Academic literature on the topic 'Soil metagenomic'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Soil metagenomic.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Journal articles on the topic "Soil metagenomic"
1
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.
Full textAbstract:
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.
2
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.
Full textAbstract:
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.
3
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.
Full textAbstract:
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.
4
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.
Full textAbstract:
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.
5
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.
Full textAbstract:
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.
6
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.
Full textAbstract:
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.
7
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.
Full textAbstract:
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.
8
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.
Full textAbstract:
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.
9
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.
Full textAbstract:
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.
10
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.
Full textAbstract:
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.
Dissertations / Theses on the topic "Soil metagenomic"
1
Goode, Ann Marie Liles Mark Russell. "Polyketide synthase pathway discovery from soil metagenomic libraries." Auburn, Ala., 2009. http://hdl.handle.net/10415/1805.
Full text
2
Shezi, Ntombifuthi. "Bio-prospecting a Soil Metagenomic Library for Carbohydrate Active Esterases." Thesis, Rhodes University, 2016. http://hdl.handle.net/10962/d1021266.
Full textAbstract:
Lignocellulosic biomass is a promising renewable resource on earth. Plant biomass contains fermentable sugars and other moieties that can be converted to biofuels or other chemicals. Enzymatic hydrolysis of these biopolymers is significant in the liberation of sugars for fermentation into desired products. Owing to its complex structure, synergistic action of enzymes is required for its degradation. Enzymes that are involved in biomass degradation include cellulases, hemicellulases and the accessory enzymes acetyl xylan esterases and ferulic acid esterases. Ferulic acid esterases (FAEs, EC 3.1.1.73), represent a subclass of carboxylester hydrolases (EC 3.1.1.-) that catalyse the release of hydroxycinnamic acids (such as ferulic acid, p-coumaric, ferulic, sinapic and caffeic acid) that are generally found esterified to polysaccharides, such as arabinoxylans. Hydroxycinnamic acids have widespread potential applications due to their antimicrobial, photoprotectant and antioxidant properties, as well as their use as flavour precursors. Therefore, this interesting group of FAEs has a potentially wide variety of applications in agriculture, food and pharmaceutical industries. In the search for novel biocatalysts, metagenomics is considered as an alternative approach to conventional microbe screening, therefore, searching for novel biocatalysts from a soil metagenome that harbours a unique diversity of biocatalyst is significant. The aim of this study was to extract DNA from soil associated with cattle manure and construct a soil metagenomic library using a fosmid based plasmid vector and subsequently functionally screen for ferulic acid esterases using ethyl ferulate as a model substrate. A total of 59 recombinant fosmids conferring ferulic acid esterase phenotypes were identified (Hit rate 1:3122) and the two fosmids that consistently showed high FAE activities were selected for further study. Following nucleotide sequencing and translational analysis, two fae encoding open reading frames (FAE9 and FAE27) of approximately 274 and 322 aa, respectively, were identified. The amino acid sequence of the two ORFs contained a classical conserved esterase/lipase G-x-S-x-G sequence motif. The two genes (fae9 and fae27) were successfully expressed in Escherichia coli BL21 (DE3) and the purified enzymes exhibited respective temperature optima of 50 °C and 40 °C, and respective pH optima of 6.0 and 7.0. Further biochemical characterisation showed that FAE9 and FAE27 have high substrate specificity, following the fact that EFA is the preferred substrate for FAE9 (kcat/Km value of 128 s−1.mM-1) and also the preferred substrate for FAE27 (kcat/Km value of 137 s−1.mM-1). This work proves that soil is a valuable environmental source for novel esterase screening through functional based metagenomic approach. Therefore, this method may be used to screen for other valuable enzymes from environmental sources using inexpensive natural sources to encourage the screening of specific enzymes. Biochemistry of the two isolated enzymes makes these enzymes to be useful in industrial applications due to broad substrate activity that could replace the specialised enzymes to complete plant biomass degradation.
3
Spiegelman, Dan. "Exploring the fusion of metagenomic library and DNA microarray technologies." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=98805.
Full textAbstract:
We explored the combination of metagenomic library and DNA microarray technologies into a single platform as a novel way to rapidly screen metagenomic libraries for genetic targets. In the "metagenomic microarray" system, metagenomic library clone DNA is printed on a microarray surface, and clones of interest are detected by hybridization to single-gene probes. This study represents the initial steps in the development of this technology. We constructed two 5,000-clone large-insert metagenomic libraries from two diesel-contaminated Arctic soil samples. We developed and optimized an automated fosmid purification protocol to rapidly-extract clone DNA in a high-throughput 96-well format. We then created a series of small prototype arrays to optimize various parameters of microarray printing and hybridization, to identify and resolve technical challenges, and to provide proof-of-principle of this novel application. Our results suggest that this method shows promise, but more experimentation must be done to establish the feasibility of this approach.
