The aquatic microbiome is the community of microorganisms living in water. It plays a vital role in both freshwater and marine ecosystems. These microorganisms affect water quality, ecosystem balance, the health of other aquatic organisms and can serve as indicators of ecological status or pollution. Knowledge of the composition of the aquatic microbiome allows a better understanding of the dynamics of aquatic ecosystems and can provide useful data for their management, water quality improvement or commercial use.
For whom is the acquatic microbiome analysis in our laboratory intended?
- Water resource managers - A systematic review of the microbial composition of water will allow you to better monitor water quality, identify possible pollution or improve the efficiency of water treatment.
- Water managers - Using microbiome analysis, you can monitor microbial activity in wastewater or water treatment and optimize processes that lead to improved water quality and public health protection.
- Ecologists - Knowledge of the composition of the aquatic microbiome is key to understanding ecological processes, biodiversity and the impact of human activity on the aquatic environment.
- Farmers and Fishermen - The aquatic microbiome affects the quality of the water you use for irrigation or fish farming. Analyzing the microbial composition can help you understand the effect the microbiome has on the health of your water sources and the productivity of your farms, it can detect any pathogenic microorganisms, etc.
- Industrial enterprises - Companies that use water in their processes can monitor water quality and prevent the formation of unwanted biofilms or microbial contamination, which increases the efficiency of production processes and minimizes maintenance costs.
Case study - Monitoring of the recirculation aquaculture system (RAS) for intensive fish farming
Recirculating aquaculture systems (RAS) are the future of intensive fish farming. Only in the RAS is it possible to breed fish intensively and in a fully controlled environment. At the same time, however, ecologically and sustainably, with minimal impacts on the surrounding ecosystems.
For example, in a healthy RAS system, conditions are maintained to support adequate growth of nitrifying bacteria. A change in conditions or the unintended introduction of unwanted bacteria can throw the existing microbiome out of balance. Undesirable bacterial populations can begin to grow beyond acceptable limits, which can lead to negative consequences such as disease in farmed fish, low gains or mortality. The ability to regularly monitor the state of the microbiome in a RAS system can be a very valuable tool that allows operators to prevent these situations and the costs associated with their remediation.
Analysis of the microbiome by DNA sequencing techniques addresses several limitations of traditional microbial testing methods. This technology has the ability to identify and quantify all types of microorganisms present. It also does this more accurately than traditional testing methods and allows you to detect potential unwanted microorganisms that you didn't even know you should be looking for in your water.
Technology
The analysis of the microbiome can be performed in basically two ways. One of them is the analysis of selected informative markers such as the 16S rRNA gene and other standard or specifically selected markers suitable for evaluating the diversity of microbial populations. Any such appropriately chosen marker is capable of capturing changes in the diversity of the bacterial community, however this analysis is typically limited purely to the detection of the microorganisms present.
If we want to analyze the microbiome in more detail, an alternative technique called deep or shot-gun sequencing comes into play. With this method, we not only reveal the identity of the organisms present, but we are also able to perform functional profiling. In functional profiling, the present biosynthetic pathways of the microorganisms represented in the microbiome are reconstructed - the analysis thus at least partly tells about what is "going on" in the microbiome.
Both methodological approaches have their pros and cons, and their choice is a matter of assignment and discussion.
How does a custom microbiome analysis work?
- Study design - Based on your specification, we will jointly determine the objectives of the analysis of the microbiome in your samples, including the broader context, typically the collection of metadata in connection with the collection of samples. We will explain to you the possibilities of analyzing the microbiome using sequencing techniques, taking into account the nature of the study and what questions you can and cannot expect to be answered.
- Sampling - We will provide you with instructions for collection, storage and transport and recommend suitable sampling kits. In case of interest and if it is technically possible, we will carry out or assist in the collection of samples.
- DNA Extraction - After receiving the samples, we extract the microbial DNA.
- Sequencing - We analyze the microbial composition of the sample using DNA sequencing techniques.
- Bioinformatics analysis - We process sequencing data using tools and databases that enable accurate identification of microorganisms, their functional capabilities and their representation in the sample.
- Report and interpretation of results - We will provide you with a clear report on the composition of the microbiome in the analyzed samples. In cooperation with you and based on all the data obtained, we will try to interpret the results to the maximum extent possible so that you can draw conclusions from them with regard to the set goals of the project.
If you are interested in our services in aquatic microbiome analysis, contact us.