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Lee ES, Park SY, Kim CG. Comparison of anaerobic digestion of starch- and petro-based bioplastic under hydrogen-rich conditions. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 175:133-145. [PMID: 38194798 DOI: 10.1016/j.wasman.2023.12.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
To identify an economically viable waste management system for bioplastics, thermoplastic starch (TPS) and poly(butylene adipate-co-terephthalate) (PBAT) were anaerobically digested under hydrogen (H2)/carbon dioxide (CO2) and nitrogen (N2) gas-purged conditions to compare methane (CH4) production and biodegradation. Regardless of the type of bioplastics, CH4 production was consistently higher with H2/CO2 than with N2. The highest amount of CH4 was produced at 307.74 mL CH4/g volatile solids when TPS digested with H2/CO2. A stepwise increased in CH4 yield was observed, with a nominal initial increment followed by accelerated methanogenesis conversion as H2 was depleted. This may be attributed to a substantial shift in the microbial structure from hydrogenotrophic methanogen (Methanobacteriales and Methanomicrobiales) to heterotrophs (Spirochaetia). In contrast, no significant change was observed with PBAT, regardless of the type of purged gas. TPS was broken down into numerous derivatives, including volatile fatty acids. TPS produced more byproducts with H2/CO2 (i.e., 430) than with N2 (i.e., 320). In contrast, differential scanning calorimetry analysis on PBAT revealed an increase in crystallinity from 10.20 % to 12.31 % and 11.36 % in the H2/CO2- and N2-purged conditions, respectively, after 65 days of testing. PBAT surface modifications were characterized via Fourier transform infrared spectroscopy and scanning electron microscopy. The results suggest that the addition of H2/CO2 can enhance the CH4 yield and increase the breakdown rate of TPS more than that of PBAT. This study provides novel insights into the CH4 production potential of two bioplastics with different biodegradabilities in H2/CO2-mediated anaerobic digestion systems.
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Affiliation(s)
- Eun Seo Lee
- Program in Environmental and Polymer Engineering, INHA University, Incheon 22212, Republic of Korea
| | - Seon Yeong Park
- Institute of Environmental Research, INHA University, Incheon 22212, Republic of Korea
| | - Chang Gyun Kim
- Program in Environmental and Polymer Engineering, INHA University, Incheon 22212, Republic of Korea; Department of Environmental Engineering, INHA University, Incheon 22212, Republic of Korea.
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2
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Lin TY, Liu WT. Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor. WATER RESEARCH 2023; 243:120358. [PMID: 37481999 DOI: 10.1016/j.watres.2023.120358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.
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Affiliation(s)
- Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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3
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Mohana Rangan S, Rao S, Robles A, Mouti A, LaPat-Polasko L, Lowry GV, Krajmalnik-Brown R, Delgado AG. Decoupling Fe 0 Application and Bioaugmentation in Space and Time Enables Microbial Reductive Dechlorination of Trichloroethene to Ethene: Evidence from Soil Columns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4167-4179. [PMID: 36866930 PMCID: PMC10018760 DOI: 10.1021/acs.est.2c06433] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/28/2022] [Accepted: 02/14/2023] [Indexed: 06/06/2023]
Abstract
Fe0 is a powerful chemical reductant with applications for remediation of chlorinated solvents, including tetrachloroethene and trichloroethene. Its utilization efficiency at contaminated sites is limited because most of the electrons from Fe0 are channeled to the reduction of water to H2 rather than to the reduction of the contaminants. Coupling Fe0 with H2-utilizing organohalide-respiring bacteria (i.e., Dehalococcoides mccartyi) could enhance trichloroethene conversion to ethene while maximizing Fe0 utilization efficiency. Columns packed with aquifer materials have been used to assess the efficacy of a treatment combining in space and time Fe0 and aD. mccartyi-containing culture (bioaugmentation). To date, most column studies documented only partial conversion of the solvents to chlorinated byproducts, calling into question the feasibility of Fe0 to promote complete microbial reductive dechlorination. In this study, we decoupled the application of Fe0 in space and time from the addition of organic substrates andD. mccartyi-containing cultures. We used a column containing soil and Fe0 (at 15 g L-1 in porewater) and fed it with groundwater as a proxy for an upstream Fe0 injection zone dominated by abiotic reactions and biostimulated/bioaugmented soil columns (Bio-columns) as proxies for downstream microbiological zones. Results showed that Bio-columns receiving reduced groundwater from the Fe0-column supported microbial reductive dechlorination, yielding up to 98% trichloroethene conversion to ethene. The microbial community in the Bio-columns established with Fe0-reduced groundwater also sustained trichloroethene reduction to ethene (up to 100%) when challenged with aerobic groundwater. This study supports a conceptual model where decoupling the application of Fe0 and biostimulation/bioaugmentation in space and/or time could augment microbial trichloroethene reductive dechlorination, particularly under oxic conditions.
