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Li J, Xiang S, Li Y, Cheng R, Lai Q, Wang L, Li G, Dong C, Shao Z. Arcobacteraceae are ubiquitous mixotrophic bacteria playing important roles in carbon, nitrogen, and sulfur cycling in global oceans. mSystems 2024; 9:e0051324. [PMID: 38904399 PMCID: PMC11265409 DOI: 10.1128/msystems.00513-24] [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: 04/08/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous Arcobacteraceae based on our deep-sea in situ incubations and the global data. The phylogenomic tree of Arcobacteraceae is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation, denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea in situ incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of Arcobacteraceae in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized Arcobacteraceae to carbon, nitrogen, and sulfur cycling in global oceans.IMPORTANCEMarine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria Arcobacteraceae that thrived on the "hot time" of bulky particulate organic matter and exhibited mixotrophic strategy during the in situ organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of Arcobacteraceae with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths.
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Affiliation(s)
- Jianyang Li
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Shizheng Xiang
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Yufei Li
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Ruolin Cheng
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Liping Wang
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Guizhen Li
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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Torres-Herrera S, Palomares-Cortés J, González-Cortés JJ, Cubides-Páez DF, Gamisans X, Cantero D, Ramírez M. Biodesulfurization of landfill biogas by a pilot-scale bioscrubber: Operational limits and microbial analysis. ENVIRONMENTAL RESEARCH 2024; 246:118164. [PMID: 38211717 DOI: 10.1016/j.envres.2024.118164] [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: 10/28/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
Biogas serves as a crucial renewable energy vector to ensure a more sustainable energy future. However, the presence of hydrogen sulfide (H2S) limits its application in various sectors, emphasizing the importance of effective H2S removal techniques for maximizing its potential. In the present study, the limits of a pilot-scale bioscrubber for biogas desulfurization was study in a real scenario. An increase in the superficial liquid velocity resulted in significant improvements in the H2S removal efficiency, increasing from 76 ± 8% (elimination capacity of 6.2 ± 0.5 gS-H2S m-3 h-1) to 97.7 ± 0.5% (elimination capacity of 8 ± 1 gS-H2S m-3 h-1) as the superficial liquid velocity increased from 50 ± 3 m h-1 to 200 ± 8 m h-1. A USL of 161.4 ± 0.5 m h-1 was able to achieve outlet H2S concentrations as low as 3 ± 1 ppmv (H2S removal efficiency of 97 ± 1%) for 7 days. High superficial liquid velocity favoured the aerobic H2S oxidation reducing the nitrate demand. The maximum EC reached throughout the operation was 50.8 ± 0.6 gS-H2S m-3 h-1 (H2S removal efficiency of 96 ± 1%) and a sulfur production of 60%. Studies in batch flocculation experiments showed sulfur removal rates up to 97.6 ± 0.9% with a cationic flocculant dose of 75 mg L-1. Microbial analysis revealed that the predominant genus with sulfo-oxidant capacity during periods of low H2S inlet load was Thioalkalispira-sulfurivermis (61-69%), while in periods of higher H2S inlet load, family Arcobacteraceae was the most prevalent (11%).
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Affiliation(s)
- S Torres-Herrera
- Department of Chemical Engineering and Food Technologies, Wine and Agrifood Research Institute (IVAGRO). Faculty of Sciences, University of Cadiz, Puerto Real, Cadiz, 11510, Spain
| | - J Palomares-Cortés
- Department of Chemical Engineering and Food Technologies, Wine and Agrifood Research Institute (IVAGRO). Faculty of Sciences, University of Cadiz, Puerto Real, Cadiz, 11510, Spain
| | - J J González-Cortés
- Department of Chemical Engineering and Food Technologies, Wine and Agrifood Research Institute (IVAGRO). Faculty of Sciences, University of Cadiz, Puerto Real, Cadiz, 11510, Spain
| | - D F Cubides-Páez
- Eurecat, Centre Tecnològic de Catalunya, Sustainability Area, Plaça de la Ciencia 2, Manresa, Barcelona, 08242, Spain
| | - X Gamisans
- Department of Mining, Industrial and ICT Engineering, Manresa School of Engineering, Universitat Politècnica de Catalunya, Manresa, Barcelona, 08242, Spain
| | - D Cantero
- Department of Chemical Engineering and Food Technologies, Wine and Agrifood Research Institute (IVAGRO). Faculty of Sciences, University of Cadiz, Puerto Real, Cadiz, 11510, Spain
| | - M Ramírez
- Department of Chemical Engineering and Food Technologies, Wine and Agrifood Research Institute (IVAGRO). Faculty of Sciences, University of Cadiz, Puerto Real, Cadiz, 11510, Spain.
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Howard RD, Schul MD, Rodriguez Bravo LM, Altieri AH, Meyer JL. Shifts in the coral microbiome in response to in situ experimental deoxygenation. Appl Environ Microbiol 2023; 89:e0057723. [PMID: 37916820 PMCID: PMC10686059 DOI: 10.1128/aem.00577-23] [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: 04/06/2023] [Accepted: 09/12/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Marine hypoxia is a threat for corals but has remained understudied in tropical regions where coral reefs are abundant. Though microbial symbioses can alleviate the effects of ecological stress, we do not yet understand the taxonomic or functional response of the coral microbiome to hypoxia. In this study, we experimentally lowered oxygen levels around Siderastrea siderea and Agaricia lamarcki colonies in situ to observe changes in the coral microbiome in response to deoxygenation. Our results show that hypoxia triggers a stochastic change of the microbiome overall, with some bacterial families changing deterministically after just 48 hours of exposure. These families represent an increase in anaerobic and opportunistic taxa in the microbiomes of both coral species. Thus, marine deoxygenation destabilizes the coral microbiome and increases bacterial opportunism. This work provides novel and fundamental knowledge of the microbial response in coral during hypoxia and may provide insight into holobiont function during stress.
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Affiliation(s)
- Rachel D. Howard
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, Florida, USA
| | - Monica D. Schul
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, Florida, USA
| | - Lucia M. Rodriguez Bravo
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Andrew H. Altieri
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie L. Meyer
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, Florida, USA
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Cheng H, Lee W, Wen C, Dai H, Cheng F, Lu X. A sustainable integrated anoxic/aerobic bio-contactor process for simultaneously in-situ deodorization and pollutants removal from decentralized domestic sewage. Heliyon 2023; 9:e22339. [PMID: 38045187 PMCID: PMC10689935 DOI: 10.1016/j.heliyon.2023.e22339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 12/05/2023] Open
Abstract
The integration of anoxic filter and aerobic rotating biological contactor shows promise in treating rural domestic sewage. It offers high efficiency, low sludge production, and strong shock resistance. However, further optimization is needed for odor control, pollutant removal, and power consumption. In this study, the investigation on a one-pump-drive lab-scale device of retention anoxic filter (RAF) integrated with hydraulic rotating bio-contactor (HRBC) and its optimal operation mode were conducted. During the 50-day operation, optimal operation parameters were investigated. These parameters included a 175 % reflux ratio (RR), 5-h hydraulic retention time in the RAF (HRTRAF), and 2.5-h hydraulic retention time in the HRBC (HRTHRBC). Those conditions characterized a micro-aerobic environment (DO: 0.6-0.8 mg/L) in RAF, inducing improved deodorization (89.3 % sulfide removal) and denitrification (85.9 % nitrate removal) simultaneously. During the operation period, 84.79 ± 3.87 % COD, 82.71± 2.06 % NH 4 + -N, 74.83 ± 2.06 % TN, 91.68± 2.12 % S2-, and 89.04 ± 1.68 % TON were removed in RAF-HRBC. Based on large amount of operational data, organic loading rate curves of RAF-HRBC were validated and calibrated as a crucial reference to aid in full-scale designs and applications. The richness of microbial community was improved in both RAF and HRBC. In the RAF, the autotrophic sulfide-oxidizing nitrate-reducing bacteria (a-son) and heterotrophic sulfide-oxidizing nitrate-reducing bacteria (h-son) were selectively enriched, which intensified the sulfide removal and denitrification process. In the two-stage HRBC system, the 1st stage RBC was primarily composed of organics degraders, while the 2nd stage RBC consisted mainly of ammonium oxidizers. Overall, the integrated RAF-HRBC process holds significant potential for simultaneously improving pollutant removal and in-situ odor mitigation in decentralized domestic sewage treatment. This process specifically contributes to enhancing environmental sustainability and operational efficiency.
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Affiliation(s)
- Helai Cheng
- School of Energy and Environment, Southeast University, No. 2 Sipailou Road, Nanjing 210096, China
- ERC Taihu Lake Water Environment (Yixing, Wuxi), No. 1 Puzhubeilu Road, Yixing, Wuxi 214226, China
| | - Wenhua Lee
- School of Energy and Environment, Southeast University, No. 2 Sipailou Road, Nanjing 210096, China
- ERC Taihu Lake Water Environment (Yixing, Wuxi), No. 1 Puzhubeilu Road, Yixing, Wuxi 214226, China
| | - Cangxiang Wen
- School of Energy and Environment, Southeast University, No. 2 Sipailou Road, Nanjing 210096, China
- ERC Taihu Lake Water Environment (Yixing, Wuxi), No. 1 Puzhubeilu Road, Yixing, Wuxi 214226, China
| | - Hongliang Dai
- School of Energy and Environment, Southeast University, No. 2 Sipailou Road, Nanjing 210096, China
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, No. 2 Mengxi Road, Zhenjiang 212018, China
| | - Fangkui Cheng
- School of Energy and Environment, Southeast University, No. 2 Sipailou Road, Nanjing 210096, China
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, No. 2 Mengxi Road, Zhenjiang 212018, China
| | - Xiwu Lu
- School of Energy and Environment, Southeast University, No. 2 Sipailou Road, Nanjing 210096, China
- ERC Taihu Lake Water Environment (Yixing, Wuxi), No. 1 Puzhubeilu Road, Yixing, Wuxi 214226, China
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Aerts JW, Sarbu SM, Brad T, Ehrenfreund P, Westerhoff HV. Microbial Ecosystems in Movile Cave: An Environment of Extreme Life. Life (Basel) 2023; 13:2120. [PMID: 38004260 PMCID: PMC10672346 DOI: 10.3390/life13112120] [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: 09/29/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Movile Cave, situated in Romania close to the Black Sea, constitutes a distinct and challenging environment for life. Its partially submerged ecosystem depends on chemolithotrophic processes for its energetics, which are fed by a continuous hypogenic inflow of mesothermal waters rich in reduced chemicals such as hydrogen sulfide and methane. We sampled a variety of cave sublocations over the course of three years. Furthermore, in a microcosm experiment, minerals were incubated in the cave waters for one year. Both endemic cave samples and extracts from the minerals were subjected to 16S rRNA amplicon sequencing. The sequence data show specific community profiles in the different subenvironments, indicating that specialized prokaryotic communities inhabit the different zones in the cave. Already after one year, the different incubated minerals had been colonized by specific microbial communities, indicating that microbes in Movile Cave can adapt in a relatively short timescale to environmental opportunities in terms of energy and nutrients. Life can thrive, diversify and adapt in remote and isolated subterranean environments such as Movile Cave.
