SAMPLE COLLECTION
The collection of samples for bacterial analyses may be an important step if we want to avoid potential contaminations. Bacteria are almost ubiquitous and highly diverse, and therefore the composition of complex bacterial communities can be altered by the procedures and tools used during sample collection.
Sediment samples
Sediment core and grab samplers are commonly used to collect bottom sediments from marine and freshwater environments. Only 250-400 mg of sediment are sufficient to carry out DNA/RNA extractions, so 1-3 grams of sediment are usually collected by a sterile mini scoop into an Eppendorf tube. If the samples need to be stored until further analysis, it is recommended to immediately freeze the tubes at -20 °C - (-80) °C. Liquid nitrogen is commonly used to ensure a better preservation. OmiBox allows the processing of samples immediately after collection, so there is no need for preservation at freezing temperatures.
While the grab samplers provides a mixture of the sediments dragged from the sampling area, the core samples allow us to obtain vertical columns where the different sediment layers can be distinguished and therefore collected separately. Considering the different physicochemical and biological composition throughout these different layers, this approach is certainly useful for detailed studies of aquatic sediments. (add picture of grab and core samplers.
Soil samples
Collection of soil material is similar to the collection of aquatic sediments. Grab sampling techniques are also employed using a scoop or similar tools. However, the sediment layers are destroyed and mixed, and therefore this method is not the most appropriate for detailed layer profile studies. For that purpose, core samplers are commonly used, such as the split spoon technique, where a drilling rig or a hand auger are used to insert a split spoon into the soil to collect undisturbed cores. T-handle core samplers are also commonly used to easily extract cores from relatively soft soils without the need for mechanical equipment.
Water samples
Collecting environmental DNA and RNA from water samples is usually a more complex procedure since the biomass contained in the water must be concentrated in order to obtain sufficient amounts of DNA and RNA. This process is usually conducted using filtration systems where water is filtrated onto a membrane filter with a pore size dependent of the organisms of interest. For prokaryotic organisms, 0.2 µm pore size filters are used, as virtually all prokaryotes are considered to be bigger than 0.2 µm. Eukaryotic organisms exhibit larger dimensions and, therefore, filters with greater pore sizes can be employed.
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Another aspect worth considering is the "pre-fixation" of the sampled water after its collection. Due to technical constrains during some sampling procedures in the field or in the lab, the time period spanning between the water collection and its filtration may be prolonged by hours. In these cases, the organisms contained in the samples are exposed to environmental conditions that may significantly differ from the natural environment, which can affect the functioning and even the composition of the original communities. This is particularly important in prokaryotes, as their cellular activity and division can be altered in time-lapses as short as half an hour. In order to stop the cellular activity and avoid DNA/RNA degradation, a phenol– ethanol solution can be added to the water samples right after the collection. See Rodríguez et al. 2022 as an example.