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Affiliation(s)
- Srivatsan Mohana Rangan
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Center for Health Through Microbiomes, Arizona
State University, Tempe, Arizona 85287, United States
| | - Shefali Rao
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
| | - Aide Robles
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
| | - Aatikah Mouti
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
| | | | - Gregory V. Lowry
- Center
for Environmental Implications of Nanotechnology (CEINT), Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department
of Civil & Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rosa Krajmalnik-Brown
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Center for Health Through Microbiomes, Arizona
State University, Tempe, Arizona 85287, United States
| | - Anca G. Delgado
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
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4
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Anaerobic membrane bioreactor-based treatment of poultry slaughterhouse wastewater: Microbial community adaptation and antibiotic resistance gene profiles. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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5
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Gam ZBA, Thioye A, Cayol JL, Postec A, Bartoli-Joseph M, Vandecasteele C, Erauso G, Labat M. Thermospira aquatica gen. nov., sp. nov., a novel thermophilic spirochete isolated from a Tunisian hot spring, and description of the novel family Thermospiraceae. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748411 DOI: 10.1099/ijsem.0.005690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A novel thermophilic, anaerobic bacterium, strain F1F22T, was isolated from hot spring water collected in northern Tunisia. The cells were non-motile, Gram-negative and helical with hooked ends, 0.5×10-32 µm in size. Growth of the strain was observed at 45-70 °C (optimum, 55 °C), in 0.0-1.0 % (w/v) NaCl (optimum without NaCl) and at pH 6.5-8.5 (optimum, pH 7.5). Yeast extract was required for growth, and the strain grew on glucose, sucrose and maltose. The major fatty acids were C16:0 (40.2 %), iso-C16: 0 (30.2 %) and C16 :0 DMA (14.5 %). The genome consisted of a circular chromosome (2.5 Mb) containing 2672 predicted protein-encoding genes with a G+C content of 43.15 mol %. Based on a comparative 16S rRNA gene sequence analysis, strain F1F22T formed a deeply branching lineage within the phylum Spirochaetota, class Spirochaetia, order Brevinematales, and had only low sequence similarity to other species of the phylum (lower than 83 %). Genome-based analysis of average nucleotide identity and digital DNA-DNA hybridization of strain F1F22T with Treponema caldarium DSM 7334T, Brevinema andersonii ATCC 43811T and Spirochaeta thermophila DSM 6578T showed values between 63.26 and 63.52 %, and between 20 and 25 %. Hence, we propose strain F1F22T as a representative of a novel family (Thermospiraceae fam. nov.), genus and species of Brevinematales: Thermospira aquatica gen. nov., sp. nov. (type strain F1F22T=JCM 31314T=DSM 101182T).
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Affiliation(s)
- Zouhaier Ben Ali Gam
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | - Abdoulaye Thioye
- Université Cheikh Anta Diop, Ecole Supérieure Polytechnique, Laboratoire de Microbiologie Appliquée et de Génie Industriel, BP 5005, Dakar-Fann, Dakar, Sénégal
| | - Jean-Luc Cayol
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | - Anne Postec
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | - Manon Bartoli-Joseph
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | | | - Gaël Erauso
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | - Marc Labat
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
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6
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Obtainment of lignocellulose degradation microbial community: the effect of acid–base combination after restrictive enrichment. Arch Microbiol 2022; 204:683. [DOI: 10.1007/s00203-022-03195-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 11/06/2022]
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7
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Tomita R, Yoshida N, Meng L. Formate: A promising electron donor to enhance trichloroethene-to-ethene dechlorination in Dehalococcoides-augmented groundwater ecosystems with minimal bacterial growth. CHEMOSPHERE 2022; 307:136080. [PMID: 35988762 DOI: 10.1016/j.chemosphere.2022.136080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 08/05/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Various substrates have been used to stimulate habitat microbes in chloroethene-contaminated groundwater, however, the specific efficiency and minimum growth of microbes have rarely been studied. This study investigated the effects of seven substrates on trichloroethene (TCE) dechlorination by augmentation of groundwater with Dehalococcoides mccartyi NIT01 and its contribution to the microbial community. Three out of eight test groups completed dechlorination of 1 mM TCE-to-ethene in varying durations; groundwater supplemented with formate (FOR) required 78 days, whereas the microcosms with lactate (LAC) and citrate (CIT) required approximately twice as long (143 days). The calculated efficiency of how much produced H2 was used in dechlorination indicated a higher efficiency in FOR (36%) compared with LAC (1.9%) or CIT (2.9%). FOR showed lower microbial growth (3.4 × 105 copies/mL) than LAC (1.5 × 106) or CIT (4.4 × 106), and maintained a higher Shannon diversity index (5.65) than LAC (4.97) and CIT (4.30). The rapid and higher H2 transfer efficiency with lower bacterial growth by using formate was attributed to the slightly positive Gibbs free energy identified in H2 production requiring a H2-utilizer, lower carbon in the molecule, and adaptation to metabolic potential of the original groundwater microbiome. Formate is, therefore, a promising electron donor for rapid Dehalococcoides-augmented remediation with minimum bacterial growth. Sequential transferring of the FOR culture successfully maintained TCE-to-ethene dechlorination activity and enriched the members of genera Dehalococcoides (33%), Methanosphaerula (23%), Rectinema (13%), and Desulfitobacterium (5.6%). This suggests that formate is transferred to H2 and acetate, and provided to Dehalococcoides.
