Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance

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.

Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils

“…The bacterial communities in the recovered soils were more similar to communities in reference soils than fire-affected soils (Lee et al, 2017). As fire-affected soils cooled over seven consecutive years, we further observed directional changes in the bacterial community structure, with the community becoming more similar to the unaffected reference communities over time (Barnett and Shade, 2024a) No studies have examined soil viral dynamics under long-term soil heating conditions like those in Centralia. Furthermore, it is not clear how much soil viral communities change over multiple years.…”

“…Finally, we wanted to compare the beta diversity of the viral community (vOTUs) to that of the bacterial communities (OTU). Bacterial OTU were processed as previously described (Barnett and Shade, 2024a). As the previous study had more sites than included here, we removed samples not included in metagenome sequencing and rarefied the resulting OTU table to the lowest sequencing depth (161,171 reads).…”

“…Soils were collected from each site from 2015 to 2021 in the first or second week of October. Twenty cm depth soil cores were collected as described (Barnett and Shade, 2024a), sieved at 4 mm, hand-homogenized, and flash-frozen in liquid nitrogen. In situ, soil, and air temperatures were collected with an electronic thermometer.…”

“…In situ, soil, and air temperatures were collected with an electronic thermometer. Soil moisture was measured (Barnett and Shade, 2024a), soil temperature across the fire-affected sites decreased over the seven sampling years as the fire gradually advanced and those soils began to cool (Fig S1B).…”

“…For example, phages can remain dormant for extended periods, as is expected in soils, as phages have been experimentally shown to persist for weeks in soils without a host (DiPietro et al, 2023). We used the unique temperature disturbance gradient in Centralia, Pennsylvania, USA, to examine phage community diversity and 7-year dynamics as soils recover from a decades-old underground coal seam fire (Barnett and Shade, 2024a). The fires under Centralia have been burning along two roughly linear coal seams since 1962, elevating surface soil temperatures and releasing combustion products through soil vents (Elick, 2011).…”