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He G, Chen G, Xie Y, Swift CM, Ramirez D, Cha G, Konstantinidis KT, Radosevich M, Löffler FE. Sustained bacterial N 2O reduction at acidic pH. Nat Commun 2024; 15:4092. [PMID: 38750010 PMCID: PMC11096178 DOI: 10.1038/s41467-024-48236-x] [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: 01/12/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
Nitrous oxide (N2O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N2O to dinitrogen (N2) is the major consumption process but microbial N2O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N2O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N2O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N2O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N2O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N2O reduction between pH 4.5 and 6, highlighting microbial N2O reduction potential in acidic soils.
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Affiliation(s)
- Guang He
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Gao Chen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Yongchao Xie
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Cynthia M Swift
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Diana Ramirez
- Department of Microbiology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Frank E Löffler
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Department of Microbiology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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Egas RA, Kurth JM, Boeren S, Sousa DZ, Welte CU, Sánchez-Andrea I. A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans. mSystems 2024; 9:e0096723. [PMID: 38323850 PMCID: PMC10949509 DOI: 10.1128/msystems.00967-23] [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: 09/09/2023] [Accepted: 12/25/2023] [Indexed: 02/08/2024] Open
Abstract
The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.
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Affiliation(s)
- Reinier A. Egas
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Julia M. Kurth
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Microcosm Earth Centre, Philipps-Universität Marburg & Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Cornelia U. Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Department of Environmental Sciences for Sustainability, IE University, Segovia, Spain
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Cuevas M, Francisco I, Díaz-González F, Diaz M, Quatrini R, Beamud G, Pedrozo F, Temporetti P. Nutrient structure dynamics and microbial communities at the water-sediment interface in an extremely acidic lake in northern Patagonia. Front Microbiol 2024; 15:1335978. [PMID: 38410393 PMCID: PMC10895001 DOI: 10.3389/fmicb.2024.1335978] [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: 11/09/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024] Open
Abstract
Lake Caviahue (37° 50 'S and 71° 06' W; Patagonia, Argentina) is an extreme case of a glacial, naturally acidic, aquatic environment (pH ~ 3). Knowledge of the bacterial communities in the water column of this lake, is incipient, with a basal quantification of the bacterioplankton abundance distribution in the North and South Basins of Lake Caviahue, and the described the presence of sulfur and iron oxidizing bacteria in the lake sediments. The role that bacterioplankton plays in nutrient utilization and recycling in this environment, especially in the phosphorus cycle, has not been studied. In this work, we explore this aspect in further depth by assessing the diversity of pelagic, littoral and sediment bacteria, using state of the art molecular methods and identifying the differences and commonalties in the composition of the cognate communities. Also, we investigate the interactions between the sediments of Lake Caviahue and the microbial communities present in both sediments, pore water and the water column, to comprehend the ecological relationships driving nutrient structure and fluxes, with a special focus on carbon, nitrogen, and phosphorus. Two major environmental patterns were observed: (a) one distinguishing the surface water samples due to temperature, Fe2+, and electrical conductivity, and (b) another distinguishing winter and summer samples due to the high pH and increasing concentrations of N-NH4+, DOC and SO42-, from autumn and spring samples with high soluble reactive phosphorus (SRP) and iron concentrations. The largest bacterial abundance was found in autumn, alongside higher levels of dissolved phosphorus, iron forms, and increased conductivity. The highest values of bacterial biomass were found in the bottom strata of the lake, which is also where the greatest diversity in microbial communities was found. The experiments using continuous flow column microcosms showed that microbial growth over time, in both the test and control columns, was accompanied by a decrease in the concentration of dissolved nutrients (SRP and N-NH4+), providing proof that sediment microorganisms are active and contribute significantly to nutrient utilization/mobilization.
