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Shcherbakova VA, Rechkina VI, Trubitsyn VE. Metagenome-assembled genomes of the methanogenic enrichment obtained from drilling fluid wastes stored in permafrost. Microbiol Resour Announc 2024:e0115923. [PMID: 38602400 DOI: 10.1128/mra.01159-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/21/2024] [Indexed: 04/12/2024] Open
Abstract
We studied methanogenic enrichment (Kha) from spent drilling fluid stored in permafrost, Kharasavey (71°10'50″N 66°51'50″E) gas field located in the western part of the Yamal Peninsula. The metagenome-assembled genomes showed that Kha consists of representatives of Methanosarcina, Methanobacterium, Proteinifillum, and Synergistetes genera.
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Affiliation(s)
- V A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow, Russia
| | - V I Rechkina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow, Russia
| | - V E Trubitsyn
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow, Russia
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2
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Pereira AR, Assis NVD, Paranhos AGDO, Lima DRS, Baeta BEL, Aquino SFD, Silva SDQ. Effect of inoculum composition on the microbial community involved in the anaerobic digestion of sugarcane bagasse. Environ Technol 2024; 45:2205-2217. [PMID: 36632771 DOI: 10.1080/09593330.2023.2166877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
In anaerobic digestion (AD), the choice of inoculum type seems to be relevant for methane production for complex substrates, such as lignocellulosic material. Previous work demonstrated that the addition of fresh manure and ruminal fluid to anaerobic sludge improved methane productivity and kinetics of AD of crude sugarcane bagasse (CSB). Considering that the improvement of methane production could be a result of a more adapted microbial community, the present study performed the Next Generation Sequencing analysis to identify changes in the microbiome of anaerobic sludge inoculum, resulting from fresh manure and ruminal fluid addition. In comparison with AD performed only with anaerobic sludge inoculum (50:50, U), accumulated methane production was 15% higher with anaerobic sludge plus ruminal fluid inoculum (50:50, UR) and even higher (68%) with anaerobic sludge with fresh bovine manure inoculum (50:50, UFM), reaching the value of 143 NmLCH4.gVS-1. Clostridium species were highly abundant in all inocula, playing an important role during the hydrolysis and fermentation of CSB, and detoxifying potential inhibitors. Microbial composition also revealed the occurrence of Pseudomonas and Anaerobaculum at UFM inoculum that seem to have contributed to the higher methane production rate, mainly due to their hydrolytic and fermentative ability on lignocellulosic substrates. On the other hand, the presence of Alcaligenes might have had a negative effect on methane production due to their ability to perform methane oxidation.
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Affiliation(s)
- Andressa Rezende Pereira
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Nathália Vercelli de Assis
- Graduate Program in Biotechnology, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Diego Roberto Sousa Lima
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Bruno Eduardo Lobo Baeta
- Department of Chemistry, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Silvana de Queiroz Silva
- Department of Biological Sciences, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
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3
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Kuehnast T, Kumpitsch C, Mohammadzadeh R, Weichhart T, Moissl-Eichinger C, Heine H. Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system. FEBS J 2024. [PMID: 38555566 DOI: 10.1111/febs.17123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
This Review aims to coalesce existing knowledge on the human archaeome, a less-studied yet critical non-bacterial component of the human microbiome, with a focus on its interaction with the immune system. Despite a largely bacteria-centric focus in microbiome research, archaea present unique challenges and opportunities for understanding human health. We examine the archaeal distribution across different human body sites, such as the lower gastrointestinal tract (LGT), upper aerodigestive tract (UAT), urogenital tract (UGT), and skin. Variability in archaeal composition exists between sites; methanogens dominate the LGT, while Nitrososphaeria are prevalent on the skin and UAT. Archaea have yet to be classified as pathogens but show associations with conditions such as refractory sinusitis and vaginosis. In the LGT, methanogenic archaea play critical metabolic roles by converting bacterial end-products into methane, correlating with various health conditions, including obesity and certain cancers. Finally, this work looks at the complex interactions between archaea and the human immune system at the molecular level. Recent research has illuminated the roles of specific archaeal molecules, such as RNA and glycerolipids, in stimulating immune responses via innate immune receptors like Toll-like receptor 8 (TLR8) and 'C-type lectin domain family 4 member E' (CLEC4E; also known as MINCLE). Additionally, metabolic by-products of archaea, specifically methane, have demonstrated immunomodulatory effects through anti-inflammatory and anti-oxidative pathways. Despite these advancements, the mechanistic underpinnings of how archaea influence immune activity remain a fertile area for further investigation.
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Affiliation(s)
- Torben Kuehnast
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Christina Kumpitsch
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Rokhsareh Mohammadzadeh
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Thomas Weichhart
- Institute of Medical Genetics, Medical University of Vienna, Austria
| | - Christine Moissl-Eichinger
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
- BioTechMed Graz, Austria
| | - Holger Heine
- Research Center Borstel - Leibniz Lung Center, Division of Innate Immunity, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
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4
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Roques S, Martinez-Fernandez G, Ramayo-Caldas Y, Popova M, Denman S, Meale SJ, Morgavi DP. Recent Advances in Enteric Methane Mitigation and the Long Road to Sustainable Ruminant Production. Annu Rev Anim Biosci 2024; 12:321-343. [PMID: 38079599 DOI: 10.1146/annurev-animal-021022-024931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Mitigation of methane emission, a potent greenhouse gas, is a worldwide priority to limit global warming. A substantial part of anthropogenic methane is emitted by the livestock sector, as methane is a normal product of ruminant digestion. We present the latest developments and challenges ahead of the main efficient mitigation strategies of enteric methane production in ruminants. Numerous mitigation strategies have been developed in the last decades, from dietary manipulation and breeding to targeting of methanogens, the microbes that produce methane. The most recent advances focus on specific inhibition of key enzymes involved in methanogenesis. But these inhibitors, although efficient, are not affordable and not adapted to the extensive farming systems prevalent in low- and middle-income countries. Effective global mitigation of methane emissions from livestock should be based not only on scientific progress but also on the feasibility and accessibility of mitigation strategies.
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Affiliation(s)
- Simon Roques
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
| | | | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, Caldes de Montbui, Spain;
| | - Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
| | - Stuart Denman
- Agriculture and Food, CSIRO, St. Lucia, Queensland, Australia; ,
| | - Sarah J Meale
- School of Agriculture and Food Sustainability, Faculty of Science, University of Queensland, Gatton, Queensland, Australia;
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
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Cisek AA, Szymańska E, Aleksandrzak-Piekarczyk T, Cukrowska B. The Role of Methanogenic Archaea in Inflammatory Bowel Disease-A Review. J Pers Med 2024; 14:196. [PMID: 38392629 PMCID: PMC10890621 DOI: 10.3390/jpm14020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Methanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Edyta Szymańska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | | | - Bożena Cukrowska
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
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6
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Ungerfeld EM, Cancino-Padilla N, Vera-Aguilera N, Scorcione MC, Saldivia M, Lagos-Pailla L, Vera M, Cerda C, Muñoz C, Urrutia N, Martínez ED. Effects of type of substrate and dilution rate on fermentation in serial rumen mixed cultures. Front Microbiol 2024; 15:1356966. [PMID: 38389534 PMCID: PMC10883771 DOI: 10.3389/fmicb.2024.1356966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Forages and concentrates have consistently distinct patterns of fermentation in the rumen, with forages producing more methane (CH4) per unit of digested organic matter (OM) and higher acetate to propionate ratio than concentrates. A mechanism based on the Monod function of microbial growth has been proposed to explain the distinct fermentation pattern of forages and concentrates, where greater dilution rates and lower pH associated with concentrate feeding increase dihydrogen (H2) concentration through increasing methanogens growth rate and decreasing methanogens theoretically maximal growth rate, respectively. Increased H2 concentration would in turn inhibit H2 production, decreasing methanogenesis, inhibit H2-producing pathways such as acetate production via pyruvate oxidative decarboxylation, and stimulate H2-incorporating pathways such as propionate production. We examined the hypothesis that equalizing dilution rates in serial rumen cultures would result in a similar fermentation profile of a high forage and a high concentrate substrate. Under a 2 × 3 factorial arrangement, a high forage and a high concentrate substrate were incubated at dilution rates of 0.14, 0.28, or 0.56 h-1 in eight transfers of serial rumen cultures. Each treatment was replicated thrice, and the experiment repeated in two different months. The high concentrate substrate accumulated considerably more H2 and formate and produced less CH4 than the high forage substrate. Methanogens were nearly washed-out with high concentrate and increased their initial numbers with high forage. The effect of dilution rate was minor in comparison to the effect of the type of substrate. Accumulation of H2 and formate with high concentrate inhibited acetate and probably H2 and formate production, and stimulated butyrate, rather than propionate, as an electron sink alternative to CH4. All three dilution rates are considered high and selected for rapidly growing bacteria. The archaeal community composition varied widely and inconsistently. Lactate accumulated with both substrates, likely favored by microbial growth kinetics rather than by H2 accumulation thermodynamically stimulating electron disposal from NADH into pyruvate reduction. In this study, the type of substrate had a major effect on rumen fermentation largely independent of dilution rate and pH.
