Title
Low abundant soil bacteria can be metabolically versatile and fast-growing.
Introduction
It is not yet known what causes rarity and abundance in soil bacteria. The aim of this
experiment is to investigate if the growth rate and utilization of substrates affect the abundance
of soil bacterial species. The abundance of species is affected by several factors including
abiotic conditions and biotic interactions within a species (Kurm, 2018). In general, rare species
are assumed to be slow growing, their small cell sizes suggest that they can escape predation
and lysis. In this experiment, three hypotheses were investigated to test the aim of this
experiment. The first one states that rare bacterial species are assumed to have a slower
growth rate than abundant bacteria. The second hypothesis states that abundant bacterial
species should use more carbon sources than rare/low abundance bacterial species. Lastly,
from the first two hypotheses, one can assume that bacteria that use fewer carbon sources,
should also have a lower growth rate. The opposite would be true for fast-growing bacterial
species (Kurm et al., 2017).
Methodology
Bacteria were isolated from soil samples collected from previously arable land. The bacteria
were isolated using flow cytometry and dilution plating. Different culture media was used to
cultivate a wider range of bacterial species from the samples. A soil solution, as well as a
control, was prepared. Both solutions were stained with SYBR green stain. The particles that
had a low intensity of fluorescence and a cell size of about 0.5 micrometres were plated onto
different media. The composition of the dilution plating was suitable for isolating various soil
bacteria taxa. Colony-PCR was done to amplify the 16S rRNA gene of the pure isolated
bacteria. The partial 16S rRNA gene was then compared to a sequence database of soil
samples. An estimation of the growth rate was measured by plating precultures on low and
high nutrient microplates. The substrate utilization was profiled for the isolates using 31
different substrates as the sole carbon source.
Conclusion
It was found that there was a positive correlation between the growth rate and the substrates
that a species could use. Hypothesis one and two were rejected because there was no direct
correlation between growth rate, the number of substrates and relative abundance (Kurm,
2018). A relationship was however discovered between the growth rate and rRNA gene copy
number of the isolates. To summarize, the growth rate and substrate use of bacterial species
in the soil is not the only factor that affects the abundance of these species. Enrichment bias
skews the results of this experiment. Further experiments are therefore required to investigate
if other factors affect the relative abundance of soil bacteria.
Next step
Only ex-arable soil was used, and the report was concerned about lack of taxa, further
experiments should include soils of varying pH, temperature and oxygen levels. Other factors
that can affect the abundance of bacteria include; competition between species, predation from
fast-growing species and abiotic factors such as mineral surfaces (Kurm et al., 2017). New
samples of soil should be taken from various locations under several conditions. The bacteria
should be isolated with different concentrations of nutrients and some of the bacteria should
be isolated with predators. This should give data about how low abundance bacteria compete
for different nutrients when they are exposed to predators.
References
Kurm, V. (2018). Causes and consequences of soil bacteria rarity. PhD Wageningen
University.
Kurm, V., van der Putten, W., de Boer, W., Naus-Wiezer, S. and Hol, W. (2017). Low abundant
soil bacteria can be metabolically versatile and fast-growing. Ecology, 98(2), pp.188-190.