Journal articles on the topic 'Soil metagenomic'
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Navarrete, Acacio Aparecido, Eliamar Aparecida Nascimbém Pedrinho, Luciano Takeshi Kishi, Camila Cesário Fernandes, Victoria Romancini Toledo, Rita de Cassia Félix Alvarez, Elisângela de Souza Loureiro, Leandro Nascimento Lemos, Siu Mui Tsai, and Eliana Gertrudes de Macedo Lemos. "Taxonomic and nitrogen-cycling microbial community functional profiles of sugarcane and adjacent forest soils in Southeast Brazil." MOJ Ecology & Environmental Sciences 6, no. 4 (July 5, 2021): 119–25. http://dx.doi.org/10.15406/mojes.2021.06.00224.
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Nowadays, due to the expansion of agricultural borders, it is highly desirable to increase the sustained productivity of sugarcane cultivars using the knowledge of soil microbial communities. In this study, twelve shotgun metagenomic datasets based on genomic DNA from soil were analyzed using the Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) and Statistical Analysis of Metagenomic Profiles (STAMP) to assess differential responses for the total soil bacterial community composition and nitrogen-cycling microbial community functional potential in soils from sugarcane field with pre-harvest burning and adjacent forest in dry and wet seasons in Southeast Brazil. The soil bacterial community revealed higher abundance for Actinobacteria in forest soil than sugarcane soil in dry and wet seasons, and an opposite pattern for Proteobacteria and Planctomycetes in these soils in both seasons. The results obtained in this study based on the KEEG map suggest that the forest soil has a higher nitrogen-cycling microbial community functional potential compared to the sugarcane soil, independently of the season. The gene sequences associated with carbohydrate metabolism were the most frequent in all soil metagenomes. Taken together, the results confirm previous findings regarding the effects of forest conversion to sugarcane production area, providing new insights regarding to this conversion through the prism of the seasonality and pre-harvesting method on microbially mediated nitrogen cycle in sugarcane production fields.
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Meier, Matthew J., E. Suzanne Paterson, and Iain B. Lambert. "Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil." Applied and Environmental Microbiology 82, no. 3 (November 20, 2015): 897–909. http://dx.doi.org/10.1128/aem.03306-15.
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ABSTRACTMetagenomics allows the study of genes related to xenobiotic degradation in a culture-independent manner, but many of these studies are limited by the lack of genomic context for metagenomic sequences. This study combined a phenotypic screen known as substrate-induced gene expression (SIGEX) with whole-metagenome shotgun sequencing. SIGEX is a high-throughput promoter-trap method that relies on transcriptional activation of a green fluorescent protein (GFP) reporter gene in response to an inducing compound and subsequent fluorescence-activated cell sorting to isolate individual inducible clones from a metagenomic DNA library. We describe a SIGEX procedure with improved library construction from fragmented metagenomic DNA and improved flow cytometry sorting procedures. We used SIGEX to interrogate an aromatic hydrocarbon (AH)-contaminated soil metagenome. The recovered clones contained sequences with various degrees of similarity to genes (or partial genes) involved in aromatic metabolism, for example,nahG(salicylate oxygenase) family genes and their respective upstreamnahRregulators. To obtain a broader context for the recovered fragments, clones were mapped to contigs derived fromde novoassembly of shotgun-sequenced metagenomic DNA which, in most cases, contained complete operons involved in aromatic metabolism, providing greater insight into the origin of the metagenomic fragments. A comparable set of contigs was generated using a significantly less computationally intensive procedure in which assembly of shotgun-sequenced metagenomic DNA was directed by the SIGEX-recovered sequences. This methodology may have broad applicability in identifying biologically relevant subsets of metagenomes (including both novel and known sequences) that can be targeted computationally byin silicoassembly and prediction tools.
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Werbin, Zoey R., Briana Hackos, Jorge Lopez-Nava, Michael C. Dietze, and Jennifer M. Bhatnagar. "The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis." F1000Research 10 (March 23, 2022): 299. http://dx.doi.org/10.12688/f1000research.51494.2.
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The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON’s shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.
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Puranik, Sampada, Rajesh Ramavadh Pal, Ravi Prabhakar More, and Hemant J. Purohit. "Metagenomic approach to characterize soil microbial diversity of Phumdi at Loktak Lake." Water Science and Technology 74, no. 9 (August 9, 2016): 2075–86. http://dx.doi.org/10.2166/wst.2016.370.
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Loktak, one of the largest freshwater lakes of India, is known for floating islands (Phumdi), being made up of a heterogeneous biomass of vegetation and soil. This ecological site represents an exclusive environmental habitat wherein the rhizospheric microbial community of Phumdi plays a key role in biogeochemical cycling of nutrients. A culture-independent whole genome shotgun sequencing based metagenomic approach was employed to unravel the composition of the microbial community and its corresponding functional potential at this environmental habitat. Proteobacteria (51%) was found to be the most dominant bacterial phylum followed by Acidobacteria (10%), Actinobacteria (9%) and Bacteroidetes (7%). Furthermore, Loktak metagenome data were compared with available metagenomes from four other aquatic habitats, varying from pristine to highly polluted eutrophic habitats. The comparative metagenomics approach aided by statistical analysis revealed that Candidatus Solibacter, Bradyrhizobium, Candidatus Koribacter, Pedosphaera, Methylobacterium, Anaeromyxobacter, Sorangium, Opitutus and Acidobacterium genera are selectively dominant at this habitat. Correspondingly, 12 different functional categories were found to be exclusively prevalent at Phumdi compared to other freshwater habitats. These differential features have been attributed to the unique habitat at Phumdi and correlated to the phenomenon of bioremediation at Loktak Lake.
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Simon, Carola, and Rolf Daniel. "Metagenomic Analyses: Past and Future Trends." Applied and Environmental Microbiology 77, no. 4 (December 17, 2010): 1153–61. http://dx.doi.org/10.1128/aem.02345-10.
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ABSTRACTMetagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. Metagenomics comprising construction and screening of metagenomic DNA libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. So far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. Recently, metagenomes of extreme environments have also been used as sources of novel biocatalysts. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body, and ocean water. Analyses of these data sets opened a window into the enormous taxonomic and functional diversity of environmental microbial communities. To assess the functional dynamics of microbial communities, metatranscriptomics and metaproteomics have been developed. The combination of DNA-based, mRNA-based, and protein-based analyses of microbial communities present in different environments is a way to elucidate the compositions, functions, and interactions of microbial communities and to link these to environmental processes.
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Huy, Pham Quang, Nguyen Kim Thoa, and Dang Thi Cam Ha. "Diversity of reductive dechlorinating bacteria and archaea in herbicide/dioxin-contaminated soils from Bien Hoa airbase using metagenomic approach." Vietnam Journal of Biotechnology 18, no. 4 (May 24, 2021): 773–84. http://dx.doi.org/10.15625/1811-4989/18/4/15799.
