1
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Krett G, Romsics C, Jurecska L, Bódai V, Erdélyi B, Márialigeti K, Nagymáté Z. Field test of a bioaugmentation agent for the bioremediation of chlorinated ethene contaminated sites. Biol Futur 2024:10.1007/s42977-024-00230-6. [PMID: 39078604 DOI: 10.1007/s42977-024-00230-6] [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: 04/29/2024] [Accepted: 07/14/2024] [Indexed: 07/31/2024]
Abstract
Chlorinated ethenes are toxic compounds that were widely used in the past, and their improper handling and storage caused notable pollutions worldwide. In situ bioremediation by reductive dechlorination of bacteria is a cost-effective and ecologically friendly way to eliminate these pollutions. During the present study, the efficiency of a previously developed bioaugmentation agent combined with biostimulation was tested under field conditions in contaminated soil. Furthermore, the preservation of dechlorinating ability was also investigated in a long-term experiment. Initially, aerobic conditions were present in the groundwater with possible presence of anaerobic micro-niches providing habitat for Brocadia related anammox bacteria. "Candidatus Omnitrophus" was also identified as a dominant member of community then. Significant changes were detected after the biostimulation, anaerobic conditions established and most of the dominant OTUs were related to fermentative taxa (e.g. Clostridium, Trichococcus and Macillibacteroides). Dominant presence of vinyl-chloride coupled with the lack of vinyl-chloride reductase gene was observed. The most notable change after the bioaugmentation was the significant decrease in the pollutant quantities and the parallel increase in the vcrA gene copy numbers. Similar to post-biostimulation state, fermentative bacteria dominated the community. Bacterial community composition transformed considerably with time after the treatment, dominance of fermentative-mainly Firmicutes related-taxa decreased and chemolithotrophic bacteria became abundant, but the dechlorinating potential of the community remained and could be induced by the reappearance of the pollutants even after 4 years.
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Affiliation(s)
- Gergely Krett
- Department of Microbiology, Eötvös Loránd University, Pázmány P. Sétány 1/C, 1117, Budapest, Hungary.
| | - Csaba Romsics
- Department of Microbiology, Eötvös Loránd University, Pázmány P. Sétány 1/C, 1117, Budapest, Hungary
| | - Laura Jurecska
- Department of Microbiology, Eötvös Loránd University, Pázmány P. Sétány 1/C, 1117, Budapest, Hungary
| | | | | | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány P. Sétány 1/C, 1117, Budapest, Hungary
| | - Zsuzsanna Nagymáté
- Department of Microbiology, Eötvös Loránd University, Pázmány P. Sétány 1/C, 1117, Budapest, Hungary
- Fermentia Ltd, Berlini Utca 47, 1045, Budapest, Hungary
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2
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Angius F, Cremers G, Frank J, Witkowski C, Pol A, van Alen TA, Jetten MSM, Op den Camp HJM, Berben T. Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles. Antonie Van Leeuwenhoek 2024; 117:94. [PMID: 38954064 PMCID: PMC11219375 DOI: 10.1007/s10482-024-01995-5] [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: 03/26/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide. Hydrogen, methane, and carbon monoxide are minor components of these emissions which together can feed large quantities of bacteria and archaea that do contribute to the removal of these notorious greenhouse gases. Here we analyzed the metagenome of samples taken from the Levante bay on Vulcano Island, Italy. Using a gene-centric approach, the hydrothermal vent community appeared to be dominated by Proteobacteria, and Sulfurimonas was the most abundant genus. Metabolic reconstructions highlight a prominent role of formaldehyde oxidation and the reverse TCA cycle in carbon fixation. [NiFe]-hydrogenases seemed to constitute the preferred strategy to oxidize H2, indicating that besides H2S, H2 could be an essential electron donor in this system. Moreover, the sulfur cycle analysis showed a high abundance and diversity of sulfate reduction genes underpinning the H2S production. This study covers the diversity and metabolic potential of the microbial soil community in Levante bay and adds to our understanding of the biogeochemistry of volcanic ecosystems.
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Affiliation(s)
- Federica Angius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jeroen Frank
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Caitlyn Witkowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
- School of Earth Sciences, Wills Memorial Building, University of Bristol, Queens Road, Clifton, BS8 1RJ, UK
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Theo A van Alen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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3
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Zhu QZ, Yin X, Taubner H, Wendt J, Friedrich MW, Elvert M, Hinrichs KU, Middelburg JJ. Secondary production and priming reshape the organic matter composition in marine sediments. SCIENCE ADVANCES 2024; 10:eadm8096. [PMID: 38758798 PMCID: PMC11100564 DOI: 10.1126/sciadv.adm8096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
Abstract
Organic matter (OM) transformations in marine sediments play a crucial role in the global carbon cycle. However, secondary production and priming have been ignored in marine biogeochemistry. By incubating shelf sediments with various 13C-labeled algal substrates for 400 days, we show that ~65% of the lipids and ~20% of the proteins were mineralized by numerically minor heterotrophic bacteria as revealed by RNA stable isotope probing. Up to 11% of carbon from the algal lipids was transformed into the biomass of secondary producers as indicated by 13C incorporation in amino acids. This biomass turned over throughout the experiment, corresponding to dynamic microbial shifts. Algal lipid addition accelerated indigenous OM degradation by 2.5 to 6 times. This priming was driven by diverse heterotrophic bacteria and sulfur- and iron-cycling bacteria and, in turn, resulted in extra secondary production, which exceeded that stimulated by added substrates. These interactions between degradation, secondary production, and priming govern the eventual fate of OM in marine sediments.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Xiuran Yin
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Heidi Taubner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jenny Wendt
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W. Friedrich
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, 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
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jack J. Middelburg
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
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4
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Zhang W, Ye J, Liu X, Zhang Y, Zhang J, Shen L, Jin Y, Zhang J, Li H. Spatiotemporal dynamics of bacterioplankton communities in the estuaries of two differently contaminated coastal areas: Composition, driving factors and ecological process. MARINE POLLUTION BULLETIN 2024; 201:116263. [PMID: 38531208 DOI: 10.1016/j.marpolbul.2024.116263] [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: 12/06/2023] [Revised: 02/05/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Seasonal variations of environmental parameters usually lead to considerable changes in microbial communities. Nevertheless, the specific response patterns of these communities in coastal areas subjected to different levels of contamination remain unclear. Our results revealed notable fluctuations in the bacterioplankton community both seasonally and spatially, with seasonal variations being particularly significant. The diversity and composition of bacterioplankton communities in the estuaries varied significantly across seasons and between seas. Some bacterial phyla that were highly abundant in the dry season (e.g., Patescibacteria and Epsilonbacteraeota) were almost absent in the wet season. Furthermore, the network analysis revealed that the bacterioplankton networks were more complex during the wet season than in the dry season. In the wet season, the estuarine bacterioplankton network in the Yellow Sea region was more complex and stable, while the opposite was true in the dry season. According to the neutral community model, stochastic processes played a more significant role in the formation of bacterioplankton communities during the wet season than during the dry season. Estuarine bacterioplankton communities in the Yellow Sea region were more affected by stochastic processes compared to those in the Bohai Sea. In summary, in the estuaries of two differently contaminated coastal areas, the seasonal increase in nutrient levels enhanced the deterministic processes and network complexity of the bacterioplankton communities.
