By T. Trevor Caughlin, Literature Coordinator

The transformation from degraded agricultural land to tropical forest is accompanied by visible changes in animal and plant biodiversity. How this transformation affects microbial communities, the invisible majority of life on earth, remains poorly understood. This knowledge gap represents a significant missing piece in our understanding of secondary succession, because fungi and bacteria play a major role in biogeochemical cycling and could be critically important for the ecosystem services tropical secondary forests provide, including belowground carbon storage. A fascinating new study, led by Peyton Smith and co-authored by PARTNERS member Erika Marín-Spiotta, addresses this knowledge gap by documenting changes in microbial communities that occur during tropical reforestation.


The study’s lead author sampling soil in Puerto Rico. Image credit: Peyton Smith.


The study was conducted in a well-replicated chronosequence of secondary forests in Puerto Rico that is broadly representative of succession in Neotropical pastures. The chronosequence sites range from actively grazed pastures, to 90-year old secondary forest, to primary forest. In addition to substituting space for decadal time scales in the chronosequence, the authors sampled each site five different times over a three year period, including both wet and dry seasons. The short-term temporal replication in the study design enabled the authors to disentangle seasonal and annual effects from differences due to successional state. While the tree composition in the study sites is well-known and provides invaluable context for interpreting changes in other taxa, measuring microbial communities is not as simple as botanical identification. The lab work required to determine microbial communities included measuring subtle differences in cell membrane fatty acids and identifying functional groups of microbes, since species-level classification is difficult (and may be meaningless for microbes that can exchange genetic material). By pairing technical expertise in cell biology with ecological context—a chronosequence of succession in tropical pastures—the authors provide a unique perspective on how microscopic life responds to reforestation.

Results indicate that forest succession is associated with significant changes in microbial community composition. Changes in microbial communities generally paralleled changes in tree community structure, although the microbial community appears far more dynamic. They observed large differences in microbial community structure between the wet and dry seasons, with more gradual changes in microbial community structure in the wet season and a sharp difference between older (70 year old to primary forest sites) and younger (pasture to 40 year old sites) in the dry season. Individual functional groups of microbes showed differences between successional stages that could lead to interesting lines of further research. For example, arbuscular mycorrhizal fungi, which assist tree roots in acquiring nutrients, were more abundant in early successional sites than later successional sites. Despite the significant differences between sites found for soil microbes, microbial enzyme activity and microbial communities in leaf litter were more strongly impacted by season than by successional stage. There were few significant differences in soil nutrient content between sites, providing further evidence that belowground microbial community changes are coupled with tree community changes.

Overall, the results suggest strong links between aboveground changes in forest composition and belowground changes in microbial communities during the course of succession. The strength of this relationship points to potential feedbacks between plants and microbes, for example, between plant root exudates and microbes, or between mycorrhizal fungi and tree roots. The interplay between microbes and trees during reforestation is a compelling research area full of interesting new questions with potential importance for applied work, including predicting ecosystem services and developing probiotic supplements for tree planting efforts. Further within-site comparisons across broad taxonomic and functional groups will likely have large pay-offs for our understanding of the ecological dynamics of reforestation.


Smith, A. P., E. Marín-Spiotta, and T. Balser. 2015. Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study. Global Change Biology: In Press. DOI: 10.1111/gcb.12947.

Featured image: fungi growing on leaf litter in Puerto Rico. Image credit: Peyton Smith.

If you have a recent publication you would like to see featured on the PARTNERS website, please email Trevor Caughlin at trevor.caughlin (at)

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