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Affiliation(s)
- Ryuya Tomita
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya, 466-8555, Japan
| | - Naoko Yoshida
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya, 466-8555, Japan.
| | - Lingyu Meng
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya, 466-8555, Japan
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8
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Ni J, Ji J, Kubota K, Li YY. Sodium hypochlorite induced inhibition in anaerobic digestion and possible approach to maintain methane fermentation performance. BIORESOURCE TECHNOLOGY 2022; 352:127096. [PMID: 35367600 DOI: 10.1016/j.biortech.2022.127096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Since sodium hypochlorite (NaClO), a commonly used chemical to deal with membrane fouling, is toxic to microorganisms, it is a major concern in the membrane cleaning process. In this study, the concentration-dependent effects of NaClO (0-9 g/L) on the biodegradation performance and microbial activity were investigated via batch experiments. The methane production (obtained approximately 140 mL) and microbial community revealed by principal coordinates analysis were almost unaffected when the NaClO concentration ranged between 0 and 3 g/L. A follow-up batch experiment was conducted and revealed that the microbial products could help protect or recover the activity of anaerobic microorganisms at a high NaClO concentration of 10 g/L. Additionally, correlation analysis was used to investigate the associations between the 15 major bacterial genera. Moreover, the microbial analysis results indicated that the top 10 operational taxonomic units most affected by NaClO were primarily coryneform and filamentous bacteria.
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Affiliation(s)
- Jialing Ni
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan; Department of Chemical Engineering, Graduate School of Engineering, Tohoku University, 6-6-07 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.
| | - Jiayuan Ji
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan; Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
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9
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Brune A, Song Y, Oren A, Paster BJ. A new family for 'termite gut treponemes': description of Breznakiellaceae fam. nov., Gracilinema caldarium gen. nov., comb. nov., Leadbettera azotonutricia gen. nov., comb. nov., Helmutkoenigia isoptericolens gen. nov., comb. nov., and Zuelzera stenostrepta gen. nov., comb. nov., and proposal of Rectinemataceae fam. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 35639582 DOI: 10.1099/ijsem.0.005439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The intestinal tracts of termites are abundantly colonized by a diverse assemblage of spirochetes. Most of them belong to 'termite cluster I', a monophyletic group within the radiation of the genus Treponema that occurs exclusively in termite guts. Phylogenomic analysis revealed that members of the genus Treponema are extremely diverse and represent two separate, family-level lineages: the Treponemataceae sensu stricto, which comprise the majority of the validly described Treponema species, and a second lineage that comprises the remaining members of the genus Treponema, including all members of 'termite cluster I' from termites and the recently isolated Breznakiella homolactica from cockroaches. Here, we present the formal description of Breznakiellaceae fam. nov. and of the new genera required to accommodate the misplaced Treponema species in the new family as new combinations (Leadbettera azotonutricia, Gracilinema caldarium, Helmutkoenigia isoptericolens and Zuelzera stenostrepta). To avoid paraphyly of Treponemataceae, we propose Rectinemataceae fam. nov. to include the genus Rectinema.
