About

Professor Francisco Dini Andreote leads research at the intersection of microbiology, ecology, and plant physiology with a focus on harnessing the plant microbiome for sustainable agriculture. His work centers on studying the collection of microbial taxa and their functional attributes across physicochemical gradients, aiming to understand how these microbiomes dynamically respond to environmental perturbations. This research integrates fundamental ecological principles to investigate the processes and mechanisms that structure microbiomes in space and time, providing novel insights into microbial diversity. Additionally, Professor Andreote's research addresses the impacts of climate change on the physiology and distribution of organisms, particularly examining how microbiomes affect and are affected by climate change with an emphasis on carbon sequestration and soil biogeochemistry. His work also explores strategies to properly manipulate and engineer microbiomes in agroecosystems to enhance agricultural productivity and sustainability.

Research topics

• Biology
• Ecology
• Botany
• Biochemistry
• Genetics
• Cartography
• Geography
• Agronomy
• Bioinformatics

Selected publications

• Contrasting physiological adaptation strategies to natural environmental change in two Red Sea coral holobionts

  ISME Communications · 2026-01-01

  articleOpen access

  Abstract Coral holobionts acquire energy and nutrients from heterotrophic feeding, Symbiodiniaceae symbiosis, and additional metabolic functions (e.g. nitrogen (N) fixation) from associated bacterial communities. Since symbioses often require stable environmental conditions, corals in environments with seasonal variability have likely evolved adaptation strategies by either maintaining (i.e. regulating) or shifting (i.e. conforming) key functional traits, but empirical data is needed. We investigated carbon (C) and N elemental and stable isotope ratios alongside bacterial community composition in the hydrocoral Millepora dichotoma and the scleractinian coral Stylophora pistillata every two months over one year. These data were integrated with environmental parameters to investigate potential adaptation strategies of the coral holobionts over a seasonal cycle. S. pistillata showed temporal changes in δ13C, δ15N and C:N ratios in both host and Symbiodiniaceae tissues (indicating stable host-Symbiodiniaceae C/N cycling), in combination with stable bacterial communities. M. dichotoma, did not exhibit temporal changes in elemental and stable isotope ratios, but higher δ15N and C:N variability, and 61% higher C:N ratios in Symbiodiniaceae compared to host tissue. Temporal shifts in bacterial communities resulted in significantly enriched predicted metabolic functions for C, N, and sulfur cycling in winter. Stable C/N cycling and bacterial community composition suggest a regulator-like life history strategy of S. pistillata, whereas variable C/N cycling and flexible bacterial communities indicate a conformer-like life history strategy for M. dichotoma. Both contrasting adaptation strategies enable these organisms to succeed amid current environmental change, yet to what extent this can be maintained under future climate scenarios remains to be investigated.

  PublisherDOI

• Silencing mitochondrial genes: a potential new frontier in plant science

  Trends in Plant Science · 2026-03-03

  article
  PublisherDOI

• 16S rRNA metabarcoding data and analysis code from throughfall and soil samples in a Neotropical forest (Ubatuba, São Paulo, Brazil)

  University of Campinas · 2026-01-01

  datasetOpen access

  This repository contains processed data and analysis code associated with a 16S rRNA gene metabarcoding study of bacterial communities in throughfall water (rainwater passing through the forest canopy) and soil samples collected in a Neotropical forest in Ubatuba, São Paulo, Brazil. The dataset was generated to investigate how epiphytic tank bromeliads influence soil bacterial community structure and microbial functioning via canopy–soil coupling mediated by throughfall. Throughfall and soil samples were collected in field conditions and processed using eDNA metabarcoding targeting the 16S rRNA gene (V4 region), following the Illumina Amplicon Protocol from the Earth Microbiome Project. Sequence data were processed using QIIME 2, with denoising and amplicon sequence variant (ASV) inference performed using DADA2, and taxonomic assignment conducted with a Naive Bayes classifier trained on the SILVA 138 database. The repository includes ASV tables, taxonomic classifications, and associated metadata. In addition to sequencing data, this repository provides R scripts used for downstream analyses, including diversity metrics (alpha and beta diversity), ordination analyses (PCoA), redundancy analysis (RDA), and structural equation modeling (piecewise SEM). Soil chemical variables (e.g., pH, organic matter, and nutrients) and microbial functional indicators—such as microbial biomass carbon, soil respiration, and β-glucosidase activity—were integrated into the analytical framework as well. The data cannot be made publicly available due to intellectual property protection restrictions. For additional information, please contact the corresponding authors.