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Heavy herbicide/dioxin contamination of soil was derived a negative effect on the microbial biodiversity, soil quality, animal and human health in Central and South of Vietnam. This is the first time, the application metagenomic tools investigated soil microbial structural community of undetoxified (C - 21,605 ng TEQ/kg dry soil) and bioremediated (BHR - 13.2 ng TEQ/kg dry soil) which could not only help us to explore the potential risks associated with contaminated soils but also provide insights into possible soil bioremediation technology by stimulating indigenous microbes. Four methanogen genera, Methanosarcina (24 - 322 OTUs respectively C – BHR samples), Methanocella (13 - 63 OTUs), Methanosaeta (7 - 42 OTUs) and Methanococcus (6 - 69 OTUs) have been dominantly detected in both two metagenomes. Twenty genera of archaea belonging to the phylum Euryarchaeota were found. They could be clustered within 14 different families and nine archaeal genera including unclassified archaea (17 OTUs – C; 145 OTUs - BHR). In metagenome C and BHR, 12 genera of sulfate reducing bacteria (SRB) with different number (2 - 77; 61 - 904 OTUs) respectively were presented. Four SRB genera are dominated in C metagenome, it is linear also in BHR. The highest number is genus Desulfovibrio detected in both examined metagenomes. However, the relationship features of these bacterial groups need deeply investigation for understanding their role of reductive dechlorination, anaerobic degradation in herbicide/dioxin contaminated heavy soil and sediment. These results provide additional evidence to explain why heavy herbicide/dioxin contaminated soil was detoxified successfully at Bien Hoa airbase, Vietnam.
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Castillo Villamizar, Genis Andrés, Heiko Nacke, Marc Boehning, Kristin Herz, and Rolf Daniel. "Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases." mBio 10, no. 1 (January 29, 2019): e01966-18. http://dx.doi.org/10.1128/mbio.01966-18.
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ABSTRACTPhosphatases, including phytases, play a major role in cell metabolism, phosphorus cycle, biotechnology, and pathogenic processes. Nevertheless, their discovery by functional metagenomics is challenging. Here, soil metagenomic libraries were successfully screened for genes encoding phosphatase activity. In this context, we report the largest number and diversity of phosphatase genes derived from functional metagenome analysis. Two of the detected gene products carry domains which have never been associated with phosphatase activity before. One of these domains, the SNARE-associated domain DedA, harbors a so-far-overlooked motif present in numerous bacterial SNARE-associated proteins. Our analysis revealed a previously unreported phytase activity of the alkaline phosphatase and sulfatase superfamily (cl23718) and of purple acid phosphatases from nonvegetal origin. This suggests that the classical concept comprising four classes of phytases should be modified and indicates high performance of our screening method for retrieving novel types of phosphatases/phytases hidden in metagenomes of complex environments.IMPORTANCEPhosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth’s phosphatase pools.
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Werbin, Zoey R., Briana Hackos, Michael C. Dietze, and Jennifer M. Bhatnagar. "The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis." F1000Research 10 (April 19, 2021): 299. http://dx.doi.org/10.12688/f1000research.51494.1.
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The National Ecological Observatory Network (NEON) annually performs shotgun metagenomic sequencing to sample genes within soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data policies and programming tutorials, but there is currently no introductory tutorial for performing analyses with the soil shotgun metagenomic dataset. Here, we describe a workflow for processing raw soil metagenome sequencing reads using the Sunbeam bioinformatics pipeline. The workflow includes cleaning and processing raw reads, taxonomic classification, assembly into contigs, annotation of predicted genes using custom protein databases, and exporting assemblies to the KBase platform for downstream analysis. This workflow is designed to be robust to annual data releases from NEON, and the underlying Snakemake framework can manage complex software dependencies. The workflow presented here aims to increase the accessibility of NEON’s shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.
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Delmont, Tom O., Patrick Robe, Sébastien Cecillon, Ian M. Clark, Florentin Constancias, Pascal Simonet, Penny R. Hirsch, and Timothy M. Vogel. "Accessing the Soil Metagenome for Studies of Microbial Diversity." Applied and Environmental Microbiology 77, no. 4 (December 23, 2010): 1315–24. http://dx.doi.org/10.1128/aem.01526-10.
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ABSTRACTSoil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.
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Owen, Jeremy G., Zachary Charlop-Powers, Alexandra G. Smith, Melinda A. Ternei, Paula Y. Calle, Boojala Vijay B. Reddy, Daniel Montiel, and Sean F. Brady. "Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors." Proceedings of the National Academy of Sciences 112, no. 14 (March 23, 2015): 4221–26. http://dx.doi.org/10.1073/pnas.1501124112.
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In molecular evolutionary analyses, short DNA sequences are used to infer phylogenetic relationships among species. Here we apply this principle to the study of bacterial biosynthesis, enabling the targeted isolation of previously unidentified natural products directly from complex metagenomes. Our approach uses short natural product sequence tags derived from conserved biosynthetic motifs to profile biosynthetic diversity in the environment and then guide the recovery of gene clusters from metagenomic libraries. The methodology is conceptually simple, requires only a small investment in sequencing, and is not computationally demanding. To demonstrate the power of this approach to natural product discovery we conducted a computational search for epoxyketone proteasome inhibitors within 185 globally distributed soil metagenomes. This led to the identification of 99 unique epoxyketone sequence tags, falling into 6 phylogenetically distinct clades. Complete gene clusters associated with nine unique tags were recovered from four saturating soil metagenomic libraries. Using heterologous expression methodologies, seven potent epoxyketone proteasome inhibitors (clarepoxcins A–E and landepoxcins A and B) were produced from these pathways, including compounds with different warhead structures and a naturally occurring halohydrin prodrug. This study provides a template for the targeted expansion of bacterially derived natural products using the global metagenome.
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Djokic, Lidija, M. Savic, Tanja Narancic, and Branka Vasiljevic. "Metagenomic analysis of soil microbial communities." Archives of Biological Sciences 62, no. 3 (2010): 559–64. http://dx.doi.org/10.2298/abs1003559d.
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Ramonda serbica and Ramonda nathaliae, rare resurrection plants growing in the Balkan Peninsula, produce a high amount of phenolic compounds as a response to stress. The composition and size of bacterial communities in two rhizosphere soil samples of these plants were analyzed using a metagenomic approach. Fluorescent in situ hybridization (FISH) experiments together with DAPI staining showed that the metabolically active bacteria represent only a small fraction, approximately 5%, of total soil bacteria. Using universal bacteria - specific primers 16S rDNA genes were amplified directly from metagenomic DNAs and two libraries were constructed. The Restriction Fragment Length Polymorphism (RLFP) method was used in library screening. Amongst 192 clones, 35 unique operational taxonomic units (OTUs) were determined from the rhizosphere of R. nathaliae, and 13 OTUs out of 80 clones in total from the library of R. serbica. Representative clones from each OTU were sequenced. The majority of sequences from metagenomes showed very little similarity to any cultured bacteria. In conclusion, the bacterial communities in the studied soil samples showed quite poor diversity. .
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Zorrilla, Francisco, Filip Buric, Kiran R. Patil, and Aleksej Zelezniak. "metaGEM: reconstruction of genome scale metabolic models directly from metagenomes." Nucleic Acids Research 49, no. 21 (October 6, 2021): e126-e126. http://dx.doi.org/10.1093/nar/gkab815.
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Abstract Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozorrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species communities directly from metagenomes. The pipeline automates all steps from the extraction of context-specific prokaryotic GEMs from MAGs to community level flux balance analysis (FBA) simulations. To demonstrate the capabilities of metaGEM, we analyzed 483 samples spanning lab culture, human gut, plant-associated, soil, and ocean metagenomes, reconstructing over 14,000 GEMs. We show that GEMs reconstructed from metagenomes have fully represented metabolism comparable to isolated genomes. We demonstrate that metagenomic GEMs capture intraspecies metabolic diversity and identify potential differences in the progression of type 2 diabetes at the level of gut bacterial metabolic exchanges. Overall, metaGEM enables FBA-ready metabolic model reconstruction directly from metagenomes, provides a resource of metabolic models, and showcases community-level modeling of microbiomes associated with disease conditions allowing generation of mechanistic hypotheses.
