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Net growth of microbial populations, i.e., changes in abundances over time, can be studied using 16S rRNA fluorescence in situ hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, the copiotrophic phylum Bacteroidetes, and its genus Aurantivirga. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate the cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8 d-1 and Aurantivirga of up to 1.9 d-1 differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9 d-1, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (-0.6 to 0.5 d-1) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within one day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom-up and top-down controls.

The Amazon rain forest plays a major role in global hydrological cycling, and biogenic aerosols are likely to influence the formation of clouds and precipitation. Information about the sources and altitude profiles of primary biological aerosol particles, however, is sparse. We used fluorescence in situ hybridization (FISH), a molecular biological staining technique largely unexplored in aerosol research, to investigate the sources and spatiotemporal distribution of Amazonian bioaerosols on the domain level. We found wet season bioaerosol number concentrations in the range of 1–5 × 105 m−3 accounting for > 70 % of the coarse mode aerosol. Eukaryotic and bacterial particles predominated, with fractions of ∼ 56 % and ∼ 26 % of the intact airborne cells. Archaea occurred at very low concentrations. Vertical profiles exhibit a steep decrease in bioaerosol numbers from the understory to 325 m height on the Amazon Tall Tower Observatory (ATTO), with a stronger decrease in Eukarya compared to Bacteria. Considering earlier investigations, our results can be regarded as representative for near-pristine Amazonian wet season conditions. The observed concentrations and profiles provide new insights into the sources and dispersion of different types of Amazonian bioaerosols as a solid basis for model studies on biosphere–atmosphere interactions such as bioprecipitation cycling. Version of record

Additional file 5: Figure S5. Microscopic images of differently fixed Gramella forsetii cells after cell sorting. Shown are overlay images of the HCR-FISH signal (green) and DAPI signal (blue). All images were taken with an epifluorescence microscope with a HC409LP (DAPI) and an ET500/LP (HCR-FISH) filter. The numbers in brackets indicate the exposure time for each image with the first number corresponding to the DAPI and the second to the HCR-FISH signals.

Additional file 8: Figure S8. Genomic quality estimation of Gramella forsetii and Maribacter forsetii sequencing products after MDA of 100 and 500 sorted cells using Quast. Shown are from left to right: the number of contigs longer than 1000 bp, the total assembly lengths, N50, number of misassemblies and number of mismatches per 100 kpb. Unhybridized samples were unfixed and were not subjected to HCR-FISH, but only sorted based on their DAPI signal. Maribacter forsetii unhybridized controls were taken from a cell aliquot and have not been filtered and washed off a filter like the other controls, including the Gramella forsetii unhybridized control. Significance thresholds (p-values) of pairwise t-tests are * < 0.05, ** < 0.01, *** < 0.001.

Additional file 6: Figure S6. Exemplary images of gel electrophoresis with MDA products from sorted isolates, fixed with formaldehyde, Lugol’s solution, ethanol or unfixed. The uppermost band of the used marker LambdaDNA Hind III corresponds to 23 kb. MDA products from formaldehyde fixed cells were either not detectable or in low amount.

Additional file 3: Figure S3. Four pure cultures (Gramella forsetii, Maribacter forsetii, Escherichia coli, Micrococcus sp.) were fixed with 10 different fixation methods (formaldehyde 4%, 1%, 0.25%, 0.1%, ethanol, Lugol’s solution with and without thiosulfate, glyoxal with and without ethanol and unfixed). HCR-FISH was done on filtered cells and signal intensity was measured after washing the cells off the filter and analyzing them in the flow cytometer. Plotted are the green fluorescence (530/40 nm) from HCR-FISH and blue fluorescence (450/60 nm) from DAPI staining. The fluorescence intensity is given in relative units on a logarithmic scale. The background fluorescence (dotted line) was defined for 10 RU. N.A. = not analyzed due to disrupted cells.