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Affiliation(s)
- Weiyue Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jinqing Ye
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China.
| | - Xiaohan Liu
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Yunlei Zhang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jinyong Zhang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Lingyu Shen
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Yuan Jin
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jianheng Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China.
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5
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Biderre-Petit C, Courtine D, Hennequin C, Galand PE, Bertilsson S, Debroas D, Monjot A, Lepère C, Divne AM, Hochart C. A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin. Mol Ecol Resour 2024; 24:e13923. [PMID: 38189173 DOI: 10.1111/1755-0998.13923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/26/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide- and sulphate-poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key-role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling.
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Affiliation(s)
- Corinne Biderre-Petit
- Laboratoire Microorganismes: Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Damien Courtine
- Laboratoire Microorganismes: Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Claire Hennequin
- Laboratoire Microorganismes: Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pierre E Galand
- Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, CNRS, Sorbonne Universités, Banyuls sur Mer, France
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences and Science for Life Laboratory, Uppsala, Sweden
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Arthur Monjot
- Laboratoire Microorganismes: Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Cécile Lepère
- Laboratoire Microorganismes: Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Anna-Maria Divne
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Corentin Hochart
- Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, CNRS, Sorbonne Universités, Banyuls sur Mer, France
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6
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Park CG, Lee JS, An SA, Cho SM, Min I, Woo YC, Kim HS. Enhancement of denitrification by sulfur-based carrier in sequencing batch reactor (SBR) for advanced wastewater treatment. CHEMOSPHERE 2024; 352:141415. [PMID: 38336039 DOI: 10.1016/j.chemosphere.2024.141415] [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: 12/29/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
This study was to enhance the nitrogen removal efficiency in the sequencing batch reactor (SBR) process by adding sulfur-based carriers. The nitrogen removal efficiency of the control group was compared with that of the experimental group through a two-series operation of SBR1 without carrier and SBR2 with the carrier under the condition of no external carbon source. A total nitrogen (T-N) removal efficiency of 6.6%, 72.6%, and 79.9% was observed in SBR1, SBR2 (5%), and (10%), respectively. The T-N removal efficiency was improved in the system with carriers, which showed an increase in the removal efficiency of approximately 91.7%. The results suggest that the inclusion of the carrier led to an elevation in the sulfur ratio, implying an augmented surface area for sulfur-based denitrifying microorganisms. Additionally, CaCO3 contributed essential alkalinity for sulfur denitrification, thereby preventing a decline in pH. Regardless of the carrier, the efficiency of organic matter removal surpassed 89%, indicating that the sulfur-based carrier did not adversely affect the biological reaction associated with organic matter. Therefore, autotrophic denitrification was successfully performed using a sulfur carrier in the SBR process without an external carbon source, improving the nitrogen removal efficiency.
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Affiliation(s)
- Cheol-Gyu Park
- Department of Environmental Engineering and Energy, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do, 17058, Republic of Korea
| | - Jin-San Lee
- Department of Environmental Engineering and Energy, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do, 17058, Republic of Korea
| | - Sun-A An
- Department of Environmental Engineering and Energy, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do, 17058, Republic of Korea
| | - Seong-Min Cho
- Department of Environmental Engineering and Energy, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do, 17058, Republic of Korea
| | - Inhong Min
- K-Water Institute, 125, 1689beon-gil, Yuseong-daero, Yuseong-gu, Daejeon, 34045, Republic of Korea
| | - Yun Chul Woo
- Department of Environmental Engineering and Energy, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do, 17058, Republic of Korea.
| | - Han-Seung Kim
- Department of Environmental Engineering and Energy, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do, 17058, Republic of Korea.
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7
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Li D, Liu L, Zhang G, Ma C, Wang H. Sulfur-manganese carbonate composite autotrophic denitrification: nitrogen removal performance and biochemistry mechanism. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 272:116048. [PMID: 38309233 DOI: 10.1016/j.ecoenv.2024.116048] [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: 09/07/2023] [Revised: 01/06/2024] [Accepted: 01/27/2024] [Indexed: 02/05/2024]
Abstract
A novel composite sulfur-manganese carbonate autotrophic denitrification (SMAD) system was developed to reduce sulfate production and provide pH buffer function while improving denitrification efficiency without external organics. The average removal efficiency of total nitrogen (TN) was 98.09% and 96.29%, and that of NO3--N was 99.53% and 97.77%, respectively, in the SMAD system with a hydraulic retention time (HRT) of 6 h and 3 h. They were significantly higher than that in the controls (quartz sand, manganese carbonate ore, and sulfur systems). The H+ produced by the sulfur autotrophic denitrification (SAD) process promoted the release of Mn2+ in the SMAD system. And this system had a stable pH with no accumulation of NO2--N. The decrease of sulfate and formation of Mn oxides through Mn2+ electron donation confirmed the presence of the manganese autotrophic denitrification (MAD) process in the SMAD system. Dominant functional bacteria in the SMAD system were Thiobacillus, Chlorobium, and Sulfurimonas, which were linked to nitrogen, sulfur, and manganese conversion and promoted denitrification. Meanwhile, Flavobacterium participating in Mn2+ oxidation was found only in the SMAD system. The SMAD system provided a new strategy for advanced tailwater treatment.
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Affiliation(s)
- Duo Li
- Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, School of Eco-Environment, Hebei University, Baoding 071002, PR China; College of Chemistry & Environmental Science, Hebei University, Baoding 071002, PR China; College of Life Science, Hebei University, Baoding 071002, PR China
| | - Ling Liu
- Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, School of Eco-Environment, Hebei University, Baoding 071002, PR China; College of Life Science, Hebei University, Baoding 071002, PR China
| | - Guangming Zhang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, PR China
| | - Congli Ma
- Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, School of Eco-Environment, Hebei University, Baoding 071002, PR China; College of Life Science, Hebei University, Baoding 071002, PR China.