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Affiliation(s)
- Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Yulin Song
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Bruce J Paster
- The Forsyth Institute, 245 First St., Cambridge, MA, USA
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Kabaivanova L, Hubenov V, Dimitrova L, Simeonov I, Wang H, Petrova P. Archaeal and Bacterial Content in a Two-Stage Anaerobic System for Efficient Energy Production from Agricultural Wastes. Molecules 2022; 27:1512. [PMID: 35268611 PMCID: PMC8911581 DOI: 10.3390/molecules27051512] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 12/22/2022] Open
Abstract
Anaerobic digestion (AD) is a microbially-driven process enabling energy production. Microorganisms are the core of anaerobic digesters and play an important role in the succession of hydrolysis, acidogenesis, acetogenesis, and methanogenesis processes. The diversity of participating microbial communities can provide new information on digester performance for biomass valorization and biofuel production. In this study anaerobic systems were used, operating under mesophilic conditions that realized biodegradation processes of waste wheat straw pretreated with NaOH-a renewable source for hydrogen and methane production. These processes could be managed and optimized for hydrogen and methane separately but combining them in a two-stage system can lead to higher yields and a positive energy balance. The aim of the study was to depict a process of biohydrogen production from lignocellulosic waste followed by a second one leading to the production of biomethane. Archaeal and bacterial consortia in a two-stage system operating with wheat straw were identified for the first time and the role of the most important representatives was elucidated. The mixed cultures were identified by the molecular-biological methods of metagenomics. The results showed that biohydrogen generation is most probably due to the presence of Proteiniphilum saccharofermentans, which was 28.2% to 45.4% of the microbial community in the first and the second bioreactor, respectively. Archaeal representatives belonging to Methanobacterium formicicum (0.71% of the community), Methanosarcina spelaei (0.03%), Methanothrix soehngenii (0.012%), and Methanobacterium beijingense (0.01%) were proven in the methane-generating reactor. The correlation between substrate degradation and biogas accumulation was calculated, together with the profile of fatty acids as intermediates produced during the processes. The hydrogen concentration in the biogas reached 14.43%, and the Methane concentration was 69%. Calculations of the energy yield during the two-stage process showed 1195.89 kWh·t-1 compared to a 361.62 kWh·t-1 cumulative yield of energy carrier for a one-stage process.
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Affiliation(s)
- Lyudmila Kabaivanova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Venelin Hubenov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Lyudmila Dimitrova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Ivan Simeonov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Haoping Wang
- French-Chinese Laboratory LaFCAS, School of Automation, Nanjing University of Science and Technology, Nanjing 210094, China;
| | - Penka Petrova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
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11
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Haddad PG, Mura J, Castéran F, Guignard M, Ranchou-Peyruse M, Sénéchal P, Larregieu M, Isaure MP, Svahn I, Moonen P, Le Hécho I, Hoareau G, Chiquet P, Caumette G, Dequidt D, Cézac P, Ranchou-Peyruse A. Biological, geological and chemical effects of oxygen injection in underground gas storage aquifers in the setting of biomethane deployment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150690. [PMID: 34600980 DOI: 10.1016/j.scitotenv.2021.150690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/15/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
The last few years have seen the proliferation of anaerobic digestion plants to produce biomethane. Oxygen (O2) traces added to biogas during the desulfurization process are co-injected in the gas network and can be stored in Underground Gas Storage (UGS). However, there are no data available for the undesirable effects of O2 on these anoxic environments, especially on deep aquifers. In addition to mineral alteration, O2 can have an impact on the anaerobic autochthonous microbial life. In our study, the storage conditions of an UGS aquifer were reproduced in a high-pressure reactor and bio-geo-chemical interactions between the aqueous, gas and solid phases were studied. Sulfate was depleted from the liquid phase for three consecutive times during the first 130 days of incubation reproducing the storage conditions (36 °C, 60 bar, methane with 1% CO2). Sulfate-reducers, such as Desulfovibrionaceae, were identified from the high-pressure system. Simulations with PHREEQC were used to determine the thermodynamic equilibrium to confirm any gas consumption. CO2 quantities decreased in the gas phase, suggesting its use as carbon source by microbial life. Benzene and toluene, hydrocarbons found in traces and known to be biodegradable in storages, were monitored and a decrease of toluene was revealed and associated to the Peptococcaceae family. Afterwards, O2 was added as 1% of the gas phase, corresponding to the maximum quantity found in biomethane after desulfurization process. Re-oxidation of sulfide to sulfate was observed along with the end of sulfate reducing activity and toluene biodegradation and the disappearance of most of the community. H2 surprisingly appeared and accumulated as soon as hydrogenotrophic sulfate-reducers decreased. H2 would be produced via the necromass fermentation accomplished by microorganisms able to resist the oxic conditions of 4.42·10-4 mol.Kgw-1 of O2. The solid phase composed essentially of quartz, presented no remarkable changes.
