Does revegetation cause soil microbiota recovery? Evidence from revisiting a revegetation chronosequence 6 years after initial sampling

Abstract

The global biodiversity and land degradation crises have brought about an urgent need and great demand for restoration actions. However, restoration outcomes are often less than ideal, indicating a need for improved restoration practices. Soil microbiota are extremely diverse and functionally important and should be further considered in restoration. However, despite their importance, there remains a gap in understanding of how soil microbiota respond following native plant revegetation. Several studies have used cross-sectional study designs of restoration chronosequences to infer that revegetation causes the recovery of soil microbiota, but it is near-impossible to determine cause and effect relationships with cross-sectional study designs. Here we used high-throughput amplicon sequencing of the bacterial 16s rRNA gene from soil samples collected at two timepoints, 6 years apart, at a revegetation chronosequence in South Australia. Our results show some indications of recovery but not the additional recovery in bacterial community composition toward the reference sites as expected after this 6-year period-a result that appears at odds to the expected patterns of revegetation causing recovery of soil microbiota. Spatially dependent factors (e.g. soil chemistry), biotic and abiotic barriers, seasonal differences in sampling, and variability among the ecological reference sites could each help explain this apparent lack of additional microbial recovery. More detailed longitudinal and/or experimental manipulation work is required to further examine the cause-effect relationships. Our study contributes important new information and highlights knowledge gaps in how soil microbiota respond to revegetation, and we urge caution when attempting to infer causation from cross-sectional chronosequence studies.

Soil DNA chronosequence analysis shows bacterial community re‐assembly following post‐mining forest rehabilitation

“…This environmentally driven spatial variation of soil microbial communities highlights the need for appropriate experimental designs that limit spatial confounders where practicable or address their ecological implications. Furthermore, to experimentally test cause-effect relationships in a rehabilitation context, either experiments need to be embedded into rehabilitation sites (Gellie et al 2018) or longitudinal studies need to be done to conclusively ascertain temporal changes in soil microbiota (Lem et al 2022). Also, to investigate any potential return of key bacterial-mediated ecological functions, future studies should incorporate shotgun metagenomic data to directly ascertain changes in functional gene abundances as inferring any functional changes from 16s data alone is problematic (Sun et al 2020).…”

“…Barber et al 2017; Gellie et al 2017), while others have found either that recovery had stalled (e.g. Farrell et al 2020 b ; Lem et al 2022) or recovery is dependent on organism or topsoil handling methods (Van Der Heyde et al 2020). This presents a problem since soil microbiota are highly diverse and functionally important ecosystem components and therefore understanding their ecology and responses to both impacts and restoration or rehabilitation is integral to ecosystem restoration (Cameron et al 2018; Delgado‐Baquerizo et al 2020).…”

“…While the potential use of soil microbiota as an ecosystem indicator is beginning to be explored as part of an interrelated matrix of biotic and abiotic ecosystem components (Muñoz‐Rojas 2018; Tibbett et al 2019), cause and effect relationship regarding the response of soil microbiota post‐rehabilitation and specific drivers of any recovery remains a notable knowledge gap (Lem et al 2022). A pragmatic approach to begin to understand changes in microbiota with rehabilitation has been to use space as a proxy for time using a rehabilitation chronosequence design (i.e.…”

Integrating soil microbial communities into fundamental ecology, conservation, and restoration: examples from Australia

“…Soil microbiota are fundamentally linked to the restoration of degraded ecosystems; therefore, DNA‐based methods to characterise shifts in soil bacterial community composition have been developed to track restoration progress. Successful restoration of postagricultural landscapes back to biodiverse, functional, and self‐sustaining ecosystems is often hampered by legacies that linger from decades of unsustainable land use (Lem et al ., 2022; Peddle et al ., 2023). Developed from restoration chronosequence study datasets, a new ‘rehabilitation trajectory assessment’ (Liddicoat et al ., 2022) offers promise to help monitor and inform adaptive management practices and predict the ecological progress of restoration sites towards reference states (Craig Liddicoat, Flinders University).…”

Revegetation promotes soil microbial network stability in a novel riparian ecosystem

“…Natural regeneration, a common restoration practice without direct human interference, could increase microbial network complexity (Morrien et al, 2017). Meanwhile, active revegetation with a change in plant community composition significantly increases microbial diversity and affects soil microbial community reorganization primarily due to the increase of soil nutrient availability (Araujo et al, 2014; Lem et al, 2022; Ren et al, 2018; Wang et al, 2022; Yan et al, 2019). On the other hand, soil functional fungi including fungal decomposers, plant pathogens and mycorrhizal fungi can help plants withstand environmental challenges and maintain ecosystem functions (de Vries et al, 2020; Wagg et al, 2021; Yang et al, 2021).…”