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Affiliation(s)
- Emilio M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias, Vilcún, Chile
| | - Nathaly Cancino-Padilla
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias, Vilcún, Chile
| | - Nelson Vera-Aguilera
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias, Vilcún, Chile
| | | | - Marcelo Saldivia
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Lorena Lagos-Pailla
- Instituto de Ingeniería Agraria y Suelos, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
- Centro de Investigación de Suelos Volcánicos, Universidad Austral de Chile, Valdivia, Chile
- Centro de Humedales Río Cruces, Valdivia, Chile
| | - Milena Vera
- Instituto de Ingeniería Agraria y Suelos, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Cristián Cerda
- Departamento de Procesos Industriales, Universidad Católica de Temuco, Temuco, Chile
| | - Camila Muñoz
- Centro Regional de Investigación Remehue, Instituto de Investigaciones Agropecuarias, Osorno, Chile
| | - Natalie Urrutia
- Centro Regional de Investigación Remehue, Instituto de Investigaciones Agropecuarias, Osorno, Chile
| | - Emilio D Martínez
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
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Fausset H, Spietz RL, Cox S, Cooper G, Spurzem S, Tokmina-Lukaszewska M, DuBois J, Broderick JB, Shepard EM, Boyd ES, Bothner B. A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri. Microbiol Spectr 2024; 12:e0041823. [PMID: 38179920 PMCID: PMC10846266 DOI: 10.1128/spectrum.00418-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Iron (Fe) and sulfur (S) are required elements for life, and changes in their availability can limit the ecological distribution and function of microorganisms. In anoxic environments, soluble Fe typically exists as ferrous iron [Fe(II)] and S as sulfide (HS-). These species exhibit a strong affinity that ultimately drives the formation of sedimentary pyrite (FeS2). Recently, paradigm-shifting studies indicate that Fe and S in FeS2 can be made bioavailable by methanogens through a reductive dissolution process. However, the impact of the utilization of FeS2, as opposed to canonical Fe and S sources, on the phenotype of cells is not fully understood. Here, shotgun proteomics was utilized to measure changes in the phenotype of Methanosarcina barkeri MS grown with FeS2, Fe(II)/HS-, or Fe(II)/cysteine. Shotgun proteomics tracked 1,019 proteins overall, with 307 observed to change between growth conditions. Functional characterization and pathway analyses revealed these changes to be systemic and largely tangential to Fe/S metabolism. As a final step, the proteomics data were viewed with respect to previously collected transcriptomics data to deepen the analysis. Presented here is evidence that M. barkeri adopts distinct phenotypes to exploit specific sources of Fe and S in its environment. This is supported by observed protein abundance changes across broad categories of cellular biology. DNA adjacent metabolism, central carbon metabolism methanogenesis, metal trafficking, quorum sensing, and porphyrin biosynthesis pathways are all features in the phenotypic differentiation. Differences in trace metal availability attributed to complexation with HS-, either as a component of the growth medium [Fe(II)/HS-] or generated through reduction of FeS2, were likely a major factor underpinning these phenotypic differences.IMPORTANCEThe methanogenic archaeon Methanosarcina barkeri holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life's origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so.
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Affiliation(s)
- Hunter Fausset
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Rachel L. Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Savannah Cox
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Gwendolyn Cooper
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Scott Spurzem
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | | | - Jennifer DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric M. Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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Pilliol V, Morsli M, Terlier L, Hassani Y, Malat I, Guindo CO, Davoust B, Lamglait B, Drancourt M, Aboudharam G, Grine G, Terrer E. Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos. Microbiol Spectr 2024; 12:e0514122. [PMID: 38189277 PMCID: PMC10845953 DOI: 10.1128/spectrum.05141-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/24/2023] [Indexed: 01/09/2024] Open
Abstract
Methanosphaera stadtmanae was the sole Methanosphaera representative to be cultured and detected by molecular methods in the human gut microbiota, further associated with digestive and respiratory diseases, leaving unknown the actual diversity of human-associated Methanosphaera species. Here, a novel Methanosphaera species, Candidatus Methanosphaera massiliense (Ca. M. massiliense) sp. nov. was isolated by culture using a hydrogen- and carbon dioxide-free medium from one human feces sample. Ca. M. massiliense is a non-motile, 850 nm Gram-positive coccus autofluorescent at 420 nm. Whole-genome sequencing yielded a 29.7% GC content, gapless 1,785,773 bp genome sequence with an 84.5% coding ratio, encoding for alcohol and aldehyde dehydrogenases promoting the growth of Ca. M. massiliense without hydrogen. Screening additional mammal and human feces using a specific genome sequence-derived DNA-polymerase RT-PCR system yielded a prevalence of 22% in pigs, 12% in red kangaroos, and no detection in 149 other human samples. This study, extending the diversity of Methanosphaera in human microbiota, questions the zoonotic sources of Ca. M. massiliense and possible transfer between hosts.IMPORTANCEMethanogens are constant inhabitants in the human gut microbiota in which Methanosphaera stadtmanae was the only cultivated Methanosphaera representative. We grew Candidatus Methanosphaera massiliense sp. nov. from one human feces sample in a novel culture medium under a nitrogen atmosphere. Systematic research for methanogens in human and animal fecal samples detected Ca. M. massiliense in pig and red kangaroo feces, raising the possibility of its zoonotic acquisition. Host specificity, source of acquisition, and adaptation of methanogens should be further investigated.
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Affiliation(s)
- Virginie Pilliol
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Madjid Morsli
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Laureline Terlier
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Yasmine Hassani
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ihab Malat
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Cheick Oumar Guindo
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard Davoust
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | | | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | | | - Elodie Terrer
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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9
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Prakash O, Dewala SR, Nimonkar Y, Patil SK, Chauhan A, Yadav A, Dhotre DP, Ranade DR. Culture-based and culture-independent approach for the study of the methanogens and obligate anaerobes from different landfill sites. Front Microbiol 2024; 14:1273037. [PMID: 38348306 PMCID: PMC10860756 DOI: 10.3389/fmicb.2023.1273037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/27/2023] [Indexed: 02/15/2024] Open
Abstract
The landfill is a cheap way of solid waste management in developing countries. The majority of landfills are non-sanitary and work as open garbage dumping sites and pose threats to public and environmental health. Therefore, an in-depth understanding of the chemistry and microbiology of landfills is imperative to develop the right policies for landfill management. In the current study, we investigated the chemistry and microbiology of three Indian landfill sites using culture-based and culture-independent molecular approaches. Our data indicate that the nature of landfills varies from site to site in terms of chemistry, pollutants, and pathogens. We also enriched and cultivated three methanogens using an optimized medium and constructed two high-quality draft genomes from enriched microbiomes using metagenome-assembled genome approaches. The phylogenomic study of one draft genome showed the highest 93% sequence similarity with members of Methanomassiliicoccaceae and was always enriched with Acholoplasma and Anaerohalosphaera lusitana. Despite all the efforts, we did not isolate it in pure culture and hypothesized that for the cultivation of some not-yet-cultured methanogen, the presence of other organisms plays an important role, and their syntrophic interaction must be discerned for its successful cultivation in the future. Co-cultivation of amino acid-degrading organisms indicates that their co-culture can assist in boosting the growth of methanogens. In addition, our data indicated that landfill leachate contains a heavy load of pollutants and treatment is a must before discharge in nature or use in irrigation or biofertilizer.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Sahab Ram Dewala
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Yogesh Nimonkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Shalaka K. Patil
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Ashvini Chauhan
- Environmental Biotechnology at the School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Amit Yadav
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Dheeraj P. Dhotre
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Dilip R. Ranade
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
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10
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Prabhaharan D, Nair PS, Park H, Choi O, Sang BI. Complete genome sequence of Methanothermobacter sp. DP, a hydrogenotrophic and thermophilic methanogen. Microbiol Resour Announc 2024; 13:e0064223. [PMID: 38054708 DOI: 10.1128/mra.00642-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/04/2023] [Indexed: 12/07/2023] Open
Abstract
Here, we report the complete genome sequence of the thermophilic hydrogenotrophic methanogen Methanothermobacter sp. DP isolated in South Korea from an anaerobic digester fed with cigarette waste. The genome consists of 1,693,285 bp, with 1,772 protein-coding genes and a GC content of 48.8%.
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Affiliation(s)
- Darsha Prabhaharan
- Department of Chemical Engineering, Hanyang University, Wangsimniro, Seongdong-gu , Seoul, South Korea
| | - Pranav Sasidharan Nair
- Department of Chemical Engineering, Hanyang University, Wangsimniro, Seongdong-gu , Seoul, South Korea
| | - Hyojung Park
- Department of Chemical Engineering, Hanyang University, Wangsimniro, Seongdong-gu , Seoul, South Korea
- Center of Convergence Bioceramic Materials, Korea Institute of Ceramic Engineering and Technology, Osongsaengmyeong 1-ro, Osong-eup, Heungdeok-gu, Cheongju-si , Chungchengbuk-do, South Korea
| | - Okkyoung Choi
- Eco Lab Center, SK Ecoplant, Jong-ro, Jongno-gu , Seoul, South Korea
| | - Byoung-In Sang
- Department of Chemical Engineering, Hanyang University, Wangsimniro, Seongdong-gu , Seoul, South Korea
- Clean-Energy Research Institute, Hanyang University, Wangsimniro, Seongdong-gu , Seoul, South Korea
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11
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Cisek AA, Szymańska E, Wierzbicka-Rucińska A, Aleksandrzak-Piekarczyk T, Cukrowska B. Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity. Int J Mol Sci 2024; 25:673. [PMID: 38203843 PMCID: PMC10779203 DOI: 10.3390/ijms25010673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens-especially those focused on children-are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn's disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity assessed with the use of Pediatric Crohn's Disease Activity Index (PCDAI) and Pediatric Ulcerative Colitis Activity Index (PUCAI) indices, and fecal calprotectin (FCP) concentration, and compared with controls. There was a significant decrease in the number of total methanogens in CD and UC compared to controls. The prevalence of total methanogens was also lower in UC compared to controls. Furthermore, patients from the inactive UC group were colonized by a lower number of Mb. smithii, and demonstrated the most pronounced positive correlation between the number of Ms. stadtmanae and the FCP concentration. Our results demonstrate that gut methanogens are related to the type and activity of pediatric IBD.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathomorphology, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | - Edyta Szymańska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | - Aldona Wierzbicka-Rucińska
- Department of Biochemistry, Radioimmunology and Experimental Medicine, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | | | - Bożena Cukrowska
- Department of Pathomorphology, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
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12
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Novikova PV, Bhanu Busi S, Probst AJ, May P, Wilmes P. Functional prediction of proteins from the human gut archaeome. ISME Commun 2024; 4:ycad014. [PMID: 38486809 PMCID: PMC10939349 DOI: 10.1093/ismeco/ycad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 03/17/2024]
Abstract
The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.
