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Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades.
BackgroundCurrently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).MethodsShotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.ResultsThe three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.ConclusionThis Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades
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Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.
Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism
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The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health.
Food and human health are inextricably linked. As such, revolutionary impacts on health have been derived from advances in the production and distribution of food relating to food safety and fortification with micronutrients. During the past two decades, it has become apparent that the human microbiome has the potential to modulate health, including in ways that may be related to diet and the composition of specific foods. Despite the excitement and potential surrounding this area, the complexity of the gut microbiome, the chemical composition of food, and their interplay in situ remains a daunting task to fully understand. However, recent advances in high-throughput sequencing, metabolomics profiling, compositional analysis of food, and the emergence of electronic health records provide new sources of data that can contribute to addressing this challenge. Computational science will play an essential role in this effort as it will provide the foundation to integrate these data layers and derive insights capable of revealing and understanding the complex interactions between diet, gut microbiome, and health. Here, we review the current knowledge on diet-health-gut microbiota, relevant data sources, bioinformatics tools, machine learning capabilities, as well as the intellectual property and legislative regulatory landscape. We provide guidance on employing machine learning and data analytics, identify gaps in current methods, and describe new scenarios to be unlocked in the next few years in the context of current knowledge
Metagenome Of Matang Mangrove Forest Reveals Tree Harvesting Alter Soil Microbiome
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
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
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
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
Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition
Additional file 11: Table S7. Summary of de novo assembly results (37Â k)
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