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Affiliation(s)
- Perla G Haddad
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France
| | - Jean Mura
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France
| | - Franck Castéran
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France; Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France
| | - Marion Guignard
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Magali Ranchou-Peyruse
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France; Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Pascale Sénéchal
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, DMEX, Pau, France
| | - Marie Larregieu
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Isabelle Svahn
- Bordeaux Imaging Center (BIC), CNRS, Université de Bordeaux, Bordeaux, France
| | - Peter Moonen
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, DMEX, Pau, France
| | - Isabelle Le Hécho
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Guilhem Hoareau
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, TOTAL, LFCR, Pau, France
| | - Pierre Chiquet
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Teréga, Pau, France
| | - Guilhem Caumette
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Teréga, Pau, France
| | - David Dequidt
- STORENGY - Geosciences Department, Bois-Colombes, France
| | - Pierre Cézac
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France; Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France
| | - Anthony Ranchou-Peyruse
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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12
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Yamazaki Y, Kitamura G, Tian X, Suzuki I, Kobayashi T, Shimizu T, Inoue D, Ike M. Temperature dependence of sequential chlorinated ethenes dechlorination and the dynamics of dechlorinating microorganisms. CHEMOSPHERE 2022; 287:131989. [PMID: 34450366 DOI: 10.1016/j.chemosphere.2021.131989] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Thermally enhanced bioremediation is a promising approach to shorten the bioremediation period of tetrachloroethene (PCE) and trichloroethene (TCE). To clarify the influence that temperature has on stepwise PCE dechlorination and associated microorganisms, this study conducted dechlorination experiments using contaminated soil and groundwater under five distinct temperature conditions (i.e., 15, 20, 25, 30, and 35 °C). PCE and TCE were dechlorinated most rapidly at 25-35 °C, whereas the preferable temperatures for the dechlorination of cis-1,2- dichloroethene (cis-1,2-DCE) and vinyl chloride (VC) were 25-30 °C and 25 °C, respectively. Microbial community analysis revealed that Sulfurospirillum and Geobacter may have a dominant contribution to the dechlorination of PCE to cis-1,2-DCE, whereas Dehalococcoides harboring VC reductase genes are likely major contributors to the dechlorination of cis-1,2-DCE and VC. These results suggest that temperature influences various microbial groups, including major dechlorinating microorganisms, resulting in the different extent of PCE dechlorination. In addition, the microbial community structure greatly changed after the onset of the experiment, whereas the temperature influence of 15-30 °C on the microbial community structure was minor; however, the microbial community was significantly impacted at 35 °C. Collectively, these results suggest that thermally enhanced anaerobic dechlorination at 25 °C is useful for successful dechlorination of chlorinated ethenes in a short period.
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Affiliation(s)
- Yuji Yamazaki
- Research & Development Institute, TAKENAKA Corporation, 1-5-1 Otsuka, Inzai, Chiba, Japan; Division of Sustainable Energy and Environment Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan.
| | - Gaku Kitamura
- Research & Development Institute, TAKENAKA Corporation, 1-5-1 Otsuka, Inzai, Chiba, Japan
| | - Xiaowei Tian
- Center for Creation of Symbiosis Society with Risk, Institute of Advanced Sciences, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa, Japan
| | - Ichiro Suzuki
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa, Japan
| | - Takeshi Kobayashi
- Division of Artificial Environment and Information Research, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa, Japan
| | - Takaaki Shimizu
- Technical Headquarters, TAKENAKA Corporation, 1-1-1 Shinsuna, Koto-ku, Tokyo, Japan
| | - Daisuke Inoue
- Division of Sustainable Energy and Environment Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environment Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
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13
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Toshchakov SV, Izotova AO, Vinogradova EN, Kachmazov GS, Tuaeva AY, Abaev VT, Evteeva MA, Gunitseva NM, Korzhenkov AA, Elcheninov AG, Patrushev MV, Kublanov IV. Culture-Independent Survey of Thermophilic Microbial Communities of the North Caucasus. BIOLOGY 2021; 10:biology10121352. [PMID: 34943267 PMCID: PMC8698779 DOI: 10.3390/biology10121352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 01/04/2023]
Abstract
Simple Summary The Republic of North Ossetia-Alania, located in the southern part of the North Caucasus, possess a number of hydrothermal habitats, including both subterranean thermal reservoirs and terrestrial hot springs. At the same time, reports on microbiology of numerous geothermal sites are rather scarce for the whole North Caucasus region. In this paper, we report on the first culture-independent metabarcoding study of thermal habitats in the North Caucasus, coupled with a chemical analysis of the elemental composition of water. The results of this work include the conclusions regarding key metabolic characteristics of these habitats as well as detection of few but abundant deep lineages of uncultivated microorganisms which could be regarded as endemic. This study may represent a first step in closing the knowledge gap in extremophilic microbial communities of the North Caucasus. Abstract The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot springs. However, there are only a limited number of scientific works reporting on the microbial communities of these habitats. Moreover, all these reports concern only studies of specific microbial taxa, carried out using classical cultivation approaches. In this work, we present first culture-independent study of hydrotherms in the Republic of North Ossetia-Alania, located in the southern part of the North Caucasus. Using 16S metabarcoding, we analyzed the composition of the microbial communities of two subterranean thermal aquifers and terrestrial hot springs of the Karmadon valley. Analysis of correlations between the chemical composition of water and the representation of key taxa allowed us to identify the key factors determining the formation of microbial communities. In addition, we were able to identify a significant number of highly abundant deep phylogenetic lineages. Our study represents a first glance on the thermophilic microbial communities of the North Caucasus and may serve as a basis for further microbiological studies of the extreme habitats of this region.