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Affiliation(s)
- Polina V Novikova
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- UK Centre for Ecology and Hydrology, Wallingford, OX10 8 BB, United Kingdom
| | - Alexander J Probst
- Environmental Metagenomics, Department of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, for Environmental Microbiology and Biotechnology, University Duisburg-Essen, Duisburg 47057, Germany
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Paul Wilmes
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
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13
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Hanišáková N, Vítězová M, Vítěz T, Kushkevych I, Kotrlová E, Novák D, Lochman J, Zavada R. Microbiological insight into various underground gas storages in Vienna Basin focusing on methanogenic Archaea. Front Microbiol 2023; 14:1293506. [PMID: 38188570 PMCID: PMC10771303 DOI: 10.3389/fmicb.2023.1293506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive understanding of the microbial communities within any UGS facilities designated for hydrogen storage. In this study, underground water samples and water samples from surface technologies from 7 different UGS objects located in the Vienna Basin were studied using both molecular biology methods and cultivation methods. Results from 16S rRNA sequencing revealed that the proportion of archaea in the groundwater samples ranged from 20 to 58%, with methanogens being the predominant. Some water samples collected from surface technologies contained up to 87% of methanogens. Various species of methanogens were isolated from individual wells, including Methanobacterium sp., Methanocalculus sp., Methanolobus sp. or Methanosarcina sp. We also examined water samples for the presence of sulfate-reducing bacteria known to be involved in microbially induced corrosion and identified species of the genus Desulfovibrio in the samples. In the second part of our study, we contextualized our data by comparing it to available sequencing data from terrestrial subsurface environments worldwide. This allowed us to discern patterns and correlations between different types of underground samples based on environmental conditions. Our findings reveal presence of methanogens in all analyzed groups of underground samples, which suggests the possibility of unintended microbial hydrogen-to-methane conversion and the associated financial losses. Nevertheless, the prevalence of methanogens in our results also highlights the potential of the UGS environment, which can be effectively leveraged as a bioreactor for the conversion of hydrogen into methane, particularly in the context of Power-to-Methane technology.
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Affiliation(s)
- Nikola Hanišáková
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Monika Vítězová
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tomáš Vítěz
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Ivan Kushkevych
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eva Kotrlová
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Novák
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Roman Zavada
- Innovation Unit, NAFTA a.s., Bratislava, Slovakia
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14
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Zhu P, Somvanshi T, Bao J, Scheller S. CRISPR/Cas12a toolbox for genome editing in Methanosarcina acetivorans. Front Microbiol 2023; 14:1235616. [PMID: 38149272 PMCID: PMC10750270 DOI: 10.3389/fmicb.2023.1235616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023] Open
Abstract
Methanogenic archaea play an important role in the global carbon cycle and may serve as host organisms for the biotechnological production of fuels and chemicals from CO2 and other one-carbon substrates. Methanosarcina acetivorans is extensively studied as a model methanogen due to its large genome, versatile substrate range, and available genetic tools. Genome editing in M. acetivorans via CRISPR/Cas9 has also been demonstrated. Here, we describe a user-friendly CRISPR/Cas12a toolbox that recognizes T-rich (5'-TTTV) PAM sequences. The toolbox can manage deletions of 3,500 bp (i.e., knocking out the entire frhADGB operon) and heterologous gene insertions with positive rates of over 80%. Cas12a-mediated multiplex genome editing was used to edit two separate sites on the chromosome in one round of editing. Double deletions of 100 bp were achieved, with 8/8 of transformants being edited correctly. Simultaneous deletion of 100 bp at one site and replacement of 100 bp with the 2,400 bp uidA expression cassette at a separate site yielded 5/6 correctly edited transformants. Our CRISPR/Cas12a toolbox enables reliable genome editing, and it can be used in parallel with the previously reported Cas9-based system for the genetic engineering of the Methanosarcina species.
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Affiliation(s)
| | | | - Jichen Bao
- Laboratory of Biochemistry, Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| | - Silvan Scheller
- Laboratory of Biochemistry, Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
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15
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Hinkle JE, Mara P, Beaudoin DJ, Edgcomb VP, Teske AP. A PCR-Based Survey of Methane-Cycling Archaea in Methane-Soaked Subsurface Sediments of Guaymas Basin, Gulf of California. Microorganisms 2023; 11:2956. [PMID: 38138100 PMCID: PMC10745291 DOI: 10.3390/microorganisms11122956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases, showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity in methanogen lineages. Our survey indicates the potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin.
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Affiliation(s)
- John E. Hinkle
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Falmouth, MA 02543, USA; (P.M.); (D.J.B.); (V.P.E.)
| | - David J. Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Falmouth, MA 02543, USA; (P.M.); (D.J.B.); (V.P.E.)
| | - Virginia P. Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Falmouth, MA 02543, USA; (P.M.); (D.J.B.); (V.P.E.)
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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16
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Soza-Bolaños AI, Domínguez-Pérez RA, Ayala-Herrera JL, Pérez-Serrano RM, Soto-Barreras U, Espinosa-Cristóbal LF, Rivera-Albarrán CA, Zaldívar-Lelo de Larrea G. Presence of methanogenic archaea in necrotic root canals of patients with or without type 2 diabetes mellitus. AUST ENDOD J 2023; 49:641-647. [PMID: 37715368 DOI: 10.1111/aej.12797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/11/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023]
Abstract
Theoretically, a necrotic root canal fulfils all requirements as a niche for methanogens to inhabit. However, their presence in it and its implication in apical periodontitis (AP) is controversial. Therefore, to contribute to ending the controversy, this study aimed to detect and compare methanogens' presence in two distinct niches with supposedly different microenvironments; both were necrotic root canals associated with AP but one from patients with type 2 diabetes mellitus (T2DM) while the other from non-diabetic patients. A clinical examination was performed on 65 T2DM patients and 73 non-diabetic controls. Samples from necrotic root canals were obtained, and methanogens were identified. The presence of methanogens was three times higher (27.6%) in the T2DM group than in non-diabetic patients (8.2%). In addition, methanogens' presence was associated with a higher prevalence of periapical symptoms.
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Affiliation(s)
- Ana I Soza-Bolaños
- Laboratory of Multidisciplinary Dentistry Research, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
- Department of Endodontics, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
| | - Rubén A Domínguez-Pérez
- Laboratory of Multidisciplinary Dentistry Research, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
- Department of Endodontics, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
| | | | - Rosa M Pérez-Serrano
- Laboratorio de Genética y Biología Molecular (GENBIOM), Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
| | | | - León F Espinosa-Cristóbal
- Master Program in Dental Sciences, Stomatology Department, Institute of Biomedical Sciences, Autonomous University of Juarez, Ciudad Juarez, Mexico
| | - Claudia A Rivera-Albarrán
- Laboratory of Multidisciplinary Dentistry Research, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
| | - Guadalupe Zaldívar-Lelo de Larrea
- Laboratorio de Genética y Biología Molecular (GENBIOM), Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
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17
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Pérez G, Krause SMB, Bodelier PLE, Meima-Franke M, Pitombo L, Irisarri P. Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils. Microorganisms 2023; 11:2830. [PMID: 38137974 PMCID: PMC10745823 DOI: 10.3390/microorganisms11122830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 12/24/2023] Open
Abstract
Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.
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Affiliation(s)
- Germán Pérez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
- Laboratory of Microbiology, Department of Plant Biology, Agronomy Faculty, University of the Republic, Montevideo 12900, Uruguay;
| | - Sascha M. B. Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
| | - Leonardo Pitombo
- Department of Environmental Sciences, Federal University of São Carlos (UFSCar), São Paulo 18052-780, Brazil;
| | - Pilar Irisarri
- Laboratory of Microbiology, Department of Plant Biology, Agronomy Faculty, University of the Republic, Montevideo 12900, Uruguay;
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18
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Borrel G, Fadhlaoui K, Ben Hania W, Gaci N, Pehau-Arnaudet G, Chaudhary PP, Vandekerckove P, Ballet N, Alric M, O’Toole PW, Fardeau ML, Ollivier B, Brugère JF. Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov. Microorganisms 2023; 11:2794. [PMID: 38004804 PMCID: PMC10673518 DOI: 10.3390/microorganisms11112794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L-1 NaCl (optimum 0.12 mol.L-1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05T (JCM 31474T).