| | - Hongjie Wang
- Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, School of Eco-Environment, Hebei University, Baoding 071002, PR China; College of Life Science, Hebei University, Baoding 071002, PR China
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Jacob J, Veras I, Calderόn O, Porter-Morgan HA, Tan J, Aguilar HE, Elkins WT, Martinez Castro VP, Fulton V, Yousri WK. Possibly pathogenic bacteria in aerosols and foams as a result of aeration remediation in a polluted urban waterway. Folia Microbiol (Praha) 2024; 69:235-246. [PMID: 37777646 PMCID: PMC10876779 DOI: 10.1007/s12223-023-01096-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
Newtown Creek is a tributary of the Hudson River Estuary. It has a legacy of both industrial pollution and sewage pollution and has been designated a Superfund site. To ameliorate the chronically low levels of dissolved oxygen detected in the Creek, the New York City Department of Environmental Protection has been installing aerators. The abundance of various bacteria in the aerosols, foams, and water, at two sites in the Creek, was studied before, during, and after the aeration process. Additionally, aerosols and dispersed foams created by the aeration process were sampled and cultured to determine what unique taxa of bacteria could be grown and identified. Taxa including Actinobacteria and Firmicutes were prevalent in cultures taken from aerosols, whereas Gammaproteobacteria were prevalent in cultures taken from foam. Campylobacteria was found to have a significant presence in both samples taken after the aerators were turned off. These taxa include potentially pathogenic bacteria and are therefore of particular concern.
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Affiliation(s)
- Joby Jacob
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA.
| | - Ingrid Veras
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Olga Calderόn
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Holly A Porter-Morgan
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Joshua Tan
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Harry E Aguilar
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | | | - Veronica P Martinez Castro
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Vania Fulton
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Wesam K Yousri
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
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9
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Wang J, Zhang Y, Ding Y, Zhang Y, Xu W, Zhang X, Wang Y, Li D. Adaptive characteristics of indigenous microflora in an organically contaminated high salinity groundwater. CHEMOSPHERE 2024; 349:140951. [PMID: 38101485 DOI: 10.1016/j.chemosphere.2023.140951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
Salinity, a critical factor, could directly or indirectly affect the microbial community structure and diversity. Changes in salinity levels act as environmental filters that influence the transformation of key microbial species. This study investigates the adaptive characteristics of indigenous microflora in groundwater in relation to external organic pollutants under high salinity stress. A highly mineralized shallow groundwater in Northwest China was conducted as the study area, and six representative sampling points were chosen to explore the response of groundwater hydrochemical parameters and microflora, as well as to identify the tolerance mechanisms of indigenous microflora to combined pollution. The results revealed that the dominant genera found in high salinity groundwater contaminated with organic pollutants possess the remarkable ability to degrade such pollutants even under challenging high salinity conditions, including Halomonas, Pseudomonas, Halothiobacillus, Sphingomonas, Lutibacter, Aquabacterium, Thiomicrospira, Aequorivita, etc. The hydrochemical factors, including total dissolved solids (TDS), sulfide, nitrite, nitrate, oxidation reduction potential (ORP), NH3-N, Na, Fe, benzene series, phenols, and halogenated hydrocarbons, demonstrated a significant influence on microflora. High levels of sulphate and sulfide in groundwater can exhibit dual effects on microflora. On one hand, these compounds can inhibit the growth and metabolism of microorganisms. On the other hand, they can also serve as effective electron donors/receptors during the microbial degradation of organic pollutants. Microorganisms exhibit resilience to the inhibitory effects of high salinity and organic pollutants via a series of tolerance mechanisms, such as strengthening the extracellular membrane barrier, enhancing the synthesis of relevant enzymes, initiating novel biochemical reactions, improving cellular self-healing capabilities, responding to unfavorable environmental conditions by migration, and enhancing the S cycle for the microbial metabolism of organic pollutants.
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Affiliation(s)
- Jili Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Yuling Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China.
| | - Yang Ding
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Yi Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Weiqing Xu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Xinying Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Yiliang Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Dong Li
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
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10
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Fullerton H, Smith L, Enriquez A, Butterfield D, Wheat CG, Moyer CL. Seafloor incubation experiments at deep-sea hydrothermal vents reveal distinct biogeographic signatures of autotrophic communities. FEMS Microbiol Ecol 2024; 100:fiae001. [PMID: 38200713 PMCID: PMC10808952 DOI: 10.1093/femsec/fiae001] [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: 05/23/2023] [Revised: 10/20/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024] Open
Abstract
The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kama'ehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kama'ehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.
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Affiliation(s)
- Heather Fullerton
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - Lindsey Smith
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
| | - Alejandra Enriquez
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - David Butterfield
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington and NOAA/PMEL, John M. Wallace Hall, 3737 Brooklyn Ave NE, Seattle, WA 98105, United States
| | - C Geoffrey Wheat
- Institute of Marine Studies, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Drive, 245 O’Neill Building, PO Box 757220, Fairbanks, Alaska 99775-7220, United States
| | - Craig L Moyer
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
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11
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Keller NS, Lüders K, Hornbruch G, Birnstengel S, Vogt C, Ebert M, Kallies R, Dahmke A, Richnow HH. Rapid Consumption of Dihydrogen Injected into a Shallow Aquifer by Ecophysiologically Different Microbes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:333-341. [PMID: 38117480 PMCID: PMC10785757 DOI: 10.1021/acs.est.3c04340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023]
Abstract
The envisaged future dihydrogen (H2) economy requires a H2 gas grid as well as large deep underground stores. However, the consequences of an unintended spread of H2 through leaky pipes, wells, or subterranean gas migrations on groundwater resources and their ecosystems are poorly understood. Therefore, we emulated a short-term leakage incident by injecting gaseous H2 into a shallow aquifer at the TestUM test site and monitored the subsequent biogeochemical processes in the groundwater system. At elevated H2 concentrations, an increase in acetate concentrations and a decrease in microbial α-diversity with a concomitant change in microbial β-diversity were observed. Additionally, microbial H2 oxidation was indicated by temporally higher abundances of taxa known for aerobic or anaerobic H2 oxidation. After H2 concentrations diminished below the detection limit, α- and β-diversity approached baseline values. In summary, the emulated H2 leakage resulted in a temporally limited change of the groundwater microbiome and associated geochemical conditions due to the intermediate growth of H2 consumers. The results confirm the general assumption that H2, being an excellent energy and electron source for many microorganisms, is quickly microbiologically consumed in the environment after a leakage.
