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Soil Metagenomics

Vinod Kumar, Sabah AlMomin, Hamed Al-Aqeel, Fadila Al-Salameen, Sindhu Nair, Anisha Shajan
The role of rhizosphere microbial communities in the degradation of hydrocarbons remains poorly understood and is a field of active study. We used high throughput sequencing to explore the rhizosphere microbial diversity in the alfalfa and barley planted oil contaminated soil samples. The analysis of 16s rRNA sequences showed Proteobacteria to be the most enriched (45.9%) followed by Bacteriodetes (21.4%) and Actinobacteria (10.4%) phyla. The results also indicated differences in the microbial diversity among the oil contaminated planted soil samples...
2018: PloS One
Wentao Peng, Xiangmin Li, Chuang Wang, Hui Cao, Zhongli Cui
Multitemplate PCR is used widely for the study of microbial community diversity. Although such studies have established the abundance of different groups within many natural ecosystems, these reports are limited by uncertainties such as bias and artifacts in the PCR. Bias which is introduced by the simultaneous amplification of specific genes from complex mixtures of templates remains poorly understood. In this study, factors leading to the bias of the multitemplate PCR in bacterial communities were examined and optimized...
August 9, 2018: Journal of Basic Microbiology
Amanpreet Singh, Erica Lasek-Nesselquist, Vishnu Chaturvedi, Sudha Chaturvedi
BACKGROUND: Pseudogymnoascus destructans (Pd), the causative fungal agent of white-nose syndrome (WNS), has led to the deaths of millions of hibernating bats in the United States of America (USA) and Canada. Efficient strategies are needed to decontaminate Pd from the bat hibernacula to interrupt the disease transmission cycle without affecting the native microbes. Previously, we discovered a novel Trichoderma polysporum (Tp) strain (WPM 39143), which inhibited the growth of Pd in autoclaved soil samples...
August 8, 2018: Microbiome
M Crampon, J Bodilis, F Portet-Koltalo
The aim of this study was to understand the role of indigenous soil microbial communities on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) and to determine whether PAHs degradation potential in soils may be evaluated by analysis of bacterial diversity and potential metabolisms using a metagenomics approach. Five different soils were artificially contaminated with seven selected PAHs and the most abundant bacterial taxa were assessed by sequencing the 16S rRNA gene, and linking them to PAH biodegradation efficiencies...
July 27, 2018: Journal of Hazardous Materials
Jin Liu, Barbara J Cade-Menun, Jianjun Yang, Yongfeng Hu, Corey W Liu, Julien Tremblay, Kerry LaForge, Michael Schellenberg, Chantal Hamel, Luke D Bainard
Agriculturally-driven land transformation is increasing globally. Improving phosphorus (P) use efficiency to sustain optimum productivity in diverse ecosystems, based on knowledge of soil P dynamics, is also globally important in light of potential shortages of rock phosphate to manufacture P fertilizer. We investigated P chemical speciation and P cycling with solution 31 P nuclear magnetic resonance, P K-edge X-ray absorption near-edge structure spectroscopy, phosphatase activity assays, and shotgun metagenomics in soil samples from long-term agricultural fields containing four different land-use types (native and tame grasslands, annual croplands, and roadside ditches)...
2018: Frontiers in Microbiology
Marie E Kroeger, Tom O Delmont, A M Eren, Kyle M Meyer, Jiarong Guo, Kiran Khan, Jorge L M Rodrigues, Brendan J M Bohannan, Susannah G Tringe, Clovis D Borges, James M Tiedje, Siu M Tsai, Klaus Nüsslein
Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil...
2018: Frontiers in Microbiology
Paula Istvan, Amanda Araújo Souza, Aisel Valle Garay, Debora Farage Knupp Dos Santos, Gideane Mendes de Oliveira, Renata Henrique Santana, Fabyano Alvares Cardoso Lopes, Sonia Maria de Freitas, João Alexandre Ribeiro Gonçalves Barbosa, Ricardo Henrique Krüger
OBJECTIVE: To isolate putative lipase enzymes by screening a Cerrado soil metagenomic library with novel features. RESULTS: Of 6720 clones evaluated, Clone W (10,000 bp) presented lipolytic activity and four predicted coding sequences, one of them LipW. Characterization of a predicted esterase/lipase, LipW, showed 28% sequence identity with an arylesterase from Pseudomonas fluorescens (pdb|3HEA) from protein database (PDB). Phylogenetic analysis showed LipW clustered with family V lipases; however, LipW was clustered in different subclade belonged to family V, suggesting a different subgroup of family V...