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Affiliation(s)
- Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell, 75015 Paris, France
| | - Khaled Fadhlaoui
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS, UMR 6023 CNRS-UCA, Laboratoire Microorganismes: Génome et Environnement LMGE, 63000 Clermont-Ferrand, France
| | - Wajdi Ben Hania
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Nadia Gaci
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Gérard Pehau-Arnaudet
- Institut Pasteur, Université Paris Cité, Ultrastructural Bioimaging, 75015 Paris, France
| | - Prem Prashant Chaudhary
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Nathalie Ballet
- Lesaffre International, Lesaffre Group, 59700 Marcq-en-Barœul, France
| | - Monique Alric
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | | | - Marie-Laure Fardeau
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
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19
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Protasov E, Nonoh JO, Kästle Silva JM, Mies US, Hervé V, Dietrich C, Lang K, Mikulski L, Platt K, Poehlein A, Köhler-Ramm T, Miambi E, Boga HI, Feldewert C, Ngugi DK, Plarre R, Sillam-Dussès D, Šobotník J, Daniel R, Brune A. Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods. Front Microbiol 2023; 14:1281628. [PMID: 38033561 PMCID: PMC10684969 DOI: 10.3389/fmicb.2023.1281628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.
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Affiliation(s)
- Evgenii Protasov
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - James O. Nonoh
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Joana M. Kästle Silva
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Undine S. Mies
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kristina Lang
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lena Mikulski
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katja Platt
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
| | - Tim Köhler-Ramm
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Edouard Miambi
- Evolutionary Ecology Department, Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), University of Paris-Est Créteil (UPEC), Créteil, France
| | - Hamadi I. Boga
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Christopher Feldewert
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - David K. Ngugi
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rudy Plarre
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology (LEEC), UR 4443, Université Sorbonne Paris Nord, Villetaneuse, France
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czechia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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20
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Aryee G, Luecke SM, Dahlen CR, Swanson KC, Amat S. Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle. Microorganisms 2023; 11:2746. [PMID: 38004757 PMCID: PMC10673468 DOI: 10.3390/microorganisms11112746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.
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Affiliation(s)
- Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
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21
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Liu J, Ding Y, Qiu W, Cheng Q, Xu C, Fan G, Song G, Xiao B. Enhancing anaerobic digestion of sulphate wastewater by adding nano-zero valent iron. Environ Technol 2023; 44:3988-3996. [PMID: 35546259 DOI: 10.1080/09593330.2022.2077137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
In this paper, the effects of nano-zero valent iron (nZVI) on anaerobic digestion of sulphate wastewater with different SO 4 2 - /COD ratios, including the COD removal rate, methane yield, intermediate products and the change of microbial community structure, were investigated. The results showed that nZVI could effectively enhance the treatment efficiency and methane yield. Compared with the control group without nZVI, the methane yield increased from 348.6833 to 1007.05 mL CH4/gCODremoval with 4 g nZVI loading at SO 4 2 - /COD = 0.1. nZVI could make electron flow from sulphate reduction to methane production, which increased methane yield even at high sulphate concentration. The microbial community analysis showed that adding nZVI could increase the abundance of acetoclastic methanogens, which accelerated hydrolysis acidification.
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Affiliation(s)
- Jiacheng Liu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Yongyu Ding
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Wen Qiu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Qunpeng Cheng
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Chenxi Xu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Guozhi Fan
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Guangsen Song
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Bo Xiao
- School of Environmental Engineering, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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22
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Chanderban M, Hill CA, Dhamad AE, Lessner DJ. Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase. Appl Environ Microbiol 2023; 89:e0103323. [PMID: 37695043 PMCID: PMC10537573 DOI: 10.1128/aem.01033-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/07/2023] [Indexed: 09/12/2023] Open
Abstract
All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N2) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif, vnf, and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif, vnf, and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N2 but not with NH4Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.
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Affiliation(s)
- Melissa Chanderban
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Christopher A. Hill
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Ahmed E. Dhamad
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
- Department of Biological Sciences, Wasit University, Wasit, Iraq
| | - Daniel J. Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
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23
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Tian W, Wang H, Xiang X, Loni PC, Qiu X, Wang R, Huang X, Tuovinen OH. Water table level controls methanogenic and methanotrophic communities and methane emissions in a Sphagnum-dominated peatland. Microbiol Spectr 2023; 11:e0199223. [PMID: 37747896 PMCID: PMC10580971 DOI: 10.1128/spectrum.01992-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/27/2023] [Indexed: 09/27/2023] Open
Abstract
Peatlands are important sources of the greenhouse gas methane emissions equipoised by methanogens and methanotrophs. However, knowledge about how microbial functional groups associated with methane production and oxidation respond to water table fluctuations has been limited to date. Here, methane-related microbial communities and the potentials of methane production and oxidation were determined along sectioned peat layers in a subalpine peatland across four Sphagnum-dominated sites with different water table levels. Methane fluxes were also monitored at these sites. The results showed that mcrA gene copies for methanogens were the highest in the 10- to 15-cm peat layer, which was also characterized by the maximum potential methane production (24.53 ± 1.83 nmol/g/h). Copy numbers of the pmoA gene for type Ia and Ib methanotrophs were enriched in the 0-5 cm peat layer with the highest potential methane oxidation (43.09 ± 3.44 nmol/g/h). For the type II methanotrophs, the pmoA gene copies were higher in the 10- to 15-cm peat layer. Hydrogenotrophic methanogens and type II methanotrophs dominated the methane functional groups. Deterministic process contributed more to methanogenic and methanotrophic community assemblages in comparison with stochastic process. The level of water table significantly shaped methanogenic and methanotrophic community structures and regulated methane fluxes. Compared with vascular plants, Sphagnum mosses significantly reduced the methane emissions in peatlands. Collectively, these findings enhance a comprehensive understanding of the effect of the water table level on methane functional groups, with consequential implications for reducing methane emissions within peatland ecosystems.IMPORTANCEThe water table level is recognized as a critical factor in regulating methane emissions, which are largely dependent on the balance of methanogens and methanotrophs. Previous studies on peat methane emissions have been mostly focused on spatial-temporal variations and the relationship with meteorological conditions. However, the role of the water table level in methane emissions remains unknown. In this work, four representative microhabitats along a water table gradient in a Sphagnum-dominated peatland were sampled to gain an insight into methane functional communities and methane emissions as affected by the water table level. The changes in methane-related microbial community structure and assembly were used to characterize the response to the water table level. This study improves the understanding of the changes in methane-related microbial communities and methane emissions with water table levels in peatlands.
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Affiliation(s)
- Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- College of Resource and Environment, Anhui Science and Technology of University, Chuzhou, China
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- College of Life Science, Shangrao Normal University, Shangrao, China
| | - Prakash C. Loni
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xuan Qiu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ruicheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xianyu Huang
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, China
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
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24
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Lorca GL, Kleinsteuber S. Editorial: Women in microbial physiology and metabolism: 2022. Front Microbiol 2023; 14:1268568. [PMID: 37645220 PMCID: PMC10461555 DOI: 10.3389/fmicb.2023.1268568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023] Open
Affiliation(s)
- Graciela L. Lorca
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
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25
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Abdel Azim A, Vizzarro A, Bellini R, Bassani I, Baudino L, Pirri CF, Verga F, Lamberti A, Menin B. Perspective on the use of methanogens in lithium recovery from brines. Front Microbiol 2023; 14:1233221. [PMID: 37601371 PMCID: PMC10434214 DOI: 10.3389/fmicb.2023.1233221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Methanogenic archaea stand out as multipurpose biocatalysts for different applications in wide-ranging industrial sectors due to their crucial role in the methane (CH4) cycle and ubiquity in natural environments. The increasing demand for raw materials required by the manufacturing sector (i.e., metals-, concrete-, chemicals-, plastic- and lubricants-based industries) represents a milestone for the global economy and one of the main sources of CO2 emissions. Recovery of critical raw materials (CRMs) from byproducts generated along their supply chain, rather than massive mining operations for mineral extraction and metal smelting, represents a sustainable choice. Demand for lithium (Li), included among CRMs in 2023, grew by 17.1% in the last decades, mostly due to its application in rechargeable lithium-ion batteries. In addition to mineral deposits, the natural resources of Li comprise water, ranging from low Li concentrations (seawater and freshwater) to higher ones (salt lakes and artificial brines). Brines from water desalination can be high in Li content which can be recovered. However, biological brine treatment is not a popular methodology. The methanogenic community has already demonstrated its ability to recover several CRMs which are not essential to their metabolism. Here, we attempt to interconnect the well-established biomethanation process with Li recovery from brines, by analyzing the methanogenic species which may be suitable to grow in brine-like environments and the corresponding mechanism of recovery. Moreover, key factors which should be considered to establish the techno-economic feasibility of this process are here discussed.
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Affiliation(s)
- Annalisa Abdel Azim
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Arianna Vizzarro
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Environment, Land and Infrastructure Engineering, Politecnico di Torino, Turin, Italy
| | - Ruggero Bellini
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Ilaria Bassani
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Luisa Baudino
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Candido Fabrizio Pirri
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Francesca Verga
- Department of Environment, Land and Infrastructure Engineering, Politecnico di Torino, Turin, Italy
| | - Andrea Lamberti
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Barbara Menin
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale Delle Ricerche, Milan, Italy
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26
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Deng Z, Chen H, Wang J, Zhang N, Han Z, Xie Y, Zhang X, Fang X, Yu H, Zhang D, Yue Z, Zhang C. Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination. Environ Sci Technol 2023. [PMID: 37478352 DOI: 10.1021/acs.est.3c03738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.