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Affiliation(s)
- Mayra Cuevas
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
| | - Issotta Francisco
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Department of Molecular Genetics and Microbiology, School of Biological Sciences, P. Universidad Católica de Chile, Santiago, Chile
| | - Fernando Díaz-González
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Mónica Diaz
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
| | - Raquel Quatrini
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Guadalupe Beamud
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
| | - Fernando Pedrozo
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
| | - Pedro Temporetti
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
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Babich TL, Popova NM, Sokolova DS, Perepelov AV, Safonov AV, Nazina TN. Microbial and Monosaccharide Composition of Biofilms Developing on Sandy Loams from an Aquifer Contaminated with Liquid Radioactive Waste. Microorganisms 2024; 12:275. [PMID: 38399679 PMCID: PMC10892373 DOI: 10.3390/microorganisms12020275] [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: 01/05/2024] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The development of microbial biofilms increases the survival of microorganisms in the extreme conditions of ecosystems contaminated with components of liquid radioactive waste (LRW) and may contribute to the successful bioremediation of groundwater. The purpose of this work was to compare the composition of the microorganisms and the exopolysaccharide matrix of the biofilms formed on sandy loams collected at the aquifer from a clean zone and from a zone with nitrate and radionuclide contamination. The aquifer is polluted from the nearby surface repository for liquid radioactive waste (Russia). The phylogenetic diversity of prokaryotes forming biofilms on the sandy loams' surface was determined during 100 days using high-throughput sequencing of the V4 region of the 16S rRNA genes. Scanning electron microscopy was used to study the development of microbial biofilms on the sandy loams. The ratio of proteins and carbohydrates in the biofilms changed in the course of their development, and the diversity of monosaccharides decreased, depending on the contamination of the sites from which the rocks were selected. The presence of pollution affects biofilm formation and EPS composition along with the dominant taxa of microorganisms and their activity. Biofilms establish a concentration gradient of the pollutant and allow the microorganisms involved to effectively participate in the reduction of nitrate and sulfate; they decrease the risk of nitrite accumulation during denitrification and suppress the migration of radionuclides. These biofilms can serve as an important barrier in underground water sources, preventing the spread of pollution. Pure cultures of microorganisms capable of forming a polysaccharide matrix and reducing nitrate, chromate, uranyl, and pertechnetate ions were isolated from the biofilms, which confirmed the possibility of their participation in the bioremediation of the aquifer from nonradioactive waste components and the decrease in the radionuclides' migration.
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Affiliation(s)
- Tamara L. Babich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (T.L.B.); (D.S.S.)
| | - Nadezhda M. Popova
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (N.M.P.); (A.V.S.)
| | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (T.L.B.); (D.S.S.)
| | - Andrei V. Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia;
| | - Alexey V. Safonov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (N.M.P.); (A.V.S.)
| | - Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (T.L.B.); (D.S.S.)
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Rios-Valenciana EE, Moreno-Perlin T, Briones-Gallardo R, Sierra-Alvarez R, Celis LB. The key role of biogenic arsenic sulfides in the removal of soluble arsenic and propagation of arsenic mineralizing communities. Environ Res 2023; 220:115124. [PMID: 36563982 DOI: 10.1016/j.envres.2022.115124] [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: 07/13/2022] [Revised: 12/04/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Biogeochemical processes govern the transport and availability of arsenic in sediments. However, little is known about the transition from indigenous communities to cultivable consortia when exposed to high arsenic concentrations. Such cultivable communities could be exploited for arsenic bioremediation of waste streams and polluted sites. Thus, it is crucial to understand the dynamics and selective pressures that shape the communities during the development of customized bacterial consortia. First, from the arsenic partitioning of two sediments with high arsenic concentrations, we found that up to 55% of arsenic was bioavailable because it was associated with the soluble, carbonate, and ionically exchangeable fractions. Next, we prepared sediment enrichment cultures under arsenate- and sulfate-reducing conditions to precipitate arsenic sulfide biominerals and analyze the communities. The produced biominerals were used as the inoculum to develop bacterial consortia via successive transfers. Tracking of the 16S rRNA gene in the fresh sediments, sediment enrichments, biogenic minerals, and bacterial consortia revealed differences in the bacterial communities. Removing the sediment caused a substantial decrease in diversity and shifts toward the dominance of the Firmicutes phylum to the detriment of Proteobacteria. In agreement with the 16S rRNA gene results, the sequencing of the arrA gene confirmed the presence of phylotypes closely related to Desulfosporosinus sp. Y5 (100% similarity), highlighting the pivotal role of this genus in the removal of soluble arsenic. Here, we demonstrated for the first time that besides being important as arsenic sinks, the biogenic arsenic sulfide minerals are reservoirs of arsenic resistant/respiring bacteria and can be used to culture them.
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Affiliation(s)
- Erika E Rios-Valenciana
- División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, Camino a La Presa San José 2055, Lomas 4a. Sección, 78216, San Luis Potosí, SLP, Mexico
| | - Tonatiuh Moreno-Perlin
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma Del Estado de Morelos, Avenida Universidad 1001, Chamilpa, 62210, Cuernavaca, Mor, Mexico
| | - Roberto Briones-Gallardo
- Facultad de Ingeniería-Instituto de Metalurgia, Universidad Autónoma de San Luis Potosí, Sierra Leona 550, Lomas 2a. Sección, 78216, San Luis Potosí, SLP, Mexico
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, The University of Arizona, P.O. Box 210011, Tucson, AZ, 85721, USA
| | - Lourdes B Celis
- División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, Camino a La Presa San José 2055, Lomas 4a. Sección, 78216, San Luis Potosí, SLP, Mexico.