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Affiliation(s)
- Joost W. Aerts
- Molecular Cell Biology, A-LIFE, 01-E-57, Faculty of Science, VU University Amsterdam, Van der Boechorstraat 3, 1081 BT Amsterdam, The Netherlands
| | - Serban M. Sarbu
- “Emil Racoviţă” Institute of Speleology, Str. Frumoasă 31, 010986 Bucharest, Romania
- Department of Biological Sciences, California State University, Chico, CA 95929, USA
| | - Traian Brad
- “Emil Racoviţă” Institute of Speleology, Clinicilor 5-7, 400006 Cluj-Napoca, Romania;
| | - Pascale Ehrenfreund
- Laboratory for Astrophysics, Leiden Observatory, Leiden University, 2333 RA Leiden, The Netherlands
- Space Policy Institute, George Washington University, Washington, DC 20052, USA
| | - Hans V. Westerhoff
- Molecular Cell Biology, A-LIFE, 01-E-57, Faculty of Science, VU University Amsterdam, Van der Boechorstraat 3, 1081 BT Amsterdam, The Netherlands
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Stellenbosch Institute for Advanced Study, Stellenbosch 7600, South Africa
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Goffredi SK, Panossian B, Brzechffa C, Field N, King C, Moggioli G, Rouse GW, Martín-Durán JM, Henry LM. A dynamic epibiont community associated with the bone-eating polychaete genus Osedax. mBio 2023; 14:e0314022. [PMID: 37382438 PMCID: PMC10470745 DOI: 10.1128/mbio.03140-22] [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: 11/08/2022] [Accepted: 05/08/2023] [Indexed: 06/30/2023] Open
Abstract
Osedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-yr study, we reveal a dynamic, yet persistent, shift of Campylobacterales integrated into the epidermis of Osedax, which change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species of Osedax, which comprise 67% of the bacterial community on the trunk, appear initially dominated by the genus Arcobacter (at early time points <24 mo), the Sulfurospirillum at intermediate stages (~50 mo), and the Sulfurimonas at later stages (>140 mo) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests potential for a transition from heterotrophy to autotrophy and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free-living relatives, the Osedax epibiont genomes were enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein (ELP) domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms. IMPORTANCE Symbiotic associations are widespread in nature and we can expect to find them in every type of ecological niche. In the last twenty years, the myriad of functions, interactions and species comprising microbe-host associations has fueled a surge of interest and appreciation for symbiosis. During this 14-year study, we reveal a dynamic population of bacterial epibionts, integrated into the epidermis of 7 species of a deep-sea worm group that feeds exclusively on the remains of marine mammals. The bacterial genomes provide clues of a long evolutionary history with these enigmatic worms. On the host surface, they exchange genes and appear to undergo ecological succession, as the whale carcass habitat degrades over time, similar to what is observed for some free-living communities. These, and other annelid worms are important keystone species for diverse deep-sea environments, yet the role of attached external bacteria in supporting host health has received relatively little attention.
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Affiliation(s)
- Shana K. Goffredi
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Balig Panossian
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Camille Brzechffa
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Naomi Field
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Chad King
- Monterey Bay National Marine Sanctuary, Monterey, California, USA
| | - Giacomo Moggioli
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg W. Rouse
- Scripps Oceanography, University of California, La Jolla, California, USA
| | - José M. Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Lee M. Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
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Wada N, Iguchi A, Urabe Y, Yoshioka Y, Abe N, Takase K, Hayashi S, Kawanabe S, Sato Y, Tang SL, Mano N. Microbial mat compositions and localization patterns explain the virulence of black band disease in corals. NPJ Biofilms Microbiomes 2023; 9:15. [PMID: 37015942 PMCID: PMC10073141 DOI: 10.1038/s41522-023-00381-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
Black band disease (BBD) in corals is characterized by a distinctive, band-like microbial mat, which spreads across the tissues and often kills infected colonies. The microbial mat is dominated by cyanobacteria but also commonly contains sulfide-oxidizing bacteria (SOB), sulfate-reducing bacteria (SRB), and other microbes. The migration rate in BBD varies across different environmental conditions, including temperature, light, and pH. However, whether variations in the migration rates reflect differences in the microbial consortium within the BBD mat remains unknown. Here, we show that the micro-scale surface structure, bacterial composition, and spatial distribution differed across BBD lesions with different migration rates. The migration rate was positively correlated with the relative abundance of potential SOBs belonging to Arcobacteraceae localized in the middle layer within the mat and negatively correlated with the relative abundance of other potential SOBs belonging to Rhodobacteraceae. Our study highlights the microbial composition in BBD as an important determinant of virulence.
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Affiliation(s)
- Naohisa Wada
- Biodiversity Research Center, Academia Sinica, No.128, Sec 2, Academia Rd, Nangang, Taipei, 11529, Taiwan
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
- Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Yuta Urabe
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago-City, Okinawa, 905-2192, Japan
| | - Natsumi Abe
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Kazuki Takase
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Shuji Hayashi
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Saeko Kawanabe
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Yui Sato
- College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, No.128, Sec 2, Academia Rd, Nangang, Taipei, 11529, Taiwan.
| | - Nobuhiro Mano
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan.
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Zhang Y, Liu S, Zhang G, Peng Y, Wei Q, Jiang M, Zheng J. Evaluation of selenite reduction under salinity and sulfate stress in anaerobic membrane bioreactor. Front Bioeng Biotechnol 2023; 11:1133613. [PMID: 36970610 PMCID: PMC10036345 DOI: 10.3389/fbioe.2023.1133613] [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: 12/29/2022] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
Current microbial reduction technologies have been proven to be suitable for decontaminating industrial wastewaters containing high concentrations of selenium (Se) oxyanions, however, their application is strictly limited by the elemental Se (Se0) accumulation in the system effluents. In this work, a continuous-flow anaerobic membrane bioreactor (AnMBR) was employed for the first time to treat synthetic wastewater containing 0.2 mM soluble selenite (SeO3 2-). The SeO3 2- removal efficiency by the AnMBR was approachable to 100% in most of the time, regardless of the fluctuation in influent salinity and sulfate (SO4 2-) stress. Se0 particles were always undetectable in the system effluents, owing to their interception by the surface micropores and adhering cake layer of membranes. High salt stress led to the aggravated membrane fouling and diminished content ratio of protein to polysaccharide in the cake layer-contained microbial products. The results of physicochemical characterization suggested that the sludge-attached Se0 particles presented either sphere- or rod-like morphology, hexagonal crystalline structure and were entrapped by the organic capping layer. According to the microbial community analysis, increasing influent salinity led to the diminished population of non-halotolerant Se-reducer (Acinetobacter) and increased abundance of halotolerant sulfate reducing bacteria (Desulfomicrobium). In the absence of Acinetobacter, the efficient SeO3 2- abatement performance of the system could still be maintained, as a result of the abiotic reaction between SeO3 2- and S2- generated by Desulfomicrobium, which then gave rise to the production of Se0 and S0.
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Affiliation(s)
- Yuanyuan Zhang
- College of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, China
- Guangxi Key Laboratory of Automatic Detecting Technology and Instruments, Guilin University of Electronic Technology, Guilin, China
| | - Shuang Liu
- College of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, China
| | - Gaorong Zhang
- College of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, China
| | - Yixiang Peng
- College of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, China
| | - Qiaoyan Wei
- College of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, China
- Guangxi Key Laboratory of Automatic Detecting Technology and Instruments, Guilin University of Electronic Technology, Guilin, China
| | - Minmin Jiang
- College of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, China
- Guangxi Key Laboratory of Automatic Detecting Technology and Instruments, Guilin University of Electronic Technology, Guilin, China
| | - Junjian Zheng
- College of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, China
- Guangxi Key Laboratory of Automatic Detecting Technology and Instruments, Guilin University of Electronic Technology, Guilin, China
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Le Moine Bauer S, Lu GS, Goulaouic S, Puzenat V, Schouw A, Barreyre T, Pawlowsky-Glahn V, Egozcue JJ, Martelat JE, Escartin J, Amend JP, Nomikou P, Vlasopoulos O, Polymenakou P, Jørgensen SL. Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece. Front Microbiol 2023; 13:1060168. [PMID: 36687571 PMCID: PMC9852839 DOI: 10.3389/fmicb.2022.1060168] [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: 10/02/2022] [Accepted: 12/01/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades. However, a thorough description of the microbial communities inhabiting the bay is still missing. Methods We present the first in-depth characterization of the prokaryotic communities of Paleochori Bay by sampling eight different seafloor types that are distributed along the entire gradient of hydrothermal influence. We used deep sequencing of the 16S rRNA marker gene and complemented the analysis with qPCR quantification of the 16S rRNA gene and several functional genes to gain insights into the metabolic potential of the communities. Results We found that the microbiome of the bay is strongly influenced by the hydrothermal venting, with a succession of various groups dominating the sediments from the coldest to the warmest zones. Prokaryotic diversity and abundance decrease with increasing temperature, and thermophilic archaea overtake the community. Discussion Relevant geochemical cycles of the Bay are discussed. This study expands our limited understanding of subsurface microbial communities in acidic shallow-sea hydrothermal systems and the contribution of their microbial activity to biogeochemical cycling.
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Affiliation(s)
- Sven Le Moine Bauer
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway,*Correspondence: Sven Le Moine Bauer,
| | - Guang-Sin Lu
- Cooperative Institute for Climate, Ocean and Ecosystem Studies, University of Washington, Seattle, WA, United States,NOAA Pacific Marine Environmental Laboratory, Seattle, WA, United States
| | - Steven Goulaouic
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Valentine Puzenat
- Institut de Physique du Globe de Paris, CNRS, Université Paris Cité, Paris, France
| | - Anders Schouw
- Center for Deep Sea Research, Department of Biology, University of Bergen, Bergen, Norway
| | - Thibaut Barreyre
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Vera Pawlowsky-Glahn
- Department of Computer Science, Applied Mathematics and Statistics, University of Girona, Girona, Spain
| | - Juan José Egozcue
- Department of Civil and Environmental Engineering, University Politécnica de Cataluña, Barcelona, Spain
| | - Jean-Emmanuel Martelat
- Université de Lyon, UCBL, ENSL, CNRS, Laboratoire de Géologie LGL-TPE, Villeurbanne, France
| | - Javier Escartin
- Laboratoire de Géologie (CNRS UMR8538), Ecole Normale Supérieure de Paris, PSL University, Paris, France
| | - Jan P. Amend
- Departments of Earth Sciences and Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Paraskevi Nomikou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Othonas Vlasopoulos
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Paraskevi Polymenakou
- Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Steffen Leth Jørgensen
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
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Lazar CS, Schmidt F, Elvert M, Heuer VB, Hinrichs KU, Teske AP. Microbial diversity gradients in the geothermal mud volcano underlying the hypersaline Urania Basin. Front Microbiol 2022; 13:1043414. [PMID: 36620052 PMCID: PMC9812581 DOI: 10.3389/fmicb.2022.1043414] [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: 09/13/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Mud volcanoes transport deep fluidized sediment and their microbial communities and thus provide a window into the deep biosphere. However, mud volcanoes are commonly sampled at the surface and not probed at greater depths, with the consequence that their internal geochemistry and microbiology remain hidden from view. Urania Basin, a hypersaline seafloor basin in the Mediterranean, harbors a mud volcano that erupts fluidized mud into the brine. The vertical mud pipe was amenable to shipboard Niskin bottle and multicorer sampling and provided an opportunity to investigate the downward sequence of bacterial and archaeal communities of the Urania Basin brine, fluid mud layers and consolidated subsurface sediments using 16S rRNA gene sequencing. These microbial communities show characteristic, habitat-related trends as they change throughout the sample series, from extremely halophilic bacteria (KB1) and archaea (Halodesulfoarchaeum spp.) in the brine, toward moderately halophilic and thermophilic endospore-forming bacteria and uncultured archaeal lineages in the mud fluid, and finally ending in aromatics-oxidizing bacteria, uncultured spore formers, and heterotrophic subsurface archaea (Thermoplasmatales, Bathyarchaeota, and Lokiarcheota) in the deep subsurface sediment at the bottom of the mud volcano. Since these bacterial and archaeal lineages are mostly anaerobic heterotrophic fermenters, the microbial ecosystem in the brine and fluidized mud functions as a layered fermenter for the degradation of sedimentary biomass and hydrocarbons. By spreading spore-forming, thermophilic Firmicutes during eruptions, the Urania Basin mud volcano likely functions as a source of endospores that occur widely in cold seafloor sediments.