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Affiliation(s)
- Nina S. Keller
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Klas Lüders
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - Götz Hornbruch
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - Susann Birnstengel
- Department
of Monitoring & Exploration Technologies, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Markus Ebert
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - René Kallies
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Andreas Dahmke
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - Hans H. Richnow
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Isodetect
GmbH, Deutscher Platz
5b, 04103 Leipzig, Germany
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12
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Fu K, Kang J, Zhao J, Bian Y, Li X, Yang W, Li Z. Efficient nitrite accumulation in partial sulfide autotrophic denitrification (PSAD) system: insights of S/N ratio, pH and temperature. ENVIRONMENTAL TECHNOLOGY 2023:1-18. [PMID: 38118135 DOI: 10.1080/09593330.2023.2293678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/03/2023] [Indexed: 12/22/2023]
Abstract
To provide the necessary nitrite for the Anaerobic Ammonium Oxidation (ANAMMOX) process, the effect of nitrite accumulation in the partial sulfide autotrophic denitrification (PSAD) process was investigated using an SBR reactor. The results revealed that the effectiveness of nitrate removal was unsatisfactory when the S/N ratio (mol/mol) fell below 0.6. The optimal conditions for nitrate removal and nitrite accumulation were achieved within the S/N ratio range of 0.7-0.8, resulting in an average Nitrate Removal Efficiency (NRE) of 95.84%±4.89% and a Nitrite Accumulation Rate (NAR) of 75.31%±6.61%, respectively. It was observed that the nitrate reduction rate was three times faster than that of nitrite reduction during a typical cycle test. Furthermore, batch tests were conducted to assess the influence of pH and temperature conditions. In the pH tests, it became evident that the PSAD process performed more effectively in alkaline environment. The highest levels of nitrate removal and nitrite accumulation were achieved at an initial pH of 8.5, resulting in a NRE of 98.30%±1.93% and a NAR of 85.83%±0.47%, respectively. In the temperature tests, the most favourable outcomes for nitrate removal and nitrite accumulation were observed at 22±1 ℃, with a NRE of 100.00% and a NAR of 81.03%±1.64%, respectively. Moreover, a comparative analysis of 16S rRNA sequencing results between the raw sludge and the sulfide-enriched culture sludge sample showed that Proteobacteria (49.51%) remained the dominant phylum, with Thiobacillus (24.72%), Prosthecobacter (2.55%), Brevundimonas (2.31%) and Ignavibacterium (2.04%) emerging as the dominant genera, assuming the good nitrogen performance of the system.
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Affiliation(s)
- Kunming Fu
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Jia Kang
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Jing Zhao
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Yihao Bian
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Xiaodan Li
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Wenbing Yang
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Zirui Li
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
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13
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Cruces M, Suárez J, Nancucheo I, Schwarz A. Optimization of the chemolithotrophic denitrification of ion exchange concentrate using hydrogen-based membrane biofilm reactors. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119283. [PMID: 37839208 DOI: 10.1016/j.jenvman.2023.119283] [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: 07/17/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
A H2-based membrane biofilm reactor (MBfR) was used to remove nitrate from a synthetic ion-exchange brine made up of 23.8 g L-1 NaCl. To aid the selection of the best nitrate management strategy, our research was based on the integrated analysis of ionic exchange and MBfR processes, including a detailed cost analysis. The nitrate removal flux was not affected if key nutrients were present in the feed solution including potassium and sodium bicarbonate. Operating pH was maintained between 7 and 8. By using a H2 pressure of 15 psi, a hydraulic retention time (HRT) of 4 h, and a surface loading rate of 13.6 ± 0.2 g N m-2 d-1, the average nitrate removal flux was 3.3 ± 0.6 g N m-2 d-1. At HRTs of up to 24 h, the system was able to maintain a removal flux of 1.6 ± 0.2 g N m-2 d-1. Microbial diversity analysis showed that the consortium was dominated by the genera Sulfurimonas and Marinobacter. The estimated cost for a 200 m3/h capacity, coupled ion exchange (IX) + MBfR treatment plant is 0.43 USD/m3. This is a sustainable and competitive alternative to an IX-only plant for the same flowrate. The proposed treatment option allows for brine recycling and reduces costs by 55% by avoiding brine disposal expenses.
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Affiliation(s)
- Matias Cruces
- Departamento de Ingeniería Civil, Universidad de Concepción, P.O. Box 160-C, Concepción, 4070386, Chile
| | - José Suárez
- Departamento de Ingeniería Civil, Universidad de Concepción, P.O. Box 160-C, Concepción, 4070386, Chile
| | - Iván Nancucheo
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Lientur 1457, Concepción, 4080871, Chile
| | - Alex Schwarz
- Departamento de Ingeniería Civil, Universidad de Concepción, P.O. Box 160-C, Concepción, 4070386, Chile.
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14
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Osburn MR, Selensky MJ, Beddows PA, Jacobson A, DeFranco K, Merediz-Alonso G. Microbial biogeography of the eastern Yucatán carbonate aquifer. Appl Environ Microbiol 2023; 89:e0168223. [PMID: 37916826 PMCID: PMC10701671 DOI: 10.1128/aem.01682-23] [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: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE The extensive Yucatán carbonate aquifer, located primarily in southeastern Mexico, is pockmarked by numerous sinkholes (cenotes) that lead to a complex web of underwater caves. The aquifer hosts a diverse yet understudied microbiome throughout its highly stratified water column, which is marked by a meteoric lens floating on intruding seawater owing to the coastal proximity and high permeability of the Yucatán carbonate platform. Here, we present a biogeographic survey of bacterial and archaeal communities from the eastern Yucatán aquifer. We apply a novel network analysis software that models ecological niche space from microbial taxonomic abundance data. Our analysis reveals that the aquifer community is composed of several distinct niches that follow broader regional and hydrological patterns. This work lays the groundwork for future investigations to characterize the biogeochemical potential of the entire aquifer with other systems biology approaches.
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Affiliation(s)
- Magdalena R. Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Matthew J. Selensky
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Patricia A. Beddows
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Andrew Jacobson
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Karyn DeFranco
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Gonzalo Merediz-Alonso
- Amigos de Sian Ka'an, and Consejo de Cuenca de la Península de Yucatán, Cancún, Quintana Roo, Mexico
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15
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Matturro B, Di Franca ML, Tonanzi B, Cruz Viggi C, Aulenta F, Di Leo M, Giandomenico S, Rossetti S. Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy). Microorganisms 2023; 11:2782. [PMID: 38004793 PMCID: PMC10673493 DOI: 10.3390/microorganisms11112782] [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: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.
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Affiliation(s)
- Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Maria Letizia Di Franca
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Barbara Tonanzi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Magda Di Leo
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Santina Giandomenico
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
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16
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Grégoire DS, George NA, Hug LA. Microbial methane cycling in a landfill on a decadal time scale. Nat Commun 2023; 14:7402. [PMID: 37973978 PMCID: PMC10654671 DOI: 10.1038/s41467-023-43129-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.