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6
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Ayala-Muñoz D, Burgos WD, Sánchez-España J, Falagán C, Couradeau E, Macalady JL. Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake. Front Bioeng Biotechnol 2022; 10:867321. [PMID: 35910036 PMCID: PMC9326234 DOI: 10.3389/fbioe.2022.867321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes (MAGs) representing the most abundant populations. None of the MAGs were closely related to either cultured or non-cultured organisms from the Genome Taxonomy or NCBI databases (none with average nucleotide identity >95%). Despite oxygen concentrations that are consistently below detection in the deep layer, some archaeal and bacterial MAGs mapped transcripts of genes for sulfide oxidation coupled with oxygen reduction. Among these microaerophilic sulfide oxidizers, mixotrophic Thermoplasmatales archaea were the most numerous and represented 24% of the total community. Populations associated with the highest predicted in situ activity for sulfate reduction were affiliated with Actinobacteria, Chloroflexi, and Nitrospirae phyla, and together represented about 9% of the total community. These MAGs, in addition to a less abundant Proteobacteria MAG in the genus Desulfomonile, contained transcripts of genes in the Wood-Ljungdahl pathway. All MAGs had significant genetic potential for organic carbon oxidation. Our results indicate that novel acidophiles are contributing to biosulfidogenesis in the deep layer of Cueva de la Mora, and that in situ sulfide production is limited by organic carbon availability and sulfur oxidation.
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Affiliation(s)
- Diana Ayala-Muñoz
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, United States
- *Correspondence: Diana Ayala-Muñoz, ; Jennifer L. Macalady,
| | - William D. Burgos
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, United States
| | | | - Carmen Falagán
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Estelle Couradeau
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, United States
| | - Jennifer L. Macalady
- Department of Geosciences, The Pennsylvania State University, University Park, PA, United States
- *Correspondence: Diana Ayala-Muñoz, ; Jennifer L. Macalady,
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Sánchez-Andrea I, van der Graaf CM, Hornung B, Bale NJ, Jarzembowska M, Sousa DZ, Rijpstra WIC, Sinninghe Damsté JS, Stams AJM. Acetate Degradation at Low pH by the Moderately Acidophilic Sulfate Reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov. Front Microbiol 2022; 13:816605. [PMID: 35391737 PMCID: PMC8982180 DOI: 10.3389/fmicb.2022.816605] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/31/2022] [Indexed: 11/19/2022] Open
Abstract
In acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acidotolerant. Here, a novel species within a novel genus of moderately acidophilic SRB is described, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, able to grow at pH 3.8. Bioreactor studies with strain INE at optimum (5.0) and low (3.9) pH for growth showed that strain INE alkalinized its environment, and that this was more pronounced at lower pH. These studies also showed the capacity of strain INE to completely oxidize organic acids to CO2, which is uncommon among acidophilic SRB. Since organic acids are mainly in their protonated form at low pH, which increases their toxicity, their complete oxidation may be an acid stress resistance mechanism. Comparative proteogenomic and membrane lipid analysis further indicated that the presence of saturated ether-bound lipids in the membrane, and their relative increase at lower pH, was a protection mechanism against acid stress. Interestingly, other canonical acid stress resistance mechanisms, such as a Donnan potential and increased active charge transport, did not appear to be active.
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Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Irene Sánchez-Andrea,
| | | | - Bastian Hornung
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Monika Jarzembowska
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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Sato Y, Hamai T, Hori T, Aoyagi T, Inaba T, Hayashi K, Kobayashi M, Sakata T, Habe H. Optimal start-up conditions for the efficient treatment of acid mine drainage using sulfate-reducing bioreactors based on physicochemical and microbiome analyses. J Hazard Mater 2022; 423:127089. [PMID: 34560478 DOI: 10.1016/j.jhazmat.2021.127089] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/30/2021] [Revised: 07/29/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
Typically, sulfate-reducing bioreactors used to treat acid mine drainage (AMD) undergo an initial incubation period of a few weeks to acclimatize sulfate-reducing bacteria (SRB), although necessity of this preincubation has rarely been evaluated. To reduce time and economic cost, we developed an SRB acclimatization method using the continuous flow of AMD into bioreactors fed with rice bran, and compared with the conventional acclimatization method. We found that the SRB sufficiently acclimatized without the preincubation phase. Furthermore, we examined the performance and SRB communities in bioreactors operated for >200 days under seven different conditions, in which the amount of rice bran added and hydraulic retention times (HRTs) were varied. A comparison of the various bioreactor conditions revealed that the lowest rice bran amount (50 g) and the shortest HRT (6 h) caused a deterioration in reactor performance after day 144 and 229, respectively. In both cases, relatively aerobic environments developed due to the lack of organic matter seemed to inhibit sulfate reduction. Of the conditions tested, operation of the bioreactors with 200 g of rice bran and an HRT of 12.5 h was the most effective in treating AMD, showing a sulfate reduction rate of 20.7-77.9% during days 54-242. DATA AND MATERIALS AVAILABILITY: All data needed to evaluate the conclusions of this study are presented in the paper and/or the appendix.
