Significance We do not know how and why belowground biodiversity may change as soils develop over centuries to millennia, hampering our ability to predict the myriad of ecosystem processes regulated by belowground organisms under changing environments. We conducted a global survey of 16 soil chronosequences spanning a wide range of ecosystem types and found that in less productive ecosystems, increases in belowground biodiversity followed increases in plant cover, but in more productive ecosystems, acidification during soil development was often associated with declines in belowground biodiversity. The biodiversity of multiple soil organisms exhibited similar patterns over time, but in contrast to expectations, changes in plant diversity were not associated with corresponding changes in belowground biodiversity.

Abstract Belowground organisms play critical roles in maintaining multiple ecosystem processes, including plant productivity, decomposition, and nutrient cycling. Despite their importance, however, we have a limited understanding of how and why belowground biodiversity (bacteria, fungi, protists, and invertebrates) may change as soils develop over centuries to millennia (pedogenesis). Moreover, it is unclear whether belowground biodiversity changes during pedogenesis are similar to the patterns observed for aboveground plant diversity. Here we evaluated the roles of resource availability, nutrient stoichiometry, and soil abiotic factors in driving belowground biodiversity across 16 soil chronosequences (from centuries to millennia) spanning a wide range of globally distributed ecosystem types. Changes in belowground biodiversity during pedogenesis followed two main patterns. In lower-productivity ecosystems (i.e., drier and colder), increases in belowground biodiversity tracked increases in plant cover. In more productive ecosystems (i.e., wetter and warmer), increased acidification during pedogenesis was associated with declines in belowground biodiversity. Changes in the diversity of bacteria, fungi, protists, and invertebrates with pedogenesis were strongly and positively correlated worldwide, highlighting that belowground biodiversity shares similar ecological drivers as soils and ecosystems develop. In general, temporal changes in aboveground plant diversity and belowground biodiversity were not correlated, challenging the common perception that belowground biodiversity should follow similar patterns to those of plant diversity during ecosystem development. Taken together, our findings provide evidence that ecological patterns in belowground biodiversity are predictable across major globally distributed ecosystem types and suggest that shifts in plant cover and soil acidification during ecosystem development are associated with changes in belowground biodiversity over centuries to millennia.

Belowground organisms play critical roles in maintaining the rates and stability of multiple ecosystem processes, including plant productivity, decomposition, and nutrient cycling (1⇓–3). Complementary ecological theories have been proposed to explain belowground biodiversity patterns, including theories related to aboveground and belowground resource availability, nutrient stoichiometry, and abiotic environmental factors (1⇓⇓⇓⇓⇓⇓⇓⇓⇓⇓–12) (SI Appendix, Table S1). However, and despite a longstanding interest in the topic (4⇓⇓⇓–8), the patterns in belowground biodiversity as soils develop over centuries to millennia (pedogenesis), as well as the environmental factors responsible for those patterns, remain largely unresolved. It is also unclear whether belowground biodiversity follows a similar trend to that of plant diversity during pedogenesis (4⇓–6), which often exhibits a positive or hump-shaped relationship attributed to changes in abiotic environmental factors (e.g., acidification) and soil resource availability (e.g., soil phosphorus) as soils develop (4⇓–6). Improving our knowledge of the mechanisms driving changes in belowground biodiversity during pedogenesis is critical for predicting both global ecological patterns and the many ecosystem processes regulated by belowground organisms (1⇓–3).

There are two main reasons why we lack a mechanistic understanding of how belowground biodiversity changes during pedogenesis. First, studies of belowground biodiversity patterns with pedogenesis have mostly been conducted on a few individual soil chronosequences (13⇓⇓⇓–17), with such work focusing mainly on a single group of belowground organisms, such as bacteria (16), fungi (18) or protists (19), or on changes in microbial biomass and community structure (17). Although such studies provide valuable information, pedogenesis often follows different trajectories depending on such factors as soil parent material and climate (7, 8, 19⇓–21). Moreover, multiple taxa should be considered in concert to achieve a holistic understanding of how belowground biodiversity changes during pedogenesis. Second, most studies reported to date have focused on changes in belowground biodiversity during initial stages of primary succession (i.e., years to centuries) (13, 22), with few studies evaluating effects over much longer time scales (i.e., from centuries to thousands or millions of years) (13, 15, 16). The fate of belowground biodiversity is expected to differ between early and late stages of pedogenesis, because older ecosystems may enter a retrogressive phase (19, 23⇓–25). This stage of ecosystem development is typically characterized by reduced resource availability [e.g., soil phosphorus (P), carbon (C), plant biomass], altered soil nutrient stoichiometry [e.g., increased nitrogen (N):P ratios], and soil acidification (19, 23⇓⇓–26), which could change the long-term development of belowground biodiversity.

