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Soil Metagenomics

Alexandre Pedrinho, Lucas William Mendes, Luis Fernando Merloti, Mariley de Cassia da Fonseca, Fabiana de Souza Cannavan, Siu Mui Tsai
Amazon rainforest has been subjected to particularly high rates of deforestation caused mainly by the expansion of cattle pasture and agriculture. A commonly observed response to land-use change is a negative impact on biodiversity of plant and animal species. However, its effect on the soil microbial community and ecosystem functioning is still poorly understood. Here, we used DNA metagenomic sequencing approach to investigate the impact of land-use change on soil microbial community composition and its potential functions in three land-use systems (primary forest, pasture, and secondary forest) in the Amazon region...
December 13, 2018: FEMS Microbiology Ecology
Matteo D'Alessio, Lisa M Durso, Daniel N Miller, Brian Woodbury, Chittaranjan Ray, Daniel D Snow
The impact of commonly-used livestock antibiotics on soil nitrogen transformations under varying redox conditions is largely unknown. Soil column incubations were conducted using three livestock antibiotics (monensin, lincomycin and sulfamethazine) to better understand the fate of the antibiotics, their effect on nitrogen transformation, and their impact on soil microbial communities under aerobic, anoxic, and denitrifying conditions. While monensin was not recovered in the effluent, lincomycin and sulfamethazine concentrations decreased slightly during transport through the columns...
November 30, 2018: Environmental Pollution
Haya F Alsammar, Samina Naseeb, Lorenzo B Brancia, R Tucker Gilman, Ping Wang, Daniela Delneri
The species of the genus Saccharomyces are commonly inhabiting tree bark and the surrounding soil, but their abundance have likely been underestimated due to biases in culturing methods. Metagenomic studies have so far been unable to detect Saccharomyces species in wild environments. Here, we sequenced the mycobiome of soils surrounding different trees at various altitudes in the Italian Alps. To survey for yeasts species belonging to Saccharomyces genus rather than other fungal species, we performed a selectivity step involving the isolation of the internal transcribed spacer (ITS) region that is specific to this yeast group...
December 3, 2018: Environmental Microbiology Reports
Puleng Letuma, Yasir Arafat, Muhammad Waqas, Feifan Lin, Weiwei Lin, Yiyang Zhang, Mamello Masita, Kai Fan, Zhaowei Li, Wenxiong Lin
Generally, plant roots shape the rhizosphere fungal community but how individual plant genes involved in senescence affect this shaping is less studied. We used an early senescence leaf (esl) mutant rice and compared it with its isogenic wild type variety to evaluate the effect of the vacuolar H+ -ATPase (VHA-A1) gene mutation on the rhizosphere fungal community structure and composition using a metagenomic pyrosequencing approach. The most predominate fungal phyla identified for both isogenic lines belonged to Ascomycota, Basidiomycota and Glomeromycota, where Ascomycota were more prevalent in the esl mutant than the wild type variety...
November 30, 2018: Scientific Reports
Andrew T Crombie, Nasmille L Larke-Mejia, Helen Emery, Robin Dawson, Jennifer Pratscher, Gordon P Murphy, Terry J McGenity, J Colin Murrell
The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source...
November 29, 2018: Proceedings of the National Academy of Sciences of the United States of America
Akebe Luther King Abia, Arghavan Alisoltani, Eunice Ubomba-Jaswa, Matthys Alois Dippenaar
Recent studies have identified cemeteries as potential environmental reservoirs of multi-drug resistant pathogenic bacteria that could contaminate groundwater sources posing public health threats. However, these findings were based on the identification of culturable bacteria and at times not below burial grounds. Investigation on the bacterial diversity and functional profiles of bacterial communities above and below burial grounds in human cemeteries are few. The current study used high-throughput sequencing techniques to determine the bacterial composition and their associated functional profiles in cemetery soil samples collected at the surface and below burial ground in two South African cemeteries (Maitland Cemetery in Cape Town and Fontein Street Cemetery in Middelburg) to evaluate the potential health threat to surrounding populations through contamination of groundwater...