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Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, Université du Québec à Montréal, Montréal, QC, Canada
| | - Frauke Schmidt
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Verena B. Heuer
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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11
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Virpiranta H, Leiviskä T, Taskila S, Tanskanen J. Bioregeneration of sulfate-laden anion exchange resin. WATER RESEARCH 2022; 224:119110. [PMID: 36126630 DOI: 10.1016/j.watres.2022.119110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Ion exchange technology removes ionic compounds from waters effectively but treatment of the spent regenerant is expensive. The bioregeneration of sulfate-laden strong base anion exchange resin was successfully tested using both pure and mixed sulfate-reducing bacterial cultures. The resin was first used for removal of sulfate from neutral (pH 6.7 ± 0.5) synthetic sodium sulfate solutions, after which the spent resin was regenerated by incubating with a viable sulfate-reducing bacterial culture in batch and column modes. In the batch bioregeneration tests, the achieved bioregeneration was 36-95% of the original capacity of the fresh resin (112 mg SO42-/g) and it increased with regeneration time (1-14 days). The capacity achieved in the column tests during 24 hours of bioregeneration was 107 mg SO42-/g after the first regeneration cycle. During the bioregeneration, sulfate was mainly reduced by the sulfate-reducing bacteria (approx. 60%), but part of it was only detached from the resins (approx. 30%). The resin-attached sulfate was most likely replaced with ions present in the liquid sulfate-reducing bacterial culture (e.g., HCO3-, HS-, and Cl-). During the subsequent exhaustion cycles with the bioregenerated resin, the pH of the treated sodium sulfate solution increased from the original 6.7 ± 0.5 to around 9. The study showed that biological sulfate reduction could be used for sulfate removal in combination with ion exchange, and that the exhausted ion exchange resins could be regenerated using a liquid sulfate-reducing bacterial culture without producing any brine.
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Affiliation(s)
- Hanna Virpiranta
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014 Oulu, Finland.
| | - Tiina Leiviskä
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014 Oulu, Finland
| | - Sanna Taskila
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014 Oulu, Finland
| | - Juha Tanskanen
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014 Oulu, Finland
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12
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Zhu QZ, Wegener G, Hinrichs KU, Elvert M. Activity of Ancillary Heterotrophic Community Members in Anaerobic Methane-Oxidizing Cultures. Front Microbiol 2022; 13:912299. [PMID: 35722308 PMCID: PMC9201399 DOI: 10.3389/fmicb.2022.912299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria mediate the anaerobic oxidation of methane (AOM) in marine sediments. However, even sediment-free cultures contain a substantial number of additional microorganisms not directly related to AOM. To track the heterotrophic activity of these community members and their possible relationship with AOM, we amended meso- (37°C) and thermophilic (50°C) AOM cultures (dominated by ANME-1 archaea and their partner bacteria of the Seep-SRB2 clade or Candidatus Desulfofervidus auxilii) with L-leucine-3-13C (13C-leu). Various microbial lipids incorporated the labeled carbon from this amino acid, independent of the presence of methane as an energy source, specifically bacterial fatty acids, such as iso and anteiso-branched C15:0 and C17:0, as well as unsaturated C18:1ω9 and C18:1ω7. In natural methane-rich environments, these bacterial fatty acids are strongly 13C-depleted. We, therefore, suggest that those fatty acids are produced by ancillary bacteria that grow on 13C-depleted necromass or cell exudates/lysates of the AOM core communities. Candidates that likely benefit from AOM biomass are heterotrophic bacterial members of the Spirochetes and Anaerolineae—known to produce abundant branched fatty acids and present in all the AOM enrichment cultures. For archaeal lipids, we observed minor 13C-incorporation, but still suggesting some 13C-leu anabolism. Based on their relatively high abundance in the culture, the most probable archaeal candidates are Bathyarchaeota, Thermoplasmatales, and Lokiarchaeota. The identified heterotrophic bacterial and archaeal ancillary members are likely key players in organic carbon recycling in anoxic marine sediments.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
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Assessing Microbial Corrosion Risk on Offshore Crude Oil Production Topsides under Conditions of Nitrate and Nitrite Treatment for Souring. Microorganisms 2022; 10:microorganisms10050932. [PMID: 35630376 PMCID: PMC9145487 DOI: 10.3390/microorganisms10050932] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 01/06/2023] Open
Abstract
Oilfield souring is a detrimental effect caused by sulfate-reducing microorganisms that reduce sulfate to sulfide during their respiration process. Nitrate or nitrite can be used to mitigate souring, but may also impart a corrosion risk. Produced fluids sampled from the topside infrastructure of two floating, production, storage, and offloading (FPSO) vessels (Platform A and Platform B) were assessed for microbial corrosion under nitrate and nitrite breakthrough conditions using microcosm tests incubated at 54 °C. Microbial community compositions on each individual FPSO were similar, while those between the two FPSO vessels differed. Platform B microbial communities responded as expected to nitrate breakthrough conditions, where nitrate-reducing activity was enhanced and sulfate reduction was inhibited. In contrast, nitrate treatments of Platform A microbial communities were not as effective in preventing sulfide production. Nitrite breakthrough conditions had the strongest sulfate reduction inhibition in samples from both platforms, but exhibited the highest pitting density. Live experimental replicates with no nitrate or nitrite additive yielded the highest general corrosion rates in the study (up to 0.48 mm/year), while nitrate- or nitrite-treated fluids revealed general corrosion rates that are considered low or moderate (<0.12 mm/year). Overall, the results of this study provide a description of nitrogen- and sulfur-based microbial activities under thermophilic conditions, and their risk for MIC that can occur along fluid processing lines on FPSO topsides that process fluids during offshore oil production operations.
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Watanabe T, Kubo K, Kamei Y, Kojima H, Fukui M. Dissimilatory microbial sulfur and methane metabolism in the water column of a shallow meromictic lake. Syst Appl Microbiol 2022; 45:126320. [DOI: 10.1016/j.syapm.2022.126320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 01/04/2023]
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15
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Zhang G, Yang Z, Zhou Y, Zhu DZ, Zhang Y, Yu T, Shypanski A. Combination of nitrate and sodium nitroprusside dosing for sulfide control with low carbon source loss in sewer biofilm reactors. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127527. [PMID: 34879520 DOI: 10.1016/j.jhazmat.2021.127527] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/22/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Nitrate has been widely used in sewer systems for sulfide control. However, significant chemical consumption and the loss of carbon source were observed in previous studies. To find a feasible and cost-effective control strategy of the sulfide control, the effect of nitrate combined with sodium nitroprusside (SNP) dosage strategy was tested in lab-scale sewer biofilm reactors. Results showed that nitrate and SNP were strongly synergistic, with 30 mg N/L nitrate and 20 mg/L SNP being sufficient for sulfide control in this study. While large amount of nitrate alone (100 mg N/L) is required to achieve the same sulfide control effectiveness. Meanwhile, the nitrate combined with SNP could reduce the organic carbon source loss by 80%. Additionally, the high-throughput sequencing results showed that the relative abundance of autotrophic, nitrate reducing-sulfide oxidizing bacteria genera (a-NR-SOB) such as Arcobacter and Sulfurimonas was increased by around 18%, while the heterotrophic, nitrate-reducing bacteria (hNRB) such as Thauera was substantially reduced. It demonstrated that the sulfide control was mainly due to the a-NR-SOB activity under the nitrate and SNP dosing strategy. The microbial functional prediction further revealed that nitrate and SNP promoted the dissimilatory nitrate reduction process which utilizes sulfide as an effective electron donor. Moreover, economic assessment indicated that using the combination of nitrate and SNP for sulfide control in sewers would lower the chemical costs by approximately 35% compared with only nitrate addition.
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Affiliation(s)
- Guijiao Zhang
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China; Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Zhi Yang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Yongchao Zhou
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China.
| | - David Z Zhu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Yiping Zhang
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Tong Yu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Adam Shypanski
- Drainage Planning, EPCOR Drainage Services, Edmonton, AB T5J 3A3, Canada
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Jurado V, D'Angeli I, Martin-Pozas T, Cappelletti M, Ghezzi D, Gonzalez-Pimentel JL, Cuezva S, Miller AZ, Fernandez-Cortes A, De Waele J, Sanchez-Moral S, Saiz-Jimenez C. Dominance of Arcobacter in the white filaments from the thermal sulfidic spring of Fetida Cave (Apulia, southern Italy). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149465. [PMID: 34391144 DOI: 10.1016/j.scitotenv.2021.149465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/31/2021] [Indexed: 05/10/2023]
Abstract
The thermal spring of Fetida Cave, a still active sulfuric acid cave opening at sea level and located in Santa Cesarea Terme, southeastern Salento (Apulia region, Southern Italy) hosts abundant floating white filaments. The white filaments were mainly composed of sulfur crystals surrounded by microbial mass of the phyla Epsilonbacteraeota, Proteobacteria, Bacteroidetes, and Patescibacteria. The most abundant genus in the white filaments collected from the waters in the innermost part of the cave dominated by sulfidic exhalations was Arcobacter. This abundance can be related to the higher concentration of sulfide dissolved in water, and low oxygen and pH values. Conversely, lower Arcobacter abundances were obtained in the filaments collected in the entrance and middle part of the cave, where sulfidic water mixes with seawater, as the cave is subjected to tides and the mixing of fresh (continental) with marine water. The geochemical analysis of water and atmospheric gases confirmed these environmental constraints. In fact, the highest concentrations of H2S in the air and water were recorded closest to the spring upwelling in the innermost part of the cave, and the lowest ones near the cave entrance. The metabolic versatility of Arcobacter might provide a competitive advantage in the colonization of water bodies characterized by high sulfide, low oxygen, and dynamic fluid movement.
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Affiliation(s)
- Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, 41012 Sevilla, Spain
| | - Ilenia D'Angeli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | | | - Martina Cappelletti
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, 40126 Bologna, Italy
| | - Daniele Ghezzi
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, 40126 Bologna, Italy; Laboratory of NanoBiotechnology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | | | - Soledad Cuezva
- Departamento de Geologia, Geografia y Medio Ambiente, Universidad de Alcala de Henares, 28801 Alcala de Henares, Spain
| | - Ana Zelia Miller
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, 41012 Sevilla, Spain
| | | | - Jo De Waele
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | | | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, 41012 Sevilla, Spain.