4
Borsetto, Chiara. "Study and exploitation of diverse soil environments for novel natural product discovery using metagenomic approaches." Thesis, University of Warwick, 2017. http://wrap.warwick.ac.uk/97341/.
Full textAbstract:
Natural products with antimicrobial activity have played an important role in the treatment of infection since their discovery. The increasing emergence of pathogens resistant to multiple antibiotics has raised awareness of the urgent need for novel antibiotics. Soil microorganisms are the major source of antibiotics and Actinobacteria in particular have an impressive capacity for production of diverse bioactive secondary metabolites. However, culture-independent studies have shown a greater microbial diversity present in soil with potential for novel chemical structures and these can be explored further using metagenomic approaches capturing genes without the need to cultivate the host. Different metagenomic tools were used to study and explore microbial secondary metabolite diversity in soil. In particular, amplicon sequencing of 16S rRNA gene, NRPS and PKS biosynthetic genes allowed the identification of novel potential phylogenetic drivers of secondary metabolite diversity in the less characterized phyla Verrucomicrobia and Bacteroidetes and potential geographic hotspots harbouring unique biosynthetic diversity such as Antarctica and Cuba. The exploitation of these hotspots presented some bottlenecks in the form of DNA extraction efficiency, library creation, screening and heterologous expression. These were overcome by comparative analysis of different eDNA extraction methods to optimise fragment size and purity combined with development of new cloning tools for both DNA capture and expression. Modification of the microbial community through the amendment of the soil with chitin, highlighted the beneficial effect of microbial enrichment allowing a higher recovery of eDNA and higher detection of the biosynthetic gene of interest related to secondary metabolite production. Further additions were made to the metagenomic molecular toolbox in the form of BAC vectors (pBCaBAC and pBCkBAC) which were tested with suitable heterologous host systems (Streptomyces sp. and the engineered Pseudomonas putida species) potentially facilitating heterologous expression. In conclusion this is the first study to identify the drivers of microbial secondary metabolite diversity in situ and provided a comparative analysis of a range of diverse soil types. This approach paired with new developments in metagenomic technologies will make a substantial contribution to improving the likelihood for discovery and exploitation of new drugs for treating multi-resistant pathogenic bacteria.
5
Andrews, Tucker. "Ecology Of Composted Bedded Pack And Its Impact On The Udder Microbiome With An Emphasis On Mastitis Epidemiology." ScholarWorks @ UVM, 2019. https://scholarworks.uvm.edu/graddis/989.
Full textAbstract:
Infections of the cow udder leading to mastitis and lower milk quality are a critical challenge facing northeast organic dairy farmers. Limited mastitis treatment options are available to organic producers and bedding systems impact cow health, including mastitis risk. Composted bedded pack, a system touted for increased cow comfort and well-being, allows stratified accumulation of bedding and manure in the barn. This method is gaining popularity among organic producers, yet little is known about the microbiota of the accumulated pack and its interaction with the cow mammary gland. An in-depth single farm study was conducted that surveyed bedded pack (microbiome and microarthropod community), dipteran vectors of bacterial mastitis pathogens, and the teat skin and teat cistern milk microbiomes. Comparisons were made with four additional farms utilizing bedded packs to test generality of results.
Few fly pests were observed in the bedded pack. However, bedding on all farms was found to harbor the mesostigmatid mite genus Glyptholaspis, a well-established predator of nematodes and muscid fly larvae, suggesting that predators may suppress populations of biting flies in bedded pack barns. Additionally, the fungivorous genus Rhizoglyphus was commonly abundant in all farms, suggesting that the mite community regulates microbial activity at multiple trophic levels.
High-throughput sequencing of universal marker genes for bacterial and fungal communities was used to characterize the skin and milk microbiome of cows with both a healthy and infected quarter on the case study farm, and the composted bedded pack of all five farms. The bedded pack microbiome varied with bedding material and management style; fungal taxa were primarily yeasts of the Ascomycota; all farms additionally contained anaerobic fungi associated with the bovine rumen. Common bacterial genera included Acinetobacter and Pseudomonas, both of which were also commonly observed on teat skin and in milk. The udder microbiome varied through time and between skin and milk. Both healthy and infected milk microbiomes reflected a diverse group of microbial DNA sequences. Health status of the quarter changed whether taxa were shared between the teat skin, milk, and bedding. Proportion of taxa shared between healthy milk and skin was stable while taxa shared in infected quarters varied widely. Taxa shared among all habitats included yeast genus Debaryomyces and bacteria Acinetobacter guillouiaea.
