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Genome-resolved metagenomics of sugarcane vinasse bacteria. / Cassman, N.; Lourenço, Késia S.; Braga do Carmo, Janaina; Cantarella, Heitor; Kuramae, E.E. (Corresponding author).

In: Biotechnology for Biofuels, Vol. 11, 48, 2018.

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Cassman, N. ; Lourenço, Késia S. ; Braga do Carmo, Janaina ; Cantarella, Heitor ; Kuramae, E.E. / Genome-resolved metagenomics of sugarcane vinasse bacteria. In: Biotechnology for Biofuels. 2018 ; Vol. 11.

BibTeX

@article{d435527dcd4e4e59a19c8fb966209879,
title = "Genome-resolved metagenomics of sugarcane vinasse bacteria",
abstract = "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.ResultsWe 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.ConclusionsIdentification 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.",
keywords = "international",
author = "N. Cassman and Louren{\cc}o, {K{\'e}sia S.} and {Braga do Carmo}, Janaina and Heitor Cantarella and E.E. Kuramae",
note = "6473, ME; Data Archiving: Data deposited in MG-RAST with the IDs: 4678764.3, 4678762.3,4678758.3, 4678765.3, 4678752.3, 4678749.3, 4678755.3, 4678760.3, 4678754.3, 4678766.3, 4678756.3 Draft bacterial genomes are available at https://zenodo.org/record/1194340",
year = "2018",
doi = "10.1186/s13068-018-1036-9",
language = "English",
volume = "11",
journal = "Biotechnology for Biofuels",
issn = "1754-6834",
publisher = "BioMed Central",

}

RIS

TY - JOUR

T1 - Genome-resolved metagenomics of sugarcane vinasse bacteria

AU - Cassman, N.

AU - Lourenço, Késia S.

AU - Braga do Carmo, Janaina

AU - Cantarella, Heitor

AU - Kuramae, E.E.

N1 - 6473, ME; Data Archiving: Data deposited in MG-RAST with the IDs: 4678764.3, 4678762.3,4678758.3, 4678765.3, 4678752.3, 4678749.3, 4678755.3, 4678760.3, 4678754.3, 4678766.3, 4678756.3 Draft bacterial genomes are available at https://zenodo.org/record/1194340

PY - 2018

Y1 - 2018

N2 - 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.ResultsWe 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.ConclusionsIdentification 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.

AB - 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.ResultsWe 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.ConclusionsIdentification 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.

KW - international

UR - https://doi.org/10.5281/zenodo.1194340

U2 - 10.1186/s13068-018-1036-9

DO - 10.1186/s13068-018-1036-9

M3 - Article

VL - 11

JO - Biotechnology for Biofuels

JF - Biotechnology for Biofuels

SN - 1754-6834

M1 - 48

ER -

ID: 6160249