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Carver, Sarah M., Nadia Nikulin, and Jenny Kao-Kniffin. "Uncovering Plant Growth-Mediating Allelochemicals Produced by Soil Microorganisms." Weed Science 64, no. 1 (March 2016): 119–28. http://dx.doi.org/10.1614/ws-d-15-00095.1.
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Coevolving interactions between a plant population and its microbiota can potentially yield a rhizosphere enriched in metagenomes containing the blueprints for a vast array of natural products. We describe a method of isolating those metabolites through activity-based screening of soil metagenomic libraries. The method allows for the isolation of small molecules produced in vector–host expression systems containing large-insert DNA fragments extracted from the target plant rhizospheres. Allelopathic activities derived from selected clones were screened against a series of controls. Nonmetric multidimensional scaling (NMS) showed similar effects of the set of controls on lettuce growth, whereas annual bluegrass had a broader range of growth responses. Methanol extracts from clones indicating activity showed distinct patterns in grass seedling growth from the empty vector control, but the same extracts showed no effect on lettuce. The results indicate that the metagenomics method and bioassay screen of clone extracts are tools that can be used for initial determination of allelopathic activity from noncultured soil microbiota.
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Liles, Mark R., Lynn L. Williamson, Jitsupang Rodbumrer, Vigdis Torsvik, Robert M. Goodman, and Jo Handelsman. "Recovery, Purification, and Cloning of High-Molecular-Weight DNA from Soil Microorganisms." Applied and Environmental Microbiology 74, no. 10 (March 21, 2008): 3302–5. http://dx.doi.org/10.1128/aem.02630-07.
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ABSTRACT We describe here an improved method for isolating, purifying, and cloning DNA from diverse soil microbiota. Soil microorganisms were extracted from soils and embedded and lysed within an agarose plug. Nucleases that copurified with the metagenomic DNA were removed by incubating plugs with a high-salt and -formamide solution. This method was used to construct large-insert soil metagenomic libraries.
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Pinnell, Lee J., Eric Dunford, Patrick Ronan, Martina Hausner, and Josh D. Neufeld. "Recovering glycoside hydrolase genes from active tundra cellulolytic bacteria." Canadian Journal of Microbiology 60, no. 7 (July 2014): 469–76. http://dx.doi.org/10.1139/cjm-2014-0193.
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Bacteria responsible for cellulose hydrolysis in situ are poorly understood, largely because of the relatively recent development of cultivation-independent methods for their detection and characterization. This study combined DNA stable-isotope probing (DNA-SIP) and metagenomics for identifying active bacterial communities that assimilated carbon from glucose and cellulose in Arctic tundra microcosms. Following DNA-SIP, bacterial fingerprint analysis of gradient fractions confirmed isotopic enrichment. Sequenced fingerprint bands and clone library analysis of 16S rRNA genes identified active bacterial taxa associated with cellulose-associated labelled DNA, including Bacteroidetes (Sphingobacteriales), Betaproteobacteria (Burkholderiales), Alphaproteobacteria (Caulobacteraceae), and Chloroflexi (Anaerolineaceae). We also compared glycoside hydrolase metagenomic profiles from bulk soil and heavy DNA recovered from DNA-SIP incubations. Active populations consuming [13C]glucose and [13C]cellulose were distinct, based on ordinations of light and heavy DNA. Metagenomic analysis demonstrated a ∼3-fold increase in the relative abundance of glycoside hydrolases in DNA-SIP libraries over bulk-soil libraries. The data also indicate that multiple displacement amplification introduced bias into the resulting metagenomic analysis. This research identified DNA-SIP incubation conditions for glucose and cellulose that were suitable for Arctic tundra soil and confirmed that DNA-SIP enrichment can increase target gene frequencies in metagenomic libraries.
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Kim, Kyoung-Ho, Ho-Won Chang, Young-Do Nam, Seong Woon Roh, Min-Soo Kim, Youlboong Sung, Che Ok Jeon, Hee-Mock Oh, and Jin-Woo Bae. "Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil." Applied and Environmental Microbiology 74, no. 19 (August 15, 2008): 5975–85. http://dx.doi.org/10.1128/aem.01275-08.
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ABSTRACT Viruses are known to be the most numerous biological entities in soil; however, little is known about their diversity in this environment. In order to explore the genetic diversity of soil viruses, we isolated viruses by centrifugation and sequential filtration before performing a metagenomic investigation. We adopted multiple-displacement amplification (MDA), an isothermal whole-genome amplification method with φ29 polymerase and random hexamers, to amplify viral DNA and construct clone libraries for metagenome sequencing. By the MDA method, the diversity of both single-stranded DNA (ssDNA) viruses and double-stranded DNA viruses could be investigated at the same time. On the contrary, by eliminating the denaturing step in the MDA reaction, only ssDNA viral diversity could be explored selectively. Irrespective of the denaturing step, more than 60% of the soil metagenome sequences did not show significant hits (E-value criterion, 0.001) with previously reported viral sequences. Those hits that were considered to be significant were also distantly related to known ssDNA viruses (average amino acid similarity, approximately 34%). Phylogenetic analysis showed that replication-related proteins (which were the most frequently detected proteins) related to those of ssDNA viruses obtained from the metagenomic sequences were diverse and novel. Putative circular genome components of ssDNA viruses that are unrelated to known viruses were assembled from the metagenomic sequences. In conclusion, ssDNA viral diversity in soil is more complex than previously thought. Soil is therefore a rich pool of previously unknown ssDNA viruses.
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Sousa, Joana, Sara C. Silvério, Angela M. A. Costa, and Ligia R. Rodrigues. "Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water." Catalysts 12, no. 4 (March 30, 2022): 385. http://dx.doi.org/10.3390/catal12040385.
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Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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ITOH, HIDEOMI, SATOSHI ISHII, and KEISHI SENOO. "III-1. Metagenomics in agriculture: Metagenomic analysis of rice paddy field soil." NIPPON SUISAN GAKKAISHI 77, no. 2 (2011): 254. http://dx.doi.org/10.2331/suisan.77.254.
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Castillo Arteaga, Roger David, Simone Ichiwaki, Karen Massini, Leandro Maza-Garrido, Edith Mariela Burbano-Rosero, and Gabriel Padilla. "Screening of polyketide genes from Brazilian Atlantic Forest soil." Universitas Scientiarum 22, no. 1 (April 3, 2017): 87. http://dx.doi.org/10.11144/javeriana.sc22-1.sopg.
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Soil is a large source of microorganisms with potential to produce bioactive compounds. Since most of them cannot be cultured, metagenomics has become a useful tool in order to evaluate this potential. The aim of this study was to screen biosynthetic polyketide genes (PKS) present in a metagenomic library constructed from a soil sample isolated from the Brazilian Atlantic Forest. The library comprises 5000 clones with DNA inserts between 40 and 50 Kb. The characterization of the biosynthetic gene clusters of these molecules is a promising alternative to elucidate the biotechnological potential of bioactive compounds in microbial communities. The PKS genes were screened using degenerated primers. The positive clones for PKS systems were isolated, and their nucleotide sequences analysed with bioinformatics tools. The screening yielded two positive clones for PKS II genes. Furthermore, variations in the sequences of the PKS II genes from the metagenomic library were observed when compared with sequences of ketosynthases’ databases. With these findings we gain insight into the possible relation between new biosynthetic genes and the production of new secondary metabolites.