Results support an ecological interpretation of both the udder and the bedded pack environment and support the notion that mastitis can be described as an imbalance of the healthy mammary gland microbiome. Future work might compare udder health between common bedding practices, investigating the impact of bedding on the microbiota of the mammary gland in the healthy and diseased state.
6
Nesme, Joseph. "Characterization of antibiotic resistance genes abundance and diversity in soil bacteria by metagenomic approaches : what is the dissemination potential of the soil resistome?" Phd thesis, Ecole Centrale de Lyon, 2014. http://tel.archives-ouvertes.fr/tel-01068359.
Full textAbstract:
Environmental bacteria and especially soil bacteria are active producers of antibiotic molecules and most drugs used nowadays are isolated from saprophytic soil bacteria and these microorganisms have also evolved numerous resistance pathways leading to an arsenal of Antibiotic Resistance Genes Determinants (ARGD) known as the environmental resistome. A survey of ARGD prevalence is required in order to characterize this natural phenomenon with critical implications in our current infectious diseases management. In order to perform such analysis we compiled a set of 71 metagenomic datasets from various environmental origins: soils, oceans, lakes, human feces, indoor air, etc., and compared their sequences with a database of known antibiotic resistance gene determinants (ARGD). ARGD-annotated reads are found in every environment analyzed confirming their ubiquity. Soil is found to be the richest and shares a large part of ARGD with the human gut microbiome, indicating ARGD transfers between these environments. Experiments using qPCR and metagenomic DNA sequencing on soil samples from two sites with known and distinct antibiotic pollution history were conducted to understand how ARGD abundance and diversity in soil are affected when impacted by antibiotic molecules. The first site is a reference soil from a long-term experiment without history of antibiotic pollution (Rothamsted Park Grass, UK). Soil microcosms are setup with addition of either antibiotic-containg animal manure or pure molecules and incubated for 6 months to monitor changes in ARGD concentration following these perturbations. Our second study-site is a very remote settlement in French Guiana where antibiotics are available since recently and may have impacted the local soil microbial community. Soil samples are taken following a line-transect going from the village (antibiotic source) to 3km deep in the forest in a gradient of human-impact. Our results all confirm prevalence of ARGD in soil at significant abundance but also that ARGD distribution is more correlated to environmental factors such as soil type, microbial taxonomy composition or microcosms incubation conditions than antibiotic molecules exposure in both sites. Pathogens ARGD diversity is far lower than ARGD diversity found in the environment and not all the soil resistome is readily accessible for transfer. In order to characterize the soil mobile gene pool, a strategy is proposed to isolate specifically mobile DNA directly from the environment for sequencing purposes. Better knowledge on the microbial ecology factors limiting ARGD transfers to pathogens may greatly help us reduce the current threat on our limited medical antibiotic molecules resource.
7
Whissell, Gavin. "Merging metagenomic and microarray technologies to explore bacterial catabolic potential of Arctic soils." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=98518.
Full textAbstract:
A novel approach for screening metagenomic libraries by merging both metagenomic and microarray platforms was developed and optimized. This high-throughput screening strategy termed "metagenomic microarrays" involved the construction of two Arctic soil large-insert libraries and the high density arraying of the clone plasmid DNA (~50 kb) onto glass slides. A standard alkaline lysis technique used for the purification of plasmid DNA was adapted and optimized to function efficiently in a 96-well format, providing an economically viable means of producing sufficient high-quality plasmid DNA for direct printing onto microarrays. The amounts of printed material and probe, required for maximal clone detection, were optimized. To examine catabolic clone detection libraries were first screened by PCR for catabolic genes of interest. Two PCR-positive clones were printed onto microarrays, and detection of these specific clones in the printed libraries was achieved using labeled probes produced from PCR fragments of known sequence. Also, hybridizations were performed using labeled PCR fragments derived from the amplification of a catabolic gene from the total community DNA. The ability of selected probes to specifically target clones of interest was demonstrated. This merger of metagenomics and microarray technologies has shown great promise as a tool for screening the natural microbial community for catabolic potential and could also be used to profile microbial diversity in different environments.
8
NOVELLO, GIORGIA. "Exploring the microbiota of Vitis vinifera cv. Pinot Noir in two vineyards with different soil management: metagenomic and metaproteomic analysis." Doctoral thesis, Università del Piemonte Orientale, 2017. http://hdl.handle.net/11579/86922.