November 22, 2018: Science of the Total Environment
Delong Meng, Juan Li, Tianbo Liu, Yongjun Liu, Mingli Yan, Jin Hu, Xiaoqi Li, Xueduan Liu, Yili Liang, Hongwei Liu, Huaqun Yin
Understanding the role of microbes in the solubility of cadmium (Cd) is of fundamental importance for remediation of Cd toxicity. The present study aimed to identify the microbes that involved in regulating Cd solubility and to reveal possible mechanisms. Therefore, microbial communities were investigated through high-throughput sequencing approach, the molecular ecological network was constructed and metagenomes were predicted. Our results indicated that redox conditions affected both the solubility of soil Cd and the microbial communities...
January 2019: Journal of Environmental Sciences (China)
Jin Xu, Yunzeng Zhang, Pengfan Zhang, Pankaj Trivedi, Nadia Riera, Yayu Wang, Xin Liu, Guangyi Fan, Jiliang Tang, Helvécio D Coletta-Filho, Jaime Cubero, Xiaoling Deng, Veronica Ancona, Zhanjun Lu, Balian Zhong, M Caroline Roper, Nieves Capote, Vittoria Catara, Gerhard Pietersen, Christian Vernière, Abdullah M Al-Sadi, Lei Li, Fan Yang, Xun Xu, Jian Wang, Huanming Yang, Tao Jin, Nian Wang
Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes...
November 20, 2018: Nature Communications
Frederik Schulz, Lauren Alteio, Danielle Goudeau, Elizabeth M Ryan, Feiqiao B Yu, Rex R Malmstrom, Jeffrey Blanchard, Tanja Woyke
Known giant virus diversity is currently skewed towards viruses isolated from aquatic environments and cultivated in the laboratory. Here, we employ cultivation-independent metagenomics and mini-metagenomics on soils from the Harvard Forest, leading to the discovery of 16 novel giant viruses, chiefly recovered by mini-metagenomics. The candidate viruses greatly expand phylogenetic diversity of known giant viruses and either represented novel lineages or are affiliated with klosneuviruses, Cafeteria roenbergensis virus or tupanviruses...
November 19, 2018: Nature Communications
Séverine Lopez, Xavier Goux, Guillaume Echevarria, Magdalena Calusinska, Jean Louis Morel, Emile Benizri
Ultramafic (i.e. serpentine) soils are widespread in the Balkans and particularly in Albania. They account for a large part of plant endemism in that region and host several hyperaccumulator species, which are characterized by leaf nickel concentrations frequently above 1%. This rich nickel hyperaccumulating flora could serve as candidate to be used in phytoextraction and agromining. Despite recent interest in metal hyperaccumulating plants and agromining, very few studies have investigated the bacterial diversity and the influence of environmental factors on microbial gene profiles in the rhizosphere of hyperaccumulator plants growing on ultramafic soils...
November 8, 2018: Science of the Total Environment
Robert Starke, Nico Jehmlich, Felipe Bastida
Metaproteomics was established to analyse both the structure and the function of microbial communities and, particularly in soils, their contribution to ecosystem services. In this review, we provide an overview on how the study of the soil metaproteome can provide fundamental information on the role of microbial communities in soil ecosystem services. We further discuss the strengths and weaknesses of soil metaproteomics in comparison to other culture-independent OMIC techniques. We critically review its bottlenecks but also provide strategies to mitigate and possible directions for future research as the direct link of structure and function is advantageous and complementary to metagenomics, metatranscriptomics and metametabolomics...
November 13, 2018: Journal of Proteomics
Yimin You, Zhigang Wang, Weihui Xu, Chunlong Wang, Xiaosong Zhao, Yunpeng Su
Phthalic acid esters (PAEs), such as dimethyl phthalate (DMP) and dibutyl phthalate (DBP), are widely distributed as environmental pollutants. In this study, the effects of these chemicals were investigated in black soils using a metagenomics approach. The results clearly showed that DMP or DBP increased the abundance of genes involved in transcription, replication and repair in black soils. In addition, the abundances of genes associated with metabolic functions was improved following treatment with DMP or DBP, including those involved in lipid transport and metabolism, carbohydrate transport and metabolism, and energy production and conversion...