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Satoh, Soichirou, Rei Tanaka, Makio Yokono, Daiji Endoh, Tetsuo Yabuki, and Ayumi Tanaka. "Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota." PLOS ONE 18, no. 2 (February 2, 2023): e0281288. http://dx.doi.org/10.1371/journal.pone.0281288.
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Environmental factors affect the growth of microorganisms and therefore alter the composition of microbiota. Correlative analysis of the relationship between metagenomic composition and the environmental gradient can help elucidate key environmental factors and establishment principles for microbial communities. However, a reasonable method to quantitatively compare whole metagenomic data and identify the primary environmental factors for the establishment of microbiota has not been reported so far. In this study, we developed a method to compare whole proteomes deduced from metagenomic shotgun sequencing data, and quantitatively display their phylogenetic relationships as metagenomic trees. We called this method Metagenomic Phylogeny by Average Sequence Similarity (MPASS). We also compared one of the metagenomic trees with dendrograms of environmental factors using a comparison tool for phylogenetic trees. The MPASS method correctly constructed metagenomic trees of simulated metagenomes and soil and water samples. The topology of the metagenomic tree of samples from the Kirishima hot springs area in Japan was highly similarity to that of the dendrograms based on previously reported environmental factors for this area. The topology of the metagenomic tree also reflected the dynamics of microbiota at the taxonomic and functional levels. Our results strongly suggest that MPASS can successfully classify metagenomic shotgun sequencing data based on the similarity of whole protein-coding sequences, and will be useful for the identification of principal environmental factors for the establishment of microbial communities. Custom Perl script for the MPASS pipeline is available at https://github.com/s0sat/MPASS.
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Ma, Bin, Erinne Stirling, Yuanhui Liu, Kankan Zhao, Jizhong Zhou, Brajesh K. Singh, Caixian Tang, Randy A. Dahlgren, and Jianming Xu. "Soil Biogeochemical Cycle Couplings Inferred from a Function-Taxon Network." Research 2021 (March 10, 2021): 1–10. http://dx.doi.org/10.34133/2021/7102769.
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Soil biogeochemical cycles and their interconnections play a critical role in regulating functions and services of environmental systems. However, the coupling of soil biogeochemical processes with their mediating microbes remains poorly understood. Here, we identified key microbial taxa regulating soil biogeochemical processes by exploring biomarker genes and taxa of contigs assembled from metagenomes of forest soils collected along a latitudinal transect (18° N to 48° N) in eastern China. Among environmental and soil factors, soil pH was a sensitive indicator for functional gene composition and diversity. A function-taxon bipartite network inferred from metagenomic contigs identified the microbial taxa regulating coupled biogeochemical cycles between carbon and phosphorus, nitrogen and sulfur, and nitrogen and iron. Our results provide novel evidence for the coupling of soil biogeochemical cycles, identify key regulating microbes, and demonstrate the efficacy of a new approach to investigate the processes and microbial taxa regulating soil ecosystem functions.
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McGhee, Jordan J., Nick Rawson, Barbara A. Bailey, Antonio Fernandez-Guerra, Laura Sisk-Hackworth, and Scott T. Kelley. "Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics." PeerJ 8 (March 24, 2020): e8783. http://dx.doi.org/10.7717/peerj.8783.
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Background Microbial source tracking methods are used to determine the origin of contaminating bacteria and other microorganisms, particularly in contaminated water systems. The Bayesian SourceTracker approach uses deep-sequencing marker gene libraries (16S ribosomal RNA) to determine the proportional contributions of bacteria from many potential source environments to a given sink environment simultaneously. Since its development, SourceTracker has been applied to an extensive diversity of studies, from beach contamination to human behavior. Methods Here, we demonstrate a novel application of SourceTracker to work with metagenomic datasets and tested this approach using sink samples from a study of coastal marine environments. Source environment metagenomes were obtained from metagenomics studies of gut, freshwater, marine, sand and soil environments. As part of this effort, we implemented features for determining the stability of source proportion estimates, including precision visualizations for performance optimization, and performed domain-specific source-tracking analyses (i.e., Bacteria, Archaea, Eukaryota and viruses). We also applied SourceTracker to metagenomic libraries generated from samples collected from the International Space Station (ISS). Results SourceTracker proved highly effective at predicting the composition of known sources using shotgun metagenomic libraries. In addition, we showed that different taxonomic domains sometimes presented highly divergent pictures of environmental source origins for both the coastal marine and ISS samples. These findings indicated that applying SourceTracker to separate domains may provide a deeper understanding of the microbial origins of complex, mixed-source environments, and further suggested that certain domains may be preferable for tracking specific sources of contamination.
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Epihov, Dimitar Z., Kristin Saltonstall, Sarah A. Batterman, Lars O. Hedin, Jefferson S. Hall, Michiel van Breugel, Jonathan R. Leake, and David J. Beerling. "Legume–microbiome interactions unlock mineral nutrients in regrowing tropical forests." Proceedings of the National Academy of Sciences 118, no. 11 (March 8, 2021): e2022241118. http://dx.doi.org/10.1073/pnas.2022241118.
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Legume trees form an abundant and functionally important component of tropical forests worldwide with N2-fixing symbioses linked to enhanced growth and recruitment in early secondary succession. However, it remains unclear how N2-fixers meet the high demands for inorganic nutrients imposed by rapid biomass accumulation on nutrient-poor tropical soils. Here, we show that N2-fixing trees in secondary Neotropical forests triggered twofold higher in situ weathering of fresh primary silicates compared to non-N2–fixing trees and induced locally enhanced nutrient cycling by the soil microbiome community. Shotgun metagenomic data from weathered minerals support the role of enhanced nitrogen and carbon cycling in increasing acidity and weathering. Metagenomic and marker gene analyses further revealed increased microbial potential beneath N2-fixers for anaerobic iron reduction, a process regulating the pool of phosphorus bound to iron-bearing soil minerals. We find that the Fe(III)-reducing gene pool in soil is dominated by acidophilic Acidobacteria, including a highly abundant genus of previously undescribed bacteria, Candidatus Acidoferrum, genus novus. The resulting dependence of the Fe-cycling gene pool to pH determines the high iron-reducing potential encoded in the metagenome of the more acidic soils of N2-fixers and their nonfixing neighbors. We infer that by promoting the activities of a specialized local microbiome through changes in soil pH and C:N ratios, N2-fixing trees can influence the wider biogeochemical functioning of tropical forest ecosystems in a manner that enhances their ability to assimilate and store atmospheric carbon.
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Xu, Peng, Cyrus Modavi, Benjamin Demaree, Frederick Twigg, Benjamin Liang, Chen Sun, Wenjun Zhang, and Adam R. Abate. "Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery." Nucleic Acids Research 48, no. 8 (February 25, 2020): e48-e48. http://dx.doi.org/10.1093/nar/gkaa131.
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Abstract Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samples using microfluidic automated plasmid library enrichment. Our approach provides deep coverage of the target gene cluster, facilitating reassembly. We demonstrate the approach by isolating and sequencing type I polyketide synthase gene clusters from an Antarctic soil metagenome. Our method promotes the discovery of functional-related genes and biosynthetic pathways.
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Delegan, Yanina, Svetlana Sushkova, Tatiana Minkina, Andrey Filonov, Yulia Kocharovskaya, Konstantin Demin, Andrey Gorovtsov, et al. "Diversity and Metabolic Potential of a PAH-Degrading Bacterial Consortium in Technogenically Contaminated Haplic Chernozem, Southern Russia." Processes 10, no. 12 (December 1, 2022): 2555. http://dx.doi.org/10.3390/pr10122555.