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Affiliation(s)
- Stepan V. Toshchakov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Correspondence: ; Tel.: +7-911-481-1809
| | - Anna O. Izotova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Elizaveta N. Vinogradova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Gennady S. Kachmazov
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Albina Y. Tuaeva
- National Research Center Kurchatov Institute-GOSNIIGENETIKA, 1st Dorozhny Pr., 1, Moscow 117545, Russia;
| | - Vladimir T. Abaev
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Martha A. Evteeva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Natalia M. Gunitseva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Aleksei A. Korzhenkov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
| | - Maxim V. Patrushev
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
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14
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Bin Hudari MS, Vogt C, Richnow HH. Sulfidic acetate mineralization at 45°C by an aquifer microbial community: key players and effects of heat changes on activity and community structure. Environ Microbiol 2021; 24:370-389. [PMID: 34859568 DOI: 10.1111/1462-2920.15852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/28/2022]
Abstract
High-Temperature Aquifer Thermal Energy Storage (HT-ATES) is a sustainable approach for integrating thermal energy from various sources into complex energy systems. Temperatures ≥45°C, which are relevant in impact zones of HT-ATES systems, may dramatically influence the structure and activities of indigenous aquifer microbial communities. Here, we characterized an acetate-mineralizing, sulfate-reducing microbial community derived from an aquifer and adapted to 45°C. Acetate mineralization was strongly inhibited at temperatures ≤25°C and 60°C. Prolonged incubation at 12°C and 25°C resulted in acetate mineralization recovery after 40-80 days whereas acetate was not mineralized at 60°C within 100 days. Cultures pre-grown at 45°C and inhibited for 28 days by incubation at 12°C, 25°C, or 60°C recovered quickly after changing the temperature back to 45°C. Phylotypes affiliated to the order Spirochaetales and to endospore-forming sulfate reducers of the order Clostridiales were highly abundant in microcosms being active at 45°C highlighting their key role. In summary, prolonged incubation at 45°C resulted in active microbial communities mainly consisting of organisms adapted to temperatures between the typical temperature range of mesophiles and thermophiles and being resilient to temporary heat changes.
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Affiliation(s)
- Mohammad S Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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15
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Xiao Y, Lin S, Hao T. Investigating the response of electrogenic metabolism to salinity in saline wastewater treatment for optimal energy output via microbial fuel cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147092. [PMID: 34088164 DOI: 10.1016/j.scitotenv.2021.147092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
In the current study, MFCs treating saline wastewater with the different conductivities of 5.0 ± 0.2, 7.7 ± 0.6, 10.5 ± 0.9, 13.0 ± 1.0, 15.3 ± 1.0, and 16.0 ± 0.1 mS/cm were investigated. Increasing salinity drives a considerable shift of microbial communities, and it also affects metabolic pathways in MFCs. Overwhelming acetate oxidizing electron transfer with moderate conductivities between 7.7 and 13.0 mS/cm led to high energy outputs. Power generation at the low conductivities of less than 7.7 mS/cm was restricted by the competition between fermentative bacteria (e.g., Lactobacillus) and exoelectrogens (e.g., Pseudomonas and Shewanella) for substrate utilization. Increasing salinity beyond 13 mS/cm suppressed the fermentation of glucose to butyrate. It also induced sulfidogenesis; sulfide oxidizing bacteria Desulfovibrio (5.2%), Desulfuromonas (3.7%) and exoelectrogen Pseudomonas (1.1%) formed a sulfur-driven current production, thereby resulting in low energy outputs. The present study revealed the effects of ionic conductivity on electrical energy production and provided insights into the dynamics of the MFCs substrate utilization.
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Affiliation(s)
- Yihang Xiao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau
| | - Sen Lin
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tianwei Hao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau.