Full text
9
Ortiz-Ortiz, Marianyoly. "Kartchner Caverns: Habitat Scale Community Diversity and Function in a Carbonate Cave." Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/265356.
Full textAbstract:
This dissertation examines the microbial and functional diversity in Kartchner Caverns, a limestone cave in Arizona, USA. Kartchner is highly oligotrophic due to the lack of photosynthesis and the limited inputs of organic material from the surface. This characteristic poses a challenge for microbial life in the cave. The first objective of this work was to evaluate the bacterial richness, diversity and taxonomic composition of speleothems surfaces within Kartchner Caverns in order to gain insight into the distribution patterns associated with these communities. Secondly, the metabolic strategies used by cave communities to survive harsh cave conditions were investigated based on phylogenetic associations and metagenomics. Both objectives were directed toward answering the questions "who are there?" and "what are they doing?". The 454-pyrotag analysis of the V6 region of the 16S rRNA gene revealed an unexpectedly high bacterial diversity with each speleothem supporting a unique bacterial community profile. A focused study on one room of the cave revealed three community types: Type 1 was dominated by the phylum Proteobacteria; Type 2 by Actinobacteria; and Type 3 by Acidobacteria. Phylogenetic associations of the sequences generated by the 454 sequencing and by a Sanger clone library suggested cave microbial communities are supported by chemoautotrophic activities such as nitrite and iron oxidation. Results from the phylogenetic associations guided the metagenomic analysis which supports the presence of chemoautotrophic activities in the cave. Genes for two complete CO2 fixation mechanisms, the Calvin-Benson-Bashan and the rTCA cycles were identified in the cave metagenome, as well as genes for ammonia and nitrite oxidation. These genes are associated with both Bacteria and Archaea suggesting members of both domains are acting as primary producers in the cave ecosystem. Comparative analysis of cave samples to other environments suggests an overabundance of DNA repair mechanisms which could be potentially used by cave communities to overcome the toxicity due to high concentrations of calcium on the speleothem surfaces. This work provides the first comprehensive analysis of the microbial diversity and potential strategies used by microbial communities to survive under the extreme conditions found in a semi-arid limestone cave environment.
10
Grisi, Teresa Cristina Soares de Lima. "Diversidade de Bacteria e Archaea do solo do Cariri paraibano e prospecção de celulases e xilanases em clones metagenômicos e isolados bacterianos." Universidade Federal da Paraíba, 2011. http://tede.biblioteca.ufpb.br:8080/handle/tede/342.
Full textAbstract:
Made available in DSpace on 2015-04-01T12:09:01Z (GMT). No. of bitstreams: 1
arquivototal.pdf: 4073387 bytes, checksum: 8309cf98c379c11892e9d5cd2fae29dd (MD5)
Previous issue date: 2011-12-01Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
Soil samples of native pasture (site A) and of soil cultivated with grass Paspalum conjugatum, Bergius (site B) collected from Caatinga vegetation in the semi-arid region in Paraíba state (07°23‟27 S 36°31‟58 W) were utilized for constructing four metagenomic libraries, aiming the evaluation of microbial diversity through amplification of gene 16S rRNA of domains Bacteria and Archaea. The metagenomic DNAs were extracted by utilizing FastDNA® SPIN Kit for Soil (BIO 101), which were amplified by PCR, by using universal primers 27F / 1525R (Bacteria) and 20F / 958R (Archaea). The purified fragments were linked to vector pGEM Teasy and transformed by thermal shock in chemically competent Escherichia coli DH10B. Transformants were cultivated in LB/Ampicillin medium (100 μM/ml), IPTG (800 μg/mL) and XGal (80 μg/mL) at 37ºC/18-20 h. A selection of 250 clones of each library was performed, sequenced and after discarding the low quality sequences and chimerics, 64 and 68 sequences were obtained (Bacteria) and 89 and 141 sequences (Archaea) from soils of sites A and B, respectively, which were compared to public bank of data RDB and NCBI (similarity >95%). In site A the phylum Acidobacteria (48.4%) was the most abundant, followed by phyla Bacteroidetes (10.9%), Proteobacteria (10.9%), and Firmicutes (6.3%). In site B Proteobacteria (45.6%) was the most abundant, followed by Firmicutes (10.3%), Acidobacteria (8.8%), Bacterioidetes (7.3%); and also Cyanobacteria (1.5%) and Planctomycetes (1.5%) which were not found in site A. Among the sequences obtained, 23.4% (site A) and 25.0% (site B) were not classified (similarity <95%). In the domain Archaea the phyla found were Euryarchaeota (3.4 and 45.4%) and Crenarchaeota (2.2 and 3.5%), in sites A and B, respectively; it should be observed that 94.4% and 51.1% of the sequences were not classified (similarity <95%), between sites A and B, respectively. Larger diversity (Shannon‟s índex), richness (Chao 1), and distribution (equity index) of communities were observed at species level, in the phyla Bacteria and Archaea, in both sites. The metagenomic libraries 16S rRNA of Bacteria and Archaea, when compared by using the LIBSHUFF program, differed significantly (p<0.0001). The results of the present study showed the occurrence of a great diversity of bacteria and archaea in that semi-arid environment, with peculiar features of elevated temperature and hydric limitations, emphasizing the possibility of investigations on search of new genes and/or microbial isolates with biotechnological potential.