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Polycyclic aromatic hydrocarbons (PAHs) are chemically recalcitrant carcinogenic and mutagenic compounds with primarily anthropogenic origin. The investigation of the effects of emissions from energy enterprises on soil microbiomes is of a high priority for modern soil science. In this study, metagenomic profiling of technogenic contaminated soils was carried out based on bioinformatic analysis of shotgun metagenome data with PAH-degrading genes identification. The use of prokaryotic consortia has been often used as one of the bio-remediation approaches to degrade PAHs with different molecular weight. Since the process of PAH degradation predominantly includes non-culturable or yet-to-be cultured species, metagenomic approaches are highly recommended for studying the composition and metabolic abilities of microbial communities. In this study, whole metagenome shotgun sequencing of DNA from two soils with varying PAH levels was performed. In the control site, the total content of 12 priority PAHs was 262 µg kg−1. The background soil levels in the polluted site for PAHs with 3 or more rings exceeded this, at 800 µg kg−1. The abundance of genes and taxa associated with PAH degradation in these two sites were estimated. Despite differences in PAH concentrations up to 1200 µg kg−1, individual and operon-organized PAH degradation genes were almost equally abundant and diverse in pristine and highly contaminated areas. The most numerous taxa in both spots were actinobacteria from Terrabacteria group. In addition to well-known PAH degraders such as Gordonia and Rhodococcus, genes corresponding to the PAH degradation were found in Azoarcus, Burkholderia and Variovorax. The data shows non-specificity and multifunctionality of metabolic pathways encoded in the genes of PAH-degrading microorganisms.
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Ahmad, Mohd Fadzli, Hasdianty Abdullah, Muhammad Naim Hassan, Muhammad Imran Jamaludin, Ashvini Sivam, Kazuhiro Komatsu, Irni Suhayu Sapian, et al. "Topographically Distinguished Microbiome Taxonomy and Stress-Response Genes of Royal Belum Rainforest and Raja Muda Musa Peat Swamp Revealed through Metagenomic Inquisition." International Journal of Molecular Sciences 24, no. 1 (January 3, 2023): 872. http://dx.doi.org/10.3390/ijms24010872.
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Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.
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Jaswal, Pathak, III, III, Seaman, Stothard, Krivushin, Blom, Rupp, and Chauhan. "Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA." Genes 10, no. 5 (April 28, 2019): 325. http://dx.doi.org/10.3390/genes10050325.
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Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.
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Monier, Jean-Michel, Sandrine Demanèche, Tom O. Delmont, Alban Mathieu, Timothy M. Vogel, and Pascal Simonet. "Metagenomic exploration of antibiotic resistance in soil." Current Opinion in Microbiology 14, no. 3 (June 2011): 229–35. http://dx.doi.org/10.1016/j.mib.2011.04.010.
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Echeverría-Beirute, Fabián, Ingrid Varela-Benavides, Jose P Jiménez-Madrigal, Milagro Carvajal-Chacon, and Tomás Guzmán-Hernández. "eDNA extraction protocol for metagenomic studies in tropical soils." BioTechniques 71, no. 6 (December 2021): 580–86. http://dx.doi.org/10.2144/btn-2021-0057.
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The lack of knowledge about biological communities residing in soils, especially those in tropical regions, represents a constraint to management practices to take advantage of the ecological services provided by soil microbiota to agroecosystems. One of the complexities derived from describing biological diversity in such tropical conditions comes from the methods used to isolate microorganisms without altering the composition of the sample. The goal of this study was to establish a protocol for adequate soil sampling and environmental DNA extraction from a tropical region in Costa Rica. We present an up-to-date protocol optimized for tropical soils which improves sevenfold the amount of DNA extracted without significantly affecting the 260/280 and 260/230 ratios compared with commercially available kits and standard protocols.
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Rahman, Khondaker Md Jaminur, Farzana Diba, Md Sadikur Rahman Shuvo, Mohammad Anwar Siddique, M. Anwar Hossain, and Munawar Sultana. "Metagenomic investigation of bacterial community of arsenic-prone area in the northwest region of Bangladesh." Bangladesh Journal of Microbiology 39, no. 1 (January 22, 2023): 31–38. http://dx.doi.org/10.3329/bjm.v39i1.64056.
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Metagenomic analysis provides in-depth understanding of microbe mediated Arsenic (As) metabolism. The present study aims atmetagenomic analysis of the distribution, diversity, and abundance of bacteriome in arsenic affected groundwater and surrounding soils collected fromBogra district of Bangladesh. Metagenomic DNA was extracted from two groundwater samples BCW3 andBCW4 (As content10μgL-1 and 500 μgL-1, respectively), and two tube-well surrounding soil samples BSS1 and BCS5 (As content335 μgkg-1 and 492 μgkg-1),where As rich water flows off. Metagenomic analysis of six hypervariable regions of 16S rRNA gene resulted in a total of 788709 processed sequence reads and 5878 operational taxonomic units (OTUs). Bacterial richness, abundance and diversity (alpha and beta) were higher in BCW4 (85 genera) than BCW3 (19 genera) whereas both soil samples exhibited almost similar richness and diversity. Predominant genera in BCW3 were Pseudomonas, Microbacterium, Achromobacterwhereas Acinetobacter, Thiothrix, Stenotrophomonas, Paracoccus, Dechloromonas dominated in BCW4. Soils were co-dominated with more than hundreds of genera with a high relative abundance of Bacillus, Rhodoplanesand Pseudomonas.Metagenomic investigation explored potentialarsenotrophicbacteriome. Exploring microbial community might help to understand the biogeochemistry of As affected groundwater and surrounding soil environment.
Bangladesh J Microbiol, Volume 39, Number 1, June 2022, pp 31-38
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Sanchez-Cid, Concepcion, Romie Tignat-Perrier, Laure Franqueville, Laurence Delaurière, Trista Schagat, and Timothy M. Vogel. "Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery." Biomolecules 12, no. 3 (February 25, 2022): 364. http://dx.doi.org/10.3390/biom12030364.
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Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the soil microbiome and its ecosystem function. In this study, we compared the effects of DNA extraction and sequencing depth on bacterial richness discovery from two soil samples. Four DNA extraction methods were used, and sequencing duplicates were generated for each DNA sample. The V3–V4 region of the 16S rRNA gene was sequenced to determine the taxonomical richness measured by each method at the amplicon sequence variant (ASV) level. Both the overall functional richness and antibiotic resistance gene (ARG) richness were evaluated by metagenomics sequencing. Despite variable DNA extraction methods, sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Sequencing duplicates from the same sample provided access to different portions of bacterial richness, and this was related to differences in the sequencing depth. Thus, the sequencing depth introduced biases in the comparison of DNA extraction methods. An optimisation of the soil metagenomics workflow is needed in order to sequence at a sufficient and equal depth. This would improve the accuracy of metagenomic comparisons and soil microbiome profiles.
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Kim, Jin-Wook, Young-Kyu Hong, Hyuck-Soo Kim, Eun-Ji Oh, Yong-Ha Park, and Sung-Chul Kim. "Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil after Soil Remediation." Toxics 9, no. 12 (November 24, 2021): 319. http://dx.doi.org/10.3390/toxics9120319.