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Affiliation(s)
- Daniel S Grégoire
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
- Department of Chemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada.
| | - Nikhil A George
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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17
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Chen Z, Lou M, Fang P, Xiao D, Zhu W, Chen H, Qian W. Impact of different sulfur sources on the structure and function of sulfur autotrophic denitrification bacteria. Sci Rep 2023; 13:19404. [PMID: 37938235 PMCID: PMC10632486 DOI: 10.1038/s41598-023-46829-y] [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: 06/26/2023] [Accepted: 11/06/2023] [Indexed: 11/09/2023] Open
Abstract
Nitrate pollution in surface water has become a significant environmental concern. Sulfur autotrophic denitrification (SAD) technology is gaining attention for its cost-effectiveness and efficiency in nitrate removal. This study aimed to investigate the structure and function of sulfur autotrophic denitrification microbial communities in systems using sodium thiosulfate (Group A) and elemental sulfur (Group B) as the sole electron donors. Metagenomic amplicon sequencing and physicochemical analysis were performed to examine the microbial communities. The results revealed that on day 13, the nitrate nitrogen removal rate in Group A was significantly higher (89.2%) compared to Group B (74.4%). The dominant genus in both Groups was Thiobacillus, with average abundances of 34.15% and 16.34% in Groups A and B, respectively. β-diversity analysis based on species level showed significant differences in bacterial community structure between the two Groups (P < 0.001). Group A exhibited a greater potential for nitrate reduction and utilized both thiosulfate and elemental sulfur (P < 0.01) compared to Group B. This study provides a sufficient experimental basis for improving the start-up time and operating cost of SAD system through sulfur source switching and offers new prospects for in-depth mechanistic analysis.
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Affiliation(s)
- Zhenguo Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
- Suzhou Fangzhou Environmental Protection Technology Co., Ltd, Suzhou, China
| | - Minlan Lou
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Peizhen Fang
- Zhejiang Construction Environmental Protection Engineering Co., Ltd, Hangzhou, China
| | - Dunquan Xiao
- Zhejiang Construction Environmental Protection Engineering Co., Ltd, Hangzhou, China
| | - Wenting Zhu
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Suzhou Polytechnic Institute of Agriculture, Suzhou, China
| | - Hongwei Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Wei Qian
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China.
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18
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Bernardini I, Quagliariello A, Peruzza L, Martino ME, Dalla Rovere G, Iori S, Asnicar D, Ciscato M, Fabrello J, Corami F, Cecchetto M, Giubilato E, Carrer C, Bettiol C, Semenzin E, Marcomini A, Matozzo V, Bargelloni L, Milan M, Patarnello T. Contaminants from dredged sediments alter the transcriptome of Manila clam and induce shifts in microbiota composition. BMC Biol 2023; 21:234. [PMID: 37880625 PMCID: PMC10601118 DOI: 10.1186/s12915-023-01741-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The reuse of dredged sediments in ports and lagoons is a big issue as it should not affect the quality and the equilibrium of ecosystems. In the lagoon of Venice, sediment management is of crucial importance as sediments are often utilized to built-up structures necessary to limit erosion. However, the impact of sediment reuse on organisms inhabiting this delicate area is poorly known. The Manila clam is a filter-feeding species of high economic and ecological value for the Venice lagoon experiencing a drastic decline in the last decades. In order to define the molecular mechanisms behind sediment toxicity, we exposed clams to sediments sampled from different sites within one of the Venice lagoon navigable canals close to the industrial area. Moreover, we investigated the impacts of dredged sediments on clam's microbial communities. RESULTS Concentrations of the trace elements and organic chemicals showed increasing concentrations from the city of Venice to sites close to the industrial area of Porto Marghera, where PCDD/Fs and PCBs concentrations were up to 120 times higher than the southern lagoon. While bioaccumulation of organic contaminants of industrial origin reflected sediments' chemical concentrations, metal bioaccumulation was not consistent with metal concentrations measured in sediments probably due to the activation of ABC transporters. At the transcriptional level, we found a persistent activation of the mTORC1 signalling pathway, which is central in the coordination of cellular responses to chemical stress. Microbiota characterization showed the over-representation of potential opportunistic pathogens following exposure to the most contaminated sediments, leading to host immune response activation. Despite the limited acquisition of new microbial species from sediments, the latter play an important role in shaping Manila clam microbial communities. CONCLUSIONS Sediment management in the Venice lagoon will increase in the next years to maintain and create new canals as well as to allow the operation of the new mobile gates at the three Venice lagoon inlets. Our data reveal important transcriptional and microbial changes of Manila clams after exposure to sediments, therefore reuse of dredged sediments represents a potential risk for the conservation of this species and possibly for other organisms inhabiting the Venice lagoon.
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Affiliation(s)
- Ilaria Bernardini
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Maria Elena Martino
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Davide Asnicar
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padua, Italy
- Aquatic Bioscience, Huntsman Marine Science Centre, 1 Lower Campus Road, E5B 2L7, St Andrews, New Brunswick, Canada
| | - Maria Ciscato
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Jacopo Fabrello
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Fabiana Corami
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
- Institute of Polar Sciences, CNR-ISP, Foscari University of Venice, Campus Scientifico - CaVia Torino, 155, 30172, Venice-Mestre, Italy
| | - Martina Cecchetto
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Elisa Giubilato
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Claudio Carrer
- Thetis S.P.a. C/o laboratorio del Provveditorato Interregionale Alle Opere Pubbliche Per Il Veneto, Il Trentino Alto Adige E Il Friuli Venezia Giulia, Venice-Mestre, Italy
| | - Cinzia Bettiol
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Elena Semenzin
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Antonio Marcomini
- Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari University of Venice, Via Torino, 155, 30172, Venice-Mestre, Italy
| | - Valerio Matozzo
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy.
- NFBC, National Future Biodiversity Center, Palermo, Italy.
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università 16, Agripolis, 35020, Legnaro, PD, Italy
- NFBC, National Future Biodiversity Center, Palermo, Italy
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19
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Adam-Beyer N, Laufer-Meiser K, Fuchs S, Schippers A, Indenbirken D, Garbe-Schönberg D, Petersen S, Perner M. Microbial ecosystem assessment and hydrogen oxidation potential of newly discovered vent systems from the Central and South-East Indian Ridge. Front Microbiol 2023; 14:1173613. [PMID: 37886064 PMCID: PMC10598711 DOI: 10.3389/fmicb.2023.1173613] [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: 02/24/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
In order to expand the knowledge of microbial ecosystems from deep-sea hydrothermal vent systems located on the Central and South-East Indian Ridge, we sampled hydrothermal fluids, massive sulfides, ambient water and sediments of six distinct vent fields. Most of these vent sites were only recently discovered in the course of the German exploration program for massive sulfide deposits and no previous studies of the respective microbial communities exist. Apart from typically vent-associated chemosynthetic members of the orders Campylobacterales, Mariprofundales, and Thiomicrospirales, high numbers of uncultured and unspecified Bacteria were identified via 16S rRNA gene analyses in hydrothermal fluid and massive sulfide samples. The sampled sediments however, were characterized by an overall lack of chemosynthetic Bacteria and the presence of high proportions of low abundant bacterial groups. The archaeal communities were generally less diverse and mostly dominated by members of Nitrosopumilales and Woesearchaeales, partly exhibiting high proportions of unassigned Archaea. Correlations with environmental parameters were primarily observed for sediment communities and for microbial species (associated with the nitrogen cycle) in samples from a recently identified vent field, which was geochemically distinct from all other sampled sites. Enrichment cultures of diffuse fluids demonstrated a great potential for hydrogen oxidation coupled to the reduction of various electron-acceptors with high abundances of Hydrogenovibrio and Sulfurimonas species. Overall, given the large number of currently uncultured and unspecified microorganisms identified in the vent communities, their respective metabolic traits, ecosystem functions and mediated biogeochemical processes have still to be resolved for estimating consequences of potential environmental disturbances by future mining activities.
