3,894 research outputs found

    Metagenome Of Matang Mangrove Forest Reveals Tree Harvesting Alter Soil Microbiome

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    Hutan Simpan Paya Bakau Matang di Malaysia telah diiktiraf sebagai hutan bakau yang diurus terbaik di seluruh dunia. Pengetahuan sangat terhad mengenai kesan penggunaan tanah pada komuniti mikrobial tanah dan keupayaan fungsinya Matang Mangrove Forest Reserve (MMFR) in Malaysia has been recognized as the best-managed mangrove forest in the world. There is limited knowledge about the effects of land use changes on soil microbial diversity and its functional capabilit

    Soil Metagenomics: Concepts and Applications

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    Soil is a living entity of the Earth, and considered as one of the main reservoir of microbial diversity. Studying the soil microbial diversity is very much necessary, as they play an important role in maintaining the health of soil by recycling the nutrients, creating soil structure and humus. However, the culture dependent approaches fail to provide clear estimates of the diversity and untapped resources. Hence, study of the microbial diversity using culture independent approaches become necessary. The field of metagenomics helps in studying the genomes of the diverse soil organisms collectively in their natural habitat which holds the promising for accessing novel genetic resources. Application of the metagenomics to the soil environment is very challenging due to several difficulties; one of which is co-extraction of humic acid with nucleic acids which hinder downstream high throughout processes. However, applying sequencing methods to soil microbial communities will help in uncovering the hidden resources like novel genes, biomolecules and other valuable products which are yet to be discovered or still unknown. Different culture independent techniques and applications of the metagenomics to study the abundant microflora of the complex and changing environment of soil discussed herein

    Metagenomic tools in microbial ecology research

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    Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.publishedVersio

    The Influence of Conservation Tillage and Conventional Tillage on Soil Bacterial Diversity in Southern Illinois

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    Agriculture in the Midwest United States (Illinois, Indiana, Iowa, Michigan, Minnesota, Ohio, and Wisconsin) is a critically important component of the United States economy and also for world exports of food grain. This is well reflected in the 2012 Census of Agriculture which showed that these states had a market value of crop and livestock products sold in excess of $80,000,000,000 (USDA, 2012). Within the U.S. the three Midwest states, Illinois, Iowa, and Minnesota are ranked 2nd, 3rd, and 4th for the economic value of crops sold. This economic value of agriculture in the Midwest encompasses not only corn, soybeans, livestock, vegetables, fruits, tree nuts, and berries but also nursery and many greenhouse plants. Soil is the one common underlying platform for agriculture and if agriculture has to remain profitable and sustainable, a scientific understanding of soils and their relationship to plant productivity is critical. Soils harbor probably the most diverse microbial ecosystems on Earth (Delmont et al., 2011) and we are just beginning to understand the full extent of this diversity and how it influences agricultural productivity and how in turn agricultural practices influence the microbial diversity. Estimations indicate that approximately 1,000 Giga base pairs (Gbp) of microbial genomic sequences exist per gram of soil (Vogel et al., 2009). Microorganisms occupy almost every available niche on Earth and directly affect the environment and agricultural systems by a range of mechanisms that include biological nitrogen fixation (Hungria, Franchini, Campo, & Graham, 2005), suppression of diseases (Mendes et al., 2011), decomposition of organic components (Schmidt et al., 2011), plant growth promotion (Bhattacharya & Jha, 2012), soil nutrient cycling (Brussard, 2012) and bioremediation (Ali et al., 2012). Soil microbial community structure and its associated and interdependent biological processes can be affected by the way land is used and managed. Since a vast majority of soil microorganisms do not respond to traditional culturing techniques (Delmont et al., 2011), it has been difficult to study and characterize the functional and phylogenetic diversity of these important ecosystems until recent advances in next-generation DNA sequencing which have begun to unravel what is beneath our feet (Caporaso et al., 2010). According to Food and Agricultural Organization (FAO), the amount of land used for agriculture is about 11% (http://www.fao.org/docrep/005/y4252e/y4252e06.htm) and the emissions which can have serious environmental and health effects from agricultural food production far outweigh the total emissions from all the other industries combined (Bauer, Tsigardis, & Miller, 2016). Thus, any steps to fine-tune the management practices and the way the agricultural land is utilized can go a long way in sustaining our way of life while maintaining a healthy environment. The purpose of this study is to examine the shifts in the taxonomic diversity of bacteria in soils at phylum, class and order level between two distinct agricultural practices – Conventional Tillage (CT) and Conservation Tillage (NT) in Southern Illinois along with changes in soil compaction and soil phosphatase activity. The larger idea, based on results reported here and elsewhere, is to encourage conservative tillage practices using a combination of diverse cover crop systems and continuous soil cover which seem to enhance functional microbial diversity in the soil (Ajay & Ngouajio, 2012; Verzeaux et al., 2016). Research also indicates the presence of higher numbers of bacteria of varied trophic groups, as well as increased species richness in bacteria in well-managed soils with minimal tilling and this, may correspond to more resilience to drying and rewetting disturbances in the soil (Anne et al., 2006). This research may be the first to reconstruct the entire soil bacterial community in agricultural fields of Southern Illinois and will also hopefully be a precursor for more studies aimed at not only understanding soil from a biological bacterial perspective but also in deciphering interesting patterns that can help correlate changes in land management practices and how they impact bacterial communities. It may help us in developing a methodology to use bacterial taxa as indicators of soil management practices. The study will also detect previously unreported rare bacterial taxa-specific for this region and regional geochemistry
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