Amostras do solo da pastagem nativa (sítio A) e sob cultivo do capim marrequinho (Paspalum conjugatum, Bergius) (sítio B), coletadas na região semi-árida do bioma Caatinga, Paraíba, (07°23‟27 S 36°31‟58 O), foram utilizadas para construção de quatro bibliotecas de clones metagenômicos, para avaliação da diversidade microbiana pela amplificação do gene 16S rRNA dos domínios Bacteria e Archaea. Os DNA metagenômicos foram extraídos utilizando FastDNA® SPIN Kit for Soil (BIO 101), os quais foram amplificados por PCR utilizando primers universais, 27F / 1525R (Bacteria) e 20F / 958R (Archaea). Os fragmentos purificados foram ligados ao vetor pGEM Teasy e transformados por choque térmico em Escherichia coli DH10B quimicamente competente. Os transformantes foram cultivados em meio Agar LB/Ampicilina (100 μ/mL), IPTG (800 μg/μL) e XGal (80 μg/μL), a 37ºC/18-20 h. Foram selecionados 250 clones de cada biblioteca os quais foram sequenciados e após descarte das sequências de baixa qualidade e quiméricas, foram obtidas 64 e 68, 89 e 141 sequências para Bacteria e Archaea, nos solos dos sítios A e B, respectivamente, as quais foram comparadas em banco de dados públicos RDB e NCBI (≥95% de similaridade). No sítio A o filo Acidobacteria (48,4%) foi o mais abundante, seguido dos filos Bacteroidetes (10,9%), Proteobacteria (10,9%), e Firmicutes (6,3%). No sítio B Proteobacteria (45,6%) foi o de maior destaque, seguido de Firmicutes (10,3%), Acidobacteria (8,8%), Bacterioidetes (7,3%); e ainda Cyanobacteria (1,5%) e Planctomycetes (1,5%), que não foram encontrados no sítio A. Entre as sequências geradas, 23,4% (sítio A) e 25,0% (sítio B) não foram classificadas (similaridade <95%). No domínio Archaea foram encontrados os filos Euryarchaeota (3,4 e 45,4%) e Crenarchaeota (2,2 e 3,5%), nos sítios A e B, respectivamente; destacando-se que 94,4% e 51,1% das sequências não foram classificadas (similaridade <95%), entre os sítios A e B, respectivamente. Uma maior diversidade (índice de Shannon), riqueza (índice Chao 1) e distribuição (índice de equidade) das comunidades foram observadas no nível de espécies, tanto para Bacteria como para Archaea, nos dois sítios. As bibliotecas de clones metagenômicos 16S rRNA de Bacteria e Archaea, quando comparadas, utilizando-se o programa LIBSHUFF, diferiram significativamente (p<0,0001). Os resultados desse estudo mostraram a ocorrência de uma grande diversidade de bactérias e arqueas, nesse tipo de ambiente pouco estudado e com características peculiares de temperatura elevada e limitações hídricas, com possibilidade de busca de novos genes e/ou isolados microbianos, com potencial biotecnológico.
Books on the topic "Soil metagenomic"
1
Accademia economico-agraria dei georgofili (Florence, Italy). Biodiversità e il metagenoma del terreno agrario. Firenze: Edizioni Polistampa, 2011.
Find full text
2
Japan) MARCO Workshop (5th 2009 Tsukuba. Perspectives of Metagenomics in Agricultural Research: MARCO Workshop 5 : abstract : 6-7 October 2009, Tsukuba, Japan : Epochal Tsukuba (Tsukuba International Congress Center). Tsukuba, Japan: National Institute for Agro-Environmental Sciences, 2009.
Find full text
3
Sugitha, T. C. K., Asish K. Binodh, K. Ramasamy, and U. Sivakumar. Soil Metagenomics. Taylor & Francis Group, 2020.