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Affiliation(s)
- Nicole Adam-Beyer
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Katja Laufer-Meiser
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sebastian Fuchs
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | | | | | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Mirjam Perner
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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20
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Heinze BM, Küsel K, Jehmlich N, von Bergen M, Taubert M. Metabolic versatility enables sulfur-oxidizers to dominate primary production in groundwater. WATER RESEARCH 2023; 244:120426. [PMID: 37597444 DOI: 10.1016/j.watres.2023.120426] [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: 05/13/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023]
Abstract
High rates of CO2 fixation and the genetic potential of various groundwater microbes for autotrophic activity have shown that primary production is an important source of organic C in groundwater ecosystems. However, the contribution of specific chemolithoautotrophic groups such as S-oxidizing bacteria (SOB) to groundwater primary production and their adaptation strategies remain largely unknown. Here, we stimulated anoxic groundwater microcosms with reduced S and sampled the microbial community after 1, 3 and 6 weeks. Genome-resolved metaproteomics was combined with 50at-% 13CO2 stable isotope probing to follow the C flux through the microbial food web and infer traits expressed by active SOB in the groundwater microcosms. Already after 7 days, 90% of the total microbial biomass C in the microcosms was replaced by CO2-derived C, increasing to 97% at the end of incubation. Stable Isotope Cluster Analysis revealed active autotrophs, characterized by a uniform 13C-incorporation of 45% in their peptides, to dominate the microbial community throughout incubation. Mixo- and heterotrophs, characterized by 10 to 40% 13C-incorporation, utilized the primarily produced organic C. Interestingly, obligate autotrophs affiliated with Sulfuricella and Sulfuritalea contained traits enabling the storage of elemental S in globules to maintain primary production under energy limitation. Others related to Sulfurimonas seemed to rapidly utilize substrates for fast proliferation, and most autotrophs further maximized their energy yield via efficient denitrification and the potential for H2 oxidation. Mixotrophic SOB, belonging to Curvibacter or Polaromonas, enhanced metabolic flexibility by using organic compounds to satisfy their C requirements. Time series data spanning eight years further revealed that key taxa of our microcosms composed up to 15% of the microbial groundwater community, demonstrating their in-situ importance. This showed that SOB, by using different metabolic strategies, are able to account for high rates of primary production in groundwater, especially at sites limited to geogenic nutrient sources. The widespread presence of SOB with traits such as S storage, H2 oxidation, and organic C utilization in many aquatic habitats further suggested that metabolic versatility governs S-fueled primary production in the environment.
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Affiliation(s)
- Beatrix M Heinze
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, Jena 07743, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, Jena 07743, Germany; The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, UFZ, Permoserstr. 15, Leipzig 04318, Germany
| | - Martin von Bergen
- The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany; Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, UFZ, Permoserstr. 15, Leipzig 04318, Germany; Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Brüderstr. 32, Leipzig 04103, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, Jena 07743, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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21
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Wang L, Liu J, Li Y, Liu Z, Zhang L, Che H, Cui H, Zhang Y. Elemental sulfur-driven autotrophic denitrification process for effective removal of nitrate in mariculture wastewater: Performance, kinetics and microbial community. CHEMOSPHERE 2023; 337:139354. [PMID: 37394184 DOI: 10.1016/j.chemosphere.2023.139354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/29/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
To date, there is a lack of systematic investigation on the elemental sulfur-driven autotrophic denitrification (SDAD) process for removing nitrate (NO3--N) from mariculture wastewater deficient in organic carbon sources. Therefore, a packed-bed reactor was established and continuously operated for 230 days to investigate the operation performance, kinetic characteristics and microbial community of SDAD biofilm process. Results indicate that the NO3--N removal efficiencies and rates varied with the operational conditions including HRT (1-4 h), influent concentrations of NO3--N (25-100 mg L-1) and DO (0.2-7.0 mg L-1), and temperature (10oC-30 °C), in the ranges of 51.4%-98.6% and 0.054-0.546 g L-1 d-1, respectively. Limestone could partially neutralize the produced acidity. Small portions of NO3--N were converted to nitrite (<4.5%) and ammonia (<2.8%) in the reactor. Operational conditions also influenced the production of acidity, nitrite and ammonia as well as sulfate. Shortening HRT and increasing influent NO3--N concentration turned the optimal fitting model depicting the NO3--N removal along the reactor from half-order to zero-order. Furthermore, the NO3--N removal was accelerated by a higher temperature and influent NO3--N concentration and a lower HRT and influent DO concentration. Microbial richness, evenness and diversity gradually decreased during the autotrophic denitrifier enrichment cultivation and the reactor start-up and operation. Sulfurimonas constituted the predominate genus and the primary functional bacteria in the reactor. This study highlights the SDAD as a promising way to control the coastal eutrophication associated with mariculture wastewater discharge.
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Affiliation(s)
- Lu Wang
- Laoshan Laboratory, Qingdao, 266237, China
| | - Jun Liu
- Laoshan Laboratory, Qingdao, 266237, China; First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yongfu Li
- College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Zhihao Liu
- Laoshan Laboratory, Qingdao, 266237, China
| | - Long Zhang
- National Fisheries Technology Extension Center, China Society of Fisheries, Beijing, 100125, China
| | - Hong Che
- Laoshan Laboratory, Qingdao, 266237, China
| | - Hongwu Cui
- Laoshan Laboratory, Qingdao, 266237, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
| | - Ying Zhang
- Ocean University of China, Qingdao, 266100, China.
