An Initial Proteomic Analysis of Biogas-Related Metabolism of Euryarchaeota Consortia in Sediments from the Santiago River, México

In this paper, sediments from the Santiago River were characterized to look for an alternative source of inoculum for biogas production. A proteomic analysis of methane-processing archaea present in these sediments was carried out. The Euryarchaeota superkingdom of archaea is responsible for methane production and methane assimilation in the environment. The Santiago River is a major river in México with great pollution and exceeded recovery capacity. Its sediments could contain nutrients and the anaerobic conditions for optimal growth of Euryarchaeota consortia. Batch bioreactor experiments were performed, and a proteomic analysis was conducted with current database information. The maximum biogas production was 266 NmL·L−1·g VS−1, with 33.34% of methane, and for proteomics, 3206 proteins were detected from 303 species of 69 genera. Most of them are metabolically versatile members of the genera Methanosarcina and Methanosarcinales, both with 934 and 260 proteins, respectively. These results showed a diverse euryarcheotic species with high potential to methane production. Although related proteins were found and could be feeding this metabolism through the methanol and acetyl-CoA pathways, the quality obtained from the biogas suggests that this metabolism is not the main one in carbon use, possibly the sum of several conditions including growth conditions and the pollution present in these sediments

[1]  L. Jiménez-Garcia,et al.  Ultrastructural and proteomic evidence for the presence of a putative nucleolus in an Archaeon , 2023, Frontiers in Microbiology.

[2]  E. Ríos-Castro,et al.  Venom comparisons of endemic and micro-endemic speckled rattlesnakes Crotalus mitchellii, C. polisi and C. thalassoporus from Baja California Peninsula. , 2023, Toxicon : official journal of the International Society on Toxinology.

[3]  S. Bell.  Form and function of archaeal genomes , 2022, Biochemical Society transactions.

[4]  D. Grahame,et al.  The two-electron reduced A cluster in acetyl-CoA synthase: Preparation, characteristics and mechanistic implications. , 2022, Journal of Inorganic Biochemistry.

[5]  J. W. Peters,et al.  The pathway for coenzyme M biosynthesis in bacteria , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[6]  S. Gribaldo,et al.  Diversity and Evolution of Methane-Related Pathways in Archaea. , 2022, Annual review of microbiology.

[7]  F. Pérez-Guevara,et al.  Surface water quality in the upstream of the highly contaminated Santiago River (Mexico) during the COVID-19 lockdown , 2022, Environmental Earth Sciences.

[8]  M. Xue,et al.  Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake , 2022, Animal microbiome.

[9]  E. Koonin,et al.  Evolutionary plasticity and functional versatility of CRISPR systems , 2022, PLoS biology.

[10]  R. Schmitz,et al.  Small Proteins in Archaea, a Mainly Unexplored World , 2021, Journal of bacteriology.

[11]  T. Ettema,et al.  Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future. , 2021, Annual review of microbiology.

[12]  Christian Sohlenkamp.  Crossing the lipid divide , 2021, Journal of Biological Chemistry.

[13]  H. Prommer,et al.  Carbon and methane cycling in arsenic-contaminated aquifers. , 2021, Water research.

[14]  A. VanderZaag,et al.  Understanding methane emission from stored animal manure: A review to guide model development. , 2021, Journal of environmental quality.

[15]  R. Kaushik,et al.  Archaea: An Agro-Ecological Perspective , 2021, Current Microbiology.

[16]  J. Banfield,et al.  Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways , 2021, Nature communications.

[17]  Yahai Lu,et al.  Putative Extracellular Electron Transfer in Methanogenic Archaea , 2021, Frontiers in Microbiology.

[18]  M. Jung,et al.  Ammonia-oxidizing archaea in biological interactions , 2021, Journal of Microbiology.

[19]  A. Stams,et al.  Anaerobic microbial methanol conversion in marine sediments , 2021, Environmental microbiology.

[20]  R. Zeng,et al.  Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea. , 2020, The Science of the total environment.

[21]  S. Rittmann,et al.  Archaea biotechnology. , 2020, Biotechnology advances.

[22]  L. Arellano-García,et al.  Unsafe waters: the hydrosocial cycle of drinking water in Western Mexico , 2020 .

[23]  M. Li,et al.  Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments , 2020, Microbiome.

[24]  G. F. Souza,et al.  Quantitative proteomic analysis of MARC-145 cells infected with a Mexican Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) strain using Label-free based DIA approach. , 2020, Journal of the American Society for Mass Spectrometry.

[25]  Sameh Magdeldin,et al.  UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase). , 2019, Journal of proteomics.

[26]  T. Hu,et al.  Patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge in Lhasa River. , 2019, Ecotoxicology and environmental safety.

[27]  Yue Li,et al.  Enhancement of methane production in anaerobic digestion process: A review , 2019, Applied Energy.

[28]  F. Werner,et al.  The cutting edge of archaeal transcription , 2018, Emerging topics in life sciences.

[29]  M. F. White,et al.  DNA repair in the archaea-an emerging picture. , 2018, FEMS microbiology reviews.

[30]  F. Pfeiffer,et al.  Archaeal cell surface biogenesis , 2018, FEMS microbiology reviews.