Find full text
4
Sugitha, T. C. K., Asish K. Binodh, K. Ramasamy, and U. Sivakumar. Soil Metagenomics. Taylor & Francis Group, 2020.
Find full text
5
Sugitha, T. C. K., Asish K. Binodh, K. Ramasamy, and U. Sivakumar. Soil Metagenomics. Taylor & Francis Group, 2020.
Find full text
6
Sugitha, T. C. K., Asish K. Binodh, K. Ramasamy, and U. Sivakumar. Soil Metagenomics. Taylor & Francis Group, 2020.
Find full text
7
Sugitha, T. C. K., Asish K. Binodh, K. Ramasamy, and U. Sivakumar. Soil Metagenomics. Taylor & Francis Group, 2020.
Find full text
8
Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Environmental DNA for functional diversity. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0010.
Full textAbstract:
Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.
9
Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Introduction to environmental DNA (eDNA). Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0001.
Full textAbstract:
Chapter “Introduction to environmental DNA (eDNA)” defines the central concepts of this book. Environmental DNA (eDNA) corresponds to a mixture of genomic DNA from many different organisms found in an environmental sample such as water, soil, or feces. DNA metabarcoding can be defined as the simultaneous DNA-based identification of many taxa found in the same eDNA extract. It is usually based on the analysis of a metabarcode (i.e., a short and taxonomically informative DNA region). Metagenomics refers to the assembly and functional analysis of the different genomes found in an environmental sample, while metatranscriptomics examines gene expression and regulation at the sampling time based on the set of RNAs extracted from such a sample. Chapter also presents a brief history of eDNA, highlights the different steps of an eDNA study, and gives an overview of the different eDNA methods implemented in ecological research or biodiversity management.
10
Kirchman, David L. Genomes and meta-omics for microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0005.
Full textAbstract:
The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far. Genomic studies have also highlighted the importance of genes exchanged (“horizontal gene transfer”) between organisms, seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use metagenomics to sequence all microbes in a community. This approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Genomes from single cells isolated by flow cytometry have also provided insights about the ecophysiology of both bacteria and protists. Oligotrophic bacteria have streamlined genomes, which are usually small but with a high fraction of genomic material devoted to protein-encoding genes, and few transcriptional control mechanisms. The study of all transcripts from a natural community, metatranscriptomics, has been informative about the response of eukaryotes as well as bacteria to changing environmental conditions.
Book chapters on the topic "Soil metagenomic"
1
Kathi, Srujana. "Emerging Metagenomic Strategies for Assessing Xenobiotic Contaminated Sites." In Soil Biology, 89–100. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-47744-2_7.
Full text
2
Delmont, Tom O., Laure Franqueville, Samuel Jacquiod, Pascal Simonet, and Timothy M. Vogel. "Soil Metagenomic Exploration of the Rare Biosphere." In Handbook of Molecular Microbial Ecology I, 287–98. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118010518.ch33.
Full text
3
Unno, Yusuke, and Takuro Shinano. "Metagenomic Analysis of the Rhizosphere Soil Microbial Community." In Molecular Microbial Ecology of the Rhizosphere, 1099–103. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118297674.ch104.
Full text
4
Misra, Sankalp, Vijay Kant Dixit, Swapnil Pandey, Shashank Kumar Mishra, Nikita Bisht, and Puneet Singh Chauhan. "Exploration of Soil Resistome Through a Metagenomic Approach." In Antibacterial Drug Discovery to Combat MDR, 313–25. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-9871-1_15.
Full text
5
Parsley, Larissa C., Chengcang Wu, David Mead, Robert M. Goodman, and Mark R. Liles. "Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications." In Handbook of Molecular Microbial Ecology II, 109–15. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118010549.ch11.
Full text
6
Wommack, K. Eric, Sharath Srinivasiah, Mark R. Liles, Jaysheel Bhavsar, Shellie Bench, Kurt E. Williamson, and Shawn W. Polson. "Metagenomic Contrasts of Viruses in Soil and Aquatic Environments." In Handbook of Molecular Microbial Ecology II, 25–36. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118010549.ch4.
Full text
7
Rajesh, T., J. Rajendhran, P. Lavanya Pushpam, and P. Gunasekaran. "Methods in Metagenomic DNA, RNA, and Protein Isolation from Soil." In Handbook of Molecular Microbial Ecology II, 93–107. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118010549.ch10.
Full text
8
Colagiero, Mariantonietta, Isabella Pentimone, Laura Cristina Rosso, and Aurelio Ciancio. "A Metagenomic Study on the Effect of Aboveground Plant Cover on Soil Bacterial Diversity." In Soil Biological Communities and Ecosystem Resilience, 97–106. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-63336-7_6.
