Optimising the extraction of bacteria, heterotrophic protists and diatoms, and estimating their abundance and biomass from intertidal sandy sediments
Lee, W.J.; Patterson, D.J.
Journal of the Korean Society of Oceanography e; 37(2): 58-65
The study of microbial communities in sediments is impaired by the lack of reliable extraction methods. This study reports on the efficiency of recovery of a method for extracting bacteria, protists and diatoms from sandy sediments using a modified decant/fix method. The best extractions were achieved after fixation with a microtubule stabilising fixative and subsequent sonication for 80 seconds. We estimate that the efficiencies of recovery of bacteria and mixed heterotrophic flagellate were 96.4 plus or minus 3.5% and 96.9 plus or minus 4.6%, respectively. Diatoms were recovered with an efficiency of 38-83% and varied considerably from species to species. This study suggests that the decant/fix method effective in extracting small cells such as bacteria and heterotrophic flagellates, and that the efficiency of recovery of the method varies due to cell length and different types of organisms. When the factors to correct inaccuracies were applied to field data from Port Botany, we found that the total microbial carbon biomass had been underestimated by up to 32%, with much of that relating to larger cells such as microalgae and ciliates. We note that the corrected abundances may be still be a subset of the total numbers present.