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16
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C Campbell B, Gong S, Greenfield P, J Midgley D, T Paulsen I, C George S. Aromatic compound-degrading taxa in an anoxic coal seam microbiome from the Surat Basin, Australia. FEMS Microbiol Ecol 2021; 97:6206826. [PMID: 33791788 DOI: 10.1093/femsec/fiab053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Methane is an important energy resource internationally, and a large proportion of this methane is produced by microbial communities living in coal seams. Despite the value of this resource for human energy security, our understanding of the metabolic roles played by specific taxa during the biodegradation of coal to methane in situ is quite limited. In order to develop a greater understanding of microbial catabolism on coal, a community from a coal seam in the Surat Basin, Australia, was incubated on 10 different aromatic organic compounds: coronene, benzo[a]pyrene, pyrene, phenanthrene, naphthalene, ethylbenzene, phenol, benzoate, vanillate and syringate. Each of these aromatic compounds either occurs in coal or is a possible product of the coal biodegradation process. 16S rRNA sequencing revealed substantial changes to each community in response to each aromatic carbon substrate provided. Abundant taxa from these substrate-specific communities were identified and their probable catabolic roles proposed based on literature searches of related taxa. This study is the first to link specific coal seam taxa to aromatic substrates available in coal seam environments. Two conceptual models of the putative degradation pathways and key taxa responsible are proposed.
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Affiliation(s)
- Bronwyn C Campbell
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia.,Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Se Gong
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Paul Greenfield
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - David J Midgley
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Simon C George
- Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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17
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Karnachuk OV, Lukina AP, Kadnikov VV, Sherbakova VA, Beletsky AV, Mardanov AV, Ravin NV. Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere. Environ Microbiol 2020; 23:3585-3598. [DOI: 10.1111/1462-2920.15218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Vitaly V. Kadnikov
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Viktoria A. Sherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms Federal Research Center ‘Pushchino Scientific Center for Biological Research, Russian Academy of Sciences’ Pushchino Moscow 142290 Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
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18
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Momper L, Semler A, Lu GS, Miyazaki M, Imachi H, Amend JP. Rectinema subterraneum sp. nov, a chemotrophic spirochaete isolated from the deep terrestrial subsurface. Int J Syst Evol Microbiol 2020; 70:4739-4747. [PMID: 32730198 DOI: 10.1099/ijsem.0.004339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, obligately anaerobic bacterium (strain SURF-ANA1T) was isolated from deep continental subsurface fluids at a depth of 1500 m below surface in the former Homestake Gold Mine (now Sanford Underground Research Facility, in Lead, South Dakota, USA). Cells of strain SURF-ANA1T were Gram-negative, helical, non-spore-forming and were 0.25-0.55×5.0-75.0 µm with a wavelength of 0.5-0.62 µm. Strain SURF-ANA1T grew at 15-50 °C (optimally at 40 °C), at pH 4.8-9.0 (pH 7.2) and in 1.0-40.0 g l-1 NaCl (10 g l-1 NaCl). The strain grew chemoheterotrophically with hydrogen or mono-, di- and polysaccharides as electron donors. The major cellular fatty acids in order of decreasing abundance (comprising >5% of total) were 10-methyl C16:0, iso-C15:0, C18:2 and C18:0 dimethyl acetal (DMA) and C20:0 methylene-nonadecanoic acid. Phylogenetic analysis based on the 16S rRNA gene sequence of strain SURF-ANA1T indicated a closest relationship with the recently characterized Rectinema cohabitans (99%). Despite high sequence identity, because of its distinct physiology, morphology and fatty acid profile, strain SURF-ANA1T is considered to represent a novel species within the genus Rectinema, for which the name Rectinema subterraneum sp. nov. is proposed. To our knowledge, this is the first report of an isolate within the phylum Spirochaetes from the deep (>100 m) terrestrial subsurface. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and genomic sequences of strain SURF-ANA1T are KU359248 and GCF 009768935.1, respectively. The type strain of Rectinema subterraneum is SURF-ANA1T (=ATCC TSD-67=JCM 32656).