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Genus-Specific Carbon Fixation Activity Measurements Reveal Distinct Responses to Oxygen Among Hydrothermal Vent Campylobacteria. Appl Environ Microbiol 2021; 88:e0208321. [PMID: 34788061 DOI: 10.1128/aem.02083-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (prev. Epsilonproteobacteria) often dominate the microbial community and that three genera - Arcobacter, Sulfurimonas and Sulfurovum - frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in-situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO2 in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ. Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances. Importance: Sulfidic environments worldwide are often dominated by sulfur-oxidizing, carbon-fixing Campylobacteria. Environmental factors associated with this group's dominance are now understood, but far less is known about the ecology and physiology of members of subgroups of chemoautotrophic Campylobacteria. In this study, we used a novel method to differentiate the genus-specific chemoautotrophic activity of three subtypes of Campylobacteria. In combination with evidence from microscopic counts, chemical consumption/production during incubations, and DNA-based measurements, our data show that oxygen concentration affects both community composition and chemoautotrophic function in situ. These results help us better understand factors controlling microbial diversity at deep-sea hydrothermal vents, and provide first-order insights into the ecophysiological differences between these distinct microbial taxa.
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Yan X, Du Q, Mu Q, Tian L, Wan Y, Liao C, Zhou L, Yan Y, Li N, Logan BE, Wang X. Long-Term Succession Shows Interspecies Competition of Geobacter in Exoelectrogenic Biofilms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14928-14937. [PMID: 34676765 DOI: 10.1021/acs.est.1c03010] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Geobacter spp. are well-known exoelectrogenic microorganisms that often predominate acetate-fed biofilms in microbial fuel cells (MFCs) and other bioelectrochemical systems (BESs). By using an amplicon sequence variance analysis (at one nucleotide resolution), we observed a succession between two closely related species (98% similarity in 16S RNA), Geobacter sulfurreducens and Geobacter anodireducens, in the long-term studies (20 months) of MFC biofilms. Geobacter spp. predominated in the near-electrode portion of the biofilm, while the outer layer contained an abundance of aerobes, which may have helped to consume oxygen but reduced the relative abundance of Geobacter. Removal of the outer aerobes by norspermidine washing of biofilms revealed a transition from G. sulfurreducens to G. anodireducens. This succession was also found to occur rapidly in co-cultures in BES tests even in the absence of oxygen, suggesting that oxygen was not a critical factor. G. sulfurreducens likely dominated in early biofilms by its relatively larger cell size and production of extracellular polymeric substances (individual advantages), while G. anodireducens later predominated due to greater cell numbers (quantitative advantage). Our findings revealed the interspecies competition in the long-term evolution of Geobacter genus, providing microscopic insights into Geobacter's niche and competitiveness in complex electroactive microbial consortia.
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Affiliation(s)
- Xuejun Yan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Qing Du
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Quanhua Mu
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | - Lili Tian
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Yuxuan Wan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Chengmei Liao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Lean Zhou
- School of Hydraulic Engineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Yuqing Yan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
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Conspicuous Smooth and White Egg-Shaped Sulfur Structures on a Deep-Sea Hydrothermal Vent Formed by Sulfide-Oxidizing Bacteria. Microbiol Spectr 2021; 9:e0095521. [PMID: 34468192 PMCID: PMC8557937 DOI: 10.1128/spectrum.00955-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conspicuous egg-shaped, white, and smooth structures were observed at a hydrothermal vent site in the Guaymas Basin, Gulf of California. The gelatinous structures decomposed within hours after sampling. Scanning electron microscopy (SEM) and light microscopy showed that the structure consisted of filaments of less than 0.1 μm thickness, similar to those observed for "Candidatus Arcobacter sulfidicus." SEM-energy-dispersive X-ray spectroscopy (EDS) showed that the filaments were sulfur rich. According to 16S rRNA gene amplicon and fluorescence in situ hybridization (FISH) analyses, Arcobacter, a sulfide oxidizer that is known to produce filamentous elemental sulfur, was among the dominant species in the structure and was likely responsible for its formation. Arcobacter normally produces woolly snowflake like structures in opposed gradients of sulfide and oxygen. In the laboratory, we observed sulfide consumption in the anoxic zone of the structure, suggesting an anaerobic conversion. The sulfide oxidation and decomposition of the structure in the laboratory may be explained by dissolution of the sulfur filaments by reaction with sulfide under formation of polysulfides. IMPORTANCE At the deep-sea Guaymas Basin hydrothermal vent system, sulfide-rich hydrothermal fluids mix with oxygenated seawater, thereby providing a habitat for microbial sulfur oxidation. Microbial sulfur oxidation in the deep sea involves a variety of organisms and processes and can result in the excretion of elemental sulfur. Here, we report on conspicuous white and smooth gelatinous structures found on hot vents. These strange egg-shaped structures were often observed on previous occasions in the Guaymas Basin, but their composition and formation process were unknown. Our data suggest that the notable and highly ephemeral structure was likely formed by the well-known sulfide-oxidizing Arcobacter. While normally Arcobacter produces loose flocs or woolly layers, here smooth gel-like structures were found.
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Iqbal MM, Nishimura M, Haider MN, Sano M, Ijichi M, Kogure K, Yoshizawa S. Diversity and Composition of Microbial Communities in an Eelgrass (Zostera marina) Bed in Tokyo Bay, Japan. Microbes Environ 2021; 36. [PMID: 34645731 PMCID: PMC8674447 DOI: 10.1264/jsme2.me21037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Zostera marina (eelgrass) is a widespread seagrass species that forms diverse and productive habitats along coast lines throughout much of the northern hemisphere. The present study investigated the microbial consortia of Z. marina growing at Futtsu clam-digging beach, Chiba prefecture, Japan. The following environmental samples were collected: sediment, seawater, plant leaves, and the root-rhizome. Sediment and seawater samples were obtained from three sampling points: inside, outside, and at the marginal point of the eelgrass bed. The microbial composition of each sample was analyzed using 16S ribosomal gene amplicon sequencing. Microbial communities on the dead (withered) leaf surface markedly differed from those in sediment, but were similar to those in seawater. Eelgrass leaves and surrounding seawater were dominated by the bacterial taxa Rhodobacterales (Alphaproteobacteria), whereas Rhodobacterales were a minor group in eelgrass sediment. Additionally, we speculated that the order Sphingomonadales (Alphaproteobacteria) acts as a major degrader during the decomposition process and constantly degrades eelgrass leaves, which then spread into the surrounding seawater. Withered eelgrass leaves did not accumulate on the surface sediment because they were transported out of the eelgrass bed by wind and residual currents unique to the central part of Tokyo Bay.
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Affiliation(s)
- Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo
| | | | - Md Nurul Haider
- Atmosphere and Ocean Research Institute, The University of Tokyo.,Department of Fisheries Technology, Faculty of Fisheries, Bangladesh Agricultural University
| | - Masayoshi Sano
- Atmosphere and Ocean Research Institute, The University of Tokyo.,National Institute of Polar Research
| | - Minoru Ijichi
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo
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21
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Sylvestre MN, Jean-Louis P, Grimonprez A, Bilas P, Collienne A, Azède C, Gros O. Candidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environment. Can J Microbiol 2021; 68:1-14. [PMID: 34461021 DOI: 10.1139/cjm-2021-0101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A large (47.75 ± 3.56 µm in diameter) Thiovulum bacterial strain forming white veils is described from a marine mangrove ecosystem. High sulfide concentrations (up to 8 mM of H2S) were measured on sunken organic matter (wood/bone debris) under laboratory conditions. This sulfur-oxidizing bacterium colonized the organic matter, forming a white veil. According to conventional scanning electron microscope (SEM) observations, bacterial cells are ovoid and slightly motile by numerous small flagella present on the cell surface. Large intracytoplasmic internal sulfur granules were observed, suggesting a sulfidic-based metabolism. Observations were confirmed by elemental sulfur distribution detected by energy-dispersive X-ray spectroscopy (EDXS) analysis using an environmental scanning electron microscope (ESEM) on non-dehydrated samples. Phylogenetic analysis of the partial sequence of 16S rDNA obtained from purified fractions of this Epsilonproteobacteraeota strain indicates that this bacterium belongs to the Thiovulaceae cluster and could be one of the largest Thiovulum ever described. We propose to name this species Candidatus Thiovulum sp. strain imperiosus.
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Affiliation(s)
- Marie-Noëlle Sylvestre
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Patrick Jean-Louis
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Adrien Grimonprez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Philippe Bilas
- Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane (C3MAG), UFR des Sciences Exactes et Naturelles, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
- Groupe de Technologie des Surfaces et des Interfaces, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Amandine Collienne
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Catherine Azède
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
- Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane (C3MAG), UFR des Sciences Exactes et Naturelles, Université des Antilles, BP 592 - 97159 Pointe-à-Pitre, Guadeloupe
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22
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Mori F, Umezawa Y, Kondo R, Nishihara GN, Wada M. Potential oxygen consumption and community composition of sediment bacteria in a seasonally hypoxic enclosed bay. PeerJ 2021; 9:e11836. [PMID: 34434647 PMCID: PMC8362671 DOI: 10.7717/peerj.11836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a sharp increase in the relative abundance of sulfate reducing bacteria toward hypoxia. In addition, a notable shift in other bacterial compositions was observed before and after the INT assay incubation. It was Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, that increased markedly during the assay period in the summer samples. These findings have implications not only for members of Delta- and Gammaproteobacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.
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Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan.,Institute for East China Sea Research, Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Nagasaki, Japan.,Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kochi, Japan
| | - Yu Umezawa
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Fukui, Japan
| | - Gregory N Nishihara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan.,Institute for East China Sea Research, Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Nagasaki, Japan
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
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23
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Iwanowicz DD, Jonas RB, Schill WB, Marano-Briggs K. Novel microbiome dominated by Arcobacter during anoxic excurrent flow from an ocean blue hole in Andros Island, The Bahamas. PLoS One 2021; 16:e0256305. [PMID: 34411155 PMCID: PMC8375975 DOI: 10.1371/journal.pone.0256305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/03/2021] [Indexed: 11/18/2022] Open
Abstract
Andros Island, The Bahamas, composed of porous carbonate rock, has about 175 inland blue holes and over 50 known submerged ocean caves along its eastern barrier reef. These ocean blue holes can have both vertical and horizontal zones that penetrate under the island. Tidal forces drive water flow in and out of these caves. King Kong Cavern has a vertical collapse zone and a deep penetration under Andros Island that emits sulfidic, anoxic water and masses of thin, mucoid filaments ranging to meters in length and off-white turbid water during ebb flow. Our objective was to determine the microbial composition of this mucoid material and the unconsolidated water column turbidity based on the concept that they represent unique lithoautotrophic microbial material swept from the cave into the surrounding ocean. Bacterial DNA extracted from these filaments and surrounding turbid water was characterized using PCR that targeted a portion of the 16S rRNA gene. The genus Arcobacter dominated both the filaments and the water column above the cave entrance. Arcobacter nitrofigilis and Arcobacter sp. UDC415 in the mucoid filaments accounted for as much as 80% of mapped DNA reads. In the water column Arcobacter comprised from 65% to over 85% of the reads in the depth region from about 18 m to 34 m. Bacterial species diversity was much higher in surface water and in water deeper than 36 m than in the intermediate zone. Community composition indicates that ebb flow from the cavern influences the entire water column at least to within 6 m of the surface and perhaps the near surface as well.