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Affiliation(s)
- Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Haixin Chen
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Jun Wang
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Ning Zhang
- Department of Environmental Engineering, School of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Zhiqiang Han
- Department of Marine Resources and Environment, Fishery College, Zhejiang Ocean University, Zhoushan 316002, Zhejiang, China
| | - Yeting Xie
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | - Xiaoyan Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | | | - Hao Yu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Zhen Yue
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
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27
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Zhang F, Hou H, Fu J, Bastidas-Oyanedel JR. Editorial: Anaerobic digestion of waste organics: toxicity and management. Front Microbiol 2023; 14:1243205. [PMID: 37533833 PMCID: PMC10392921 DOI: 10.3389/fmicb.2023.1243205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023] Open
Affiliation(s)
- Fang Zhang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huijie Hou
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Fu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Juan-Rodrigo Bastidas-Oyanedel
- SDU-Department of Chemical Engineering, Biotechnology, and Environmental Technology, University of Southern Denmark, Odense, Denmark
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28
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Brown JL, Gierke T, Butkovich LV, Swift CL, Singan V, Daum C, Barry K, Grigoriev IV, O’Malley MA. High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi. Front Fungal Biol 2023; 4:1171100. [PMID: 37746117 PMCID: PMC10512310 DOI: 10.3389/ffunb.2023.1171100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 09/26/2023]
Abstract
Anaerobic fungi produce biomass-degrading enzymes and natural products that are important to harness for several biotechnology applications. Although progress has been made in the development of methods for extracting nucleic acids for genomic and transcriptomic sequencing of these fungi, most studies are limited in that they do not sample multiple fungal growth phases in batch culture. In this study, we establish a method to harvest RNA from fungal monocultures and fungal-methanogen co-cultures, and also determine an optimal time frame for high-quality RNA extraction from anaerobic fungi. Based on RNA quality and quantity targets, the optimal time frame in which to harvest anaerobic fungal monocultures and fungal-methanogen co-cultures for RNA extraction was 2-5 days of growth post-inoculation. When grown on cellulose, the fungal strain Anaeromyces robustus cocultivated with the methanogen Methanobacterium bryantii upregulated genes encoding fungal carbohydrate-active enzymes and other cellulosome components relative to fungal monocultures during this time frame, but expression patterns changed at 24-hour intervals throughout the fungal growth phase. These results demonstrate the importance of establishing methods to extract high-quality RNA from anaerobic fungi at multiple time points during batch cultivation.
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Affiliation(s)
- Jennifer L. Brown
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Taylor Gierke
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lazarina V. Butkovich
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Candice L. Swift
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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29
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Li Y, Chen J, Tang S, Xi Z. Microbial Communities Affected by Hydraulic Fracturing and Environmental Factors within an In Situ Coal Reservoir. Microorganisms 2023; 11:1657. [PMID: 37512830 PMCID: PMC10385777 DOI: 10.3390/microorganisms11071657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
The rise of coalbed methane bioengineering enables the conversion and utilization of carbon dioxide through microbial action and the carbon cycle. The environment of underground coal reservoirs is the result of a comprehensive effort by microorganisms. Some studies on reservoir microorganisms have progressed in laboratory conditions. However, it does not replicate the interaction between microorganisms and the environment on site. Hydraulic fracturing is an engineering technology to improve the natural permeability of tight reservoirs and is also a prerequisite for increasing biomethane production. In addition to expanding the pore and fracture systems of coal reservoirs, hydraulic fracturing also improves the living conditions of microbial communities in underground space. The characteristics of microbial communities in the reservoir after hydraulic fracturing are unclear. To this end, we applied the 16S rRNA sequencing technique to coalbed methane production water after hydraulic fracturing south of the Qinshui Basin to analyze the microbial response of the hydraulic fracturing process in the coal reservoir. The diversity of microbial communities associated with organic degradation was improved after hydraulic fracturing in the coal reservoir. The proportion of Actinobacteria in the reservoir water of the study area increased significantly, and the abundance of Aminicenantes and Planctomycetes increased, which do not exist in non-fracturing coalbed methane wells or exist at very low abundance. There are different types of methanogens in the study area, especially in fracturing wells. Ecological factors also determine the metabolic pathway of methanogens in coal seams. After hydraulic fracturing, the impact on the reservoir's microbial communities remains within months. Hydraulic fracturing can strengthen the carbon circulation process, thereby enhancing the block's methane and carbon dioxide circulation. The study provides a unique theoretical basis for microbially enhanced coalbed methane.
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Affiliation(s)
- Yang Li
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China
- The Key Laboratory of Universities in Anhui Province for Prevention of Mine Geological Disasters, Anhui University of Science and Technology, Huainan 232001, China
- Key Laboratory of Petroleum Resources and Prospecting, China University of Petroleum, Beijing 102249, China
| | - Jian Chen
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China
- The Key Laboratory of Universities in Anhui Province for Prevention of Mine Geological Disasters, Anhui University of Science and Technology, Huainan 232001, China
| | - Shuheng Tang
- School of Energy Resource, China University of Geosciences, Beijing 100083, China
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, Ministry of Education, Beijing 100083, China
- Key Laboratory of Strategy Evaluation for Shale Gas, Ministry of Land and Resources, Beijing 100083, China
| | - Zhaodong Xi
- School of Energy Resource, China University of Geosciences, Beijing 100083, China
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, Ministry of Education, Beijing 100083, China
- Key Laboratory of Strategy Evaluation for Shale Gas, Ministry of Land and Resources, Beijing 100083, China
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Fuchs W, Rachbauer L, Rittmann SKMR, Bochmann G, Ribitsch D, Steger F. Eight Up-Coming Biotech Tools to Combat Climate Crisis. Microorganisms 2023; 11:1514. [PMID: 37375016 DOI: 10.3390/microorganisms11061514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.
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Affiliation(s)
- Werner Fuchs
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Lydia Rachbauer
- Lawrence Berkeley National Laboratory, Deconstruction Division at the Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria
| | - Günther Bochmann
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Franziska Steger
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
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Jia Z, Lipus D, Burckhardt O, Bussert R, Sondermann M, Bartholomäus A, Wagner D, Kallmeyer J. Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO 2 terrestrial subsurface environments. Front Microbiol 2023; 14:1105259. [PMID: 37293225 PMCID: PMC10246774 DOI: 10.3389/fmicb.2023.1105259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/25/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction Long-term stability of underground CO2 storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO2 makes the Eger Rift in the Czech Republic a natural analogue to underground CO2 storage. The Eger Rift is a seismically active region and H2 is produced abiotically during earthquakes, providing energy to indigenous microbial communities. Methods To investigate the response of a microbial ecosystem to high levels of CO2 and H2, we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H2/CO2 headspace to simulate a seismically active period with elevated H2. Results and discussion Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50-60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H2 and CO2, specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO2 driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO2 and H2-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO2 concentrations, similar to those found in CCS sites.
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Affiliation(s)
- Zeyu Jia
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Oliver Burckhardt
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Robert Bussert
- Applied Geochemistry, Institute of Applied Geosciences, Technische Universität Berlin, Berlin, Germany
| | - Megan Sondermann
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | | | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
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Webster G, Cragg BA, Rinna J, Watkins AJ, Sass H, Weightman AJ, Parkes RJ. Methanogen activity and microbial diversity in Gulf of Cádiz mud volcano sediments. Front Microbiol 2023; 14:1157337. [PMID: 37293223 PMCID: PMC10244519 DOI: 10.3389/fmicb.2023.1157337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
The Gulf of Cádiz is a tectonically active continental margin with over sixty mud volcanoes (MV) documented, some associated with active methane (CH4) seepage. However, the role of prokaryotes in influencing this CH4 release is largely unknown. In two expeditions (MSM1-3 and JC10) seven Gulf of Cádiz MVs (Porto, Bonjardim, Carlos Ribeiro, Captain Arutyunov, Darwin, Meknes, and Mercator) were analyzed for microbial diversity, geochemistry, and methanogenic activity, plus substrate amended slurries also measured potential methanogenesis and anaerobic oxidation of methane (AOM). Prokaryotic populations and activities were variable in these MV sediments reflecting the geochemical heterogeneity within and between them. There were also marked differences between many MV and their reference sites. Overall direct cell numbers below the SMTZ (0.2-0.5 mbsf) were much lower than the general global depth distribution and equivalent to cell numbers from below 100 mbsf. Methanogenesis from methyl compounds, especially methylamine, were much higher than the usually dominant substrates H2/CO2 or acetate. Also, CH4 production occurred in 50% of methylated substrate slurries and only methylotrophic CH4 production occurred at all seven MV sites. These slurries were dominated by Methanococcoides methanogens (resulting in pure cultures), and prokaryotes found in other MV sediments. AOM occurred in some slurries, particularly, those from Captain Arutyunov, Mercator and Carlos Ribeiro MVs. Archaeal diversity at MV sites showed the presence of both methanogens and ANME (Methanosarcinales, Methanococcoides, and ANME-1) related sequences, and bacterial diversity was higher than archaeal diversity, dominated by members of the Atribacterota, Chloroflexota, Pseudomonadota, Planctomycetota, Bacillota, and Ca. "Aminicenantes." Further work is essential to determine the full contribution of Gulf of Cádiz mud volcanoes to the global methane and carbon cycles.
