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Yadav S, Koenen M, Bale NJ, Reitsma W, Engelmann JC, Stefanova K, Damsté JSS, Villanueva L. Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria. MICROBIOME 2024; 12:98. [PMID: 38797849 PMCID: PMC11129491 DOI: 10.1186/s40168-024-01816-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/15/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea. RESULTS We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1T and A2), Spirochaetota (strains M1T, M2, and S2), Bacteroidota (strains B1T, B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea. CONCLUSIONS This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract.
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Affiliation(s)
- Subhash Yadav
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Wietse Reitsma
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Julia C Engelmann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Kremena Stefanova
- Institute of Oceanology "Fridtjof Nansen", Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands.
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands.
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Centurion VB, Rossi A, Orellana E, Ghiotto G, Kakuk B, Morlino MS, Basile A, Zampieri G, Treu L, Campanaro S. A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes. ENVIRONMENTAL MICROBIOME 2024; 19:1. [PMID: 38167520 PMCID: PMC10762816 DOI: 10.1186/s40793-023-00545-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production. RESULTS The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs. CONCLUSIONS This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization.
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Affiliation(s)
| | - Alessandro Rossi
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Esteban Orellana
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Gabriele Ghiotto
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, 12 Somogyi B. U. 4., Szeged, 6720, Hungary
| | - Maria Silvia Morlino
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Arianna Basile
- MRC Toxicology Unit, University of Cambridge, Gleeson Building Tennis Court Road, Cambridge, UK
| | - Guido Zampieri
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy.
| | - Laura Treu
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
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Grégoire DS, George NA, Hug LA. Microbial methane cycling in a landfill on a decadal time scale. Nat Commun 2023; 14:7402. [PMID: 37973978 PMCID: PMC10654671 DOI: 10.1038/s41467-023-43129-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.
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Affiliation(s)
- Daniel S Grégoire
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
- Department of Chemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada.
| | - Nikhil A George
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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Kalamaras SD, Christou ML, Tzenos CA, Vasileiadis S, Karpouzas DG, Kotsopoulos TA. Investigation of the Critical Biomass of Acclimated Microbial Communities to High Ammonia Concentrations for a Successful Bioaugmentation of Biogas Anaerobic Reactors with Ammonia Inhibition. Microorganisms 2023; 11:1710. [PMID: 37512885 PMCID: PMC10386354 DOI: 10.3390/microorganisms11071710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
This study aimed to investigate the role of the bioaugmented critical biomass that should be injected for successful bioaugmentation for addressing ammonia inhibition in anaerobic reactors used for biogas production. Cattle manure was used as a feedstock for anaerobic digestion (AD). A mixed microbial culture was acclimated to high concentrations of ammonia and used as a bioaugmented culture. Different volumes of bioaugmented culture were injected in batch anaerobic reactors under ammonia toxicity levels i.e., 4 g of NH4+-N L-1. The results showed that injecting a volume equal to 65.62% of the total working reactor volume yielded the best methane production. Specifically, this volume of bioaugmented culture resulted in methane production rates of 196.18 mL g-1 Volatile Solids (VS) and 245.88 mL g-1 VS after 30 and 60 days of AD, respectively. These rates were not significantly different from the control reactors (30d: 205.94 mL CH4 g-1 VS and 60d: 230.26 mL CH4 g-1 VS) operating without ammonia toxicity. Analysis of the microbial community using 16S rRNA gene sequencing revealed the dominance of acetoclastic methanogen members from the genus Methanosaeta in all reactors.
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Affiliation(s)
- Sotirios D Kalamaras
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria Lida Christou
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christos A Tzenos
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Sotirios Vasileiadis
- Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Thomas A Kotsopoulos
- Department of Hydraulics, Soil Science and Agricultural Engineering, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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