Microbial Ecology

, Volume 79, Issue 1, pp 110–122 | Cite as

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion

  • Dennis Goss-Souza
  • Lucas William MendesEmail author
  • Jorge Luiz Mazza Rodrigues
  • Siu Mui Tsai
Plant Microbe Interactions


Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.


Metagenomics Microbial dispersal Neutral theory Selection Soybean rhizosphere 


Author Contributions

DG-S and SMT designed the project. DG-S collected the soil samples. DG-S conducted the experiment. DG-S and LWM performed the metagenome analyses. DG-S and LWM analyzed the metadata. DG-S, LWM, JLMR, and SMT wrote the manuscript.

Funding Information

This study was funded by the São Paulo Research Foundation (FAPESP/CNPq No. 2008/58114-3 and FAPESP/NSF No. 2014/50320-4). DG-S received a scholarship from National Council for Scientific and Technological Development (PRONEX-CNPq # 140317/2014-7). SMT thanks CNPq (CNPq-PQ 311008/2016-0).

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

248_2019_1401_MOESM1_ESM.pdf (1 mb)
ESM 1 (PDF 1074 kb)


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Authors and Affiliations

  1. 1.Center for Nuclear Energy in AgricultureUniversity of São PauloPiracicabaBrazil
  2. 2.Department of Land, Air and Water ResourcesUniversity of California – DavisDavisUSA
  3. 3.Department of Soils and Natural ResourcesSanta Catarina State UniversityLagesBrazil
  4. 4.Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyUSA

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