Full text
9
Kielak, Anna M., and George A. Kowalchuk. "Targeting Major Soil-Borne Bacterial Lineages Using Large-Insert Metagenomic Approaches." In Handbook of Molecular Microbial Ecology II, 135–41. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118010549.ch14.
Full text
10
Pershina, E. V., E. E. Andronov, A. G. Pinaev, and N. A. Provorov. "Recent Advances and Perspectives in Metagenomic Studies of Soil Microbial Communities." In Management of Microbial Resources in the Environment, 141–66. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-5931-2_7.
Full textConference papers on the topic "Soil metagenomic"
1
Melnichuk, T. N., A. Yu Egovtseva, S. F. Abdurashitov, E. R. Abdurashytova, E. N. Turin, V. V. Gorelova, and A. A. Zubochenko. "Microbiocenosis of southern chernozem under the influence of no-till." In CURRENT STATE, PROBLEMS AND PROSPECTS OF THE DEVELOPMENT OF AGRARIAN SCIENCE. Federal State Budget Scientific Institution “Research Institute of Agriculture of Crimea”, 2020. http://dx.doi.org/10.33952/2542-0720-2020-5-9-10-114.
Full textAbstract:
The purpose of the research was to assess microbocenosis of the southern chernozem under the influence of no-till and microbial preparations. A metagenomic analysis of the southern chernozem revealed 12 phyla, including 11 bacteria and 1 archaeon. The number of cellulolytic microorganisms increased under the influence of farming systems compared to virgin soil. The use of microbial preparations contributed to an increase in the number of microorganisms of ecological-trophic groups and the representation of the majority of phyla, which also depended on the farming system.
2
Tereshchenko, Natalya, Tatiana Zyubanova, Elena Akimova, and Oksana Minaeva. "The assessment of soil suitability for reproduction of healthy seed potatoes based on metagenomic analysis of the soil microbial community and the level of soil suppressive activity." In MODERN SYNTHETIC METHODOLOGIES FOR CREATING DRUGS AND FUNCTIONAL MATERIALS (MOSM2020): PROCEEDINGS OF THE IV INTERNATIONAL CONFERENCE. AIP Publishing, 2021. http://dx.doi.org/10.1063/5.0069257.
Full text
3
Taura, Usman, Sara Al-Araimi, Saif Al-Bahry, Yahya Al-Wahaibi, and Lujain Al-Rashdi. "Isolation of Autochthonous Consortium for the Bioremediation of Oil Contaminated Produced Water." In SPE Nigeria Annual International Conference and Exhibition. SPE, 2022. http://dx.doi.org/10.2118/212024-ms.
Full textAbstract:
Abstract In this research, we isolated indigenous bacteria capable of remediating oil-contaminated produced water in an efficient, cost-effective and environmentally friendly manner. Nine different produced water samples were collected from Omani oil fields and analysed for their physicochemical properties and microbial communities present. Different technologies were performed to extract the DNA of the microbial community cultured in different media. Metagenomic classification of the microbial community showed that the abundant genera are the Acidithiobacillus, Proteinphilum and Marinobacter. The isolated microbes that showed the highest efficiency in oil degradation were further evaluated for liquid-based biodegradation as well as in naturally occurring and artificially contaminated soil. Fourteen bacteria samples were found to be efficient in bioremediating the three environments tested. In the liquid-based media, the isolates were able to degrade the heavy oil carbon chains (C14-C20) by at least 50% after 1 week period, while some of the most potent isolates have achieved more than 95% or completely degraded all the hydrocarbon chains. Similarly, in the naturally contaminated soil, the isolates demonstrated a complete degradation of the lighter carbon molecules from C10-C16 and also achieved a higher than 90% degradation for the heavier components. Likewise, the isolates have exhibited similar biodegradation ability when exposed to an induced contaminated soil where all the lower carbon chains (C12-C17) were mostly degraded by the microbes in the samples.
4
Kawulok, Jolanta, and Michal Kawulok. "Environmental Metagenome Classification for Soil-based Forensic Analysis." In 9th International Conference on Bioinformatics Models, Methods and Algorithms. SCITEPRESS - Science and Technology Publications, 2018. http://dx.doi.org/10.5220/0006659301820187.
Full text
5
Dzombak, Rebecca M., and Nathan D. Sheldon. "USING PAIRED GEOCHEMISTRY AND METAGENOMICS TO EXPLORE SOIL CRUSTS AS ANCIENT TERRESTRIAL ANALOGUES." In 54th Annual GSA North-Central Section Meeting - 2020. Geological Society of America, 2020. http://dx.doi.org/10.1130/abs/2020nc-347938.