October 28, 2018: Science of the Total Environment
Garrett J Smith, Jordan C Angle, Lindsey M Solden, Mikayla A Borton, Timothy H Morin, Rebecca A Daly, Michael D Johnston, Kay C Stefanik, Richard Wolfe, Bohrer Gil, Kelly C Wrighton
Microbial carbon degradation and methanogenesis in wetland soils generate a large proportion of atmospheric methane, a highly potent greenhouse gas. Despite their potential to mitigate greenhouse gas emissions, knowledge about methane-consuming methanotrophs is often limited to lower-resolution single-gene surveys that fail to capture the taxonomic and metabolic diversity of these microorganisms in soils. Here our objective was to use genome-enabled approaches to investigate methanotroph membership, distribution, and in situ activity across spatial and seasonal gradients in a freshwater wetland near Lake Erie...
November 6, 2018: MBio
Jackson W Sorensen, Taylor K Dunivin, Tammy C Tobin, Ashley Shade
Small bacterial and archaeal genomes provide insights into the minimal requirements for life1 and are phylogenetically widespread2 . However, the precise environmental pressures that constrain genome size in free-living microorganisms are unknown. A study including isolates has shown that thermophiles and other bacteria with high optimum growth temperatures often have small genomes3 . It is unclear whether this relationship extends generally to microorganisms in nature4,5 and more specifically to microorganisms that inhabit complex and highly variable environments, such as soils3,6,7 ...
November 5, 2018: Nature Microbiology
M Ganuza, N Pastor, M Boccolini, J Erazo, S Palacios, C Oddino, M M Reynoso, M Rovera, A M Torres
AIM: To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils. METHODS AND RESULTS: Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of Córdoba, Argentina...
November 1, 2018: Journal of Applied Microbiology
Kunjukrishnan Kamalakshi Sivakala, Polpass Arul Jose, Rangasamy Anandham, Thangathurai Thinesh, Solomon Robinson David Jebakumar, Sandipan Samaddar, Poulami Chatterjee, Natesan Sivakumar, Tongmin Sa
Investigating the bacterial diversity and their metabolic capabilities are 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...
September 28, 2018: Journal of Microbiology and Biotechnology
Xiaogang Li, Alexandre Jousset, Wietse de Boer, Víctor J Carrión, Taolin Zhang, Xingxiang Wang, Eiko E Kuramae
Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation...
October 27, 2018: ISME Journal
Laura Rago, Sarah Zecchin, Federica Villa, Andrea Goglio, Anna Corsini, Lucia Cavalca, Andrea Schievano
A new approach to microbial electrosynthesis is proposed, aimed at producing whole biomass from N2 and inorganic carbon, by electrostimulation of complex microbial communities. On a carbon-based conductor under constant polarization (-0.7 V vs SHE), an electroactive biofilm was enriched with autotrophic nitrogen fixing microorganims and led to biomass synthesis at higher amounts (up to 18 fold), as compared to controls kept at open circuit (OC). After 110 days, the electron transfer had increased by 30-fold, as compared to abiotic conditions...
February 2019: Bioelectrochemistry
Agota Aučynaitė, Rasa Rutkienė, Daiva Tauraitė, Rolandas Meškys, Jaunius Urbonavičius
Cytosine is one of the four letters of a standard genetic code, found both in DNA and in RNA. This heterocyclic base can be converted into uracil upon the action of the well-known cytosine deaminase. Isocytosine (2-aminouracil) is an isomer of cytosine, yet the enzymes that could convert it into uracil were previously mainly overlooked. In order to search for the isocytosine deaminases we used a selection strategy that is based on uracil auxotrophy and the metagenomic libraries, which provide a random pool of genes from uncultivated soil bacteria...
2018: Frontiers in Microbiology
Hong-Yi Li, Hang Wang, Hai-Tiao Wang, Pei-Yong Xin, Xin-Hua Xu, Yun Ma, Wei-Ping Liu, Chang-Yun Teng, Cheng-Liang Jiang, Li-Ping Lou, Wyatt Arnold, Lauren Cralle, Yong-Guan Zhu, Jin-Fang Chu, Jack A Gilbert, Zhi-Jian Zhang
BACKGROUND: Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged ultrahigh-resolution mass spectrometry, amplicon, and metagenomic sequencing to characterize the molecular distribution of DOM and the taxonomic and functional microbial diversity in paddy soils across China. We hypothesized that variances in microbial community significantly associate with changes in soil DOM molecular composition...
October 19, 2018: Microbiome
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