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Affiliation(s)
- Gordon Webster
- Microbiomes, Microbes and Informatics Group, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Barry A. Cragg
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Joachim Rinna
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
- Aker BP ASA, Lysaker, Norway
| | - Andrew J. Watkins
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
- The Wales Research and Diagnostic Positron Emission Tomography Imaging Centre (PETIC), School of Medicine, Cardiff University, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Henrik Sass
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Andrew J. Weightman
- Microbiomes, Microbes and Informatics Group, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - R. John Parkes
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
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Li Y, Tang S, Chen J, Xi Z. Research Progress and Prospects on Microbial Response and Gas Potential in the Coal Gasification Process. Microorganisms 2023; 11:1293. [PMID: 37317267 DOI: 10.3390/microorganisms11051293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
As an essential unconventional natural gas resource, China's coalbed methane resources are only commercially exploited in a few areas, such as the Qinshui Basin and the Ordos. The rise of coalbed methane bioengineering makes it possible to realize the conversion and utilization of carbon dioxide through microbial action and the carbon cycle. According to the metabolic behavior of the underground microbial community, if the coal reservoir is modified, it may stimulate the microorganism to continuously produce biomethane to prolong the production life of depleted coalbed methane wells. This paper systematically discusses the microbial response to promoting microbial metabolism by nutrients (microbial stimulation), introducing exogenous microorganisms or domestication of in situ microorganisms (microbial enhancement), pretreating coal to change its physical or chemical properties to improve bioavailability, and improving environmental conditions. However, many problems must be solved before commercialization. The whole coal reservoir is regarded as a giant anaerobic fermentation system. Some issues still need to be solved during the implementation of coalbed methane bioengineering. Firstly, the metabolic mechanism of methanogenic microorganisms should be clarified. Secondly, it is urgent to study the optimization of high-efficiency hydrolysis bacteria and nutrient solutions in coal seams. Finally, the research on the underground microbial community ecosystem and biogeochemical cycle mechanism must be improved. The study provides a unique theory for the sustainable development of unconventional natural gas resources. Furthermore, it provides a scientific basis for realizing the carbon dioxide reuse and carbon element cycle in coalbed methane reservoirs.
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Affiliation(s)
- Yang Li
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China
- The Key Laboratory of Universities in Anhui Province for Prevention of Mine Geological Disasters, Anhui University of Science and Technology, Huainan 232001, China
- State Key Laboratory of Petroleum Resources and Prospecting, China University of Petroleum, Beijing 102249, China
| | - Shuheng Tang
- School of Energy Resource, China University of Geosciences, Beijing 100083, China
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, Ministry of Education, Beijing 100083, China
- Key Laboratory of Strategy Evaluation for Shale Gas, Ministry of Land and Resources, Beijing 100083, China
| | - Jian Chen
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China
- The Key Laboratory of Universities in Anhui Province for Prevention of Mine Geological Disasters, Anhui University of Science and Technology, Huainan 232001, China
| | - Zhaodong Xi
- School of Energy Resource, China University of Geosciences, Beijing 100083, China
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, Ministry of Education, Beijing 100083, China
- Key Laboratory of Strategy Evaluation for Shale Gas, Ministry of Land and Resources, Beijing 100083, China
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Karadagli F, Marcus A, Rittmann BE. Microbiological hydrogen (H 2 ) thresholds in anaerobic continuous-flow systems: Effects of system characteristics. Biotechnol Bioeng 2023. [PMID: 37148477 DOI: 10.1002/bit.28415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/20/2023] [Accepted: 04/24/2023] [Indexed: 05/08/2023]
Abstract
Hydrogen (H2 ) concentrations that were associated with microbiological respiratory processes (RPs) such as sulfate reduction and methanogenesis were quantified in continuous-flow systems (CFSs) (e.g., bioreactors, sediments). Gibbs free energy yield (ΔǴ ~ 0) of the relevant RP has been proposed to control the observed H2 concentrations, but most of the reported values do not align with the proposed energetic trends. Alternatively, we postulate that system characteristics of each experimental design influence all system components including H2 concentrations. To analyze this proposal, a Monod-based mathematical model was developed and used to design a gas-liquid bioreactor for hydrogenotrophic methanogenesis with Methanobacterium bryantii M.o.H. Gas-to-liquid H2 mass transfer, microbiological H2 consumption, biomass growth, methane formation, and Gibbs free energy yields were evaluated systematically. Combining model predictions and experimental results revealed that an initially large biomass concentration created transients during which biomass consumed [H2 ]L rapidly to the thermodynamic H2 -threshold (≤1 nM) that triggerred the microorganisms to stop H2 oxidation. With no H2 oxidation, continuous gas-to-liquid H2 transfer increased [H2 ]L to a level that signaled the methanogens to resume H2 oxidation. Thus, an oscillatory H2 -concentration profile developed between the thermodynamic H2 -threshold (≤1 nM) and a low [H2 ]L (~10 nM) that relied on the rate of gas-to-liquid H2 -transfer. The transient [H2 ]L values were too low to support biomass synthesis that could balance biomass losses through endogenous oxidation and advection; thus, biomass declined continuously and disappeared. A stable [H2 ]L (1807 nM) emerged as a result of abiotic H2 -balance between gas-to-liquid H2 transfer and H2 removal via advection of liquid-phase.
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Affiliation(s)
- Fatih Karadagli
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
| | - Andrew Marcus
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- Skyology Inc., San Francisco, California, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
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Wang L, Guo Q, Wu G, Yu Z, Ninin JML, Planer-Friedrich B. Methanogens-Driven Arsenic Methylation Preceding Formation of Methylated Thioarsenates in Sulfide-Rich Hot Springs. Environ Sci Technol 2023; 57:7410-7420. [PMID: 37134202 DOI: 10.1021/acs.est.2c08814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hot springs represent a major source of arsenic release into the environment. Speciation is typically reported to be dominated by arsenite, arsenate, and inorganic thiolated arsenates. Much less is known about the relevance and formation of methylated thioarsenates, a group with species of high mobility and toxicity. In hot spring samples taken from the Tengchong volcanic region in China, methylated thioarsenates contributed up to 13% to total arsenic. Enrichment cultures were obtained from the corresponding sediment samples and incubated to assess their capability to convert arsenite into methylated thioarsenates over time and in the presence of different microbial inhibitors. In contrast to observations in other environmental systems (e.g., paddy soils), there was no solid evidence, supporting that the sulfate-reducing bacteria contributed to the arsenic methylation. Methanosarcina, the sole genus of methanogens detected in the enrichment cultures, as well as Methanosarcina thermophila TM-1, a pure strain within the genus, did methylate arsenic. We propose that methylated thioarsenates in a typical sulfide-rich hot spring environment like Tengchong form via a combination of biotic arsenic methylation driven by thermophilic methanogens and arsenic thiolation with either geogenic sulfide or sulfide produced by sulfate-reducing bacteria.
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Affiliation(s)
- Luxia Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
| | - Qinghai Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
| | - Zhicheng Yu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
| | - José Miguel Léon Ninin
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Britta Planer-Friedrich
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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36
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Jordan D, Kominoski JS, Servais S, Mills D. Salinity Impacts the Functional mcrA and dsrA Gene Abundances in Everglades Marshes. Microorganisms 2023; 11:1180. [PMID: 37317154 DOI: 10.3390/microorganisms11051180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Coastal wetlands, such as the Everglades, are increasingly being exposed to stressors that have the potential to modify their existing ecological processes because of global climate change. Their soil microbiomes include a population of organisms important for biogeochemical cycling, but continual stresses can disturb the community's composition, causing functional changes. The Everglades feature wetlands with varied salinity levels, implying that they contain microbial communities with a variety of salt tolerances and microbial functions. Therefore, tracking the effects of stresses on these populations in freshwater and brackish marshes is critical. The study addressed this by utilizing next generation sequencing (NGS) to construct a baseline soil microbial community. The carbon and sulfur cycles were studied by sequencing a microbial functional gene involved in each process, the mcrA and dsrA functional genes, respectively. Saline was introduced over two years to observe the taxonomic alterations that occurred after a long-term disturbance such as seawater intrusion. It was observed that saltwater dosing increased sulfite reduction in freshwater peat soils and decreased methylotrophy in brackish peat soils. These findings add to the understanding of microbiomes by demonstrating how changes in soil qualities impact communities both before and after a disturbance such as saltwater intrusion.
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Affiliation(s)
- Deidra Jordan
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- International Forensic Research Institute, Florida International University, Miami, FL 33199, USA
| | - John S Kominoski
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Institute of the Environment, Florida International University, Miami, FL 33199, USA
| | - Shelby Servais
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Institute of the Environment, Florida International University, Miami, FL 33199, USA
| | - DeEtta Mills
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- International Forensic Research Institute, Florida International University, Miami, FL 33199, USA
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García-Maldonado JQ, Latisnere-Barragán H, Escobar-Zepeda A, Cadena S, Ramírez-Arenas PJ, Vázquez-Juárez R, Rojas-Contreras M, López-Cortés A. Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities. Microorganisms 2023; 11:microorganisms11030812. [PMID: 36985385 PMCID: PMC10059902 DOI: 10.3390/microorganisms11030812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023] Open
Abstract
Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.
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Affiliation(s)
- José Q García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida 97310, Yucatán, Mexico
| | - Hever Latisnere-Barragán
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | | | - Santiago Cadena
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Patricia J Ramírez-Arenas
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Ricardo Vázquez-Juárez
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Maurilia Rojas-Contreras
- Departamento de Agronomía, Universidad Autónoma de Baja California Sur, La Paz 23080, Baja California Sur, Mexico
| | - Alejandro López-Cortés
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
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Abstract
Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.
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Affiliation(s)
| | - Dongying Wu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Obregon Alvarez D, Fonseca de Souza L, Mendes LW, de Moraes MT, Tosi M, Venturini AM, Meyer KM, Barbosa de Camargo P, Bohannan BJM, Mazza Rodrigues JL, Dunfield KE, Tsai SM. Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin. Mol Ecol 2023. [PMID: 36896778 DOI: 10.1111/mec.16912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.