Full text
6
Rahman, Jessica S., Jinyan Li, Juanying Xie, Shoshana Fogelman, and Michael Blumenstein. "Connectivity Based Method for Clustering Microbial Communities from Metagenomics Data of Water and Soil Samples." In 2018 International Joint Conference on Neural Networks (IJCNN). IEEE, 2018. http://dx.doi.org/10.1109/ijcnn.2018.8489220.
Full text
7
"Fungal metagenome of Chernevaya Taiga soils: taxonomic composition, differential abundance and factors related to plant gigantism." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-167.
Full textReports on the topic "Soil metagenomic"
1
House, Geoffrey Lehman, Laverne A. Gallegos-Graves, and Patrick Sam Guy Chain. Overview of the Soil Metagenomics and Carbon Cycling SFA Fungal Collection. Office of Scientific and Technical Information (OSTI), November 2018. http://dx.doi.org/10.2172/1483488.
Full text
2
Crowley, David E., Dror Minz, and Yitzhak Hadar. Shaping Plant Beneficial Rhizosphere Communities. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7594387.bard.
Full textAbstract:
PGPR bacteria include taxonomically diverse bacterial species that function for improving plant mineral nutrition, stress tolerance, and disease suppression. A number of PGPR are being developed and commercialized as soil and seed inoculants, but to date, their interactions with resident bacterial populations are still poorly understood, and-almost nothing is known about the effects of soil management practices on their population size and activities. To this end, the original objectives of this research project were: 1) To examine microbial community interactions with plant-growth-promoting rhizobacteria (PGPR) and their plant hosts. 2) To explore the factors that affect PGPR population size and activity on plant root surfaces. In our original proposal, we initially prqposed the use oflow-resolution methods mainly involving the use of PCR-DGGE and PLFA profiles of community structure. However, early in the project we recognized that the methods for studying soil microbial communities were undergoing an exponential leap forward to much more high resolution methods using high-throughput sequencing. The application of these methods for studies on rhizosphere ecology thus became a central theme in these research project. Other related research by the US team focused on identifying PGPR bacterial strains and examining their effective population si~es that are required to enhance plant growth and on developing a simulation model that examines the process of root colonization. As summarized in the following report, we characterized the rhizosphere microbiome of four host plant species to determine the impact of the host (host signature effect) on resident versus active communities. Results of our studies showed a distinct plant host specific signature among wheat, maize, tomato and cucumber, based on the following three parameters: (I) each plant promoted the activity of a unique suite of soil bacterial populations; (2) significant variations were observed in the number and the degree of dominance of active populations; and (3)the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This research demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations. Based on the studies from the US team, we suggest that the effective population size PGPR should be maintained at approximately 105 cells per gram of rhizosphere soil in the zone of elongation to obtain plant growth promotion effects, but emphasize that it is critical to also consider differences in the activity based on DNA-RNA correspondence. The results ofthis research provide fundamental new insight into the composition ofthe bacterial communities associated with plant roots, and the factors that affect their abundance and activity on root surfaces. Virtually all PGPR are multifunctional and may be expected to have diverse levels of activity with respect to production of plant growth hormones (regulation of root growth and architecture), suppression of stress ethylene (increased tolerance to drought and salinity), production of siderophores and antibiotics (disease suppression), and solubilization of phosphorus. The application of transcriptome methods pioneered in our research will ultimately lead to better understanding of how management practices such as use of compost and soil inoculants can be used to improve plant yields, stress tolerance, and disease resistance. As we look to the future, the use of metagenomic techniques combined with quantitative methods including microarrays, and quantitative peR methods that target specific genes should allow us to better classify, monitor, and manage the plant rhizosphere to improve crop yields in agricultural ecosystems. In addition, expression of several genes in rhizospheres of both cucumber and whet roots were identified, including mostly housekeeping genes. Denitrification, chemotaxis and motility genes were preferentially expressed in wheat while in cucumber roots bacterial genes involved in catalase, a large set of polysaccharide degradation and assimilatory sulfate reduction genes were preferentially expressed.
3
Zhou, Jizhong, and Liyou Wu. From Structure to Functions: Metagenomics-Enabled Predictive Understanding of Soil Microbial Feedbacks to Climate Change. Office of Scientific and Technical Information (OSTI), November 2019. http://dx.doi.org/10.2172/1574023.
Full text
4
Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.
Full textAbstract:
Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report