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Soil washing and landfarming processes are widely used to remediate total petroleum hydrocarbon (TPH)-contaminated soil, but the impact of these processes on soil bacteria is not well understood. Four different states of soil (uncontaminated soil (control), TPH-contaminated soil (CS), after soil washing (SW), and landfarming (LF)) were collected from a soil remediation facility to investigate the impact of TPH and soil remediation processes on soil bacterial populations by metagenomic analysis. Results showed that TPH contamination reduced the operational taxonomic unit (OTU) number and alpha diversity of soil bacteria. Compared to SW and LF remediation techniques, LF increased more bacterial richness and diversity than SW, indicating that LF is a more effective technique for TPH remediation in terms of microbial recovery. Among different bacterial species, Proteobacteria were the most abundant in all soil groups followed by Actinobacteria, Acidobacteria, and Firmicutes. For each soil group, the distribution pattern of the Proteobacteria class was different. The most abundant classed were Alphaproteobacteria (16.56%) in uncontaminated soils, Deltaproteobacteria (34%) in TPH-contaminated soils, Betaproteobacteria (24%) in soil washing, and Gammaproteobacteria (24%) in landfarming, respectively. TPH-degrading bacteria were detected from soil washing (23%) and TPH-contaminated soils (21%) and decreased to 12% in landfarming soil. These results suggest that soil pollution can change the diversity of microbial groups and different remediation techniques have varied effective ranges for recovering bacterial communities and diversity. In conclusion, the landfarming process of TPH remediation is more advantageous than soil washing from the perspective of bacterial ecology.
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Kangabam, Rajiv Das, Yumnam Silla, Gunajit Goswami, and Madhumita Barooah. "Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes." Current Genomics 21, no. 7 (October 22, 2020): 512–24. http://dx.doi.org/10.2174/1389202921999200716104355.
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Background: Microorganisms are an important component of an aquatic ecosystem and play a critical role in the biogeochemical cycle which influences the circulation of the materials and maintains the balance in aquatic ecosystems. Objective: The seasonal variation along with the impact of anthropogenic activities, water quality, bacterial community composition and dynamics in the Loktak Lake, the largest freshwater lake of North East India, located in the Indo-Burma hotspot region was assessed during post-monsoon and winter season through metagenome analysis. Methods: Five soil samples were collected during Post-monsoon and winter season from the Loktak Lake that had undergone different anthropogenic impacts. The metagenomic DNA of the soil samples was extracted using commercial metagenomic DNA extraction kits following the manufacturer’s instruction. The extracted DNA was used to prepare the NGS library and sequenced in the Illumina MiSeq platform. Results: Metagenomics analysis reveals Proteobacteria as the predominant community followed by Acidobacteria and Actinobacteria. The presence of these groups of bacteria indicates nitrogen fixation, oxidation of iron, sulfur, methane, and source of novel antibiotic candidates. The bacterial members belonging to different groups were involved in various biogeochemical processes, including fixation of carbon and nitrogen, producing streptomycin, gramicidin and perform oxidation of sulfur, sulfide, ammonia, and methane. Conclusion: The outcome of this study provides a valuable dataset representing a seasonal profile across various land use and analysis, targeting at establishing an understanding of how the microbial communities vary across the land use and the role of keystone taxa. The findings may contribute to searches for microbial bio-indicators as biodiversity markers for improving the aquatic ecosystem of the Loktak Lake.
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Eaton, William D., Shadi Shokralla, Kathleen M. McGee, and Mehrdad Hajibabaei. "Using metagenomics to show the efficacy of forest restoration in the New Jersey Pine Barrens." Genome 60, no. 10 (October 2017): 825–36. http://dx.doi.org/10.1139/gen-2015-0199.
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The Franklin Parker Preserve within the New Jersey Pine Barrens contains 5000 acres of wetlands habitat, including old-growth Atlantic white cedar (or AWC; Chamaecyparis thyoides) swamps, cranberry bogs, and former cranberry bogs undergoing restoration into AWC forests. This study showed that the C-use efficiency was greater in the old-growth AWC soils than in soils from 8-year-old mid-stage restored AWC stands, which were greater than found in soil from 4-year-old AWC stands—the latter two stands being restored from long-term cranberry bogs. A metagenomic analysis of eDNA extracted from these soils showed that the C-cycle trends were associated with increases in the relative numbers of DNA sequences from several copiotrophic bacterial groups (Bacteroidetes and Proteobacteria), complex C-decomposing fungal groups (Sordiomycetes, Mortierellales, and Thelephorales), and collembolan and formicid invertebrates. All groups are indicators of successionally more advanced soils, and critical for soil C-cycle activities. These data suggest that the restoration activities studied are enhancing critical guilds of soil biota, and increasing C-use efficiency in the soils of restored habitats, and that the use of metagenomic analysis of soil eDNA can be used in the development of assessment models for soil recovery of wetlands following restoration.
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McMahon, Matthew D., Changhui Guan, Jo Handelsman, and Michael G. Thomas. "Metagenomic Analysis of Streptomyces lividans Reveals Host-Dependent Functional Expression." Applied and Environmental Microbiology 78, no. 10 (March 16, 2012): 3622–29. http://dx.doi.org/10.1128/aem.00044-12.
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ABSTRACTMost functional metagenomic studies have been limited by the poor expression of many genes derived from metagenomic DNA inEscherichia coli, which has been the predominant surrogate host to date. To expand the range of expressed genes, we developed tools for construction and functional screening of metagenomic libraries inStreptomyces lividans. We expanded on previously published protocols by constructing a system that enables retrieval and characterization of the metagenomic DNA from biologically active clones. To test the functionality of these methods, we constructed and screened two metagenomic libraries inS. lividans. One was constructed with pooled DNA from 14 bacterial isolates cultured from Alaskan soil and the second with DNA directly extracted from the same soil. Functional screening of these libraries identified numerous clones with hemolytic activity, one clone that produces melanin by a previously unknown mechanism, and one that induces the overproduction of a secondary metabolite native toS. lividans. All bioactive clones were functional inS. lividansbut not inE. coli, demonstrating the advantages of screening metagenomic libraries in more than one host.
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Assis, Danyelle Alves Martins, Rachel Passos Rezende, and João Carlos Teixeira Dias. "Use of Metagenomics and Isolation of Actinobacteria in Brazil’s Atlantic Rainforest Soil for Antimicrobial Prospecting." ISRN Biotechnology 2014 (March 12, 2014): 1–7. http://dx.doi.org/10.1155/2014/909601.
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Modern techniques involving molecular biology, such as metagenomics, have the advantage of exploiting a higher number of microorganisms; however, classic isolation and culture methods used to obtain antimicrobials continue to be promising, especially in the isolation of Actinobacteria, which are responsible for the production of many of these compounds. In this work, two methodologies were used to search for antimicrobial substances—isolation of Actinobacteria and metagenomics of the Atlantic Rainforest soil and of the cultivation of cocoa intercropped with acai berry in the Atlantic Rainforest. The metagenomic libraries were constructed with the CopyControl Fosmid Library kit EPICENTRE, resulting in a total of 2688 clones, 1344 of each soil sample. None of the clones presented antimicrobial activity against the microorganisms tested: S. aureus, Bacillus subtilis, and Salmonella choleraesuis. A total of 46 isolates were obtained from the isolation of soil Actinobacteria: 24 isolates from Atlantic Rainforest soil and 22 isolates from the intercrop cultivation soil. Of these, two Atlantic Rainforest soil isolates inhibited the growth of S. aureus including a clinical isolate of S. aureus MRSA—a promising result, since it is an important multidrug-resistant human pathogen.