Here we considered multiple complementary ecological theories, based on aboveground and belowground resource availability, nutrient stoichiometry, and abiotic environmental factors (SI Appendix, Table S1), to identify the predominant mechanisms driving the changes in belowground biodiversity during pedogenesis across ecosystem types (SI Appendix, Materials and Methods). Toward this aim, we conducted soil and vegetation surveys across 16 globally distributed chronosequences ranging in age from hundreds to millions of years and encompassing a wide range of climatic conditions (tropical, temperate, continental, polar, and arid), vegetation types (grasslands, shrublands, forests, and croplands), and chronosequence origins (volcanic, sedimentary, dunes, and glaciers) (Fig. 1A and SI Appendix, Tables S2 and S3). The diversity of soil organisms (bacteria, fungi, protists, and invertebrates) was measured via marker gene amplicon sequencing. Data on the dominant bacterial, fungal, protist, and invertebrate taxa detected are provided in SI Appendix, Table S4.

Fig. 1. Geographical distribution and major patterns showing the fate of belowground biodiversity during pedogenesis. Belowground biodiversity is defined as the standardized average of the diversity of soil bacteria, fungi, protists, and invertebrates. (A) Locations of the 16 soil chronosequences (87 plots) included in this study. (B) A conceptual figure summarizing the major ecological patterns observed (data provided in Figs. 2 and 3). Acronyms for each chronosequence are listed in SI Appendix, Table S2. Correlations between pH and plant cover with belowground diversity across sites are shown in SI Appendix, Fig. S26.

Materials and Methods Complete documentation of the study sites, field survey, sample collection, and laboratory procedures, as well as additional details on the statistical analyses, are provided in SI Appendix, Materials and Methods. Field data were collected between 2016 and 2017 from 16 soil age chronosequences located in nine countries from six continents (Fig. 1A). Each of the 16 chronosequences studied included between 4 and 10 chronosequence age-based stages (SI Appendix, Tables S2 and S3). At each stage, we conducted a vegetation survey and collected five composite samples of mineral soil (five soil cores 0–10 cm deep, a total of 435 soil samples) and obtained information on aboveground and belowground resource availability, nutrient stoichiometry, and other abiotic factors. The diversity of soil organisms was measured via marker gene amplicon sequencing. Belowground biodiversity was calculated as the standardized average of the diversity (i.e., richness; number of phylotypes) of soil bacteria, fungi, protists, and invertebrates. Detailed information on our regression, random forest, and hierarchical clustering analyses is provided in SI Appendix, Materials and Methods.

Acknowledgments This project received funding from the European Union’s Horizon 2020 research and innovation program under Marie Sklodowska-Curie Grant Agreement 702057. N.F. was supported through grants from the US National Science Foundation (EAR1331828, DEB 1556090). Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the US Government. An extended version of the acknowledgments is provided in SI Appendix.

Footnotes Author contributions: M.D.-B. and N.F. designed research; M.D.-B., R.D.B., P.M.V., F.T.M., M.A.W., D.J.E., H.L., S.N., A.G., L.G.-V., O.E.S., S.R.A., F.D.A., A.A.B., M.A.B., C.M.C., N.A.C., S.C.H., P.E.H., Z.-Y.H., M.K., V.M.P.-R., C.A.P., S.C.R., F.S., C.S., B.W.S., L.W.-G., and N.F. performed research; M.D.-B., F.T.M., A.G., L.G.-V., and N.F. contributed new reagents/analytic tools; M.D.-B., R.D.B., P.M.V., F.T.M., M.A.W., D.J.E., H.L., S.N., A.G., O.E.S., and N.F. analyzed data; and M.D.-B. and N.F. wrote the paper, with all authors contributing to the drafts.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The primary data used in this paper have been deposited in Figshare: https://figshare.com/s/0dc27c87f09d0a1c6ca3 (doi: 10.6084/m9.figshare.7556675).

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