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22
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Houghton KM, Carere CR, Stott MB, McDonald IR. Thermophilic methane oxidation is widespread in Aotearoa-New Zealand geothermal fields. Front Microbiol 2023; 14:1253773. [PMID: 37720161 PMCID: PMC10502179 DOI: 10.3389/fmicb.2023.1253773] [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: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
Abstract
Geothermal areas represent substantial point sources for greenhouse gas emissions such as methane. While it is known that methanotrophic microorganisms act as a biofilter, decreasing the efflux of methane in most soils to the atmosphere, the diversity and the extent to which methane is consumed by thermophilic microorganisms in geothermal ecosystems has not been widely explored. To determine the extent of biologically mediated methane oxidation at elevated temperatures, we set up 57 microcosms using soils from 14 Aotearoa-New Zealand geothermal fields and show that moderately thermophilic (>40°C) and thermophilic (>60°C) methane oxidation is common across the region. Methane oxidation was detected in 54% (n = 31) of the geothermal soil microcosms tested at temperatures up to 75°C (pH 1.5-8.1), with oxidation rates ranging from 0.5 to 17.4 μmol g-1 d-1 wet weight. The abundance of known aerobic methanotrophs (up to 60.7% Methylacidiphilum and 11.2% Methylothermus) and putative anaerobic methanotrophs (up to 76.7% Bathyarchaeota) provides some explanation for the rapid rates of methane oxidation observed in microcosms. However, not all methane oxidation was attributable to known taxa; in some methane-consuming microcosms we detected methanotroph taxa in conditions outside of their known temperature range for growth, and in other examples, we observed methane oxidation in the absence of known methanotrophs through 16S rRNA gene sequencing. Both of these observations suggest unidentified methane oxidizing microorganisms or undescribed methanotrophic syntrophic associations may also be present. Subsequent enrichment cultures from microcosms yielded communities not predicted by the original diversity studies and showed rates inconsistent with microcosms (≤24.5 μmol d-1), highlighting difficulties in culturing representative thermophilic methanotrophs. Finally, to determine the active methane oxidation processes, we attempted to elucidate metabolic pathways from two enrichment cultures actively oxidizing methane using metatranscriptomics. The most highly expressed genes in both enrichments (methane monooxygenases, methanol dehydrogenases and PqqA precursor peptides) were related to methanotrophs from Methylococcaceae, Methylocystaceae and Methylothermaceae. This is the first example of using metatranscriptomics to investigate methanotrophs from geothermal environments and gives insight into the metabolic pathways involved in thermophilic methanotrophy.
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Affiliation(s)
- Karen M. Houghton
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Carlo R. Carere
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Matthew B. Stott
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Ian R. McDonald
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
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23
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Barosa B, Ferrillo A, Selci M, Giardina M, Bastianoni A, Correggia M, di Iorio L, Bernardi G, Cascone M, Capuozzo R, Intoccia M, Price R, Vetriani C, Cordone A, Giovannelli D. Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy. Front Microbiol 2023; 14:1134114. [PMID: 37637107 PMCID: PMC10452888 DOI: 10.3389/fmicb.2023.1134114] [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: 12/29/2022] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.
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Affiliation(s)
- Bernardo Barosa
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Matteo Selci
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Marco Giardina
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Alessia Bastianoni
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Monica Correggia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Luciano di Iorio
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Martina Cascone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Rosaria Capuozzo
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Michele Intoccia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Roy Price
- School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Costantino Vetriani
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
| | - Angelina Cordone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples “Federico II”, Naples, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
- Istituto per le Risorse Biologiche e Biotecnologiche Marine, Consiglio Nazionale Delle Ricerche, CNR-IRBIM, Ancona, Italy
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, Japan
- Marine Chemistry and Geochemistry Department–Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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24
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Mugge RL, Rakocinski CF, Woolsey M, Hamdan LJ. Proximity to built structures on the seabed promotes biofilm development and diversity. BIOFOULING 2023; 39:706-718. [PMID: 37746691 DOI: 10.1080/08927014.2023.2255141] [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: 12/21/2022] [Accepted: 08/30/2023] [Indexed: 09/26/2023]
Abstract
The rapidly expanding built environment in the northern Gulf of Mexico includes thousands of human built structures (e.g. platforms, shipwrecks) on the seabed. Primary-colonizing microbial biofilms transform structures into artificial reefs capable of supporting biodiversity, yet little is known about formation and recruitment of biofilms. Short-term seafloor experiments containing steel surfaces were placed near six structures, including historic shipwrecks and modern decommissioned energy platforms. Biofilms were analyzed for changes in phylogenetic composition, richness, and diversity relative to proximity to the structures. The biofilm core microbiome was primarily composed of iron-oxidizing Mariprofundus, sulfur-oxidizing Sulfurimonas, and biofilm-forming Rhodobacteraceae. Alpha diversity and richness significantly declined as a function of distance from structures. This study explores how built structures influence marine biofilms and contributes knowledge on how anthropogenic activity impacts microbiomes on the seabed.
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Affiliation(s)
- Rachel L Mugge
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
| | - Chet F Rakocinski
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
| | - Max Woolsey
- Hydrographic Science Research Center, University of Southern Mississippi, Stennis Space Center, Mississippi, USA
| | - Leila J Hamdan
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
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25
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Mazière C, Duran R, Dupuy C, Cravo-Laureau C. Microbial mats as model to decipher climate change effect on microbial communities through a mesocosm study. Front Microbiol 2023; 14:1039658. [PMID: 37396368 PMCID: PMC10308941 DOI: 10.3389/fmicb.2023.1039658] [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: 09/08/2022] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Marine environments are expected to be one of the most affected ecosystems by climate change, notably with increasing ocean temperature and ocean acidification. In marine environments, microbial communities provide important ecosystem services ensuring biogeochemical cycles. They are threatened by the modification of environmental parameters induced by climate change that, in turn, affect their activities. Microbial mats, ensuring important ecosystem services in coastal areas, are well-organized communities of diverse microorganisms representing accurate microbial models. It is hypothesized that their microbial diversity and metabolic versatility will reveal various adaptation strategies in response to climate change. Thus, understanding how climate change affects microbial mats will provide valuable information on microbial behaviour and functioning in changed environment. Experimental ecology, based on mesocosm approaches, provides the opportunity to control physical-chemical parameters, as close as possible to those observed in the environment. The exposure of microbial mats to physical-chemical conditions mimicking the climate change predictions will help to decipher the modification of the microbial community structure and function in response to it. Here, we present how to expose microbial mats, following a mesocosm approach, to study the impact of climate change on microbial community.
