fabiano de Carvalho Balieiro
The sugarcane in Brazil is passing through a management transition that is leading to the abolition of pre-harvest burning. Without burning, large amounts of sugarcane trash is generated, and there is a discussion regarding the utilization of this biomass in the industry versus keeping it in the field to improve soil quality. To study the effects of the trash removal on soil quality, we established an experimental sugarcane plantation with different levels of trash over the soil (0%, 50% and 100% of the original trash deposition) and analyzed the structure of the bacterial and fungal community as the bioindicators of impacts...
April 2016: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
Yuan Ge, John H Priester, Monika Mortimer, Chong Hyun Chang, Zhaoxia Ji, Joshua P Schimel, Patricia A Holden
Little is known about the long-term effects of engineered carbonaceous nanomaterials (ECNMs) on soil microbial communities, especially when compared to possible effects of natural or industrial carbonaceous materials. To address these issues, we exposed dry grassland soil for 1 year to 1 mg g(-1) of either natural nanostructured material (biochar), industrial carbon black, three types of multiwalled carbon nanotubes (MWCNTs), or graphene. Soil microbial biomass was assessed by substrate induced respiration and by extractable DNA...
April 5, 2016: Environmental Science & Technology
Omri M Finkel, Tom O Delmont, Anton F Post, Shimshon Belkin
UNLABELLED: The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient...
May 2016: Applied and Environmental Microbiology
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