Genome-resolved metagenomics of sugarcane vinasse bacteria

Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments

In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).

Omics approaches in understanding the benefits of plant-microbe interactions

Plant-microbe interactions are pivotal for ecosystem dynamics and sustainable agriculture, and are influenced by various factors, such as host characteristics, environmental conditions, and human activities. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revolutionized our understanding of these interactions. Genomics elucidates key genes, transcriptomics reveals gene expression dynamics, proteomics identifies essential proteins, and metabolomics profiles small molecules, thereby offering a holistic perspective. This review synthesizes diverse microbial-plant interactions, showcasing the application of omics in understanding mechanisms, such as nitrogen fixation, systemic resistance induction, mycorrhizal association, and pathogen-host interactions. Despite the challenges of data integration and ethical considerations, omics approaches promise advancements in precision intervention and resilient agricultural practices. Future research should address data integration challenges, enhance omics technology resolution, explore epigenomics, and understand plant-microbe dynamics under diverse conditions. In conclusion, omics technologies hold immense promise for optimizing agricultural strategies and fortifying resilient plant-microbe alliances, paving the way for sustainable agriculture and environmental stewardship.

Understanding microbiome dynamics and functional responses during acidogenic fermentation of sucrose and sugarcane vinasse through metatranscriptomic analysis

Improving anaerobic digestion of sugarcane vinasse - a high-strength wastewater from ethanol distillation - is a subject of great interest, in view of the reduction of the pollutants and recovery of methane and valuable metabolites as byproducts. Through metatranscriptomic analysis, this study evaluated the active microbiome and metabolic pathways in a continuous acidogenic reactor: Stage 1S (control): 100% sucrose-based substrate (SBS); Stage 2SV (acclimation): 50% SBS and 50% vinasse; Stage 3V: 100% vinasse. Metatranscriptome obtained from each Stage was subjected to taxonomic and functional annotations. Under SBS feeding, pH dropped to pH 2.7 and biohydrogen production was observed. As vinasse was added, pH increased to 4.1-4.5, resulting in community structure and metabolite changes. In Stage 3V, biohydrogen production ceased, and propionate and acetate prevailed among the volatile fatty acids. Release of homoacetogenesis enzymes by Clostridium ljungdahlii and of uptake hydrogenase (EC 1.12.99.6) by Pectinatus frisingensis were linked to hydrogen consumption in Stages 2SV and 3V. Metabolic pathways of vinasse compounds, such as carbohydrates, malate, oxalate, glycerol, sulfate and phenol, were investigated in detail. In pyruvate metabolism, gene transcripts of oadA (oxaloacetate decarboxylase) and mdh (malate dehydrogenase), were upregulated in Stage 3V, being mostly attributed to P. frisingensis. Acetate formation from vinasse degradation was mainly attributed to Megasphaera and Clostridium, and propionate formation to P. frisingensis. Glycerol removal from vinasse exceeded 99%, and gene transcripts encoding for glpF (glycerol uptake facilitator protein), glpK (glycerol kinase) and glpABC (glycerol-3-phosphate dehydrogenase) were expressed mostly by Pectinatus and Prevotella. mRNA profiling showed that active bacteria and gene expression greatly changed when vinasse replaced sucrose, and Pectinatus was the main active bacterium degrading the searched compounds from vinasse. The identification of the main metabolic routes and the associated microorganisms achieved in this work contributes with valuable information to support further optimization of fermentation towards the desired metabolites.

Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities

Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we explored how applying organic residue, vinasse, as fertilizer in its natural state (V) versus its concentrated form (CV) impacts soil microbiota. We conducted two field experiments, evaluating soil prokaryotic and fungal communities over 24 and 45 days with vinasse (V or CV) plus N fertilizer. We used 16S rRNA gene and ITS amplicon sequencing. Inorganic N had no significant impact on bacterial and fungal diversity compared to the control. However, the varying concentrations of organic C and nutrients in vinasse significantly influenced the soil microbiome structure, with smaller effects observed for V compared to CV. Prokaryotic and fungal communities were not correlated (co-inertia: RV coefficient = 0.1517, p = 0.9708). Vinasse did not change the total bacterial but increased the total fungal abundance. A higher C input enhanced the prokaryotic but reduced the fungal diversity. Our findings highlight vinasse's role as an abiotic filter shaping soil microbial communities, with distinct effects on prokaryotic and fungal communities. Vinasse primarily selects fast-growing microorganisms, shedding light on the intricate dynamics between organic residues, nutrient concentrations, and soil microbes.