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Affiliation(s)
- Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Takaya Hamai
- Japan Oil, Gas and Metals National Corporation (JOGMEC), 2-10-1 Toranomon, Minato-ku, Tokyo 105-0001, Japan.
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Kentaro Hayashi
- Metals Technology Center, Japan Oil, Gas and Metals National Corporation (JOGMEC), 9-3 Furudate, Kosaka-kozan, Kosaka, Akita 017-0202, Japan
| | - Mikio Kobayashi
- Japan Oil, Gas and Metals National Corporation (JOGMEC), 2-10-1 Toranomon, Minato-ku, Tokyo 105-0001, Japan
| | - Takeshi Sakata
- Metals Technology Center, Japan Oil, Gas and Metals National Corporation (JOGMEC), 9-3 Furudate, Kosaka-kozan, Kosaka, Akita 017-0202, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
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Panova IA, Ikkert O, Avakyan MR, Kopitsyn DS, Mardanov AV, Pimenov NV, Shcherbakova VA, Ravin NV, Karnachuk OV. Desulfosporosinus metallidurans sp. nov., an acidophilic, metal-resistant sulfate-reducing bacterium from acid mine drainage. Int J Syst Evol Microbiol 2021; 71. [PMID: 34255623 DOI: 10.1099/ijsem.0.004876] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, spore-forming, acidophilic and metal-resistant sulfate-reducing bacterium, strain OLT, was isolated from a microbial mat in a tailing dam at a gold ore mining site. Cells were slightly curved immotile rods, 0.5 µm in diameter and 2.0-3.0 µm long. Cells were stained Gram-negative, despite the Gram-positive cell structure revealed by electron microscopy of ultrathin layers. OLT grew at pH 4.0-7.0 with an optimum at 5.5. OLT utilised H2, lactate, pyruvate, malate, formate, propionate, ethanol, glycerol, glucose, fructose, sucrose, peptone and tryptone as electron donors for sulfate reduction. Sulfate, sulfite, thiosulfate, nitrate and fumarate were used as electron acceptors in the presence of lactate. Elemental sulfur, iron (III), and arsenate did not serve as electron acceptors. The major cellular fatty acids were C16:1ω7c (39.0 %) and C16 : 0 (12.1 %). The draft genome of OLT was 5.29 Mb in size and contained 4909 protein-coding genes. The 16S rRNA gene sequence placed OLT within the phylum Firmicutes, class Clostridia, family Peptococcaceae, genus Desulfosporosinus. Desulfosporosinus nitroreducens 59.4BT was the closest relative with 97.6 % sequence similarity. On the basis of phenotypic and phylogenetic characteristics, strain OLT represents a novel species within the genus Desulfosporosinus, for which we propose the name Desulfosporosinus metallidurans sp. nov. with the type strain OLT (=DSM 104464T=VKM В-3021T).
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Affiliation(s)
- Inna A Panova
- Laboratory of Molecular Biology and Biochemistry, Tomsk State University, Tomsk 634050, Russia
| | - Olga Ikkert
- Laboratory of Molecular Biology and Biochemistry, Tomsk State University, Tomsk 634050, Russia
| | - Marat R Avakyan
- Laboratory of Molecular Biology and Biochemistry, Tomsk State University, Tomsk 634050, Russia
| | | | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Viktoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research, Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Olga V Karnachuk
- Laboratory of Molecular Biology and Biochemistry, Tomsk State University, Tomsk 634050, Russia
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10
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Flynn TM, Antonopoulos DA, Skinner KA, Brulc JM, Johnston E, Boyanov MI, Kwon MJ, Kemner KM, O’Loughlin EJ. Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment. PLoS One 2021; 16:e0251883. [PMID: 34014980 PMCID: PMC8136678 DOI: 10.1371/journal.pone.0251883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/04/2021] [Indexed: 11/19/2022] Open
Abstract
Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of FeIII reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory FeIII-reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly “sulfate-reducing” phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions.
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Affiliation(s)
- Theodore M. Flynn
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | | | - Kelly A. Skinner
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Jennifer M. Brulc
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Eric Johnston
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Maxim I. Boyanov
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Man Jae Kwon
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
- Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea
| | - Kenneth M. Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Edward J. O’Loughlin
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
- * E-mail:
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11
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Panova IA, Grigoriev MA, Glukhova LB, Avakyan MR, Karnachuk OV. Isolation of a Novel Chemolithothrophic Sulfate-Reducing Firmicute from a Tyumen Thermal Borehole. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Aoyagi T, Mori Y, Nanao M, Matsuyama Y, Sato Y, Inaba T, Aizawa H, Hayakawa T, Moriya M, Higo Y, Habe H, Hori T. Effective Se reduction by lactate-stimulated indigenous microbial communities in excavated waste rocks. J Hazard Mater 2021; 403:123908. [PMID: 33264961 DOI: 10.1016/j.jhazmat.2020.123908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/16/2020] [Revised: 08/13/2020] [Accepted: 09/04/2020] [Indexed: 06/12/2023]
Abstract
Waste rocks generated from tunnel excavation contain the metalloid selenium (Se) and its concentration sometimes exceeds the environmental standards. The possibility and effectiveness of dissolved Se removal by the indigenous microorganisms are unknown. Chemical analyses and high-throughput 16S rRNA gene sequencing were implemented to investigate the functional and structural responses of the rock microbial communities to the Se and lactate amendment. During anaerobic incubation of the amended rock slurries from two distinct sites, dissolved Se concentrations decreased significantly, which coincided with lactate degradation to acetate and/or propionate. Sequencing indicated that relative abundances of Desulfosporosinus burensis increased drastically from 0.025 % and 0.022% to 67.584% and 63.716 %, respectively, in the sites. In addition, various Desulfosporosinus spp., Symbiobacterium-related species and Brevibacillus ginsengisoli, as well as the Se(VI)-reducing Desulfitobacterium hafniense, proliferated remarkably. They are capable of incomplete lactate oxidation to acetate as only organic metabolite, strongly suggesting their involvement in dissimilatory Se reduction. Furthermore, predominance of Pelosinus fermentans that ferments lactate to propionate and acetate implied that Se served as the electron sink for its fermentative lactate degradation. These results demonstrated that the indigenous microorganisms played vital roles in the lactate-stimulated Se reduction, leading to the biological Se immobilization treatment of waste rocks.
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Affiliation(s)
- Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Yoshihiko Mori
- Central Research Laboratory, Taiheiyo Cement Co., Ltd., 2-4-2 Osaku, Sakura, Chiba 285-8655, Japan
| | - Mai Nanao
- Central Research Laboratory, Taiheiyo Cement Co., Ltd., 2-4-2 Osaku, Sakura, Chiba 285-8655, Japan
| | - Yusuke Matsuyama
- Taiheiyo Cement Co., Ltd., BUNKYO GARDEN GATE TOWER, 1-1-1 Koishikawa, Bunkyo, Tokyo 112-8503, Japan
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Hidenobu Aizawa
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Takayuki Hayakawa
- Central Research Laboratory, Taiheiyo Cement Co., Ltd., 2-4-2 Osaku, Sakura, Chiba 285-8655, Japan
| | - Masahiko Moriya
- Taiheiyo Cement Co., Ltd., BUNKYO GARDEN GATE TOWER, 1-1-1 Koishikawa, Bunkyo, Tokyo 112-8503, Japan
| | - Yasuhide Higo
- Taiheiyo Cement Co., Ltd., BUNKYO GARDEN GATE TOWER, 1-1-1 Koishikawa, Bunkyo, Tokyo 112-8503, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 395-8569, Japan.
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13
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Lukina AP, Avakyan MR, Danilova EV, Karnachuk OV. Application of Microbial Mats for the Isolation of Spore-Forming Prokaryotes from Deep Biosphere. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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14
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Gruzdev EV, Beletsky AV, Kadnikov VV, Mardanov AV, Ivanov MV, Karnachuk OV, Ravin NV. Diversity of Eukaryotic Microorganisms in the Drainage Waters of a Coal Open-Cast Mine. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720050100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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15
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Panova IA, Rusanov II, Kadnikov VV, Latygolets EA, Avakyan MR, Ivanov MV, Zyusman VC, Kovaleva AA, Ravin NV, Pimenov NV, Karnachuk OV. Sulfate Reduction in Underground Horizons of a Flooded Coal Mine in Kuzbass. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720050185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Poret-Peterson AT, Sayed N, Glyzewski N, Forbes H, González-Orta ET, Kluepfel DA. Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation. Microb Ecol 2020; 80:191-201. [PMID: 31873773 PMCID: PMC7338823 DOI: 10.1007/s00248-019-01477-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
Anaerobic soil disinfestation (ASD) is an organic amendment-based management tool for controlling soil-borne plant diseases and is increasingly used in a variety of crops. ASD results in a marked decrease in soil redox potential and other physicochemical changes, and a turnover in the composition of the soil microbiome. Mechanisms of ASD-mediated pathogen control are not fully understood, but appear to depend on the carbon source used to initiate the process and involve a combination of biological (i.e., release of volatile organic compounds) and abiotic (i.e., lowered pH, release of metal ions) factors. In this study, we examined how the soil microbiome changes over time in response to ASD initiated with rice bran, tomato pomace, or red grape pomace as amendments using growth chamber mesocosms that replicate ASD-induced field soil redox conditions. Within 2 days, the soil microbiome rapidly shifted from a diverse assemblage of taxa to being dominated by members of the Firmicutes for all ASD treatments, whereas control mesocosms maintained diverse and more evenly distributed communities. Rice bran and tomato pomace amendments resulted in microbial communities with similar compositions and trajectories that were different from red grape pomace communities. Quantitative PCR showed nitrogenase gene abundances were higher in ASD communities and tended to increase over time, suggesting the potential for altering soil nitrogen availability. These results highlight the need for temporal and functional studies to understand how pathogen suppressive microbial communities assemble and function in ASD-treated soils.
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Affiliation(s)
| | - Nada Sayed
- USDA-ARS Crops Pathology and Genetics Research Unit, University of California, Davis, USA
- University of California Davis Medical Center, Sacramento, CA, USA
| | - Nathaniel Glyzewski
- USDA-ARS Crops Pathology and Genetics Research Unit, University of California, Davis, USA
- Green Leaf Lab, Sacramento, CA, USA
| | - Holly Forbes
- USDA-ARS Crops Pathology and Genetics Research Unit, University of California, Davis, USA
| | - Enid T González-Orta
- Department of Biological Sciences, California State University, Sacramento, CA, USA
| | - Daniel A Kluepfel
- USDA-ARS Crops Pathology and Genetics Research Unit, University of California, Davis, USA
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17
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Habe H, Sato Y, Aoyagi T, Inaba T, Hori T, Hamai T, Hayashi K, Kobayashi M, Sakata T, Sato N. Design, application, and microbiome of sulfate-reducing bioreactors for treatment of mining-influenced water. Appl Microbiol Biotechnol 2020; 104:6893-6903. [PMID: 32556398 DOI: 10.1007/s00253-020-10737-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 04/14/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 11/26/2022]
Abstract
Sulfate-reducing bioreactors, also called biochemical reactors, represent a promising option for passive treatment of mining-influenced water (MIW) based on similar technology to aerobic/anaerobic-constructed wetlands and vertical-flow wetlands. MIW from each mine site has a variety of site-specific properties related to its treatment; therefore, design factors, including the organic substrates and inorganic materials packed into the bioreactor, must be tested and evaluated before installation of full-scale sulfate-reducing bioreactors. Several full-scale sulfate-reducing bioreactors operating at mine sites provide examples, but holistic understanding of the complex treatment processes occurring inside the bioreactors is lacking. With the recent introduction of high-throughput DNA sequencing technologies, microbial processes within bioreactors may be clarified based on the relationships between operational parameters and key microorganisms identified using high-resolution microbiome data. In this review, the test design procedures and precedents of full-scale bioreactor application for MIW treatment are briefly summarized, and recent knowledge on the sulfate-reducing microbial communities of field-based bioreactors from fine-scale monitoring is presented.Key points• Sulfate-reducing bioreactors are promising for treatment of mining-influenced water.• Various design factors should be tested for application of full-scale bioreactors.• Introduction of several full-scale passive bioreactor systems at mine sites.• Desulfosporosinus spp. can be one of the key bacteria within field-based bioreactors.
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Affiliation(s)
- Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Takaya Hamai
- Japan Oil, Gas and Metals National Corporation (JOGMEC), 2-10-1 Toranomon, Minato-ku, Tokyo, 105-0001, Japan.
| | - Kentaro Hayashi
- JOGMEC Metals Technology Center, 9-3 Furudate, Kosakakozan, Kosaka, Akita, 017-0202, Japan
| | - Mikio Kobayashi
- Japan Oil, Gas and Metals National Corporation (JOGMEC), 2-10-1 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | - Takeshi Sakata
- JOGMEC Metals Technology Center, 9-3 Furudate, Kosakakozan, Kosaka, Akita, 017-0202, Japan
| | - Naoki Sato
- Japan Oil, Gas and Metals National Corporation (JOGMEC), 2-10-1 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
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18
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Lukina AP, Frank YA, Ivasenko DA, Glukhova LB, Danilova EV, Avakyan MR, Karnachuk OV. Isolation of New Thermophilic Sulfidogens from Microbial Mat Associated with Groundwater Discharge in the Tunkin Valley. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719050096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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19
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Sato Y, Hamai T, Hori T, Aoyagi T, Inaba T, Kobayashi M, Habe H, Sakata T. Desulfosporosinus spp. were the most predominant sulfate-reducing bacteria in pilot- and laboratory-scale passive bioreactors for acid mine drainage treatment. Appl Microbiol Biotechnol 2019; 103:7783-7793. [DOI: 10.1007/s00253-019-10063-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/29/2022]
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20
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Hausmann B, Vandieken V, Pjevac P, Schreck K, Herbold CW, Loy A. Draft Genome Sequence of Desulfosporosinus fructosivorans Strain 63.6F T, Isolated from Marine Sediment in the Baltic Sea. Microbiol Resour Announc 2019; 8:e00427-19. [PMID: 31371535 PMCID: PMC6675983 DOI: 10.1128/mra.00427-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/12/2019] [Indexed: 11/20/2022] Open
Abstract
Desulfosporosinus fructosivorans strain 63.6FT is a strictly anaerobic, spore-forming, sulfate-reducing bacterium isolated from marine sediment in the Baltic Sea. Here, we report the draft genome sequence of D. fructosivorans 63.6FT.
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Affiliation(s)
- Bela Hausmann
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Verona Vandieken
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Katharina Schreck
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
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21
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Karnachuk OV, Frank YA, Lukina AP, Kadnikov VV, Beletsky AV, Mardanov AV, Ravin NV. Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution. ISME J 2019; 13:1947-59. [PMID: 30899075 DOI: 10.1038/s41396-019-0402-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/07/2019] [Accepted: 02/28/2019] [Indexed: 11/09/2022]
Abstract
An enigmatic uncultured member of Firmicutes, Candidatus Desulforudis audaxviator (CDA), is known by its genome retrieved from the deep gold mine in South Africa, where it formed a single-species ecosystem fuelled by hydrogen from water radiolysis. It was believed that in situ conditions CDA relied on scarce energy supply and did not divide for hundreds to thousand years. We have isolated CDA strain BYF from a 2-km-deep aquifer in Western Siberia and obtained a laboratory culture growing with a doubling time of 28.5 h. BYF uses not only H2 but also various organic electron donors for sulfate respiration. Growth required elemental iron, and ferrous iron did not substitute for it. A complex intracellular organization included gas vesicles, internal membranes, and electron-dense structures enriched in phosphorus, iron, and calcium. Genome comparison of BYF with the South African CDA revealed minimal differences mostly related to mobile elements and prophage insertions. Two genomes harbored <800 single-nucleotide polymorphisms and had nearly identical CRISPR loci. We suggest that spores with the gas vesicles may facilitate global distribution of CDA followed by colonization of suitable subsurface environments. Alternatively, a slow evolution rate in the deep subsurface could result in high genetic similarity of CDA populations at two sites spatially separated for hundreds of millions of years.
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22
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Bukhtiyarova PA, Antsiferov DV, Brasseur G, Avakyan MR, Frank YA, Ikkert OP, Pimenov NV, Tuovinen OH, Karnachuk OV. Isolation, characterization, and genome insights into an anaerobic sulfidogenic Tissierella bacterium from Cu-bearing coins. Anaerobe 2019; 56:66-77. [PMID: 30776428 DOI: 10.1016/j.anaerobe.2019.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 09/04/2018] [Revised: 01/27/2019] [Accepted: 02/14/2019] [Indexed: 01/19/2023]
Abstract
Recent reports on antimicrobial effects of metallic Cu prompted this study of anaerobic microbial communities on copper surfaces. Widely circulating copper-containing coinage was used as a potential source for microorganisms that had had human contact and were tolerant to copper. This study reports on the isolation, characterization, and genome of an anaerobic sulfidogenic Tissierella sp. P1from copper-containing brass coinage. Dissimilatory (bi)sulfite reductase dsrAB present in strain P1 genome and the visible absorbance around 630 nm in the cells suggested the presence of a desulfoviridin-type protein. However, the sulfate reduction rate measurements with 35SO42- did not confirm the dissimilatory sulfate reduction by the strain. The P1 genome lacks APS reductase, sulfate adenylyltransferase, DsrC, and DsrMK necessary for dissimilatory sulfate reduction. The isolate produced up to 0.79 mM H2S during growth, possibly due to cysteine synthase (CysK) and/or cysteine desulfhydrase (CdsH) activities, encoded in the genome. The strain can tolerate up to 2.4 mM Cu2+(150 mg/l) in liquid medium, shows affinity to metallic copper, and can survive on copper-containing coins up to three days under ambient air and dry conditions. The genome sequence of strain P1 contained cutC, encoding a copper resistance protein, which distinguishes it from all other Tissierella strains with published genomes.
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Affiliation(s)
- Polina A Bukhtiyarova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Dmitry V Antsiferov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Gael Brasseur
- Laboratoire de Chimie Bactérienne, CNRS, Mediterranean Institute of Microbiology, Marseille, France
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Olga P Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Nikolay V Pimenov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia.