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Affiliation(s)
- Deborah D. Iwanowicz
- Eastern Ecological Science Center, United States Geological Survey, Kearneysville, West Virginia, United States of America
| | - Robert B. Jonas
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, United States of America
- * E-mail:
| | - William B. Schill
- Eastern Ecological Science Center, United States Geological Survey, Kearneysville, West Virginia, United States of America
| | - Kay Marano-Briggs
- Eastern Ecological Science Center, United States Geological Survey, Kearneysville, West Virginia, United States of America
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24
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Cooccurring Activities of Two Autotrophic Pathways in Symbionts of the Hydrothermal Vent Tubeworm Riftia pachyptila. Appl Environ Microbiol 2021; 87:e0079421. [PMID: 34190607 DOI: 10.1128/aem.00794-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome and proteome data predict the presence of both the reductive citric acid cycle (rCAC; also called the reductive tricarboxylic acid cycle) and the Calvin-Benson-Bassham cycle (CBB) in "Candidatus Endoriftia persephonae," the autotrophic sulfur-oxidizing bacterial endosymbiont from the giant hydrothermal vent tubeworm Riftia pachyptila. We tested whether these cycles were differentially induced by sulfide supply, since the synthesis of biosynthetic intermediates by the rCAC is less energetically expensive than that by the CBB. R. pachyptila was incubated under in situ conditions in high-pressure aquaria under low (28 to 40 μmol · h-1) or high (180 to 276 μmol · h-1) rates of sulfide supply. Symbiont-bearing trophosome samples excised from R. pachyptila maintained under the two conditions were capable of similar rates of CO2 fixation. Activities of the rCAC enzyme ATP-dependent citrate lyase (ACL) and the CBB enzyme 1,3-bisphosphate carboxylase/oxygenase (RubisCO) did not differ between the two conditions, although transcript abundances for ATP-dependent citrate lyase were 4- to 5-fold higher under low-sulfide conditions. δ13C values of internal dissolved inorganic carbon (DIC) pools were varied and did not correlate with sulfide supply rate. In samples taken from freshly collected R. pachyptila, δ13C values of lipids fell between those collected for organisms using either the rCAC or the CBB exclusively. These observations are consistent with cooccurring activities of the rCAC and the CBB in this symbiosis. IMPORTANCE Previous to this study, the activities of the rCAC and CBB in R. pachyptila had largely been inferred from "omics" studies of R. pachyptila without direct assessment of in situ conditions prior to collection. In this study, R. pachyptila was maintained and monitored in high-pressure aquaria prior to measuring its CO2 fixation parameters. Results suggest that ranges in sulfide concentrations similar to those experienced in situ do not exert a strong influence on the relative activities of the rCAC and the CBB. This observation highlights the importance of further study of this symbiosis and other organisms with multiple CO2-fixing pathways, which recent genomics and biochemical studies suggest are likely to be more prevalent than anticipated.
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25
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Patin NV, Dietrich ZA, Stancil A, Quinan M, Beckler JS, Hall ER, Culter J, Smith CG, Taillefert M, Stewart FJ. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. THE ISME JOURNAL 2021; 15:2206-2232. [PMID: 33612832 PMCID: PMC8319197 DOI: 10.1038/s41396-021-00917-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.
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Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
- Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
| | | | - A Stancil
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - M Quinan
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - J S Beckler
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - E R Hall
- Mote Marine Laboratory, Sarasota, FL, USA
| | - J Culter
- Mote Marine Laboratory, Sarasota, FL, USA
| | - C G Smith
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA
| | - M Taillefert
- School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - F J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
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26
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Johnson MD, Scott JJ, Leray M, Lucey N, Bravo LMR, Wied WL, Altieri AH. Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. Nat Commun 2021; 12:4522. [PMID: 34312399 PMCID: PMC8313580 DOI: 10.1038/s41467-021-24777-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic community composition and microbial assemblages in a shallow tropical reef ecosystem. Conditions associated with the event precipitated coral bleaching and mass mortality, causing a 50% loss of live coral and a shift in the benthic community that persisted a year later. Conversely, the unique taxonomic and functional profile of hypoxia-associated microbes rapidly reverted to a normoxic assemblage one month after the event. The decoupling of ecological trajectories among these major functional groups following an acute event emphasizes the need to incorporate deoxygenation as an emerging stressor into coral reef research and management plans to combat escalating threats to reef persistence.
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Affiliation(s)
- Maggie D Johnson
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.
- Tennenbaum Marine Observatories Network, MarineGEO, Smithsonian Institution, Edgewater, MD, USA.
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Jarrod J Scott
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Noelle Lucey
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Lucia M Rodriguez Bravo
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - William L Wied
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Department of Biological Sciences, Center for Coastal Oceans Research, Florida International University, Miami, FL, USA
| | - Andrew H Altieri
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
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27
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The Gut Microbiota of Naturally Occurring and Laboratory Aquaculture Lytechinus variegatus Revealed Differences in the Community Composition, Taxonomic Co-Occurrence, and Predicted Functional Attributes. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1020016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sea urchins, in many instances, are collected from the wild, maintained in the laboratory aquaculture environment, and used as model animals for various scientific investigations. It has been increasingly evident that diet-driven dysbiosis of the gut microbiome could affect animal health and physiology, thereby impacting the outcome of the scientific studies. In this study, we compared the gut microbiome between naturally occurring (ENV) and formulated diet-fed laboratory aquaculture (LAB) sea urchin Lytechinus variegatus by amplicon sequencing of the V4 region of the 16S rRNA gene and bioinformatics tools. Overall, the ENV gut digesta had higher taxa richness with an abundance of Propionigenium, Photobacterium, Roseimarinus, and Flavobacteriales. In contrast, the LAB group revealed fewer taxa richness, but noticeable abundances of Arcobacter, Agarivorans, and Shewanella. However, Campylobacteraceae, primarily represented by Arcobacter spp., was commonly associated with the gut tissues of both ENV and LAB groups whereas the gut digesta had taxa from Gammaproteobacteria, particularly Vibrio spp. Similarly, the co-occurrence network displayed taxonomic organizations interconnected by Arcobacter and Vibrio as being the key taxa in gut tissues and gut digesta, respectively. Predicted functional analysis of the gut tissues microbiota of both ENV and LAB groups showed a higher trend in energy-related metabolisms, whereas amino acids, carbohydrate, and lipid metabolisms heightened in the gut digesta. This study provides an outlook of the laboratory-formulated diet-fed aquaculture L. variegatus gut microbiome and predicted metabolic profile as compared to the naturally occurring animals, which should be taken into consideration for consistency, reproducibility, and translatability of scientific studies.
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28
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Izadi P, Gey MN, Schlüter N, Schröder U. Bidirectional electroactive microbial biofilms and the role of biogenic sulfur in charge storage and release. iScience 2021; 24:102822. [PMID: 34337365 PMCID: PMC8313490 DOI: 10.1016/j.isci.2021.102822] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/09/2021] [Accepted: 07/02/2021] [Indexed: 11/18/2022] Open
Abstract
The formation of combined electrogenic/electrotrophic biofilms from marine sediments for the development of microbial energy storage systems was studied. Sediment samples from the German coasts of the Baltic and the North Sea were used as inocula for biofilm formation. Anodic biofilm cultivation was applied for a fast and reproducible biofilm formation. North-Sea- and Baltic-Sea-derived biofilms yielded comparable anodic current densities of about 7.2 A m−2. The anodic cultivation was followed by a potential reversal regime, transitioning the electrode potential from 0.2 V to −0.8 V every 2 h to switch between anodic and cathodic conditions. The charge-discharge behavior was studied, revealing an electrochemical conversion of biogenic elemental sulfur as major charge-discharge mechanism. The microbial sequencing revealed strong differences between North- and Baltic-Sea-derived biofilms; however with a large number of known sulfur-converting and electrochemically active bacteria in both biofilms. Bidirectional electroactive biofilms are cultivated from marine sediments Cultivation is based on anodic growth followed by periodic potential reversal Combined electrogenic and electrotrophic activity is shown Biogenic, elemental sulfur plays a key role in charge storage and release
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Affiliation(s)
- Paniz Izadi
- Institute of Environmental and Sustainable Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Marten Niklas Gey
- Institute of Environmental and Sustainable Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Nicolas Schlüter
- Institute of Environmental and Sustainable Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Uwe Schröder
- Institute of Environmental and Sustainable Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
- Corresponding author
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29
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Marlow JJ, Hoer D, Jungbluth SP, Reynard LM, Gartman A, Chavez MS, El-Naggar MY, Tuross N, Orphan VJ, Girguis PR. Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites. Proc Natl Acad Sci U S A 2021; 118:e2006857118. [PMID: 34161255 PMCID: PMC8237665 DOI: 10.1073/pnas.2006857118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
At marine methane seeps, vast quantities of methane move through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated Vmax, and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample's methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.
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Affiliation(s)
- Jeffrey J Marlow
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
| | - Daniel Hoer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Sean P Jungbluth
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94720
| | - Linda M Reynard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Amy Gartman
- US Geological Survey Pacific Coastal and Marine Science Center, Santa Cruz, CA 95060
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Noreen Tuross
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
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30
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Athen SR, Dubey S, Kyndt JA. The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment. Life (Basel) 2021; 11:446. [PMID: 34063450 PMCID: PMC8156497 DOI: 10.3390/life11050446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique inland salt marsh environment.
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Affiliation(s)
| | | | - John A. Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; (S.R.A.); (S.D.)
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Sulonen MLK, Baeza JA, Gabriel D, Guisasola A. Optimisation of the operational parameters for a comprehensive bioelectrochemical treatment of acid mine drainage. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:124944. [PMID: 33422754 DOI: 10.1016/j.jhazmat.2020.124944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Bioelectrochemical systems provide a promising tool for the treatment of acid mine drainage (AMD). Biological sulphate reduction powered with electrical energy consumes acidity and produces sulphide, which can precipitate metals. However, the produced sulphide and the changes in pH resulting from the biological processes affect the efficiency and the environmental impacts of this treatment significantly. In this work, the effects of pH and sulphur speciation on the sulphate reduction rate (SRR) and comprehensive AMD treatment were evaluated in two-chamber microbial electrolysis cells at a cathode potential of -0.8 V vs. NHE. The increase of initial sulphate concentration from below 1000 mg to above 1500 mg S-SO42-/L increased SRR from 121 ± 25 to 177 ± 19 mg S-SO42-/L/d. SRR further increased to 347 mg S-SO42-/L/d when the operation mode was changed from batch to periodical addition of sulphate and acidity (363 mg S-SO42-/L/d and 22.6 mmol H+/L/d, respectively). The average SRR remained above 150 mg S-SO42-/L/d even at pH above 8.5 and with the total dissolved sulphide concentration increasing above 1300 mg S-TDSu/L. Operation at pH above 8 enabled the recovery of over 90% of the sulphur as dissolved sulphide and thus assisted in minimising the formation and release of toxic H2S.