  PublisherDOI

• Macroaggregates magnify the positive feedback of trophic cascades on carbon accrual

  Journal of Integrative Agriculture · 2026-01-01

  articleOpen access

  • Fungivorous nematodes enhanced fungal-derived carbon accrual via trophic cascade. • Macroaggregates magnified trophic cascade effects on soil fungal carbon accrual. • Manure amendments strengthened nematode-fungus interactions and SOC accrual. The interactions between nematodes and fungi are important for soil carbon cycling. However, their cascading effects on soil organic carbon (SOC) accrual remain unclear, particularly the role of soil aggregates and manure amendments in mediating this trophic cascade. Using a 19-year fertilization experiment, we examined how nematode predation influences fungal necromass carbon (FNC) and glomalin-related soil proteins (GRSPs), and quantified their contributions to SOC across soil aggregates under different manure amendments. Our findings showed that nematode predation significantly enhanced fungal biomass and promoted deterministic assembly of fungal communities. These effects were strongly dependent on aggregate size, with the most pronounced responses observed in the large macroaggregate (LA) fraction. A complementary microcosm experiment confirmed that nematode predation increased fungal biomass by over 6%, particularly in the LA fraction. Manure amendments further stimulated fungal growth and reinforced deterministic community assembly, thereby enhancing trophic cascade-driven accrual of FNC and GRSPs. Of the two fungal-derived carbon sources, FNC contributed more substantially to SOC (40%) than GRSPs (17%), with the greatest contribution found in the LA fraction. Path analysis further revealed that nematode-induced changes in fungal communities mediated the positive effects of manure amendments on fungal-derived carbon accrual. Overall, these findings underscore the pivotal role of nematodes in driving positive trophic cascade impact on SOC accrual. Our study offers new insights into aggregate-scale carbon dynamics and biologically mediated strategies for soil carbon management.

  PublisherDOI

• Keystone Pseudomonas species in the wheat phyllosphere microbiome mitigate Fusarium head blight by altering host pH

  Cell Host & Microbe · 2025-11-19 · 5 citations

  article
  PublisherDOI

• Spatiotemporal changes in soil properties predict plant health at continental scale

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-10

  preprintOpen access

  Abstract Abiotic and biotic soil properties are strong predictors of plant yield globally 1–5 , but they become unreliable over large areas when plant health is threatened by pathogen 6–8 . Here we present a novel approach to predict plant health based on spatiotemporal changes in soil chemical and biological properties. We first demonstrate that plant health and soil properties consistently respond to environmental change (organic fertilization) regardless of the soil type or geographical origin. Second, we experimentally show that trackable shifts in soil properties reliably explain soil suppressiveness to the Ralstonia solanacearum bacterial pathogen and that a scalable spatiotemporal model predicts plant health with 84% accuracy across multiple climatic zones and cropping systems. Our results suggest that this tight coupling between soil properties and plant health could facilitate the development of agricultural practices aimed at sustainably improving crop yields while safeguarding crop health.

  PublisherOA PDFDOI

• Revisiting the cry-for-help hypothesis in plant–microbe interactions

  Trends in Plant Science · 2025-08-22 · 8 citations

  articleSenior author
  PublisherDOI

• Fungal genomic trait-based ecological strategies mediate plant productivity

  Trends in Plant Science · 2025-12-01

  review
  PublisherDOI

• Targeted manipulation of food webs in the plant rhizosphere

  Trends in Plant Science · 2025-03-24 · 2 citations

  article
  PublisherDOI

• Unveiling the ecological processes driving soil and lichen microbiome assembly along an urbanization gradient

  npj Biofilms and Microbiomes · 2025-06-10 · 6 citations

  articleOpen access

  Global biodiversity loss is accelerating due to the transformation of natural landscapes into agricultural and urban areas. Yet, research on the urbanization impact on environmental and host-associated microbiomes, particularly on the ecological processes that mediate their assembly and function, remains scarce. This study investigated the effects of an urbanization gradient on the diversity and assembly processes of the soil microbiome and the microbiomes of three epiphytic lichen species (Candelaria concolor, Physcia adscendens, and Xanthoria parietina). Our findings revealed that the urbanization gradient shaped the soil microbiome, while the lichen microbiomes exhibited strong host specificity and showed no significant changes in diversity along the urbanization gradient. Heterogeneous selection and dispersal limitation primarily governed the soil community assembly and higher community turnover in medium- and highly urbanized zones compared to low-urbanized zones, indicating an increased influence of environmental pressures, altered resources, and habitat fragmentation in more urbanized areas. The lichen microbiome assembly in each species was primarily governed by undominated processes regardless of urbanization level, indicating that both selection and stochasticity contributed to, but neither dominantly influenced, their assembly. The lichen microbiomes further revealed species-specific co-occurrence networks, with microbial compositional signatures and potential functions being essential for lichen fitness and urban ecosystem health. Taken together, our study contributes to understanding how microbial communities are assembled in urban environments, bridging the gap between conceptual theories and empirical findings in the urban ecology of soil and lichen-associated microbiomes.

  PublisherOA PDFDOI

Frequent coauthors

• Fernando Dini Andreote

  43 shared

• Jos M. Raaijmakers

  Netherlands Institute of Ecology

  35 shared

• Yuji Jiang

  Chinese Academy of Sciences

  26 shared

• Joana Falcão Salles

  Ecologie Microbienne Lyon

  26 shared

• Welington Luiz Araújo

  Universidade de São Paulo

  23 shared

• Lu Luan

  Institute of Soil Science

  19 shared

• Eiko E. Kuramae

  13 shared

• Wietse de Boer

  13 shared

Education

• Ph.D., Microbiology

  University of Groningen

  2016

• M.S., Genetics

  University of Sao Paulo

  2011