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Functional Microbial Ecology

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Functional Microbial Ecology

Importance of Functional Microbial Ecology

Microorganisms play an important role in biogeochemical cycles and soil nutrient reposition, They can also be a valuable indicator of soil quality, and directly affect crop development and crop health. Over the past decades, scientists have been trying to clarify questions about the diversity of species in relation to ecosystem functions. A range of biochemical, physiological, molecular, microscopic, and isotopic techniques are now available to identify and study various functional groups of microflora and their functions. The progress has now reached to a level that many technologies could be used for a reproducible, reliable assessment of the taxonomic and functional diversity and function of microbiota. Functional microbial ecology is a field to comprehensively determine population dynamics through functional diversity to the molecular regulation of key processes, which has been greatly powered by the next-generation sequencing (NGS) and bioinformatics analysis.

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Accelerate Research and Practice in Functional Microbial Ecology

We are dedicated to exploring the diversity and evolution of functional microbial groups in diverse environments utilizing NGS and long-read sequencing technologies. According to your needs, we can design optimal, validated universe primers targeting functional genes or housekeeping genes (such as 16S rRNA, nirK, nirS, nosZ, LSU, amoA), and construct custom libraries for high-throughput sequencing. We can also apply this strategy to more refined classification and evolutionary research on functional microbial groups.

The Main Research Directions

  • Molecular approaches to microbial ecology.
  • Evaluate the microbial structure, evolution, and distribution in various environments.
  • New strategies for management of plant pathogenic soil microorganisms.

What Can We Do?

  1. 1. Designed and validated universal primers for amplification of certain functional genes or housekeeping genes
  2. 2. Reveal the diversity of certain functional microbial groups in the sample
  3. 3. Evolutionary studies of certain groups of microbes

Note: Our service is for research use only, and not for therapeutic or diagnostic use.

Functional Microbial Ecology

Detectable Objects

Environmental samples, especially soil samples.

Detectable Microorganisms

Functional microorganisms The gene to be sequenced Primers Sequencing platform
Methanogens 16S rRNA gene Arch519R / Arch915R MiSeq 2×300
Sulfate-reducing bacteria (SRB) dsrB dsrF / dsrR MiSeq 2×300
Ammonia-oxidizing bacteria (AOB) 16S rRNA gene CTO189f / CTO653r MiSeq 2×300
Ammonia oxidizing bacteria (AOB) amoA amoA-1F / amoA-2R MiSeq 2×300
Ammonia-oxidizing archaea (AOA) amoA Arch amoA F / Arch amoA R 454
Nitrite oxidizing bacteria (NOB) 16S rRNA gene FGPS1269 / FGPS872 MiSeq 2×300
nxrA nxrA F / nxrA R MiSeq 2×300
Anammox (AMX) 16S rRNA gene Amx368 / Amx820R MiSeq 2×300
Denitrifying bacteria narG narG1960f / narG2650r 454
nirK F1aCu / R3Cu MiSeq 2×300
nirS cd3aF / R3cd MiSeq 2×300
nosZ nosZF / nosZR MiSeq 2×300
Pavlova gyrans LSU F / R MiSeq 2×300
Nitrogen-fixing bacteria cbbL 595F / 1387R 454
cbbM F / R MiSeq 2×300
Nitrogen-fixing bacteria nifH PoIF / PoIR MiSeq 2×300

Detection Methods

The next-generation sequencing, third-generation sequencing, gene chip analysis, SNP genotyping, real-time qPCR, Denaturant Gel Gradient Electrophoresis (DGGE), etc.

Technical Platforms

We are equipped with Illumina Hiseq/Miseq, Ion PGM, PacBio SMRT systems, Nanopore systems, PCR-DGGE (PCR-denaturing gradient gel electrophoresis), real-time qPCR, clone libraries, and other detection platforms.

Sample Requirements

    1. DNA amount > 300 ng, concentration > 10 ng/ul, and OD260/280 = 1.8-2.0.
    2. Please ensure DNA is non-degraded, and do not freeze or thaw the sample repeatedly during sample preservation.
    3. Please use enough ice bags or dry ice for sample submission.

Workflow

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

PCR-DGGE analysis process

Bioinformatics Analysis

Basic Analysis Routine Analysis (According to Customer Requirements) Advanced Data Analysis
Sequence Filtering and Trimming Heatmap Phylogenetic Tree
Sequence Length Distribution VENN LDA-Effect Size (LEfSe)
OTU Clustering and Species Annotation Principal Components Analysis (PCA) Network Analysis
Diversity Index Microbial Community Structure Analysis Correlation Analysis
Shannon-Wiener Curve α Diversity Index Analysis
Rank-Abundance Curve Matastats Analysis
Rarefaction Curve Weighted Unifrac test
Multiple Contrast CCA/RDA Analysis
Heatmap
Principal Components Analysis (PCA)

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