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Affiliation(s)
- Mira L K Sulonen
- GENOCOV Research Group, Departament d'Enginyeria Química, Biològica i Ambiental. Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Juan Antonio Baeza
- GENOCOV Research Group, Departament d'Enginyeria Química, Biològica i Ambiental. Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - David Gabriel
- GENOCOV Research Group, Departament d'Enginyeria Química, Biològica i Ambiental. Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Albert Guisasola
- GENOCOV Research Group, Departament d'Enginyeria Química, Biològica i Ambiental. Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Wang L, Tomas F, Mueller RS. Nutrient enrichment increases size of Zostera marina shoots and enriches for sulfur and nitrogen cycling bacteria in root-associated microbiomes. FEMS Microbiol Ecol 2021; 96:5861935. [PMID: 32578844 DOI: 10.1093/femsec/fiaa129] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/22/2020] [Indexed: 01/09/2023] Open
Abstract
Seagrasses are vital coastal ecosystem engineers, which are mutualistically associated with microbial communities that contribute to the ecosystem services provided by meadows. The seagrass microbiome and sediment microbiota play vital roles in belowground biogeochemical and carbon cycling. These activities are influenced by nutrient, carbon and oxygen availability, all of which are modulated by environmental factors and plant physiology. Seagrass meadows are increasingly threatened by nutrient pollution, and it is unknown how the seagrass microbiome will respond to this stressor. We investigated the effects of fertilization on the physiology, morphology and microbiome of eelgrass (Zostera marina) cultivated over 4 weeks in mesocosms. We analyzed the community structure associated with eelgrass leaf, root and rhizosphere microbiomes, and of communities from water column and bulk sediment using 16S rRNA amplicon sequencing. Fertilization led to a higher number of leaves compared with that of eelgrass kept under ambient conditions. Additionally, fertilization led to enrichment of sulfur and nitrogen bacteria in belowground communities. These results suggest nutrient enrichment can stimulate belowground biogeochemical cycling, potentially exacerbating sulfide toxicity in sediments and decreasing future carbon sequestration stocks.
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Affiliation(s)
- Lu Wang
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Fiona Tomas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA.,Instituto Mediterráneo de Estudios Avanzados (CSIC-UIB), C/ Miquel Marquès, 21 07190 Esporles Illes Balears, Spain
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
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Asplund-Samuelsson J, Hudson EP. Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes. PLoS Comput Biol 2021; 17:e1008742. [PMID: 33556078 PMCID: PMC7895386 DOI: 10.1371/journal.pcbi.1008742] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/19/2021] [Accepted: 01/25/2021] [Indexed: 11/21/2022] Open
Abstract
Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Elton P. Hudson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
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Hamood Altowayti WA, Almoalemi H, Shahir S, Othman N. Comparison of culture-independent and dependent approaches for identification of native arsenic-resistant bacteria and their potential use for arsenic bioremediation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 205:111267. [PMID: 32992213 DOI: 10.1016/j.ecoenv.2020.111267] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/16/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.
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Affiliation(s)
- Wahid Ali Hamood Altowayti
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia; Micro-pollutant Research Centre (MPRC), Department of Civil Engineering, Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Johor, Malaysia.
| | - Hafedh Almoalemi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.
| | - Shafinaz Shahir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.
| | - Norzila Othman
- Micro-pollutant Research Centre (MPRC), Department of Civil Engineering, Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Johor, Malaysia.
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Huang C, Liu Q, Chen X, Nan J, Li Z, Wang A. Bioaugmentation with Thiobacillus sp. H1 in an autotrophic denitrification desulfurization microbial reactor: Microbial community changes and relationship. ENVIRONMENTAL RESEARCH 2020; 189:109927. [PMID: 32678744 DOI: 10.1016/j.envres.2020.109927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
Thiobacillus sp. H1 was isolated and made into solid bacterial agent. The Thiobacillus sp. H1 agent was dosed into two reactor (all the agent dosed one-time, and multi-dosing bacteria evenly) and run for 40 days, a start-up with no microbial agent bioreactor as control. We found that the operational performance of multi-dosing inoculum reactor was stable, and the amount of elemental sulfur produced remained stable at 143.2-152.3 mg/L. The amount of elemental sulfur generated in the reactor without the addition of the inoculum was gradually increased, and the amount of elemental sulfur generated in the reactor with the inoculum added at one-time was decreased. Two kinds of Thiobacillus gen. and unclassified betaproteobacteria that coordinated the overall community function in the autotrophic denitrification desulfurization system with high-throughput sequencing. The trend of FccAB gene in each bioreactor was similar with the trend of elemental sulfur in the effluent. On the 5th day, the copy number of FccAB in bioreactor II was the highest among the three bioreactors, reaching 11.8 log copies L/g. This study explores the possibility of artificially synthesized denitrifying desulfurization flora in the future.
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Affiliation(s)
- Cong Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Qian Liu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Xueqi Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China.
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36
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Wang CH, Gulmann LK, Zhang T, Farfan GA, Hansel CM, Sievert SM. Microbial colonization of metal sulfide minerals at a diffuse-flow deep-sea hydrothermal vent at 9°50'N on the East Pacific Rise. GEOBIOLOGY 2020; 18:594-605. [PMID: 32336020 DOI: 10.1111/gbi.12396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/24/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Metal sulfide minerals, including mercury sulfides (HgS), are widespread in hydrothermal vent systems where sulfur-oxidizing microbes are prevalent. Questions remain as to the impact of mineral composition and structure on sulfur-oxidizing microbial populations at deep-sea hydrothermal vents, including the possible role of microbial activity in remobilizing elemental Hg from HgS. In the present study, metal sulfides varying in metal composition, structure, and surface area were incubated for 13 days on and near a diffuse-flow hydrothermal vent at 9°50'N on the East Pacific Rise. Upon retrieval, incubated minerals were examined by scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS), X-ray diffraction (XRD), and epifluorescence microscopy (EFM). DNA was extracted from mineral samples, and the 16S ribosomal RNA gene sequenced to characterize colonizing microbes. Sulfur-oxidizing genera common to newly exposed surfaces (Sulfurimonas, Sulfurovum, and Arcobacter) were present on all samples. Differences in their relative abundance between and within incubation sites point to constraining effects of the immediate environment and the minerals themselves. Greater variability in colonizing community composition on off-vent samples suggests that the bioavailability of mineral-derived sulfide (as influenced by surface area, crystal structure, and reactivity) exerted greater control on microbial colonization in the ambient environment than in the vent environment, where dissolved sulfide is more abundant. The availability of mineral-derived sulfide as an electron donor may thus be a key control on the activity and proliferation of deep-sea chemosynthetic communities, and this interpretation supports the potential for microbial dissolution of HgS at hydrothermal vents.
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Affiliation(s)
- Chloe H Wang
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Chemistry, Haverford College, Haverford, PA, USA
| | - Lara K Gulmann
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Tong Zhang
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, Tianjin, China
| | - Gabriela A Farfan
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Mineral Sciences, Smithsonian Institution, Washington, DC, USA
| | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Stefan M Sievert
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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37
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Zhang RC, Chen C, Shao B, Wang W, Xu XJ, Zhou X, Xiang YN, Zhao L, Lee DJ, Ren NQ. Heterotrophic sulfide-oxidizing nitrate-reducing bacteria enables the high performance of integrated autotrophic-heterotrophic denitrification (IAHD) process under high sulfide loading. WATER RESEARCH 2020; 178:115848. [PMID: 32361288 DOI: 10.1016/j.watres.2020.115848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/04/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Micro-aerobic enhancement technology has been developed as an effective tool to enhance simultaneous removal of sulfide, nitrate and organic carbon during the integrated autotrophic-heterotrophic denitrification (IAHD) process under high loading; however, its mechanism of enhancement for functional bacteria remains ambiguous. In this study, we discovered that heterotrophic sulfide-oxidizing nitrate-reducing bacteria (h-soNRB) are responsible for enhancing IAHD performance under micro-aerobic conditions with high sulfide loading. In a continuous IAHD bioreactor, aeration rate of 2.6 mL min-1·L-1 promoted 2 to 4 times higher removal efficiencies of sulfide, nitrate and acetate with an influent sulfide concentration of 18.75 mmol/L. Metagenomic analysis revealed that trace oxygen stimulated the abundance of genes responsible for sulfide oxidation (sqr, glpE, pdo, sox and cysK), which were upregulated by 15.2%-129.9%, and the genes encoding nitrate reductase were up-regulated by 67.4%. The increased acetate removal efficiency was attributed to upregulation of ack, pta and TCA cycle related genes. The h-NRB Pseudomonas, Azoarcus, Thauera and Halomonas were detected and regarded as h-soNRB in our bioreactor. According to Illumina MiSeq sequencing, these genera were absolutely dominant in the micro-aerobic microbial community at relative abundances ranging from 82.72% to 90.84%. The sulfide, nitrate and acetate removal rates of Pseudomonas C27, a typical h-soNRB, were at least 10 times higher under micro-aerobic conditions than under anaerobic conditions. Besides, the sulfur, nitrogen and carbon metabolic network was constructed based on the Pseudomonas C27 genome. The pdo and cysK genes found in this strain may be the most advantageous for autotrophic sulfide oxidizing nitrate reducing bacteria (a-soNRB), which are closely related to the high-efficiency sulfide, nitrate and acetate removal performance under high sulfide concentrations and a limited oxygen supply. In addition, after micro-aerobic cultivation, the anaerobic sulfide loading tolerance of the IAHD bioreactor increased from 18.75 to 37.5 mmol/L with sulfide, nitrate and acetate removal efficiencies increasing 1.5 to 3 times, which suggests that intermittent micro-aeration might be a more economical and efficient regime for high-sulfide IAHD regulation.
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Affiliation(s)
- Ruo-Chen Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China; School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China.
| | - Bo Shao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Xi-Jun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Xu Zhou
- Engineering Laboratory of Microalgal Bioenergy, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Yu-Nong Xiang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei, 106, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, 106, Taiwan
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
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38
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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Sun X, Kong T, Häggblom MM, Kolton M, Li F, Dong Y, Huang Y, Li B, Sun W. Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:6082-6093. [PMID: 32216300 DOI: 10.1021/acs.est.9b07835] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nutrient deficiency, especially bio-available nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially use inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.
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Affiliation(s)
- Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Tianle Kong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Max Kolton
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yuqing Huang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
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40
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Wu L, Qian L, Deng Z, Zhou X, Li B, Lan S, Yang L, Zhang Z. Temperature modulating sand-consolidating cyanobacterial biomass, nutrients removal and bacterial community dynamics in municipal wastewater. BIORESOURCE TECHNOLOGY 2020; 301:122758. [PMID: 31986373 DOI: 10.1016/j.biortech.2020.122758] [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: 11/17/2019] [Revised: 12/31/2019] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
Cultivating sand-consolidating cyanobacteria using wastewater has unique advantages on both nutrients recycling and ecological restoration by transferring excessive nutrients from wastewaters to desert areas. Although previous study showed that sand-consolidating cyanobacterium well adapted to synthetic domestic wastewater, no study has been carried out on actual wastewater. This study aims to investigate the sand-consolidating cyanobacterial biomass production and nutrients removal by cultivating Scytonema hyalinum in the municipal wastewater under different temperatures. The results showed that biomass accumulation increased with temperature from 20 ℃ to 30 ℃, while severely depressed at 35 ℃. More than 81.63% sCOD, 90.64% TDN and 97.08% TDP were removed by day 30 under each temperature except for 35℃. The inoculation of S. hyalinum strongly regulated the native wastewater bacterial community. These results indicated that sand-consolidating cyanobacterium S. hyalinum well adapted to municipal wastewater and temperature had remarkable effects on cyanobacterial biomass accumulation, nutrients removal and wastewater native bacterial community dynamics.