[31]  J. Armendáriz-Borunda,et al.  Buccal micronucleus cytome assay of populations under chronic heavy metal and other metal exposure along the Santiago River, Mexico , 2017, Environmental Monitoring and Assessment.

[32]  Jens Mühle,et al.  Role of atmospheric oxidation in recent methane growth , 2017, Proceedings of the National Academy of Sciences.

[33]  Yuki Amano,et al.  Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments , 2017, The ISME Journal.

[34]  M. Mezzari,et al.  Enrichment and acclimation of an anaerobic mesophilic microorganism's inoculum for standardization of BMP assays. , 2016, Bioresource technology.

[35]  K. Knittel,et al.  Thermophilic archaea activate butane via alkyl-coenzyme M formation , 2016, Nature.

[36]  S. Kittelmann,et al.  An adhesin from hydrogen-utilizing rumen methanogen Methanobrevibacter ruminantium M1 binds a broad range of hydrogen-producing microorganisms. , 2016, Environmental microbiology.

[37]  Dong Li,et al.  The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9 , 2016, Standards in genomic sciences.

[38]  V. Brovkin,et al.  The Global Methane Budget 2000–2017 , 2016, Earth System Science Data.

[39]  P. Bertin,et al.  The microbial genomics of arsenic. , 2016, FEMS microbiology reviews.

[40]  Kerstin Kuchta,et al.  Microalgae-bacteria flocs (MaB-Flocs) as a substrate for fermentative biogas production. , 2015, Bioresource technology.

[41]  C. Alvarez-Moya,et al.  Use of Comet Assay in Human Lymphocytes as a Molecular Biomarker for Simultaneous Monitoring of Genetic Damage and Genotoxicity in Residents Who Lived Nearby the Santiago River, Mexico, in 2012 , 2015 .

[42]  Nicholas D. Youngblut,et al.  Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment , 2015, The ISME Journal.

[43]  S. Zinder,et al.  Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium lacus isolated from northern peatlands. , 2014, International journal of systematic and evolutionary microbiology.

[44]  N. Boon,et al.  Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways , 2013, The ISME Journal.

[45]  A. Spang,et al.  Archaea in biogeochemical cycles. , 2013, Annual review of microbiology.

[46]  D. Raoult,et al.  A Versatile Medium for Cultivating Methanogenic Archaea , 2013, PloS one.

[47]  Tasneem Abbasi,et al.  Methane capture from livestock manure. , 2013, Journal of environmental management.

[48]  Dan Golick,et al.  Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures , 2009, Proteomics.

[49]  Michael Y. Galperin,et al.  Evolutionary primacy of sodium bioenergetics , 2008, Biology Direct.

[50]  S. Teichmann,et al.  The folding and evolution of multidomain proteins , 2007, Nature Reviews Molecular Cell Biology.

[51]  C. Baker-Austin,et al.  Extreme arsenic resistance by the acidophilic archaeon ‘Ferroplasma acidarmanus’ Fer1 , 2007, Extremophiles.

[52]  M. Mann,et al.  In-gel digestion for mass spectrometric characterization of proteins and proteomes , 2006, Nature Protocols.

[53]  M. Gorenstein,et al.  Absolute Quantification of Proteins by LCMSE , 2006, Molecular & Cellular Proteomics.

[54]  M. Adams,et al.  Posttranslational Protein Modification in Archaea , 2005, Microbiology and Molecular Biology Reviews.

[55]  Robert H. White,et al.  The Structural Determination of Phosphosulfolactate Synthase from Methanococcus jannaschii at 1.7-Å Resolution , 2003, Journal of Biological Chemistry.

[56]  Robert H. White,et al.  Identification of coenzyme M biosynthetic 2-phosphosulfolactate phosphatase. A member of a new class of Mg(2+)-dependent acid phosphatases. , 2001, European journal of biochemistry.

[57]  Robert H. White,et al.  Identification of the Gene Encoding Sulfopyruvate Decarboxylase, an Enzyme Involved in Biosynthesis of Coenzyme M , 2000, Journal of bacteriology.

[58]  Robert H. White,et al.  Identification of an Archaeal 2-Hydroxy Acid Dehydrogenase Catalyzing Reactions Involved in Coenzyme Biosynthesis in Methanoarchaea , 2000, Journal of bacteriology.

[59]  S. Shima,et al.  Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. , 1997, Science.

[60]  W. Welch,et al.  Heat shock proteins functioning as molecular chaperones: their roles in normal and stressed cells. , 1993, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[61]  Mark S. Boguski,et al.  A repeating amino acid motif in CDC23 defines a family of proteins and a new relationship among genes required for mitosis and RNA synthesis , 1990, Cell.

[62]  Roger W. Hendrix,et al.  Homologous plant and bacterial proteins chaperone oligomeric protein assembly , 1988, Nature.

[63]  M. Kalyuzhnaya,et al.  Methane Biocatalysis: Paving the Way to Sustainability , 2018, Springer International Publishing.

[64]  Andrew R. Jones,et al.  Proteome Bioinformatics , 2010, Methods in Molecular Biology™.

[65]  William Stafford Noble,et al.  Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. , 2008, Journal of proteome research.