July 30, 2018: Biotechnology Letters
Sandra Díaz-Sánchez, Angélica Hernández-Jarguín, Alessandra Torina, Isabel G Fernández de Mera, Agustín Estrada-Peña, Margarita Villar, Francesco La Russa, Valeria Blanda, Joaquín Vicente, Santo Caracappa, Christian Gortazar, José de la Fuente
Biting midges of the genus Culicoides are known vectors of arboviruses affecting human and animal health. However, little is known about Culicoides imicola microbiota and its influence on this insect's biology. In this study, the impact of biotic and abiotic factors on C. imicola microbiota was characterized using shotgun-metagenomic sequencing of whole body DNA samples. Wild-caught C. imicola adult nulliparous females were sampled in two locations from Sicily, Italy. The climatic variables of temperature and soil moisture from both localities were recorded together with potential host blood meal sources...
July 30, 2018: Insect Molecular Biology
Erick S LeBrun, Sanghoon Kang
Here we compared microbial results for the same Phosphorus (P) biogeochemical cycle genes from a GeoChip microarray and PICRUSt functional predictions from 16S rRNA data for 20 samples in the four spatially separated Gotjawal forests on Jeju Island in South Korea. The high homogeneity of microbial communities detected at each site allows sites to act as environmental replicates for comparing the two different functional analysis methods. We found that while both methods capture the homogeneity of the system, both differed greatly in the total abundance of genes detected, as well as the diversity of taxa detected...
2018: F1000Research
Bin Ma, Kankan Zhao, Xiaofei Lv, Weiqin Su, Zhongmin Dai, Jack A Gilbert, Philip C Brookes, Karoline Faust, Jianming Xu
Soil ecological functions are largely determined by the activities of soil microorganisms, which, in turn, are regulated by relevant interactions between genes and their corresponding pathways. Therefore, the genetic network can theoretically elucidate the functional organization that supports complex microbial community functions, although this has not been previously attempted. We generated a genetic correlation network based on 5421 genes derived from metagenomes of forest soils, identifying 7191 positive and 123 negative correlation relationships...
July 25, 2018: ISME Journal
Kunjukrishnan Kamalakshi Sivakala, Arul Jose, T Thinesh, R Anandham, S R D Jebakumar, Sandipan Samaddar, Poulami Chatterjee, N Sivakumar, Tongmin Sa
Investigating the bacterial diversity and their metabolic capabilitiesare crucial for interpreting ecological patterns in desert environment, and assessing the presence of exploitable microbial resources. In this study, we evaluated the spatial heterogeneity of physico-chemical parameters, soil bacterial diversity and metabolic adaptation at meter scale. Soil samples were collected from two quadrates a desert environment (Thar Desert, India) which face hot arid climate with very little rainfall and extreme temperatures...
July 12, 2018: Journal of Microbiology and Biotechnology
Darshan Baral, Bruce I Dvorak, David Admiraal, Shangang Jia, Chi Zhang, Xu Li
Stormwater runoff has been known to cause increases in bacterial loadings in urban streams. However, little is known about its impacts on antibiotic resistance genes (ARGs) in urban watersheds. This study was performed to characterize the ARG composition of various environmental compartments of an urban watershed and to quantify their contributions of microbes and ARGs to an urban stream under wet weather conditions. Shotgun metagenomic results showed that the ARG abundance in wet weather flow was significantly higher than in base flow...
July 18, 2018: Environmental Science & Technology
Joanne B Emerson, Simon Roux, Jennifer R Brum, Benjamin Bolduc, Ben J Woodcroft, Ho Bin Jang, Caitlin M Singleton, Lindsey M Solden, Adrian E Naas, Joel A Boyd, Suzanne B Hodgkins, Rachel M Wilson, Gareth Trubl, Changsheng Li, Steve Frolking, Phillip B Pope, Kelly C Wrighton, Patrick M Crill, Jeffrey P Chanton, Scott R Saleska, Gene W Tyson, Virginia I Rich, Matthew B Sullivan
Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1-7 . The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8-10 , remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden...
