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Microbial Diversity in Soil

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Microbial Diversity in Soil

Importance of Microbial Diversity in Soil

The soil microflora contains a wide range of microbial strains. Microorganisms in soil are essential for the maintenance of soil functions in both natural and managed soils due to their involvement in key processes including soil structure formation, toxin removal, decomposition of organic matter, and the recycling of carbon, nitrogen, phosphorus, and sulphur. In addition, microorganisms play vital roles in promoting plant growth, suppressing soilborne plant diseases, and in changes in vegetation. Therefore, an increasing interest has emerged with respect to the significance of microbial diversity in soil habitats, which may be used as an ecosystem indicator.

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Accelerate Research and Practice in Soil Microbiology

Traditionally, microbial diversity in soil has been analyzed by methods such as viable and culturable methods, CLPP and flow cytometry. However, the limits of these methods have been preventing us from exploring further. We provide PCR, next-generation sequencing (NGS), and long-read sequencing approaches (PacBio SMRT sequencing and Nanopore sequencing) to identify, quantify, and characterize both culturable and unculturable microorganisms present in soil habitats. These techniques provide a more accurate method for measuring the microbial diversity and abundance, as well as exploring microbial function.

What Can We Do?

  1. 1. Identification of soil microflora
  2. 2. Quantitation of soil microorganisms
  3. 3. Study the evolutionary relationship of soil microorganisms
  4. 4. Study the relationship between soil microbiome and the environment

Note: Our service are for research use only, not for disease diagnosis or treatment.

Detectable Objects

DNA samples of soil microbiome from diverse soil types can be tested.

Detectable Microorganisms

Viruses, fungi, bacteria, archaea, mycoplasma, etc.

Technical Platforms

We are equipped with Illumina Hiseq/Miseq, PacBio SMRT systems, and Nanopore systems for 16S/18S/ITS sequencing and metagenomics, PCR-DGGE (PCR-denaturing gradient gel electrophoresis), real-time qPCR, clone library, and other analytical platforms.

Sample Requirements

    1. DNA sample: DNA ≥ 300 ng, concentration ≥ 10 ng/ul, and OD260/280 = 1.8-2.0.
    2. Ensure that the DNA is intact and not degraded.
    3. Avoid repeated freezing and thawing cycles.
    4. Dry ice or ice packs should be used for sample submission.

Workflow

High-throughput sequencing analysis processFigure 1. High-throughput sequencing analysis process.

PCR-DGGE analysis processFigure 2. PCR-DGGE analysis process.

Bioinformatics Analysis

OTU Clustering Distribution-Based OTU-Calling
Rarefaction Curve
Shannon-Wiener Curve
Rank Abundance Curve
Diversity Index
OTU-Based Analysis Heatmap
VENN
Principal Components Analysis (PCA)
Hierarchical Clustering
Comparative Analysis RDA/CCA
PCA/PCoA
Network Analysis
Functional analysis BLASTX, KEGG, eggNOG, CAZy, CARD, ARDB etc.
PICRUSt
TAX4Fun
Phylogenetic Analysis (Un)Weighted Unifrac
Phylogenetic Trees

References

  1. Dodd, J.C., Boddington, C.L., Rodriguez, A., Gonzalez-Chavez, C., Mansur, I., 2000. Mycelium of arbuscular mycorrhizal fungi (AMF) from different genera: form, function and detection. Plant Soil 226, 131 – 151.
  2. O’Donnell, A.G., Seasman, M., Macrae, A., Waite, I., Davies, J.T., 2001. Plants and fertilisers as drivers of change in microbial community structure and function in soils. Plant Soil 232, 135 – 145.

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