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Affiliation(s)
- Li Wu
- Hubei Key Laboratory of Mineral Resources Processing and Environment, School of Resources and Environmental Engineering, State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430072, China
| | - Long Qian
- Hubei Key Laboratory of Mineral Resources Processing and Environment, School of Resources and Environmental Engineering, State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430072, China
| | - Zhikang Deng
- Hubei Key Laboratory of Mineral Resources Processing and Environment, School of Resources and Environmental Engineering, State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430072, China
| | - Xiaolong Zhou
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Bolin Li
- Hubei Key Laboratory of Mineral Resources Processing and Environment, School of Resources and Environmental Engineering, State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430072, China
| | - Shubin Lan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Lie Yang
- Hubei Key Laboratory of Mineral Resources Processing and Environment, School of Resources and Environmental Engineering, State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430072, China
| | - Zulin Zhang
- Hubei Key Laboratory of Mineral Resources Processing and Environment, School of Resources and Environmental Engineering, State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430072, China; The James Hutton Institute, Craigiebuckler, Aberdeen ABI5 8QH, UK.
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Chen F, Li ZL, Lv M, Huang C, Liang B, Yuan Y, Lin XQ, Gao XY, Wang AJ. Recirculation ratio regulates denitrifying sulfide removal and elemental sulfur recovery by altering sludge characteristics and microbial community composition in an EGSB reactor. ENVIRONMENTAL RESEARCH 2020; 181:108905. [PMID: 31767354 DOI: 10.1016/j.envres.2019.108905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
Expanded granular sludge blanket (EGSB) is regarded as a promising reactor to carry out denitrifying sulfide removal (DSR) and elemental sulfur (S0) recovery. Although the recirculation ratio is an essential parameter for EGSB reactors, how it impacts the DSR process remains poorly understood. Here, three lab-scale DSR-EGSB reactors were established with the different recirculation ratios (3:1, 6:1 and 9:1) to evaluate the corresponding variations in pollutant removal, S0 recovery, anaerobic granular sludge (AGS) characteristics and microbial community composition. It was found that an intermediate recirculation ratio (6:1) could facilitate long-term reactor stability. Adequate recirculation ratio could enhance S0 recovery, but an excessive recirculation ratio (9:1) was likely to cause AGS fragmentation and biomass loss. The S0 desorbed more from sludge at higher recirculation ratios, probably due to the enhanced hydraulic disturbance caused by the increased recirculation ratios. At the low recirculation ratio (3:1), S0 accumulation as inorganic suspended solids in AGS led to a decrease in VSS/TSS ratio and mass transfer efficiency. Although typical denitrifying and sulfide-oxidizing bacteria (e.g., Azoarcus, Thauera and Arcobacter) were predominant in all conditions, facultative and heterotrophic functional bacteria (e.g., Azoarcus and Thauera) were more adaptable to higher recirculation ratios than autotrophs (e.g., Arcobacter, Thiobacillus and Vulcanibacillus), which was conducive to the formation of bacterial aggregates to response to the increased recirculation ratio. The study revealed recirculation ratio regulation significantly impacted the DSR-EGSB reactor performance by altering AGS characteristics and microbial community composition, which provides a novel strategy to improve DSR performance and S0 recovery.
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Affiliation(s)
- Fan Chen
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Miao Lv
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Cong Huang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ye Yuan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, 224051, China
| | - Xiao-Qiu Lin
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xiang-Yu Gao
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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Cron B, Henri P, Chan CS, Macalady JL, Cosmidis J. Elemental Sulfur Formation by Sulfuricurvum kujiense Is Mediated by Extracellular Organic Compounds. Front Microbiol 2019; 10:2710. [PMID: 31827465 PMCID: PMC6890823 DOI: 10.3389/fmicb.2019.02710] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/08/2019] [Indexed: 11/13/2022] Open
Abstract
Elemental sulfur [S(0)] is a central and ecologically important intermediate in the sulfur cycle, which can be used by a wide diversity of microorganisms that gain energy from its oxidation, reduction, or disproportionation. S(0) is formed by oxidation of reduced sulfur species, which can be chemically or microbially mediated. A variety of sulfur-oxidizing bacteria can biomineralize S(0), either intracellularly or extracellularly. The details and mechanisms of extracellular S(0) formation by bacteria have been in particular understudied so far. An important question in this respect is how extracellular S(0) minerals can be formed and remain stable in the environment outside of their thermodynamic stability domain. It was recently discovered that S(0) minerals could be formed and stabilized by oxidizing sulfide in the presence of dissolved organic compounds, a process called S(0) organomineralization. S(0) particles formed through this mechanism possess specific signatures such as morphologies that differ from that of their inorganically precipitated counterparts, encapsulation within an organic envelope, and metastable crystal structures (presence of the monoclinic β- and γ-S8 allotropes). Here, we investigated S(0) formation by the chemolithoautotrophic sulfur-oxidizing and nitrate-reducing bacterium Sulfuricurvum kujiense (Epsilonproteobacteria). We performed a thorough characterization of the S(0) minerals produced extracellularly in cultures of this microorganism, and showed that they present all the specific signatures (morphology, association with organics, and crystal structures) of organomineralized S(0). Using "spent medium" experiments, we furthermore demonstrated that soluble extracellular compounds produced by S. kujiense are necessary to form and stabilize S(0) minerals outside of the cells. This study provides the first experimental evidence of the importance of organomineralization in microbial S(0) formation. The prevalence of organomineralization in extracellular S(0) precipitation by other sulfur bacteria remains to be investigated, and the biological role of this mechanism is still unclear. However, we propose that sulfur-oxidizing bacteria could use soluble organics to stabilize stores of bioavailable S(0) outside the cells.
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Affiliation(s)
- Brandi Cron
- Department of Geosciences, The Pennsylvania State University, University Park, PA, United States
| | - Pauline Henri
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Jennifer L Macalady
- Department of Geosciences, The Pennsylvania State University, University Park, PA, United States
| | - Julie Cosmidis
- Department of Geosciences, The Pennsylvania State University, University Park, PA, United States
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Arcobacter peruensis sp. nov., a Chemolithoheterotroph Isolated from Sulfide- and Organic-Rich Coastal Waters off Peru. Appl Environ Microbiol 2019; 85:AEM.01344-19. [PMID: 31585991 DOI: 10.1128/aem.01344-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
Members of the epsilonproteobacterial genus Arcobacter have been identified to be potentially important sulfide oxidizers in marine coastal, seep, and stratified basin environments. In the highly productive upwelling waters off the coast of Peru, Arcobacter cells comprised 3 to 25% of the total microbial community at a near-shore station where sulfide concentrations exceeded 20 μM in bottom waters. From the chemocline where the Arcobacter population exceeded 106 cells ml-1 and where high rates of denitrification (up to 6.5 ± 0.4 μM N day-1) and dark carbon fixation (2.8 ± 0.2 μM C day-1) were measured, we isolated a previously uncultivated Arcobacter species, Arcobacter peruensis sp. nov. (BCCM LMG-31510). Genomic analysis showed that A. peruensis possesses genes encoding sulfide oxidation and denitrification pathways but lacks the ability to fix CO2 via autotrophic carbon fixation pathways. Genes encoding transporters for organic carbon compounds, however, were present in the A. peruensis genome. Physiological experiments demonstrated that A. peruensis grew best on a mix of sulfide, nitrate, and acetate. Isotope labeling experiments further verified that A. peruensis completely reduced nitrate to N2 and assimilated acetate but did not fix CO2, thus coupling heterotrophic growth to sulfide oxidation and denitrification. Single-cell nanoscale secondary ion mass spectrometry analysis of samples taken from shipboard isotope labeling experiments also confirmed that the Arcobacter population in situ did not substantially fix CO2 The efficient growth yield associated with the chemolithoheterotrophic metabolism of A. peruensis may allow this Arcobacter species to rapidly bloom in eutrophic and sulfide-rich waters off the coast of Peru.IMPORTANCE Our multidisciplinary approach provides new insights into the ecophysiology of a newly isolated environmental Arcobacter species, as well as the physiological flexibility within the Arcobacter genus and sulfide-oxidizing, denitrifying microbial communities within oceanic oxygen minimum zones (OMZs). The chemolithoheterotrophic species Arcobacter peruensis may play a substantial role in the diverse consortium of bacteria that is capable of coupling denitrification and fixed nitrogen loss to sulfide oxidation in eutrophic, sulfidic coastal waters. With increasing anthropogenic pressures on coastal regions, e.g., eutrophication and deoxygenation (D. Breitburg, L. A. Levin, A. Oschlies, M. Grégoire, et al., Science 359:eaam7240, 2018, https://doi.org/10.1126/science.aam7240), niches where sulfide-oxidizing, denitrifying heterotrophs such as A. peruensis thrive are likely to expand.
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Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments. Sci Rep 2019; 9:16341. [PMID: 31704947 PMCID: PMC6841974 DOI: 10.1038/s41598-019-51432-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/25/2019] [Indexed: 11/20/2022] Open
Abstract
Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.
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Zhao Y, Huang C, Ma X, Chen F, Liang B, Wang A. Bioaugmentation with the sulfur oxidizing Thauera sp. HDD1 for shortening the startup time in the denitrifying sulfide removal process. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.100192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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D'Angeli IM, Ghezzi D, Leuko S, Firrincieli A, Parise M, Fiorucci A, Vigna B, Addesso R, Baldantoni D, Carbone C, Miller AZ, Jurado V, Saiz-Jimenez C, De Waele J, Cappelletti M. Geomicrobiology of a seawater-influenced active sulfuric acid cave. PLoS One 2019; 14:e0220706. [PMID: 31393920 PMCID: PMC6687129 DOI: 10.1371/journal.pone.0220706] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 07/22/2019] [Indexed: 12/16/2022] Open
Abstract
Fetida Cave is an active sulfuric acid cave influenced by seawater, showing abundant microbial communities that organize themselves under three main different morphologies: water filaments, vermiculations and moonmilk deposits. These biofilms/deposits have different cave distribution, pH, macro- and microelement and mineralogical composition, carbon and nitrogen content. In particular, water filaments and vermiculations had circumneutral and slightly acidic pH, respectively, both had abundant organic carbon and high microbial diversity. They were rich in macro- and microelements, deriving from mineral dissolution, and, in the case of water filaments, from seawater composition. Vermiculations had different color, partly associated with their mineralogy, and unusual minerals probably due to trapping capacities. Moonmilk was composed of gypsum, poor in organic matter, had an extremely low pH (0-1) and low microbial diversity. Based on 16S rRNA gene analysis, the microbial composition of the biofilms/deposits included autotrophic taxa associated with sulfur and nitrogen cycles and biomineralization processes. In particular, water filaments communities were characterized by bacterial taxa involved in sulfur oxidation and reduction in aquatic, aphotic, microaerophilic/anoxic environments (Campylobacterales, Thiotrichales, Arenicellales, Desulfobacterales, Desulforomonadales) and in chemolithotrophy in marine habitats (Oceanospirillales, Chromatiales). Their biodiversity was linked to the morphology of the water filaments and their collection site. Microbial communities within vermiculations were partly related to their color and showed high abundance of unclassified Betaproteobacteria and sulfur-oxidizing Hydrogenophilales (including Sulfuriferula), and Acidiferrobacterales (including Sulfurifustis), sulfur-reducing Desulfurellales, and ammonia-oxidizing Planctomycetes and Nitrospirae. The microbial community associated with gypsum moonmilk showed the strong dominance (>60%) of the archaeal genus Thermoplasma and lower abundance of chemolithotrophic Acidithiobacillus, metal-oxidizing Metallibacterium, Sulfobacillus, and Acidibacillus. This study describes the geomicrobiology of water filaments, vermiculations and gypsum moonmilk from Fetida Cave, providing insights into the microbial taxa that characterize each morphology and contribute to biogeochemical cycles and speleogenesis of this peculiar seawater-influenced sulfuric acid cave.