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Affiliation(s)
- Dasiel Obregon Alvarez
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | | | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Kyle M Meyer
- Department of Integrative Biology, University of California-Berkeley, Berkeley, California, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | | | | | - Jorge L Mazza Rodrigues
- Department of Land, Air, and Water Resources, University of California-Davis, Davis, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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Downing BE, Gupta D, Nayak DD. The dual role of a multi-heme cytochrome in methanogenesis: MmcA is important for energy conservation and carbon metabolism in Methanosarcina acetivorans. Mol Microbiol 2023; 119:350-363. [PMID: 36660820 DOI: 10.1111/mmi.15029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
Methanogenic archaea belonging to the Order Methanosarcinales conserve energy using an electron transport chain (ETC). In the genetically tractable strain Methanosarcina acetivorans, ferredoxin donates electrons to the ETC via the Rnf (Rhodobacter nitrogen fixation) complex. The Rnf complex in M. acetivorans, unlike its counterpart in Bacteria, contains a multiheme c-type cytochrome (MHC) subunit called MmcA. Early studies hypothesized MmcA is a critical component of Rnf, however recent work posits that the primary role of MmcA is facilitating extracellular electron transport. To explore the physiological role of MmcA, we characterized M. acetivorans mutants lacking either the entire Rnf complex (∆mmcA-rnf) or just the MmcA subunit (∆mmcA). Our data show that MmcA is essential for growth during acetoclastic methanogenesis but neither Rnf nor MmcA is required for methanogenic growth on methylated compounds. On methylated compounds, the absence of MmcA alone leads to a more severe growth defect compared to a Rnf deletion likely due to different strategies for ferredoxin oxidation that arise in each strain. Transcriptomic data suggest that the ∆mmcA mutant might oxidize ferredoxin by upregulating the cytosolic Wood-Ljundahl pathway for acetyl-CoA synthesis, whereas the ∆mmcA-rnf mutant may repurpose the F420 dehydrogenase complex (Fpo) to oxidize ferredoxin coupled to proton translocation. Beyond energy conservation, the deletion of rnf or mmcA leads to global transcriptional changes of genes involved in methanogenesis, carbon assimilation and regulation. Overall, our study provides systems-level insights into the non-overlapping roles of the Rnf bioenergetic complex and the associated MHC, MmcA.
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Affiliation(s)
- Blake E Downing
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Dinesh Gupta
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Dipti D Nayak
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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Dick JM, Boyer GM, Canovas PA, Shock EL. Using thermodynamics to obtain geochemical information from genomes. Geobiology 2023; 21:262-273. [PMID: 36376996 DOI: 10.1111/gbi.12532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Thermodynamic characterization of the relative stabilities of chemical compounds is a pillar of conceptual models in various fields of geosciences. Analogous models applied to genomes can yield new information about the relationship between genomes and their geochemical environments. In this perspective article, we present a chemical and thermodynamic analysis of prokaryotic lineages that have been the target of previous phylogenomic studies of evolutionary adaptation to varying redox conditions. The thermodynamic model development begins by quantifying the effects of hydrogen activity (aH2 ) and temperature on the relative stabilities of organic compounds with different carbon oxidation state. When applied to proteins instead of metabolites, the same techniques can be used to identify combinations of aH2 and temperature at which reference proteomes for Class I or Class II methanogens are relatively stable. The calculated aH2 values are compatible with reported measurements for habitats of methanogens ranging from highly reducing submarine hydrothermal systems to less reducing environments including methanogenic sediments. In contrast to the transition between the two classes of methanogenic archaea, that between basal and terrestrial groups of Thaumarchaeota (denoting the origin of ammonia-oxidizing archaea) occurs at a less-reducing redox boundary. These examples reveal the consequences of energy minimization driving evolution and show how geochemical calculations involving biomolecules can be used to quantify and better understand the coevolution of the geosphere and biosphere.
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Affiliation(s)
- Jeffrey M Dick
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, China
| | - Grayson M Boyer
- School of Earth & Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Peter A Canovas
- School of Earth & Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Everett L Shock
- School of Earth & Space Exploration, Arizona State University, Tempe, Arizona, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
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Iqbal MF, Zhang Y, Kong P, Wang Y, Cao K, Zhao L, Xiao X, Fan X. High-yielding nitrate transporter cultivars also mitigate methane and nitrous oxide emissions in paddy. Front Plant Sci 2023; 14:1133643. [PMID: 36909410 PMCID: PMC9992815 DOI: 10.3389/fpls.2023.1133643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Development of high yield rice varieties is critical to ensuring global food security. However, the emission of greenhouse gases (GHG) such as Methane (CH4) and Nitrous oxide (N2O) from paddy fields threatens environmental sustainability. In this study, we selected overexpressed high-affinity nitrate transporters (NRT2.3 along with their partner protein NAR2.1) cultivars, which are effective nitrogen use efficient transgenic lines pOsNAR2.1: OsNAR2.1 (Ox2) and p35S:OsNRT2.3b (O8). We used high (270 kg N/ha) and low (90 kg N/ha) nitrogen (N) fertilizers in paddy fields to evaluate morphophysiological traits, including GHG emission. We found that Ox2 and O8 reduced CH4 emissions by 40% and 60%, respectively, compared to their wild type (WT). During growth stages, there was no consistent N2O discharge pattern between WT and transgenics (Ox2, O8) in low and high N application. However, total cumulative N2O in a cropping season reduced in O8 and increased in Ox2 cultivars, compared to WT. Root aerenchyma formation reduced by 30-60% in transgenic lines. Methanogens like mcrA in low and high N were also reduced by up to 50% from rhizosphere of Ox2 and O8. However, the nitrifying bacterial population such as nosZ reduced in both transgenics significantly, but nirK and nirS did not show a consistent variation. The high yield of transgenic rice with limited aerenchyma mitigates the discharge of CH4 and N2O by reducing root exudates that provide substrates for GHG. Our results improve understanding for breeders to serve the purpose of sustainable development.
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Affiliation(s)
- Muhammad Faseeh Iqbal
- National Key Laboratory of Crop Genetics, Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice improvement, Nanjing, China
| | - Pulin Kong
- National Key Laboratory of Crop Genetics, Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yulong Wang
- National Key Laboratory of Crop Genetics, Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Kaixun Cao
- College of Resource and Environment, Anhui Science and Technology University, Chuzhou, China
| | - Limei Zhao
- National Key Laboratory of Crop Genetics, Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin Xiao
- College of Resource and Environment, Anhui Science and Technology University, Chuzhou, China
- College of Resource and Environment, Anqing Normal University, Anqing, China
| | - Xiaorong Fan
- National Key Laboratory of Crop Genetics, Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Zhongshan Biological Breeding Laboratory, Nanjing, China
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Dzofou Ngoumelah D, Kuchenbuch A, Harnisch F, Kretzschmar J. Combining Geobacter spp. Dominated Biofilms and Anaerobic Digestion Effluents─The Effect of Effluent Composition and Electrode Potential on Biofilm Activity and Stability. Environ Sci Technol 2023; 57:2584-2594. [PMID: 36731122 DOI: 10.1021/acs.est.2c07574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The combination of anaerobic digestion (AD) and microbial electrochemical technologies (METs) offers different opportunities to increase the efficiency and sustainability of AD processes. However, methanogenic archaea and/or particles may partially hinder combining MET and AD processes. Furthermore, it is unclear if the applied anode potential affects the activity and efficiency of electroactive microorganisms in AD-MET combinations as it is described for more controlled experimental conditions. In this study, we confirm that 6-week-old Geobacter spp. dominated biofilms are by far more active and stable in AD-effluents than 3-week-old Geobacter spp. dominated biofilms. Furthermore, we show that the biofilms are twice as active at -0.2 V compared to 0.4 V, even under challenging conditions occurring in AD-MET systems. Paired-end amplicon sequencing at the DNA level using 16S-rRNA and mcrA gene shows that hydrogenotrophic methanogens incorporate into biofilms immersed in AD-effluent without any negative effect on biofilm stability and electrochemical activity.
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Affiliation(s)
- Daniel Dzofou Ngoumelah
- Department of Biochemical Conversion, DBFZ Deutsches Biomasseforschungszentrum gemeinnützige GmbH (German Biomass Research Centre), Leipzig04347, Saxony, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig04318, Saxony, Germany
| | - Anne Kuchenbuch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig04318, Saxony, Germany
| | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig04318, Saxony, Germany
| | - Jörg Kretzschmar
- Department of Biochemical Conversion, DBFZ Deutsches Biomasseforschungszentrum gemeinnützige GmbH (German Biomass Research Centre), Leipzig04347, Saxony, Germany
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Fu L, Lai S, Zhou Z, Chen Z, Cheng L. Seasonal variation of microbial community and methane metabolism in coalbed water in the Erlian Basin, China. Front Microbiol 2023; 14:1114201. [PMID: 36846781 PMCID: PMC9953142 DOI: 10.3389/fmicb.2023.1114201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
Coalbed water is a semi-open system connecting underground coalbeds with the external environment. Microorganisms in coalbed water play an important role in coal biogasification and the carbon cycle. The community assemblages of microorganisms in such a dynamic system are not well understood. Here, we used high-throughput sequencing and metagenomic analysis to investigate microbial community structure and identify the potential functional microorganisms involved in methane metabolism in coalbed water in the Erlian Basin, a preferred low-rank coal bed methane (CBM) exploration and research area in China. The results showed that there were differences in the responses of bacteria and archaea to seasonal variation. Bacterial community structure was affected by seasonal variation but archaea was not. Methane oxidation metabolism dominated by Methylomonas and methanogenesis metabolism dominated by Methanobacterium may exist simultaneously in coalbed water.
