Gabriel Silvestre Rocha

Gabriel Silvestre Rocha MSc

PhD Candidate

Bezoekadres

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands

Netwerk

Over

Passionate microbial ecologist dedicated to sustainable agriculture. I steer microbial communities for sustainability and efficient nutrient cycling. On my PhD I will focus on mitigating N losses via crop selection for biological nitrification inhibition.

Biografie

I'm a Bachelor in Environmental Sciences from the Federal University of the State of Rio de Janeiro (UNIRIO) and Master in Sciences from the Graduate Program in Sciences at the Center for Nuclear Energy in Agriculture (CENA) of the University of São Paulo (USP), with a specialized focus on Agriculture and Environment Biology. During my master's program, I conducted research projects that centered on analyzing the microbiome associated with plants of the Urochloa genus (Syn. Brachiaria) and explored methods to improve Phosphorus availability in tropical soils.

Throughout my academic journey, I actively collaborated on diverse research projects across different Brazilian biomes, including the Atlantic Forest, Cerrado (Brazilian savanna), and the Amazon. My experience includes bioinformatics and molecular biology, with emphasis on soil microbiome analysis and microbial ecology.

Currently, I am pursuing a PhD in the Microbial Ecology department at the Netherlands Institute of Ecology (NIOO-KNAW), where my research focuses on mitigating greenhouse gas emissions, with a particular interest in addressing the challenge of reducing N2O emissions through crop selection to promote biological nitrification inhibition. My commitment to advancing sustainable agriculture through microbial ecology and molecular biology continues to drive my academic and research goals.

Onderzoeksgroepen

CV

Employment

2023–Present
PhD Student (NIOO-KNAW)

Education

  • 2023–Present
    PhD Student (NIOO-KNAW)
  • 2021–2023
    Master's in Sciences (USP)
  • 2016–2021
    Bachelor in Environmental Sciences (UNIRIO)

Publicaties

Peer-reviewed publicaties

  • BMC Microbiology
    17-01-2025

    Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery

    Anderson Santos de Freitas, Luís Felipe Guandalin Zagatto, Gabriel Silvestre Rocha, Franciele Muchalak, Rogério Eiji Hanada, Aleksander Westphal Muniz, Siu Mui Tsai
    Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil’s most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.
    https://doi.org/10.1186/s12866-024-03741-3
  • ISME Communications
    01-2025

    Improved methane mitigation potential and modulated methane cycling microbial communities in arable soil by compost addition

    Stijn van den Bergh, Iris Chardon, Marion Meima-Franke, German Perez, Gabriel Silvestre Rocha, Kristof Brenzinger, Gerard Korthals, Jochen Mayer, Mathias Cougnon, Dirk Reheul, Wietse de Boer, Paul Bodelier

    The global atmospheric concentration of the potent greenhouse gas methane (CH4) is rising rapidly, and agriculture is responsible for 30%-50% of the yearly CH4 emissions. To limit its global warming effects, strong and sustained reductions are needed. Sustainable agricultural management strategies, as the use of organic amendments like compost, have previously proven to have a potent CH4 mitigation effect in laboratory experiments. Here we investigated, using an extensive field study, the effect of organic amendments on the CH4 mitigation potential and CH4 cycling microbial communities of arable soils. Organic-amended soils had higher potential CH4 uptake rates and an improved potential to oxidize CH4 to sub-atmospheric concentrations. Also, we showed for the first time that the methanotrophic and methanogenic microbial communities of arable soils were unequivocally altered after organic amendment application by increasing in size while getting less diverse. Compost-amended soils became dominated by the compost-originating methanotroph Methylocaldum szegediense and methanogen Methanosarcina horonobensis, replacing the indigenous methane cycling community members. However, multivariate analyses didn't point out type Ib methanotrophs like M. szegediense as significant driving factors for the observed improved soil CH4 uptake potential. Conventional type IIa methanotrophs like Methylocystis sp. also had higher differential abundances in organic-amended soils and are speculated to contribute to the improved CH4 uptake potential. Altogether, the results showed that compost serves as a vector for the introduction of CH4 cycling microbes and improves the soil's CH4 uptake potential, which emphasizes the potential of organic fertilization with compost to contribute to CH4 mitigation in agricultural soils.

    https://doi.org/10.1093/ismeco/ycaf139
  • Microbiology Resource Announcements
    04-06-2024

    Bacterial genomes recovered from litter’s metagenomes in Amazonian Dark Earths

    Anderson Santos de Freitas, Luís Felipe Guandalin Zagatto, Gabriel Silvestre Rocha, Thierry Alexandre Pellegrinetti, Letícia de Cássia Malho Alves, Vitor Moreira de Lara, Jéssica A. Mandro, Aleksander Westphal Muniz, Rogério Eiji Hanada, Luiz Fernando Würdig Roesch, Siu Mui Tsai
    Here, we report 27 metagenome-assembled bacterial genomes (MAGs) from litter samples of a secondary forest located in Brazil over an Amazonian Dark Earth pool. The data set includes members from the phyla Pseudomonadata (14 MAGs), Actinomycetota (7 MAGs), Bacteroidota (4 MAGs), Bacillota (1 MAG), and Bdellovibrionota (1 MAG).
    https://doi.org/10.1128/mra.00422-24

Projecten & samenwerkingen

Projecten

  • ClipsMicro: Climate proof soils by steering soil and residue microbiomes

    Project 2022–2028
    To mitigate climate change, global agricultural soils needs to store more carbon and emit less greenhouse gasses (GHG). In ClipsMicro, together with partners in agro-business, this is realised by steering soil microbes by application of novel, refined compost and crops that can reduce emissions of GHG.
    Soil from 70 year composting trial

Outreach

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