meth_1.11 Seagrass Zostera muelleri and Surficial Sediment Sampling for Marine Microbes Coastal Project

Contributor(s):

Citation:

AM Project ID: Legacy

Equipment:

  • Van Veen grab
  • Liquid nitrogen dewar (to be used both, on site and in the lab)
  • 8 mL Nunc Cryotube vials
  • Cryolabels
  • Aluminium foil
  • Gloves
  • Scissors
  • 250 mL glass jar
  • 100 mL specimen jars
  • Esky and ice
  • Black bag
  • Plastic resealable bags

General Notes:

First time the site is visited, abundance of Zostera muelleri will be measured over 10 randomly thrown 50 cm x 50 cm quadrats.

1.11.1 Surficial Sediment Sampling

NOTE: samples to be collected immediately before seagrass samples (for each plant, both surficial sediment and plant tissue will be collected).

  1. Pull out a seagrass plant and, out of water, collect surficial sediment, using sterile gloves onto a clean tray.
  2. Homogenize sediments with gloved hands and avoid collecting roots/rhizome.
  3. Fill a 1.8 mL Nunc cryotube vial up to the top (collect up to 3 cryotube vials/sample). Label tubes according to the scheme outlined in the spreadsheet “sample_schedule”.
  4. Flash freeze cryotube vials in liquid nitrogen, using the dewar brought to the field, and keep the samples on ice for transport to the laboratory.
  5. Store samples in -80 °C freezer for further analysis.
  6. RNA and DNA should be extracted from sediment within 2 weeks.
  7. Collect ~200 mL sediment in a standard glass jar and store in black bag in esky on ice (for nutrients and TOC analyses). Label according to the scheme outlined in the spreadsheet “sample_schedule”.
  8. Store glass jars in -20 °C freezer to be analysed within 2 weeks.
  9. Collect ~60 mL sediment in a standard plastic jar (for grain size analyses). Label according to the scheme outlined in the spreadsheet “sample_schedule”.
  10. Store plastic jars at room temperature for further analysis.

1.11.2   Seagrass Sampling

NOTE: samples to be collected immediately after surficial sediment samples (for each plant, both surficial sediment and plant tissue will be collected).

  1. Collect seagrass healthy plants, using sterile gloves. Select only green, no-damaged plants.
  2. Separate only the leaves (above ground biomass) from the rest of plant tissues by using sterile scissors (section at the interface between leaves and roots).
  3. Discard the seagrass roots/rhizome tissue (below ground biomass), making sure that necrotic/dark plant tissue is not
  4. Wash seagrass leaves with seawater directly in the ocean until all sediment and littler is detached. Be careful not to damage the leaves.
  5. Pack the seagrass leaves without sediment into aluminium foil envelopes previously labelled according to the scheme outlined in the spreadsheet “sample_schedule”, and flash freeze these envelopes in liquid nitrogen (or place in dewar).
  6. After return to the laboratory, store aluminium envelops in a labelled box in -80 °C freezer for further analysis.
  7. RNA should be extracted from leaves within 2 weeks.