Ground Zero? Let’s get real on regeneration! Report 1: State of the art and indicator selection

The urgency with which the world needs to combat climate change has led to ambitious commitments by leading food companies such as Nestlé. Given that a large proportion of emissions in supply chains occur during the production of commodities, focus has converged on Regenerative Agriculture as a key strategy to achieve those goals. The Regenerative Agriculture agenda coalesces around three main goals: • Reduce the Carbon Footprint • Enhance Soil Health • Enhance and safeguard Biodiversity alongside commitments to enhance smallholder producers’ incomes, to avoid child labour and to ensure a sustainable supply. The Ground Zero project aims to provide a framework of robust, easily measurable and verifiable indicators and methods for the assessment of the carbon footprint, soil health and biodiversity in cocoa and coffee production systems. The project is organised around four work packages (WPs): WP1 – Coordination; WP2 – Carbon Footprints; WP3 – Soil Health; WP4 – Biodiversity. Here we report on the state-of-the-art for each of these topics and in a final chapter we indicate the next steps that will be taken in the project

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop

Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization

Genome-resolved metagenomics of sugarcane vinasse bacteria

Abstract Background The production of 1 L of ethanol from sugarcane generates up to 12 L of vinasse, which is a liquid waste containing an as-yet uncharacterized microbial assemblage. Most vinasse is destined for use as a fertilizer on the sugarcane fields because of the high organic and K content; however, increased N2O emissions have been observed when vinasse is co-applied with inorganic N fertilizers. Here we aimed to characterize the microbial assemblage of vinasse to determine the gene potential of vinasse microbes for contributing to negative environmental effects during fertirrigation and/or to the obstruction of bioethanol fermentation. Results We measured chemical characteristics and extracted total DNA from six vinasse batches taken over 1.5 years from a bioethanol and sugar mill in Sao Paulo State. The vinasse microbial assemblage was characterized by low alpha diversity with 5–15 species across the six vinasses. The core genus was Lactobacillus. The top six represented bacterial genera across the samples were Lactobacillus, Megasphaera and Mitsuokella (Phylum Firmicutes, 35–97% of sample reads); Arcobacter and Alcaligenes (Phylum Proteobacteria, 0–40%); Dysgonomonas (Phylum Bacteroidetes, 0–53%); and Bifidobacterium (Phylum Actinobacteria, 0–18%). Potential genes for denitrification but not nitrification were identified in the vinasse metagenomes, with putative nirK and nosZ genes the most represented. Binning resulted in 38 large bins with between 36.0 and 99.3% completeness, and five small mobile element bins. Of the large bins, 53% could be classified at the phylum level as Firmicutes, 15% as Proteobacteria, 13% as unknown phyla, 13% as Bacteroidetes and 6% as Actinobacteria. The large bins spanned a range of potential denitrifiers; moreover, the genetic repertoires of all the large bins included the presence of genes involved in acetate, CO2, ethanol, H2O2, and lactose metabolism; for many of the large bins, genes related to the metabolism of mannitol, xylose, butyric acid, cellulose, sucrose, “3-hydroxy” fatty acids and antibiotic resistance were present based on the annotations. In total, 21 vinasse bacterial draft genomes were submitted to the genome repository. Conclusions Identification of the gene repertoires of vinasse bacteria and assemblages supported the idea that organic carbon and nitrogen present in vinasse together with microbiological variation of vinasse might lead to varying patterns of N2O emissions during fertirrigation. Furthermore, we uncovered draft genomes of novel strains of known bioethanol contaminants, as well as draft genomes unknown at the phylum level. This study will aid efforts to improve bioethanol production efficiency and sugarcane agriculture sustainability

Mineralização e nitrificação do nitrogênio proveniente da cama de aves aplicada ao solo

RESUMO A eficiência fertilizante da cama de aves depende da capacidade de mineralização de seus nutrientes que se encontram na forma orgânica. O potencial poluente deste resíduo, por outro lado, depende, dentre outros fatores, da rapidez da nitrificação dos compostos nitrogenados. O presente estudo objetivou quantificar a mineralização líquida e a nitrificação do N presente na cama de aves após sua aplicação em um Cambissolo Húmico álico. Os tratamentos consistiram na incubação com o solo de doses de cama (equivalente a 0; 4; 8; 16 Mg ha-1) e uma dose de ureia (204 kg ha-1 de N), todas incorporadas ou aplicadas sobre a superfície do solo. Determinaram-se os teores de amônio e nitrato no solo aos 2, 6, 12, 19, 26, 32 e 48 dias após o início da incubação. Os teores de amônio diminuíram e os de nitrato aumentaram com o tempo de incubação em função do processo de nitrificação; esta conversão foi mais rápida quando a cama de aves foi incorporada ao solo em relação à aplicação na superfície. A recuperação do N da cama de aves na forma mineral foi pequena, independentemente da forma de aplicação ao solo, com valores que decresceram em função da dose de 22,0 para 15,7% para as doses 4 e 16 Mg ha-1, respectivamente, aos 48 dias de incubação

Correction to: Genome-resolved metagenomics of sugarcane vinasse bacteria

The original version of the article contained a mistake. The accession number has been incorrectly published in the Availability of data and materials section

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop

Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization