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Kim M, Jung S, Kang S, Rhie MN, Song M, Shin J, Shin SG, Lee J. Magnetite particles accelerate methanogenic degradation of highly concentrated acetic acid in anaerobic digestion process. ENVIRONMENTAL RESEARCH 2024; 255:119132. [PMID: 38735380 DOI: 10.1016/j.envres.2024.119132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024]
Abstract
The anaerobic digestion (AD) process has become significant for its capability to convert organic wastewater into biogas, a valuable energy source. Excessive acetic acid accumulation in the anaerobic digester can inhibit methanogens, ultimately leading to the deterioration of process performance. Herein, the effect of magnetite particles (MP) as an enhancer on the methanogenic degradation of highly-concentrated acetate (6 g COD/L) was examined through long-term sequential AD batch tests. Bioreactors with (AM) and without (AO) MP were compared. AO experienced inhibition and its methane production rate (qm) converged to 0.45 L CH4/g VSS/d after 10 sequential batches (AO10, the 10th batch in a series of the sequential batch tests conducted using bioreactors without MP addition). In contrast, AM achieved 3-425% higher qm through the sequential batches, indicating that MP could counteract the inhibition caused by the highly-concentrated acetate. MP addition to inhibited bioreactors (AO10) successfully restored them, achieving qm of 1.53 L CH4/g VSS/d, 3.4 times increase from AO10 after 8 days lag time, validating its potential as a recovery strategy for inhibited digesters with acetate accumulation. AM exhibited higher microbial populations (1.8-3.8 times) and intracellular activity (9.3 times) compared to AO. MP enriched Methanosaeta, Peptoclostridium, Paraclostridium, OPB41, and genes related to direct interspecies electron transfer and acetate oxidation, potentially driving the improvement of qm through MP-mediated methanogenesis. These findings demonstrated the potential of MP supplementation as an effective strategy to accelerate acetate-utilizing methanogenesis and restore an inhibited anaerobic digester with high acetate accumulation.
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Affiliation(s)
- Minjae Kim
- Division of Earth Environmental System Science (Major of Environmental Engineering), Pukyong National University, Busan, 48513, Republic of Korea
| | - Sungyun Jung
- Division of Earth Environmental System Science (Major of Environmental Engineering), Pukyong National University, Busan, 48513, Republic of Korea
| | - Seonmin Kang
- Division of Earth Environmental System Science (Major of Environmental Engineering), Pukyong National University, Busan, 48513, Republic of Korea
| | - Mi Na Rhie
- Division of Earth Environmental System Science (Major of Environmental Engineering), Pukyong National University, Busan, 48513, Republic of Korea; National Fishery Products Quality Management Service, Busan, 49111, Republic of Korea
| | - Minsu Song
- Institute of Sustainable Earth and Environmental Dynamics (SEED), Pukyong National University, Busan, 48547, Republic of Korea
| | - Juhee Shin
- Department of Energy Engineering, Future Convergence Technology Research Institute, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Seung Gu Shin
- Department of Energy Engineering, Future Convergence Technology Research Institute, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Joonyeob Lee
- Division of Earth Environmental System Science (Major of Environmental Engineering), Pukyong National University, Busan, 48513, Republic of Korea.
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Resitano M, Tucci M, Mezzi A, Kaciulis S, Matturro B, D'Ugo E, Bertuccini L, Fazi S, Rossetti S, Aulenta F, Cruz Viggi C. Anaerobic treatment of groundwater co-contaminated by toluene and copper in a single chamber bioelectrochemical system. Bioelectrochemistry 2024; 158:108711. [PMID: 38626620 DOI: 10.1016/j.bioelechem.2024.108711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/18/2024]
Abstract
Addressing the simultaneous removal of multiple coexisting groundwater contaminants poses a significant challenge, primarily because of their different physicochemical properties. Indeed, different chemical compounds may necessitate establishing distinct, and sometimes conflicting, (bio)degradation and/or removal pathways. In this work, we investigated the concomitant anaerobic treatment of toluene and copper in a single-chamber bioelectrochemical cell with a potential difference of 1 V applied between the anode and the cathode. As a result, the electric current generated by the bioelectrocatalytic oxidation of toluene at the anode caused the abiotic reduction and precipitation of copper at the cathode, until the complete removal of both contaminants was achieved. Open circuit potential (OCP) experiments confirmed that the removal of copper and toluene was primarily associated with polarization. Analogously, abiotic experiments, at an applied potential of 1 V, confirmed that neither toluene was oxidized nor copper was reduced in the absence of microbial activity. At the end of each experiment, both electrodes were characterized by means of a comprehensive suite of chemical and microbiological analyses, evidencing a highly selected microbial community competent in the biodegradation of toluene in the anodic biofilm, and a uniform electrodeposition of spherical Cu2O nanoparticles over the cathode surface.
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Affiliation(s)
- Marco Resitano
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, (RM), Italy
| | - Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, (RM), Italy
| | - Alessio Mezzi
- Institute for the Study of Nanostructured Materials, National Research Council (CNR), 00010 Montelibretti, (RM), Italy
| | - Saulius Kaciulis
- Institute for the Study of Nanostructured Materials, National Research Council (CNR), 00010 Montelibretti, (RM), Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, (RM), Italy; National Biodiversity Future Center, Palermo 90133, Italy
| | - Emilio D'Ugo
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Stefano Fazi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, (RM), Italy
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, (RM), Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, (RM), Italy; National Biodiversity Future Center, Palermo 90133, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, (RM), Italy.
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Khomyakova MA, Merkel AY, Slobodkin AI. Anaerobaca lacustris gen. nov., sp. nov., an obligately anaerobic planctomycete of the widespread SG8-4 group, isolated from a coastal lake, and proposal of Anaerobacaceae fam. nov. Syst Appl Microbiol 2024; 47:126522. [PMID: 38852331 DOI: 10.1016/j.syapm.2024.126522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
One of the numerous and widespread lineages of planctomycetes is the hitherto uncultured SG8-4 group inhabiting anoxic environments. A novel anaerobic, mesophilic, alkalitolerant, chemoorganotrophic bacterium (strain M17dextrT) was isolated from anaerobic sediment of a coastal lake (Taman Peninsula, Russia). The cell were mainly non-motile cocci, 0.3 to 1.0 µm in diameter forming chains or aggregates. The cells had a Gram-negative cell wall and divided by binary fission. The temperature range for growth was 20-37 0C (optimum at 30 0C). The pH range for growth was 6.5-10.0, with an optimum at pH 8.0-8.5. Strain M17dextrT fermented mono-, di- and polysaccharides (starch, xanthan gum, dextran, N-acetylglucosamine), but did not utilized proteinaceous compounds. Major cellular fatty acids were C16:0 and C18:0. The genome of strain M17dextrT had a size of 5.7 Mb with a G + C content of 62.49 %. The genome contained 345 CAZyme genes. The closest cultured phylogenetic relatives of strain M17dextrT were members of the order Sedimentisphaerales, class Phycisphaerae. Among characterized planctomycetes, the highest 16S rRNA gene sequence similarity (88.3 %) was observed with Anaerohalosphaera lusitana. According to phylogenomic analysis strain M17dextrT together with many uncultured representatives of Sedimentisphaerales forms a separate family-level lineage. We propose to assign strain M17dextrT to a novel genus and species, Anaerobaca lacustris gen. nov., sp. nov.; the type strain is M17dextrT (=VKM B-3571 T = DSM 113417 T = JCM 39238 T = KCTC 25381 T = UQM 41474 T). This genus is placed in a novel family, Anaerobacaceae fam. nov. within the order Sedimentisphaerales.
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Affiliation(s)
- M A Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia.
| | - A Y Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
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Chen M, Grégoire DS, Bain JG, Blowes DW, Hug LA. Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities. Appl Environ Microbiol 2024; 90:e0014324. [PMID: 38814057 PMCID: PMC11218620 DOI: 10.1128/aem.00143-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.
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Affiliation(s)
- Molly Chen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Daniel S. Grégoire
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Jeffrey G. Bain
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - David W. Blowes
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Laura A. Hug
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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5
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Ouyang W, Huang Y, Li C, Xue C, Liu M, Ma J, Yuan S, Liu H. Response of TCE biodegradation to elevated H 2 and O 2: Implication for electrokinetic-enhanced bioremediation. ENVIRONMENTAL RESEARCH 2024; 248:118338. [PMID: 38316390 DOI: 10.1016/j.envres.2024.118338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/14/2024] [Accepted: 01/27/2024] [Indexed: 02/07/2024]
Abstract
The study investigated the influences of pure H2 and O2 introduction, simulating gases produced from the electrokinetic-enhanced bioremediation (EK-Bio), on TCE degradation, and the dynamic changes of the indigenous microbial communities. The dissolved hydrogen (DH) and oxygen (DO) concentrations ranged from 0.2 to 0.7 mg/L and 2.6 to 6.6 mg/L, respectively. The biological analysis was conducted by 16S rRNA sequencing and functional gene analyses. The results showed that the H2 introduction enhanced TCE degradation, causing a 90.4% TCE removal in the first 4 weeks, and 131.1 μM was reduced eventually. Accordingly, cis-dichloroethylene (cis-DCE) was produced as the only product. The following three ways should be responsible for this promoted TCE degradation. Firstly, the high DH rapidly reduced the oxidation-reduction potential (ORP) value to around -500 mV, beneficial to TCE microbial dechlorination. Secondly, the high DH significantly changed the community and promoted the enrichment of TCE anaerobic dechlorinators, such as Sulfuricurvum, Sulfurospirillum, Shewanella, Geobacter, and Desulfitobacterium, and increased the abundance of dechlorination gene pceA. Thirdly, the high DH promoted preferential TCE dechlorination and subsequent sulfate reduction. However, TCE bio-remediation did not occur in a high DO environment due to the reduced aerobic function or lack of functional bacteria or co-metabolic substrate. The competitive dissolved organic carbon (DOC) consumption and unfriendly microbe-microbe interactions also interpreted the non-degradation of TCE in the high DO environment. These results provided evidence for the mechanism of EK-Bio. Providing anaerobic obligate dechlorinators, and aerobic metabolic bacteria around the electrochemical cathodes and anodes, respectively, or co-metabolic substrates to the anode can be feasible methods to promote remediation of TCE-contaminated shallow aquifer under EK-Bio technology.
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Affiliation(s)
- Weiwei Ouyang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, 430078, PR China
| | - Yao Huang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, 430078, PR China
| | - Cui Li
- Hubei Ecology Polytechnic College, Wuhan, Hubei, 430200, PR China
| | - Chen Xue
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, 430078, PR China
| | - Minghui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, 430078, PR China
| | - Jie Ma
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, Hubei, 430062, PR China
| | - Songhu Yuan
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, 430078, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, 430078, PR China
| | - Hui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, 430078, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, 430078, PR China.
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6
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Shen W, Zhao M, Xu W, Shi X, Ren F, Tu P, Gao N, Shan J, Gao B. Sex-Specific Effects of Polystyrene Microplastic and Lead(II) Co-Exposure on the Gut Microbiome and Fecal Metabolome in C57BL/6 Mice. Metabolites 2024; 14:189. [PMID: 38668317 PMCID: PMC11051764 DOI: 10.3390/metabo14040189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
The wide spread of microplastics has fueled growing public health concern globally. Due to their porous structure and large surface area, microplastics can serve as carriers for other environmental pollutants, including heavy metals. Although the toxic effects of microplastics or heavy metals have been reported previously, investigations into the sex-differential health effects of combined exposure to microplastics and heavy metals are lacking. In the present study, the effects of polystyrene microplastics and lead(II) co-exposure on the gut microbiome, intestinal permeability, and fecal metabolome were examined in both male and female mice. Combined exposure of polystyrene microplastics and lead(II) increased intestinal permeability in both male and female mice. Sex-specific responses to the co-exposure were found in gut bacteria, fungi, microbial metabolic pathways, microbial genes encoding antibiotic resistance and virulence factors, as well as fecal metabolic profiles. In particular, Shannon and Simpson indices of gut bacteria were reduced by the co-exposure only in female mice. A total of 34 and 13 fecal metabolites were altered in the co-exposure group in female and male mice, respectively, among which only three metabolites were shared by both sexes. These sex-specific responses to the co-exposure need to be taken into consideration when investigating the combined toxic effects of microplastics and heavy metals on the gut microbiota.
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Affiliation(s)
- Weishou Shen
- School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (W.S.); (M.Z.); (X.S.)
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative In-Novation Center of Atmospheric Environment and Equipment Technology, Nanjing 210044, China
- Institute of Soil Health and Climate-Smart Agriculture, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Meng Zhao
- School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (W.S.); (M.Z.); (X.S.)
| | - Weichen Xu
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing 210023, China; (W.X.); (J.S.)
| | - Xiaochun Shi
- School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (W.S.); (M.Z.); (X.S.)
| | - Fangfang Ren
- School of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (F.R.); (N.G.)
| | - Pengcheng Tu
- Department of Environmental Health, Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou 310051, China;
| | - Nan Gao
- School of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (F.R.); (N.G.)
| | - Jinjun Shan
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing 210023, China; (W.X.); (J.S.)
| | - Bei Gao
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China
- Key Laboratory of Hydrometeorological Disaster Mechanism and Warning of Ministry of Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China
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Slobodkina G, Merkel A, Novikov A, Slobodkin A. Pseudodesulfovibrio pelocollis sp. nov. a Sulfate-Reducing Bacterium Isolated from a Terrestrial Mud Volcano. Curr Microbiol 2024; 81:120. [PMID: 38528188 DOI: 10.1007/s00284-024-03644-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/17/2024] [Indexed: 03/27/2024]
Abstract
Terrestrial mud volcanoes (TMVs), surface expressions of a deep-subterranean sedimentary volcanism, are widespread throughout the world. The methane and sulfur cycles are recognized as the most important biogeochemical cycles in these environments. Only few anaerobic bacterial strains were recovered from TMVs. We have isolated a novel sulfate-reducing bacterium (strain SB368T) from TMV located at Taman Peninsula, Russia. Optimum growth of strain SB368T was observed at 30 °C, pH 8.0 and 1% NaCl. Strain SB368T utilized lactate, pyruvate and fumarate in the presence of sulfate, sulfite or thiosulfate. Growth with molecular hydrogen was observed only in the presence of acetate. Fermentative growth occurred on pyruvate. Phylogenetic analysis revealed that strain SB368T belongs to the genus Pseudodesulfovibrio but is distinct from all described species. Based on its genomic and phenotypic properties, a new species, Pseudodesulfovibrio pelocollis sp. nov. is proposed with strain SB368T (= DSM 111087 T = VKM B-3585 T) as a type strain.
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Affiliation(s)
- Galina Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia.
| | - Alexander Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia
| | - Andrei Novikov
- Gubkin University, Leninsky Prospect, 65/1, 119991, Moscow, Russia
| | - Alexander Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia
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8
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Stroeva AR, Klyukina AA, Vidishcheva ON, Poludetkina EN, Solovyeva MA, Pyrkin VO, Gavirova LA, Birkeland NK, Akhmanov GG, Bonch-Osmolovskaya EA, Merkel AY. Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea. Microorganisms 2024; 12:387. [PMID: 38399791 PMCID: PMC10892650 DOI: 10.3390/microorganisms12020387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.
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Affiliation(s)
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | | | | | | | | | | | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
| | | | - Elizaveta A. Bonch-Osmolovskaya
- Lomonosov Moscow State University, 119234 Moscow, Russia
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexander Y. Merkel
- Lomonosov Moscow State University, 119234 Moscow, Russia
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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9
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Zavarzina DG, Merkel AY, Klyukina AA, Elizarov IM, Pikhtereva VA, Rusakov VS, Chistyakova NI, Ziganshin RH, Maslov AA, Gavrilov SN. Iron or sulfur respiration-an adaptive choice determining the fitness of a natronophilic bacterium Dethiobacter alkaliphilus in geochemically contrasting environments. Front Microbiol 2023; 14:1108245. [PMID: 37520367 PMCID: PMC10376724 DOI: 10.3389/fmicb.2023.1108245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, geologically ancient yet widespread ecosystems supposed to harbor relict microbial communities. We compared metabolic features and their determinants in two strains of the natronophilic species Dethiobacter alkaliphilus, the only cultured representative of the class "Dethiobacteria" (Bacillota). The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1T was described as a facultative chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered the iron reducing ability of strain AHT1T and the ability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both D. alkaliphilus strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This hypothesis was supported by a meta-analysis of Dethiobacterial genomes and by the enrichment of a novel phylotype from a subsurface alkaline aquifer under Fe(III)-reducing conditions. Genome analysis revealed multiheme c-type cytochromes to be the most probable determinants of iron and sulfur redox transformations in D. alkaliphilus. Phylogeny reconstruction showed that all the respiratory processes in this organism are likely provided by evolutionarily related early forms of unconventional octaheme tetrathionate and sulfite reductases and their structural analogs, OmhA/OcwA Fe(III)-reductases. Several phylogenetically related determinants of anaerobic Fe(II) oxidation were identified in the Z-1002 genome, and the oxidation process was experimentally demonstrated. Proteomic profiling revealed two distinct sets of multiheme cytochromes upregulated in iron(III)- or thiosulfate-respiring cells and the cytochromes peculiar for Fe(II) oxidizing cells. We suggest that maintaining high variation in multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline environments. We propose that sulfur-enriched soda lakes could be secondary habitats for D. alkaliphilus compared to Fe-rich serpentinites, and that the ongoing evolution of Dethiobacterales could retrace the evolutionary path that may have occurred in prokaryotes at a turning point in the biosphere's history, when the intensification of the sulfur cycle outweighed the global significance of the iron cycle.
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Affiliation(s)
- Daria G. Zavarzina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Yu Merkel
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ivan M. Elizarov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Valeria A. Pikhtereva
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Maslov
- Faculty of Geology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
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