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Affiliation(s)
- Lily Momper
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA.,Exponent Inc. 1055 East Colorado Blvd, Pasadena, CA, USA
| | - Amanda Semler
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Guang Sin Lu
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Masayuki Miyazaki
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA
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19
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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20
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Mei R, Nobu MK, Narihiro T, Yu J, Sathyagal A, Willman E, Liu WT. Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors. WATER RESEARCH 2018; 147:403-412. [PMID: 30336343 DOI: 10.1016/j.watres.2018.10.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 05/20/2023]
Abstract
To determine whether the addition of conductive materials could enhance methane production by direct interspecies electron transfer (DIET), we operated three anaerobic reactors amended with non-conductive (ceramic) or conductive materials (anthracite and granular activated carbon (GAC)). Throughout eight months of operation, ethanol was consistently detected as the major fermentation product. The specific yield in the anthracite and GAC-added reactors increased by 31.5% and 43.3%, respectively, compared to the ceramic-added reactor. 16S rRNA gene sequencing results indicated Geobacter was dominant (up to 55% of total sequences), whereas acids-degrading syntrophic bacteria were low in abundance (<2%). Using metagenomic analysis, the draft genome of the dominant Geobacter population (bin GAC1) was reconstructed and observed to possess genetic abilities of ethanol oxidation, hydrogen production, and extracellular electron transfer, and represented a phylogenetically novel Geobacter species. While Methanosaeta was the dominant methanogen, reactors containing conductive materials harbored more diverse and abundant archaeal populations, as revealed by FISH, qPCR, and metagenomics. Our findings suggested that a novel Geobacter population could oxidize ethanol and employed both hydrogen transfer and DIET depending on the accessibility of conductive materials. Thermodynamic advantages of DIET over hydrogen production could lead to enhanced methane production in reactors with conductive materials.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Jimmy Yu
- PepsiCo Research and Development, Hawthorne, NY, USA
| | | | - Eric Willman
- PepsiCo Research and Development, Hawthorne, NY, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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21
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Himmelberg AM, Brüls T, Farmani Z, Weyrauch P, Barthel G, Schrader W, Meckenstock RU. Anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture. Environ Microbiol 2018; 20:3589-3600. [DOI: 10.1111/1462-2920.14335] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/21/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Anne M. Himmelberg
- Institute of Groundwater Ecology; Helmholtz Zentrum München; Neuherberg Germany
| | - Thomas Brüls
- CEA, DRF, Institut Jacob, Genoscope; Evry France
- CNRS-UMR8030; Université Paris-Saclay; Evry France
| | - Zahra Farmani
- Biofilm Centre; University of Duisburg-Essen; Essen Germany
- Max-Planck-Institut für Kohlenforschung; Mülheim Germany
| | | | - Gabriele Barthel
- Institute of Groundwater Ecology; Helmholtz Zentrum München; Neuherberg Germany
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22
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Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. ISME JOURNAL 2018; 12:2039-2050. [PMID: 29849169 PMCID: PMC6052044 DOI: 10.1038/s41396-018-0148-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 11/08/2022]
Abstract
Spirochaetes are frequently detected in anoxic hydrocarbon- and organohalide-polluted groundwater, but their role in such ecosystems has remained unclear. To address this, we studied a sulfate-reducing, naphthalene-degrading enrichment culture, mainly comprising the sulfate reducer Desulfobacterium N47 and the rod-shaped Spirochete Rectinema cohabitans HM. Genome sequencing and proteome analysis suggested that the Spirochete is an obligate fermenter that catabolizes proteins and carbohydrates, resulting in acetate, ethanol, and molecular hydrogen (H2) production. Physiological experiments inferred that hydrogen is an important link between the two bacteria in the enrichment culture, with H2 derived from fermentation by R. cohabitans used as reductant for sulfate reduction by Desulfobacterium N47. Differential proteomics and physiological experiments showed that R. cohabitans utilizes biomass (proteins and carbohydrates) released from dead cells of Desulfobacterium N47. Further comparative and community genome analyses indicated that other Rectinema phylotypes are widespread in contaminated environments and may perform a hydrogenogenic fermentative lifestyle similar to R. cohabitans. Together, these findings indicate that environmental Spirochaetes scavenge detrital biomass and in turn drive necromass recycling at anoxic hydrocarbon-contaminated sites and potentially other habitats.
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Shivani Y, Subhash Y, Sasikala C, Ramana CV. Characterisation of a newly isolated member of a candidatus lineage, Marispirochaeta aestuarii gen. nov., sp. nov. Int J Syst Evol Microbiol 2017; 67:3929-3936. [DOI: 10.1099/ijsem.0.002224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. Shivani
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Y. Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
- Present address: Department of Life Science, College of Natural Science, Kyonggi University, 94-6 Iui- 6 dong Yeongtong-gu, Suwon 443-760, Republic of Korea
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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24
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Subhash Y, Lee SS. Description of Oceanispirochaeta sediminicola gen. nov., sp. nov., an obligately anaerobic bacterium isolated from coastal marine sediments, and reclassification of Spirochaeta litoralis as Oceanispirochaeta litoralis comb. nov. Int J Syst Evol Microbiol 2017; 67:3403-3409. [DOI: 10.1099/ijsem.0.002130] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
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