Environmental Microbial Analysis

Microbial Diversity in Environmental Samples

FISH and rRNA targeting oligonucleotide probes have developed into valuable molecular tools for identifying microorganisms in the environment. Complex samples from water bodies or other environments may have the difficulty of having a small number of cells to be tested. For example, most bacteria in aquatic habitats are small, grow slowly or starving, so the number of ribosomes may be small. Based on the use of horseradish peroxidase (HRP) labeled oligonucleotide probes and tyramide signal amplification, also known as catalytic reporter gene deposition (CARD) methods have gradually developed methods other than CARD-FISH. The combination of CARD and nucleic acid probes is commonly used in histology and cytochemistry to locate specific nucleic acid sequences (DNA, RNA) in microscopic preparations of tissues, cells, and chromosomes. The probe-coupled HRP-activated tyramide will covalently bind to tyrosine residues in the target cell, and each HRP catalyzes the deposition of many labeled tyramines. This method improves the low sensitivity of single FISH hybridization. FISH can be used to detect, identify, and enumerate environmental microorganisms without cultivation, so it can be used to help clarify the microbial ecology of many habitats, including water bodies and sediments. Our environmental microbiological analysis FISH service is designed to help researchers who have environmental sample microbiological analysis in scientific research projects quickly analyze and improve efficiency.

Schematic depiction of FISH, CARD-FISH, and two-pass TSA-FISH. (Kubota K, et al. 2013)Fig 1. Schematic depiction of FISH, CARD-FISH, and two-pass TSA-FISH. (Kubota K, et al. 2013)

CARD-FISH Services

CARD-FISH is the same as FISH in many steps, including preparation of biological materials, selection of nucleic acid probes, hybridization with labeled probes, cytochemical probe detection and microscopic examination. Our environmental microbiological analysis FISH service can be customized on the CARD-FISH general experimental program according to the customer's sample type and research purpose, to provide customers with the best solution to the greatest extent. The basic process of the service includes experimental protocol customization, sample pretreatment, probe preparation, hybridization detection, image acquisition and data analysis. We can provide analysis and testing services for various samples such as soil, engineering sludge, sediment, and water samples.

  • The pre-treatment of the sample includes the separation of conventional immobilized microorganisms. The optional microbial enrichment step in the sample can increase the sensitivity, and a sample evaluation report will be generated in this step.
  • The probe preparation link provides customers with optional prefabricated and customized probe products, as well as a variety of probe labeling methods.
  • In the hybridization stage, different permeabilization strategies are adopted according to the cell wall and immobilization method of the target microorganism, such as treatment with various enzymes, diluted HCl or detergent.
  • The detection stage can be processed according to the probe type, and high-quality image data can be harvested.
  • In the data analysis stage, our bioinformatics team completes statistics, annotations and chart production.

Our universal CARD-FISH protocol. - Creative BioarrayFig 2. Our universal CARD-FISH protocol.

Creative Bioarray provides CARD-FISH services related to environmental microbial analysis and identification and provides assistance to customers who need to analyze microbial samples in water bodies or sediments. We provide one-stop analysis and testing services and carry out quality control in multiple links. Our goal is to improve sensitivity and sample utilization while quickly completing analysis and testing. You will benefit from our technical expertise and equipment platform, and work with you to find the best solution. If you are interested in our environmental microbial detection CARD-FISH service, please contact us for cooperation. We look forward to cooperating with you in the near future.


  1. Kubota K. CARD-FISH for environmental microorganisms: technical advancement and future applications[J]. Microbes and environments, 2013, 28(1): 3-12.
  2. Pernthaler A, Pernthaler J. Fluorescence in situ hybridization for the identification of environmental microbes[M]//Protocols for nucleic acid analysis by nonradioactive probes. Humana Press, 2007: 153-164.
  3. Wendeberg A. Fluorescence in situ hybridization for the identification of environmental microbes[J]. Cold Spring Harbor Protocols, 2010, 2010(1): pdb. prot5366.
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