August 2018: Nature Microbiology
Min Li, Xu Zhang, Huanhuan Yang, Xinxin Li, Zhaojie Cui
The soil ecosystem is critical for agricultural production, affecting many aspects of human health. Soil has more unknown biodiversity and edaphic parameters than any other ecosystem especially when polluted. Metagenomics and metatranscriptomics were applied to research on toxicological characteristics of Pb and resistance mechanism of flavonols. Rhizosphere microorganisms-plants system, a unified system closely related to soil environment was taken as research object. Results emphasize gene expression changes in different test groups...
July 12, 2018: Environmental Science and Pollution Research International
Hyunmin Koo, Joseph A Hakim, Casey D Morrow, Michael R Crowley, Dale T Andersen, Asim K Bej
This study describes microbial community compositions, and various cold-responsive stress genes, encompassing cold-induced proteins (CIPs) and cold-associated general stress-responsive proteins (CASPs) in selected Antarctic lake water, sediment, and soil metagenomes. Overall, Proteobacteria and Bacteroidetes were the major taxa in all metagenomes. Prochlorococcus and Thiomicrospira were highly abundant in waters, while Myxococcus , Anaeromyxobacter , Haliangium, and Gloeobacter were dominant in the soil and lake sediment metagenomes...
July 11, 2018: Life
Cauã A Westmann, Luana de Fátima Alves, Rafael Silva-Rocha, María-Eugenia Guazzaroni
Although functional metagenomics has been widely employed for the discovery of genes relevant to biotechnology and biomedicine, its potential for assessing the diversity of transcriptional regulatory elements of microbial communities has remained poorly explored. Here, we experimentally mined novel constitutive promoter sequences in metagenomic libraries by combining a bi-directional reporter vector, high-throughput fluorescence assays and predictive computational methods. Through the expression profiling of fluorescent clones from two independent soil sample libraries, we have analyzed the regulatory dynamics of 260 clones with candidate promoters as a set of active metagenomic promoters in the host Escherichia coli ...
2018: Frontiers in Microbiology
Evan P Starr, Shengjing Shi, Steven J Blazewicz, Alexander J Probst, Donald J Herman, Mary K Firestone, Jillian F Banfield
BACKGROUND: The transformation of plant photosynthate into soil organic carbon and its recycling to CO2 by soil microorganisms is one of the central components of the terrestrial carbon cycle. There are currently large knowledge gaps related to which soil-associated microorganisms take up plant carbon in the rhizosphere and the fate of that carbon. RESULTS: We conducted an experiment in which common wild oats (Avena fatua) were grown in a 13 CO2 atmosphere and the rhizosphere and non-rhizosphere soil was sampled for genomic analyses...
July 3, 2018: Microbiome
Xuanxuan Li, Jia Guo, Yimin Hu, Yumeng Yang, Junwei Jiang, Fang Nan, Shenglu Wu, Zhihong Xin
A cosmid metagenomic library containing 1.3 × 105 clones was created from a soil sample. A novel gene (fae-xuan) encoding a feruloyl esterase was identified through functional screening. Primary sequence analysis showed that the gene consisted of 759 base pairs and encoded a protein of 252 amino acids. The gene was expressed in Escherichia coli BL21 (DE3) and the corresponding purified recombinant enzyme exhibited a molecular weight of 29 kDa. The FAE-Xuan showed high activity (40.0 U/mg) toward methyl ferulate with an optimal temperature and pH of 30 °C and 5...
July 3, 2018: Applied Biochemistry and Biotechnology
Junqi Zhao, Chao Guo, Lu Zhang, Chaoguang Tian
The lignocellulosic biomass usually need pre-treatment with acid at high temperature or solved in ionic liquid (IL) before cellulases hydrolysis. Thus, thermoacidophilic, thermostable and IL-tolerant cellulases are greatly desired, but rarely reported. In this study, a novel endo-β-1,4-glucanase gene nmGH45 was directly cloned from saline-alkaline lake soil microbial metagenomic DNA and expressed in Pichia pastoris. Recombinant NMgh45 was active and stable at pH 3.0-9.0, with maximum activity at pH 4.5 and >80% residual activities at pH 3...
June 28, 2018: International Journal of Biological Macromolecules
Caitlin M Singleton, Carmody K McCalley, Ben J Woodcroft, Joel A Boyd, Paul N Evans, Suzanne B Hodgkins, Jeffrey P Chanton, Steve Frolking, Patrick M Crill, Scott R Saleska, Virginia I Rich, Gene W Tyson
The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data...
June 28, 2018: ISME Journal
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