VINASSE FROM THE BRAZILIAN LIGNOCELLULOSIC ETHANOL PROCESS: CHEMICAL COMPOSITION AND POTENTIAL FOR BIOPROCESSES

Brazil is the second-largest producer of ethanol and the alcoholic fermentation wastes have become a concern for both environmental and economic reasons. Recently, the Brazilian industry has implemented the second generation (2G) process to attend the growing for biofuel. In this study, we aimed to investigate whether the 2G vinasse faces the same environmental challenges that first generation (1G) vinasses do, meaning vinasses from ethanol processes using sugarcane juice and/or molasses. Thus, vinasse was obtained from one of the recently-started 2G ethanol facilities in São Paulo State and then chemically characterized. Considering glycerol, mannitol, residual sugars, and organic acids concentrations altogether, it was determined that 2G vinasse had a total carbon source of 23,050 mg L-1 (compared to 4,800 mg L-1 in 1G vinasse). Magnesium, calcium, potassium, and others salts were determined as well. Based on its chemical composition, vinasses could be considered as nutrient sources for other bioprocesses. Finally, we brought some perspectives into bioprocesses with nutritional requirements that might be fully or partially provided by vinasses, leading to the production of bioenergy or bioproducts.

Novel insights on the versatility of biohydrogen production from sugarcane vinasse via thermophilic dark fermentation: Impacts of pH-driven operating strategies on acidogenesis metabolite profiles

An innovative application of the anaerobic structured-bed reactor (AnSTBR) in thermophilic dark fermentation of sugarcane vinasse targeting biohydrogen (bioH₂) production was assessed. A detailed metabolite monitoring program identified the major substrates and primary metabolic pathways within the system. Increasing the applied organic loading rate positively affected bioH₂ production, reaching 2074 N mL-H₂ L^-1 d^-1 and indicating an optimal load of approximately 70 kg-COD m^-3 d^-1. Controlling the fermentation pH (5.0-5.5) was the primary strategy to maintain bioH₂-producing conditions, offsetting negative impacts associated with the compositional variability of vinasse. Metabolic correlations pointed out lactate as the primary substrate for bioH₂ production, indicating its accumulation as evidence of impaired reactors. The versatility of the acidogenic system was confirmed by identifying three major metabolic pathways according to the pH, i.e., lactate-producing (pH <5.0), bioH₂-/butyrate-producing (pH = 5.0-5.5) and bioH₂-producing/sulfate-reducing (pH >6.0) systems, which enables managing the operation of the reactors for diversified purposes in practical aspects.

Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop

The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on 16S rRNA sequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar to Lysinibacillus, encode for nirK gene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.

Application of microbial fuel cell technology for vinasse treatment and bioelectricity generation

OBJECTIVE

Our study evaluated the performance of different two-chambered microbial fuel cell (MFC) prototypes, operated with variable distance between electrodes and Nafion membrane and specific inoculum concentration, applied for vinasse treatment.

RESULTS

The performance of the developed MFC resulted in a maximum current density of 1200 mA m^-2 and power density of 800 mW m^-2 in a period of 61 days. MFC performed a chemical oxygen demand removal at a rate ranging from 51 to 60%.

CONCLUSIONS

Taking our preliminary results into consideration, we concluded that the MFC technology presents itself as highly promising for the treatment of vinasse.

Correction to: Genome-resolved metagenomics of sugarcane vinasse bacteria

[This corrects the article DOI: 10.1186/s13068-018-1036-9.].

Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion

BACKGROUND

Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of vinasse on soil microbiome dynamics are unknown. Here, we evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen, or a combination of both during the sugarcane crop-growing season (389 days). Additionally, we evaluated the resistance of the resident soil microbial community to the vinasse microbiome.

RESULTS

Vinasse applied alone or 30 days prior to N resulted in similar changes in the soil microbial community. Furthermore, the impact of the application of vinasse together with N fertilizer on the soil microbial community differed from that of N fertilizer alone. Organic vinasse is a source of microbes, nutrients, and organic matter, and the combination of these factors drove the changes in the resident soil microbial community. However, these changes were restricted to a short period of time due to the capacity of the soil community to recover. The invasive bacteria present in the vinasse microbiome were unable to survive in the soil conditions and disappeared after 31 days, with the exception of the Acetobacteraceae (native in the soil) and Lactobacillaceae families.

CONCLUSION

Our analysis showed that the resident soil microbial community was not resistant to vinasse and inorganic N application but was highly resilient.