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Srinivasiah, Sharath, Jacqueline Lovett, Shawn Polson, Jaysheel Bhavsar, Dhritiman Ghosh, Krishnakali Roy, Jeffry J. Fuhrmann, Mark Radosevich, and K. Eric Wommack. "Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA." Applied and Environmental Microbiology 79, no. 18 (June 21, 2013): 5450–57. http://dx.doi.org/10.1128/aem.00268-13.
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ABSTRACTViruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity.
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Nelkner, Johanna, Christian Henke, Timo Wentong Lin, Wiebke Pätzold, Julia Hassa, Sebastian Jaenicke, Rita Grosch, Alfred Pühler, Alexander Sczyrba, and Andreas Schlüter. "Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes." Genes 10, no. 6 (June 3, 2019): 424. http://dx.doi.org/10.3390/genes10060424.
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To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe–plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant–growth–promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.
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Gorman, Myranda, Ruijie Xu, Dhani Prakoso, Liliana C. M. Salvador, and Sreekumari Rajeev. "Leptospira enrichment culture followed by ONT metagenomic sequencing allows better detection of Leptospira presence and diversity in water and soil samples." PLOS Neglected Tropical Diseases 16, no. 10 (October 26, 2022): e0010589. http://dx.doi.org/10.1371/journal.pntd.0010589.
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Background Leptospirosis, a life-threatening disease in humans and animals, is one of the most widespread global zoonosis. Contaminated soil and water are the major transmission sources in humans and animals. Clusters of disease outbreaks are common during rainy seasons. Methodology/Principal findings In this study, to detect the presence of Leptospira, we applied PCR, direct metagenomic sequencing, and enrichment culture followed by PCR and metagenomic sequencing on water and soil samples. Direct sequencing and enrichment cultures followed by PCR or sequencing effectively detected pathogenic and nonpathogenic Leptospira compared to direct PCR and 16S amplification-based metagenomic sequencing in soil or water samples. Among multiple culture media evaluated, Ellinghausen-McCullough-Johnson-Harris (EMJH) media containing antimicrobial agents was superior in recovering and detecting Leptospira from the environmental samples. Our results show that enrichment culture followed by PCR can be used to confirm the presence of pathogenic Leptospira in environmental samples. Additionally, metagenomic sequencing on enrichment cultures effectively detects the abundance and diversity of Leptospira spp. from environmental samples. Conclusions/Significance The selection of methodology is critical when testing environmental samples for the presence of Leptospira. Selective enrichment culture improves Leptospira detection efficacy by PCR or metagenomic sequencing and can be used successfully to understand the presence and diversity of pathogenic Leptospira during environmental surveillance.
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Wu, Lin Hui, Jian Li Liu, Jing Zeng, and Ji Zhao. "Comparison of DNA Extraction and Purification Methods from Different Soils for Metagenomic Sequencing." Advanced Materials Research 955-959 (June 2014): 306–9. http://dx.doi.org/10.4028/www.scientific.net/amr.955-959.306.
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There is an increased interest in the extraction of nucleic acids from various environmental samples, since only a minority of naturally occurring microbes can be cultured using standard techniques. Nucleic acids extraction and purification from soils are extremely challenging due to the low biomass, high organic contents and high variability of soil types. This has been regarded as one of the major difficulties that hamper the development of soil microbial ecology study. No commercial nucleic acids kits currently available are capable of preparing the DNAs without modifications. The cost can be very high for DNA extraction from extreme environmental soil samples, such as soils that have extreme high or low pHs. In this work, we developed and optimized soil DNA extraction and purification methods on different soils and compared the impact of three different DNA extraction protocols on DNA yield and purity. For the three different types of soil we used, direct extraction obtained the highest DNA recover rate, but required more cleanup steps. MoBio PowerSoil® DNA Isolation Kit yields less but do not require as many downstream cleaning steps. Both of the two methods obtained a more abundant microbial community than Meta-G-NomeTMDNA Isolation Kit.
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Ordine, João Vitor Wagner, Gabrielle Messias de Souza, Gustavo Tamasco, Stela Virgilio, Ana Flávia Tonelli Fernandes, Rafael Silva-Rocha, and María-Eugenia Guazzaroni. "Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil." Antibiotics 12, no. 2 (February 5, 2023): 334. http://dx.doi.org/10.3390/antibiotics12020334.
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Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities’ structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.
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Forsberg, Kevin J., Sanket Patel, Evan Witt, Bin Wang, Tyler D. Ellison, and Gautam Dantas. "Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes." Applied and Environmental Microbiology 82, no. 2 (November 6, 2015): 528–37. http://dx.doi.org/10.1128/aem.02838-15.
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ABSTRACTThe production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. These harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. We applied small-insert functional metagenomic selections to discover genes that confer microbial tolerance to these inhibitors, identifying both individual genes and general biological processes associated with tolerance to multiple inhibitory compounds. Having screened over 248 Gb of DNA cloned from 16 diverse soil metagenomes, we describe gain-of-function tolerance against acid, alcohol, and aldehyde inhibitors derived from hemicellulose and lignin, demonstrating that uncultured soil microbial communities hold tremendous genetic potential to address the toxicity of pretreated lignocellulose. We recovered genes previously known to confer tolerance to lignocellulosic inhibitors as well as novel genes that confer tolerance via unknown functions. For instance, we implicated galactose metabolism in overcoming the toxicity of lignin monomers and identified a decarboxylase that confers tolerance to ferulic acid; this enzyme has been shown to catalyze the production of 4-vinyl guaiacol, a valuable precursor to vanillin production. These metagenomic tolerance genes can enable the flexible design of hardy microbial catalysts, customized to withstand inhibitors abundant in specific bioprocessing applications.
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Riffiani, Rini, Nunik Sulistinah, and Bambang Sunarko. "Gene Encoding Nitrilase from Soil Sample of Lombok Gold Mine Industry using Metagenomics Approach." KnE Life Sciences 3, no. 4 (March 27, 2017): 201. http://dx.doi.org/10.18502/kls.v3i4.705.
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<p class="Els-body-text">This paper describes a efficient screening gene nitrilase from contaminated soil from Lombok gold mine industry. DNA was extracted directly from soil using the soil DNA isolation kit based on enzymatic, chemical and mechanical lysis. The existence of nitrilase gene in soil sample can be identified by nitrilase gene amplification using H1F˗H1R primer. BLASTN analysis result revealed that the nitrilase gene fragment which was amplified by H1F˗H1R primer has a high homology with <em>Rhodococcus rhodochrous </em>strain<em> tg1˗A6 nitrilase gene</em>. These amplification and DNA fragment sequencing results indicated that nitrilase gene existence on soil sample can be identified by metagenomic approach</p><p class="Els-Abstract-text"> </p><div><p class="Els-keywords"><strong>Keywords:</strong> Metagenomics; nitrilase gene; <em>Rhodococcus rhodochrous</em>; soil.</p></div>
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Demanèche, Sandrine, Laurent Philippot, Maude M. David, Elisabeth Navarro, Timothy M. Vogel, and Pascal Simonet. "Characterization of Denitrification Gene Clusters of Soil Bacteria via a Metagenomic Approach." Applied and Environmental Microbiology 75, no. 2 (November 14, 2008): 534–37. http://dx.doi.org/10.1128/aem.01706-08.
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ABSTRACT We characterized operons encoding enzymes involved in denitrification, a nitrogen-cycling process involved in nitrogen losses and greenhouse gas emission, using a metagenomic approach which combines molecular screening and pyrosequencing. Screening of 77,000 clones from a soil metagenomic library led to the identification and the subsequent characterization of nine denitrification gene clusters.
