Biodiversitymonitoring 2.0

 

Mixed samples from malaise traps, sticky traps, soil samples, fecal samples, stomach contents, water samples, processed foods, etc. can be analyzed with the so-called metabarcoding. All species in the sample are recorded using this method.

 

 

 

#1 Sampling

Mixed samples are collected in the field, e.g. Malaise traps, nets, yellow trays, stem traps, soil samples, bat dung, bark, macrozoobenthos samples, processed food or feed.

#2 Sample

The samples should be stored in high percentage alcohol, preferably cool and dark. Even dried samples are possible. Faeces, bark and soil samples are ideally dried and shipped as soon as possible.

#3 DNA Extraction

From the mixed samples, the DNA of all organisms in the sample is extracted.

#4 Amplification of the barcoding-Region

The gene required for DNA barcoding is amplified and the DNA pieces of each sample are given a unique marker and sequenced.

#5 Data Quality Control

In the first bioinformatic step, the quality of the sequences and data is checked and the data prepared for database comparison.

#6 Comparisons of the sequences with the databases

The sequences are aligned with the publicly accessible databases of BOLD and Genebank / NCBI.

#7 Preparation of the species lists, graphs and reports adapted to the customer

Depending on the customers' questions, detailed species lists of the individual samples / locations / times are created and further metadata (red list status, FFH status, invasion potential, occurrence, etc.) are added. In addition, statistical evaluations can be made on customer request. The graphical representation of the data is inserted in the customer report.

 

 

Biodiversity monitoring in the digitization age

Biomonitoring 1.0

Determination of large, known, red list / FFH species.

 

Requires taxonomic expertise and capacities of taxonomists.

Maximum number of samples limited.


Within a certain time, only a few individuals can be identified.

 

Example: Ssymank & Doczkal 2017 - catches of 20 malaise traps (411 empties), so far 1 million insects were evaluated in 9 years and after 3800 hours of work almost 10% of the animals are identified.

 

Comparability of different studies often difficult due to different evaluations and different data.

Biomonitoring 2.0

Determination of the entire mixed sample including the "residual samples".

Requires genetic background, laboratory and bioinformatic knowledge.

Parallelization of many samples possible.


Ten thousands individuals can be analyzed simultaneously in one analysis run.

 

Comparability of different locations and time intervals possible using bioinformatics.

 

With a fraction of the budget and a much lower expenditure of time and personnel, about 95% of the animals in a sample can be identified by metabarcoding.

 

Current limits of metabarcoding

Quantification

So far not a reliable method for the determination of the individuals' density

Databases

You can only prove what has been entered in the databases.

 

Protocols & Workflows

Problems with extraction or amplification can occur e.g., due to inhibitors.

Cryptic diversity

Some species demonstrate problems with unique identification.

 

 

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