In order to detect significant net growth or loss of populations, the cell numbers of different microbes in situ have to be determined at a standardized level of precision. This requires manual quantification of the percentage of FISH-stained microbes by epifluorescence microscopy (217). Other potential counting approaches, e.g., flow cytometry (5), so far have failed to provide working alternatives to this tedious evaluation strategy. Eventually, a rapid quantification of bacterial populations by means of automated microscopy (219) might allow us to expand the scale of investigations from a few point measurements to a spatial or temporal resolution that better reflects the true population dynamics of heterotrophic aquatic picoplankton.
A conversion of cell numbers into biomass is required for the reconstruction of carbon fluxes through microbial food webs. Bacterial cell sizes and the relationship between cell size and dry mass can be determined empirically, e.g., by image analyzed microscopy (174, 274) and appropriate conversion factors (159, 197, 233). Some microbial taxa in the plankton form significantly larger cells than others (16), and population changes within such groups may thus contribute disproportionally to changes in total biomass (132, 222). The most extreme example are the filamentous bacteria in the water column of many lakes (130). Such morphotypes rarely form more than a few percent of total cell numbers, but they may temporarily constitute half of total microbial biomass or more (130, 286) (Fig. 5). Therefore, the biomasses of different microbial populations may need to be determined separately in order to assess their respective roles in the carbon flux through aquatic systems (46, 132, 216, 237).
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