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Affiliation(s)
- Ilenia M D'Angeli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefan Leuko
- DLR Institute of Aerospace Medicine, Radiation Biology, Köln, Germany
| | - Andrea Firrincieli
- School of Environmental and Forest Science, University of Washington, Seattle, WA, United States of America
| | - Mario Parise
- Department of Geological and Environmental Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Adriano Fiorucci
- Department of Environment, Land and Infrastructure Engineering, Polytechnic University of Turin, Torino, Italy
| | - Bartolomeo Vigna
- Department of Environment, Land and Infrastructure Engineering, Polytechnic University of Turin, Torino, Italy
| | - Rosangela Addesso
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Daniela Baldantoni
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Cristina Carbone
- DISTAV, Department of Geological, Environmental and Biological Sciences, University of Genoa, Genoa, Italy
| | | | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Sevilla, Spain
| | | | - Jo De Waele
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Andreetto F, Dela Pierre F, Gibert L, Natalicchio M, Ferrando S. Potential Fossilized Sulfide-Oxidizing Bacteria in the Upper Miocene Sulfur-Bearing Limestones From the Lorca Basin (SE Spain): Paleoenvironmental Implications. Front Microbiol 2019; 10:1031. [PMID: 31164872 PMCID: PMC6536631 DOI: 10.3389/fmicb.2019.01031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 04/24/2019] [Indexed: 12/26/2022] Open
Abstract
The sulfur-bearing limestones interbedded in the upper Miocene diatomaceous sediments (Tripoli Formation) of the Lorca Basin (SE Spain) are typified, as other Mediterranean coeval carbonate and gypsum deposits, by filamentous, circular and rod-shaped microstructures of controversial origin. These features have been interpreted both as fecal pellets of brine shrimps and/or of copepods, remains of algae or cyanobacteria and fossilized sulfide-oxidizing bacteria. To shed light on their origin, a multidisciplinary study including optical, UV and scanning electron microscopy, Raman microspectroscopy, and geochemical (carbon and oxygen stable isotopes) analyses has been carried out on three carbonate beds exposed along the La Serrata ridge. The different composition of the filamentous and circular objects with respect to the rod-shaped microstructures suggest that the former represent remains of bacteria, while the latter fecal pellets of deposit- or suspension-feeder organisms. Size and shape of the filamentous and circular microfossils are consistent with their assignment to colorless sulfide-oxidizing bacteria like Beggiatoa (or Thioploca) and Thiomargarita, which is further supported by the presence, only within the microfossil body, of tiny pyrite grains. These grains possibly result from early diagenetic transformation of original sulfur globules stored by the bacteria, which are a diagnostic feature of this group of prokaryotes. The development of microbial communities dominated by putative sulfide-oxidizing bacteria at Lorca was favored by hydrogen sulfide flows generated through degradation of organic matter by sulfate-reducing bacteria thriving in underlying organic-rich sediments.
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Affiliation(s)
- Federico Andreetto
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Turin, Italy
| | | | - Luis Gibert
- Departament de Mineralogia, Petrologia i Geologia Aplicada, Universitat de Barcelona, Barcelona, Spain
| | - Marcello Natalicchio
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Turin, Italy
| | - Simona Ferrando
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Turin, Italy
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Phan VTH, Bernier-Latmani R, Tisserand D, Bardelli F, Le Pape P, Frutschi M, Gehin A, Couture RM, Charlet L. As release under the microbial sulfate reduction during redox oscillations in the upper Mekong delta aquifers, Vietnam: A mechanistic study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 663:718-730. [PMID: 30731417 DOI: 10.1016/j.scitotenv.2019.01.219] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/14/2018] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
The impact of seasonal fluctuations linked to monsoon and irrigation generates redox oscillations in the subsurface, influencing the release of arsenic (As) in aquifers. Here, the biogeochemical control on As mobility was investigated in batch experiments using redox cycling bioreactors and As- and SO42--amended sediment. Redox potential (Eh) oscillations between anoxic (-300-0 mV) and oxic condition (0-500 mV) were implemented by automatically modulating an admixture of N2/CO2 or compressed air. A carbon source (cellobiose, a monomer of cellulose) was added at the beginning of each reducing cycle to stimulate the metabolism of the native microbial community. Results show that successive redox cycles can decrease arsenic mobility by up to 92% during reducing conditions. Anoxic conditions drive mainly the conversion of soluble As(V) to As(III) in contrast to oxic conditions. Phylogenetic analyses of 16S rRNA amplified from the sediments revealed the presence of sulfate and iron - reducing bacteria, confirming that sulfate and iron reduction are key factors for As immobilization from the aqueous phase. As and S K-edge X-ray absorption spectroscopy suggested the association of Fe-(oxyhydr)oxides and the importance of pyrite (FeS2(s)), rather than poorly ordered mackinawite (FeS(s)), for As sequestration under oxidizing and reducing conditions, respectively. Finally, these findings suggest a role for elemental sulfur in mediating aqueous thioarsenates formation in As-contaminated groundwater of the Mekong delta.
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Affiliation(s)
- Van T H Phan
- University Grenoble Alps, CNRS, IRD, IFSTTAR, Institut des Sciences de la Terre (ISTerre), 38000 Grenoble, France; Ho Chi Minh City University of Technology (HCMUT), Vietnam National University - Ho Chi Minh City (VNU-HCM), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Viet Nam.
| | - Rizlan Bernier-Latmani
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Environmental Microbiology Laboratory (EML), EPFL-ENAC-IIE-EML, Station 6, CH-1015 Lausanne, Switzerland
| | - Delphine Tisserand
- University Grenoble Alps, CNRS, IRD, IFSTTAR, Institut des Sciences de la Terre (ISTerre), 38000 Grenoble, France
| | | | - Pierre Le Pape
- Institut de Mineralogie, de Physique des Materiaux et de Cosmochimie (IMPMC), UMR 7590 CNRS-UPMC-IRD-MNHN, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Manon Frutschi
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Environmental Microbiology Laboratory (EML), EPFL-ENAC-IIE-EML, Station 6, CH-1015 Lausanne, Switzerland
| | - Antoine Gehin
- University Grenoble Alps, CNRS, IRD, IFSTTAR, Institut des Sciences de la Terre (ISTerre), 38000 Grenoble, France
| | - Raoul-Marie Couture
- Département de Chimie, Université Laval, 1045 Avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Laurent Charlet
- University Grenoble Alps, CNRS, IRD, IFSTTAR, Institut des Sciences de la Terre (ISTerre), 38000 Grenoble, France
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Thomas F, Morris JT, Wigand C, Sievert SM. Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities. PLoS One 2019; 14:e0215767. [PMID: 31034478 PMCID: PMC6488055 DOI: 10.1371/journal.pone.0215767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/08/2019] [Indexed: 01/23/2023] Open
Abstract
Coastal climate adaptation strategies are needed to build salt marsh resiliency and maintain critical ecosystem services in response to impacts caused by climate change. Although resident microbial communities perform crucial biogeochemical cycles for salt marsh functioning, their response to restoration practices is still understudied. One promising restoration strategy is the placement of sand or sediment onto the marsh platform to increase marsh resiliency. A previous study examined the above- and below-ground structure, soil carbon dioxide emissions, and pore water constituents in Spartina alterniflora-vegetated natural marsh sediments and sand-amended sediments at varying inundation regimes. Here, we analyzed samples from the same experiment to test the effect of sand-amendments on the microbial communities after 5 months. Along with the previously observed changes in biogeochemistry, sand amendments drastically modified the bacterial communities, decreasing richness and diversity. The dominant sulfur-cycling bacterial community found in natural sediments was replaced by one dominated by iron oxidizers and aerobic heterotrophs, the abundance of which correlated with higher CO2-flux. In particular, the relative abundance of iron-oxidizing Zetaproteobacteria increased in the sand-amended sediments, possibly contributing to acidification by the formation of iron oxyhydroxides. Our data suggest that the bacterial community structure can equilibrate if the inundation regime is maintained within the optimal range for S. alterniflora. While long-term effects of changes in bacterial community on the growth of S. alterniflora are not clear, our results suggest that analyzing the microbial community composition could be a useful tool to monitor climate adaptation and restoration efforts.
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Affiliation(s)
- François Thomas
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - James T. Morris
- Belle Baruch Institute for Marine & Coastal Sciences, University of South Carolina, Columbia, SC, United States of America
| | - Cathleen Wigand
- U.S. EPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Narragansett, RI, United States of America
| | - Stefan M. Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
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50
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Hakim JA, Schram JB, Galloway AWE, Morrow CD, Crowley MR, Watts SA, Bej AK. The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence. Microorganisms 2019; 7:E35. [PMID: 30691133 PMCID: PMC6406795 DOI: 10.3390/microorganisms7020035] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/13/2019] [Accepted: 01/21/2019] [Indexed: 12/13/2022] Open
Abstract
The sea urchin Strongylocentrotus purpuratus (order Camarodonta, family Strongylocentrotidae) can be found dominating low intertidal pool biomass on the southern coast of Oregon, USA. In this case study, three adult sea urchins were collected from their shared intertidal pool, and the bacteriome of their pharynx, gut tissue, and gut digesta, including their tide pool water and algae, was determined using targeted high-throughput sequencing (HTS) of the 16S rRNA genes and bioinformatics tools. Overall, the gut tissue demonstrated Arcobacter and Sulfurimonas (Epsilonproteobacteria) to be abundant, whereas the gut digesta was dominated by Psychromonas (Gammaproteobacteria), Propionigenium (Fusobacteria), and Flavobacteriales (Bacteroidetes). Alpha and beta diversity analyses indicated low species richness and distinct microbial communities comprising the gut tissue and digesta, while the pharynx tissue had higher richness, more closely resembling the water microbiota. Predicted functional profiles showed Kyoto Encyclopedia of Genes and Genomes (KEGG) Level-2 categories of energy metabolism, membrane transport, cell motility, and signal transduction in the gut tissue, and the gut digesta represented amino acid, carbohydrate, vitamin and cofactor metabolisms, and replication and repair. Co-occurrence network analysis showed the potential relationships and key taxa, such as the highly abundant Arcobacter and Propionigenium, influencing population patterns and taxonomic organization between the gut tissue and digesta. These results demonstrate a trend of microbial community integration, allocation, predicted metabolic roles, and taxonomic co-occurrence patterns in the S. purpuratus gut ecosystem.
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Affiliation(s)
- Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.
| | - Julie B Schram
- Oregon Institute of Marine Biology, University of Oregon, 63466 Boat Basin Rd, Charleston, OR 97420, USA.
| | - Aaron W E Galloway
- Oregon Institute of Marine Biology, University of Oregon, 63466 Boat Basin Rd, Charleston, OR 97420, USA.
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA.
| | - Michael R Crowley
- Department of Genetics, Heflin Center Genomics Core, School of Medicine, University of Alabama at Birmingham, 705 South 20th Street, Birmingham, AL 35294, USA.
| | - Stephen A Watts
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.
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