Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance
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Abstract
Long‐term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions. This study leverages a 7‐year time series of a 60‐year‐old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the ‘whole’ bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall structural resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.
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We used 16S rRNA gene and 16S rRNA amplicon sequencing of co-extracted DNA and reverse-transcribed RNA to assess community structure across our samples
I see from this reference (https://journals.asm.org/doi/full/10.1128/mSystems.00003-19) that this method has been benchmarked against cell activity staining. Have you considered benchmarking the 16S rRNA ratio approach against a cell activity analysis used for metagenomic sequencing (like iRep, (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538567/)) to see how it performs?
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Figure 6:
It is extremely hard to get any information of the phyla color distribution outside of the first few bars. If you want to display this information, maybe removing the black lines between the phyla would make the colors more visible.
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Figure 1:
There seem to be some white text boxes covering up things that they shouldn't in this figure. For example, under FireClassification, 'recovered' looks half-covered up & 'SiteID' looks maybe a little cut off on the bottom. Maybe just a format conversion issue but you might want to check.
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to heating
do you mean "in response to heating"?
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The gradual advancement of the fire along the coal seams allows for direct comparisons across a gradient of disturbance intensities
This is a really cool opportunity/sampling site!
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by combining 16S rRNA with 16S rRNA gene amplicon sequencing
I think that this sentence could be reworded to maybe make it more clear what you mean by combining 16S rRNA with amplicon sequencing. I had to read further into the introduction to understand. Maybe something like this : "The active subset of the whole community was determined based on a threshold for the ratio of RNA sequencing reads to DNA reads for 16S rRNA genes."
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