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Affiliation(s)
- Li Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Shouchao Lai
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Zhuo Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Zhenhong Chen
- Research Institute of Petroleum Exploration and Development, Beijing, China,*Correspondence: Zhenhong Chen, ✉
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China,Lei Cheng, ✉
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Méndez G, Trueba G, Sierra-Alvarez R, Ochoa-Herrera V. Treatment of acid rock drainage using a sulphate-reducing bioreactor with a limestone precolumn. Environ Technol 2023; 44:185-196. [PMID: 34380378 DOI: 10.1080/09593330.2021.1968039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Sulphate reducing bacteria (SRB) offer promise for the treatment of mine waste due to their effectiveness removing toxic heavy metals as highly insoluble metal sulphides and their ability to generate alkalinity. The main objective of this study was to develop a treatment composed of a sulphate-reducing bioreactor with a limestone precolumn for the removal of Cu(II) from a synthetic ARD. The purpose of the limestone column was to increase the pH values and decrease the level of Cu in the effluent to prevent SRB inhibition. The system was fed with a pH-2.7 synthetic ARD containing Cu(II) (10-40 mg/L), sulphate (2000 mg/L) and acetate (2.5 g COD/L) for 150 days. Copper removal efficiencies in the two-stage system were very high (95-99%), with a final concentration of 0.53 mg/L Cu, and almost complete removal occurred in the limestone precolumn. In the same manner, the acidity of the synthetic ARD was effectively reduced in the limestone precolumn to 7.3 and the pH was raised in the bioreactor (7.3-8.0). COD consumption by methanogens was predominant from day 0-118, but SRB dominated at the end of the experiment (day 150) when the average COD removal and sulphide production were 74.8% and 61.7%, respectively. Study of the microbial taxonomic composition in the bioreactor revealed that Methanosarcina and Methanosaeta were the most prevalent methanogens while the genera Desulfotomaculum and Syntrophobacter were the dominant SRB. Among the SRB identified Desulfotomaculum intricatum (99% identity) and Desulfotomaculum acetoxidans (96%) were the most abundant sequences of bacteria capable of using acetate.
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Affiliation(s)
- Gabriela Méndez
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
- Colegio de Ciencias e Ingenierías, Instituto Biósfera, Universidad San Francisco de Quito, Quito, Ecuador
| | - Gabriel Trueba
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, The University of Arizona, Tucson, AZ, USA
| | - Valeria Ochoa-Herrera
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
- Colegio de Ciencias e Ingenierías, Instituto Biósfera, Universidad San Francisco de Quito, Quito, Ecuador
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
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Maslać N, Sidhu C, Teeling H, Wagner T. Comparative Transcriptomics Sheds Light on Remodeling of Gene Expression during Diazotrophy in the Thermophilic Methanogen Methanothermococcus thermolithotrophicus. mBio 2022; 13:e0244322. [PMID: 36409126 DOI: 10.1128/mbio.02443-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Some marine thermophilic methanogens are able to perform energy-consuming nitrogen fixation despite deriving only little energy from hydrogenotrophic methanogenesis. We studied this process in Methanothermococcus thermolithotrophicus DSM 2095, a methanogenic archaeon of the order Methanococcales that contributes to the nitrogen pool in some marine environments. We successfully grew this archaeon under diazotrophic conditions in both batch and fermenter cultures, reaching the highest cell density reported so far. Diazotrophic growth depended strictly on molybdenum and, in contrast to other diazotrophs, was not inhibited by tungstate or vanadium. This suggests an elaborate control of metal uptake and a specific metal recognition system for the insertion into the nitrogenase cofactor. Differential transcriptomics of M. thermolithotrophicus grown under diazotrophic conditions with ammonium-fed cultures as controls revealed upregulation of the nitrogenase machinery, including chaperones, regulators, and molybdate importers, as well as simultaneous upregulation of an ammonium transporter and a putative pathway for nitrate and nitrite utilization. The organism thus employs multiple synergistic strategies for uptake of nitrogen nutrients during the early exponential growth phase without altering transcription levels for genes involved in methanogenesis. As a counterpart, genes coding for transcription and translation processes were downregulated, highlighting the maintenance of an intricate metabolic balance to deal with energy constraints and nutrient limitations imposed by diazotrophy. This switch in the metabolic balance included unexpected processes, such as upregulation of the CRISPR-Cas system, probably caused by drastic changes in transcription levels of putative mobile and virus-like elements. IMPORTANCE The thermophilic anaerobic archaeon M. thermolithotrophicus is a particularly suitable model organism to study the coupling of methanogenesis to diazotrophy. Likewise, its capability of simultaneously reducing N2 and CO2 into NH3 and CH4 with H2 makes it a viable target for biofuel production. We optimized M. thermolithotrophicus cultivation, resulting in considerably higher cell yields and enabling the successful establishment of N2-fixing bioreactors. Improved understanding of the N2 fixation process would provide novel insights into metabolic adaptations that allow this energy-limited extremophile to thrive under diazotrophy, for instance, by investigating its physiology and uncharacterized nitrogenase. We demonstrated that diazotrophic growth of M. thermolithotrophicus is exclusively dependent on molybdenum, and complementary transcriptomics corroborated the expression of the molybdenum nitrogenase system. Further analyses of differentially expressed genes during diazotrophy across three cultivation time points revealed insights into the response to nitrogen limitation and the coordination of core metabolic processes.
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Abstract
Methanogens are anaerobic archaea which conserve energy by producing methane. Found in nearly every anaerobic environment on earth, methanogens serve important roles in ecology as key organisms of the global carbon cycle, and in industry as a source of renewable biofuels. Environmentally, methanogenic archaea play an essential role in the reintroducing unavailable carbon to the carbon cycle by anaerobically converting low-energy, terminal metabolic degradation products such as one and two-carbon molecules into methane which then returns to the aerobic portion of the carbon cycle. In industry, methanogens are commonly used as an inexpensive source of renewable biofuels as well as serving as a vital component in the treatment of wastewater though this is only the tip of the iceberg with respect to their metabolic potential. In this review we will discuss how the efficient central metabolism of methanoarchaea could be harnessed for future biotechnology applications.
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Yue Y, Wang F, Pan J, Chen XP, Tang Y, Yang Z, Ma J, Li M, Yang M. Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load. FEMS Microbiol Ecol 2022; 98:6701916. [PMID: 36111740 DOI: 10.1093/femsec/fiac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/16/2022] [Accepted: 09/14/2022] [Indexed: 01/21/2023] Open
Abstract
Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.
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Affiliation(s)
- Yihong Yue
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Fushun Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Xue-Ping Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Yi Tang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Zhihong Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jing Ma
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
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Spietz RL, Payne D, Szilagyi R, Boyd ES. Reductive biomining of pyrite by methanogens. Trends Microbiol 2022; 30:1072-1083. [PMID: 35624031 DOI: 10.1016/j.tim.2022.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/13/2023]
Abstract
Pyrite (FeS2) is the most abundant iron sulfide mineral in Earth's crust. Until recently, FeS2 has been considered a sink for iron (Fe) and sulfur (S) at low temperature in the absence of oxygen or oxidative weathering, making these elements unavailable to biology. However, anaerobic methanogens can transfer electrons extracellularly to reduce FeS2 via direct contact with the mineral. Reduction of FeS2 occurs through a multistep process that generates aqueous sulfide (HS-) and FeS2-associated pyrrhotite (Fe1-xS). Subsequent dissolution of Fe1-xS provides Fe(II)(aq), but not HS-, that rapidly complexes with HS-(aq) generated from FeS2 reduction to form soluble iron sulfur clusters [nFeS(aq)]. Cells assimilate nFeS(aq) to meet Fe/S nutritional demands by mobilizing and hyperaccumulating Fe and S from FeS2. As such, reductive dissolution of FeS2 by methanogens has important implications for element cycling in anoxic habitats, both today and in the geologic past.
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Affiliation(s)
- Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Robert Szilagyi
- Department of Chemistry, University of British Columbia - Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA.
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Min BR, Willis W, Casey K, Castleberry L, Waldrip H, Parker D. Condensed and Hydrolyzable Tannins for Reducing Methane and Nitrous Oxide Emissions in Dairy Manure-A Laboratory Incubation Study. Animals (Basel) 2022; 12. [PMID: 36290258 DOI: 10.3390/ani12202876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
The objectives of this study were to (1) examine the effects of plant condensed (CT) and hydrolyzable tannin (HT) extracts on CH4 and N2O emissions; (2) identify the reactions responsible for manure-derived GHG emissions, and (3) examine accompanying microbial community changes in fresh dairy manure. Five treatments were applied in triplicate to the freshly collected dairy manure, including 4% CT, 8% CT, 4% HT, 8% HT (V/V), and control (no tannin addition). Fresh dairy manure was placed into 710 mL glass incubation chambers. In vitro composted dairy manure samples were collected at 0, 24, 48, and 336 h after the start of incubation. Fluxes of N2O and CH4 were measured for 5-min/h for 14 d at a constant ambient incubation temperature of 39 °C. The addition of quebracho CT significantly decreased the CH4 flux rates compared to the tannin-free controls (215.9 mg/m2/h), with peaks of 75.6 and 89.6 mg/m2/h for 4 and 8% CT inclusion rates, respectively. Furthermore, CT significantly reduced cumulative CH4 emission by 68.2 and 57.3% at 4 and 8% CT addition, respectively. The HT treatments failed to affect CH4 reduction. However, both CT and HT reduced (p < 0.001) cumulative and flux rates of N2O emissions. The decrease in CH4 flux with CT was associated with a reduction in the abundance of Bacteroidetes and Proteobacteria.
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