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23
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Hausmann B, Pelikan C, Rattei T, Loy A, Pester M. Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. mBio 2019; 10:e02189-18. [PMID: 30755506 PMCID: PMC6372793 DOI: 10.1128/mbio.02189-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/04/2019] [Indexed: 01/05/2023] Open
Abstract
Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize "Candidatus Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of "Ca. Desulfosporosinus infrequens" increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.
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Affiliation(s)
- Bela Hausmann
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claus Pelikan
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Microorganisms, Leibniz Institute DSMZ, Braunschweig, Germany
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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24
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Liu S, Chen Q, Ma T, Wang M, Ni J. Genomic insights into metabolic potentials of two simultaneous aerobic denitrification and phosphorus removal bacteria, Achromobacter sp. GAD3 and Agrobacterium sp. LAD9. FEMS Microbiol Ecol 2018; 94:4834001. [DOI: 10.1093/femsec/fiy020] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/31/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shufeng Liu
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Qian Chen
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Tao Ma
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Ming Wang
- Yellow River Institute of Hydraulic Research, Zhengzhou 450003, China
| | - Jinren Ni
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
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25
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Vandieken V, Marshall IPG, Niemann H, Engelen B, Cypionka H. Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea. Front Microbiol 2018; 8:2614. [PMID: 29354105 PMCID: PMC5760507 DOI: 10.3389/fmicb.2017.02614] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial communities in deep subsurface sediments are challenged by the decrease in amount and quality of organic substrates with depth. In sediments of the Baltic Sea, they might additionally have to cope with an increase in salinity from ions that have diffused downward from the overlying water during the last 9000 years. Here, we report the isolation and characterization of four novel bacteria of the Bacteroidetes from depths of 14–52 m below seafloor (mbsf) of Baltic Sea sediments sampled during International Ocean Discovery Program (IODP) Expedition 347. Based on physiological, chemotaxonomic and genotypic characterization, we propose that the four strains represent two new species within a new genus in the family Marinifilaceae, with the proposed names Labilibaculum manganireducens gen. nov., sp. nov. (type strain 59.10-2MT) and Labilibaculum filiforme sp. nov. (type strains 59.16BT) with additional strains of this species (59.10-1M and 60.6M). The draft genomes of the two type strains had sizes of 5.2 and 5.3 Mb and reflected the major physiological capabilities. The strains showed gliding motility, were psychrotolerant, neutrophilic and halotolerant. Growth by fermentation of mono- and disaccharides as well as pyruvate, lactate and glycerol was observed. During glucose fermentation, small amounts of electron equivalents were transferred to Fe(III) by all strains, while one of the strains also reduced Mn(IV). Thereby, the four strains broaden the phylogenetic range of prokaryotes known to reduce metals to the group of Bacteroidetes. Halotolerance and metal reduction might both be beneficial for survival in deep subsurface sediments of the Baltic Sea.
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Affiliation(s)
- Verona Vandieken
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Ian P G Marshall
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Helge Niemann
- Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel, Switzerland.,CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, University of Tromsø, Tromsø, Norway.,Departments of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, and Utrecht University, Netherlands
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Heribert Cypionka
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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26
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Antsiferov DV, Fyodorova TS, Kovalyova AA, Lukina A, Frank YA, Avakyan MR, Banks D, Tuovinen OH, Karnachuk OV. Selection for novel, acid-tolerant Desulfovibrio spp. from a closed Transbaikal mine site in a temporal pH-gradient bioreactor. Antonie van Leeuwenhoek 2017; 110:1669-79. [DOI: 10.1007/s10482-017-0917-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022]
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27
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Karnachuk OV, Kadnikov VV, Panova IA, Mardanov AV, Beletsky AV, Danilova EV, Avakyan MR, Ravin NV. Genome sequence of the copper resistant and acid-tolerant Desulfosporosinus sp. BG isolated from the tailings of a molybdenum-tungsten mine in the Transbaikal area. Genom Data 2017; 11:106-8. [PMID: 28116241 DOI: 10.1016/j.gdata.2016.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/11/2016] [Indexed: 01/15/2023]
Abstract
Here, we report on the draft genome of a copper-resistant and acidophilic Desulfosporosinus sp. BG, isolated from the tailings of a molybdenum-tungsten mine in Transbaikal area. The draft genome has a size of 4.52 Mb and encodes transporters of heavy metals. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain BG clusters together with the other acidophilic copper-resistant strains Desulfosporosinus sp. OT and Desulfosporosinus sp. I2. The K+-ATPase, Na+/H+ antiporter and amino acid decarboxylases may participate in enabling growth at low pH. The draft genome sequence and annotation have been deposited at GenBank under the accession number NZ_MASS00000000.
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