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Czarny, Jakub, Justyna Staninska-Pięta, Jolanta Powierska-Czarny, Jacek Nowak, Łukasz Wolko, and Agnieszka Piotrowska-Cyplik. "Metagenomic Analysis of Soil Bacterial Community and Level of Genes Responsible for Biodegradation of Aromatic Hydrocarbons." Polish Journal of Microbiology 66, no. 3 (September 27, 2017): 345–52. http://dx.doi.org/10.5604/01.3001.0010.4865.
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The aim of the studies was to compare the composition of soil bacterial metabiomes originating from urbanized areas and areas con¬taminated with hydrocarbons with those from agricultural soil and forest soil obtained from a protected wild-life park area. It should be noted that hydrocarbons are everywhere therefore bacteria capable of their utilization are present in every soil type. In the hydrocarbon-contaminated soil and in the soil of anthropogenic origin, the bacteria belonging to Gammaproteobacteria were dominant (28.4–36.6%), whereas in the case of agricultural soil and protected wild-life park soil their ratios decreased (22.8–23.0%) and were similar to that of Alphaproteobacteria. No statistically significant changes were observed in terms of the Operational Taxonomic Unit identified in the studies soils, however, based on the determined alpha-diversity it can be established that contaminated soils were characterized by lower biodiversity indices compared to agricultural and forest soils. Furthermore, the dioxygenase level was also evaluated in the studied soils, which are genes encoding crucial enzymes for the decomposition of mono- and polycyclic aromatic hydrocarbons during the biodegradation of diesel oil (PAHRHDαGN, PAHRHDαGP, xylE, Cat 2,3, ndoB). It was concluded that both the population structure of the soil metabiome and the number of genes crucial for biodegradation processes differed significantly between the soils. The level of analysed genes showed a similar trend, as their highest number in relations to genes encoding 16S RNA was determined in urban and hydrocarbon-contaminated soil.
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Eltokhy, Mohamed A., Bishoy T. Saad, Wafaa N. Eltayeb, Ibrahim S. Yahia, Khaled M. Aboshanab, and Mohamed S. E. Ashour. "Exploring the Nature of the Antimicrobial Metabolites Produced by Paenibacillus ehimensis Soil Isolate MZ921932 Using a Metagenomic Nanopore Sequencing Coupled with LC-Mass Analysis." Antibiotics 11, no. 1 (December 22, 2021): 12. http://dx.doi.org/10.3390/antibiotics11010012.
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The continuous emergence of multidrug-resistant (MDR) pathogens poses a global threat to public health. Accordingly, global efforts are continuously conducted to find new approaches to infection control by rapidly discovering antibiotics, particularly those that retain activities against MDR pathogens. In this study, metagenomic nanopore sequence analysis coupled with spectroscopic methods has been conducted for rapid exploring of the various active metabolites produced by Paenibacillus ehimensis soil isolate. Preliminary soil screening resulted in selection of a Gram-positive isolate identified via 16S ribosomal RNA gene sequencing as Paenibacillus ehimensis MZ921932. The isolate showed a broad range of activity against MDR Gram-positive, Gram-negative, and Candida spp. A metagenomics sequence analysis of the soil sample harboring Paenibacillus ehimensis isolate MZ921932 (NCBI GenBank accession PRJNA785410) revealed the presence of conserved biosynthetic gene clusters of petrobactin, tridecaptin, locillomycin (β-lactone), polymyxin, and macrobrevin (polyketides). The liquid chromatography/mass (LC/MS) analysis of the Paenibacillus ehimensis metabolites confirmed the presence of petrobactin, locillomycin, and macrobrevin. In conclusion, Paenibacillus ehimensis isolate MZ921932 is a promising rich source for broad spectrum antimicrobial metabolites. The metagenomic nanopore sequence analysis was a rapid, easy, and efficient method for the preliminary detection of the nature of the expected active metabolites. LC/MS spectral analysis was employed for further confirmation of the nature of the respective active metabolites.
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Lu, Xinda, Katherine R. Heal, Anitra E. Ingalls, Andrew C. Doxey, and Josh D. Neufeld. "Metagenomic and chemical characterization of soil cobalamin production." ISME Journal 14, no. 1 (September 6, 2019): 53–66. http://dx.doi.org/10.1038/s41396-019-0502-0.
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Fierer, Noah, Mya Breitbart, James Nulton, Peter Salamon, Catherine Lozupone, Ryan Jones, Michael Robeson, et al. "Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil." Applied and Environmental Microbiology 73, no. 21 (September 7, 2007): 7059–66. http://dx.doi.org/10.1128/aem.00358-07.
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ABSTRACT Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.
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Kao-Kniffin, Jenny, Sarah M. Carver, and Antonio DiTommaso. "Advancing Weed Management Strategies Using Metagenomic Techniques." Weed Science 61, no. 2 (June 2013): 171–84. http://dx.doi.org/10.1614/ws-d-12-00114.1.
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Global occurrences of herbicide resistant weed populations have increased the demand for development of new herbicides targeting novel mechanisms of action. Metagenomic approaches to natural drug discovery offer potential for isolating weed suppressive compounds from microorganisms. In past research, traditional techniques entailed isolating compounds from living organisms, whereas metagenomic approaches involve extracting fragments of DNA from soil and exploring for compounds of interest produced by the transformed hosts. Several herbicidal compounds have been isolated from soil bacteria through culturing methods and have led to the development of popular herbicides, such as glufosinate. In this review, we discuss the emergence of metagenomic approaches for weed management in the context of natural product discovery using traditional culture-dependent isolation and the more recent culture-independent methods. The same techniques can be used to isolate herbicide resistance genes. Adoption of metagenomic approaches in pest management research can lead to novel control strategies in cropping and landscape systems.
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Ehrhardt, Linda, P. Mike Günther, Manfred Böhme, J. Michael Köhler, and Jialan Cao. "Three Soil Bacterial Communities from an Archaeological Excavation Site of an Ancient Coal Mine near Bennstedt (Germany) Characterized by 16S r-RNA Sequencing." Environments 9, no. 9 (September 5, 2022): 115. http://dx.doi.org/10.3390/environments9090115.
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This metagenomics investigation of three closely adjacent sampling sites from an archaeological excavation of a pre-industrial coal mining exploration shaft provides detailed information on the composition of the local soil bacterial communities. The observed significant differences between the samples, reflected in the 16S r-RNA analyses, were consistent with the archaeologically observed situation distinguishing the coal seam, the rapidly deposited bright sediment inside an exploration shaft, and the topsoil sediment. In general, the soils were characterized by a dominance of Proteobacteria, Actinobacteria, Acidobacteria, and Archaea, whereas the coal seam was characterized by the highest proportion of Proteobacteria; the topsoil was characterized by very high proportions of Archaea—in particular, Nitrosotaleaceae—and Acidobacteria, mainly of Subgroup 2. Interestingly, the samples of the fast-deposited bright sediment showed a rank function of OTU abundances with disproportional values in the lower abundance range. This could be interpreted as a reflection of the rapid redeposition of soil material during the refilling of the exploration shaft in the composition of the soil bacterial community. This interpretation is supported by the observation of a comparatively high proportion of reads relating to bacteria known to be alkaliphilic in this soil material. In summary, these investigations confirm that metagenomic analyses of soil material from archaeological excavations can provide valuable information about the local soil bacterial communities and the historical human impacts on them.