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Affiliation(s)
- C. Mazière
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM UMR 525—Bât. IBEAS, BP1155, Pau, France
- La Rochelle Université, CNRS, UMR 7266 LIENSs (Littoral Environnement et Sociétés)—2, rue Olympe de Gouges, Bât. ILE, La Rochelle, France
| | - R. Duran
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM UMR 525—Bât. IBEAS, BP1155, Pau, France
| | - C. Dupuy
- La Rochelle Université, CNRS, UMR 7266 LIENSs (Littoral Environnement et Sociétés)—2, rue Olympe de Gouges, Bât. ILE, La Rochelle, France
| | - C. Cravo-Laureau
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM UMR 525—Bât. IBEAS, BP1155, Pau, France
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26
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Radouani F, Sanchez-Cid C, Silbande A, Laure A, Ruiz-Valencia A, Robert F, Vogel TM, Salvin P. Evolution and interaction of microbial communities in mangrove microbial fuel cells and first description of Shewanella fodinae as electroactive bacterium. Bioelectrochemistry 2023; 153:108460. [PMID: 37224603 DOI: 10.1016/j.bioelechem.2023.108460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023]
Abstract
Understanding exoelectrogenic bacteria mechanisms and their interactions in complex biofilm is critical for the development of microbial fuel cells (MFCs). In this article, assumptions concerning the benefits of the complex sediment microbial community for electricity production were explored with both the complex microbial community and isolates identified as Shewanella. Analysis of the microbial community revealed a strong influence of the sediment community on anodes and electrolytes compared to that of only water. Moreover, while Pelobacteraceae-related genera were dominant in our MFCs instead of Desulfuromonas and Geobacter as usually reported, the electroactive Shewanella algae and Shewanella fodinae were isolated and cultivated from the anodic biofilm. S. fodinae, described for the first time as an electroactive bacterium to the best of our knowledge, led to a maximal current density of 3.6 A/m2 set as 0.3 V/SCE in a three-electrode set-up fed with lactate. S. algae, in a complex medium containing several available substrates, showed several preferential oxidative behaviors including a diauxic behavior. In pure culture and under our conditions, S. fodinae and S. algae were not able to use acetate as a sole electron donor. However, their presence in our acetate-fed MFCs and the adaptive behavior of S. algae hint a syntrophic interaction between the bacteria to optimize the use of the substrate in a complex environment.
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Affiliation(s)
- Fatima Radouani
- Laboratoire des Matériaux et Molécules en Milieu Agressif, UR4_1, UFR STE, Université des Antilles, Schoelcher, France
| | - Concepcion Sanchez-Cid
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
| | - Adèle Silbande
- Laboratoire des Matériaux et Molécules en Milieu Agressif, UR4_1, UFR STE, Université des Antilles, Schoelcher, France
| | - Adeline Laure
- Laboratoire des Matériaux et Molécules en Milieu Agressif, UR4_1, UFR STE, Université des Antilles, Schoelcher, France
| | - Azariel Ruiz-Valencia
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
| | - Florent Robert
- Laboratoire des Matériaux et Molécules en Milieu Agressif, UR4_1, UFR STE, Université des Antilles, Schoelcher, France
| | - Timothy M Vogel
- Université de Lyon, Université Claude Bernard Lyon 1, UMR 5557, UMR INRAe 1418, VetAgro Sup, Écologie Microbienne, équipe BEER, F-69622 Villeurbanne, France
| | - Paule Salvin
- Laboratoire des Matériaux et Molécules en Milieu Agressif, UR4_1, UFR STE, Université des Antilles, Schoelcher, France.
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27
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Seidel L, Broman E, Nilsson E, Ståhle M, Ketzer M, Pérez-Martínez C, Turner S, Hylander S, Pinhassi J, Forsman A, Dopson M. Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities. THE ISME JOURNAL 2023; 17:855-869. [PMID: 36977742 DOI: 10.1038/s41396-023-01395-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023]
Abstract
Besides long-term average temperature increases, climate change is projected to result in a higher frequency of marine heatwaves. Coastal zones are some of the most productive and vulnerable ecosystems, with many stretches already under anthropogenic pressure. Microorganisms in coastal areas are central to marine energy and nutrient cycling and therefore, it is important to understand how climate change will alter these ecosystems. Using a long-term heated bay (warmed for 50 years) in comparison with an unaffected adjacent control bay and an experimental short-term thermal (9 days at 6-35 °C) incubation experiment, this study provides new insights into how coastal benthic water and surface sediment bacterial communities respond to temperature change. Benthic bacterial communities in the two bays reacted differently to temperature increases with productivity in the heated bay having a broader thermal tolerance compared with that in the control bay. Furthermore, the transcriptional analysis showed that the heated bay benthic bacteria had higher transcript numbers related to energy metabolism and stress compared to the control bay, while short-term elevated temperatures in the control bay incubation experiment induced a transcript response resembling that observed in the heated bay field conditions. In contrast, a reciprocal response was not observed for the heated bay community RNA transcripts exposed to lower temperatures indicating a potential tipping point in community response may have been reached. In summary, long-term warming modulates the performance, productivity, and resilience of bacterial communities in response to warming.
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Affiliation(s)
- Laura Seidel
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Emelie Nilsson
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Magnus Ståhle
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Marcelo Ketzer
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Clara Pérez-Martínez
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Stephanie Turner
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Samuel Hylander
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
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28
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Nosalova L, Kiskova J, Fecskeova LK, Piknova M, Pristas P. Bacterial Community Structure of Two Cold Sulfur Springs in Slovakia (Central Europe). Curr Microbiol 2023; 80:145. [PMID: 36949342 DOI: 10.1007/s00284-023-03251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023]
Abstract
Sulfur-oxidizing bacteria, especially those from hot springs, have attracted the attention of microbiologists for more than 150 years. In contrast, the microbial diversity of cold sulfur springs remains largely unrecognized. Culture-dependent and culture-independent approaches were used to study the diversity of sulfur-oxidizing bacterial communities in two cold sulfur springs in Slovakia. Geological conditions and resulting spring water chemistry appear to be major factors influencing the composition of the sulfur-oxidizing bacterial community. Bacterial communities in both springs were found to be dominated by Proteobacteria with Epsilonproteobacteria being prevalent in the high-salinity Stankovany spring and Alpha- and Gammaproteobacteria in the low-salinity Jovsa spring. Limited overlap was found between culture-dependent and culture-independent approaches with multiple taxa of cultivated sulfur-oxidizing bacteria not being detected by the culture-independent metagenomics approach. Moreover, four cultivated bacterial isolates could represent novel taxa based on the low similarity of their 16S rRNA gene sequence (similarity lower than 98%) to sequences of known bacteria. Our study supports the current view that multiple approaches are required to assess the bacterial diversity in natural habitats and indicates that sulfur springs in Slovakia harbor unique, yet-undescribed microorganisms.
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Affiliation(s)
- Lea Nosalova
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, 041 54, Kosice, Slovakia
| | - Jana Kiskova
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, 041 54, Kosice, Slovakia
| | - Livia Kolesar Fecskeova
- Associated Tissue Bank, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, Trieda SNP 1, 040 11, Kosice, Slovakia
| | - Maria Piknova
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, 041 54, Kosice, Slovakia.
| | - Peter Pristas
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, 041 54, Kosice, Slovakia
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, Soltesovej 4-6, 040 01, Kosice, Slovakia
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29
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Molari M, Hassenrueck C, Laso-Pérez R, Wegener G, Offre P, Scilipoti S, Boetius A. A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nat Microbiol 2023; 8:651-665. [PMID: 36894632 PMCID: PMC10066037 DOI: 10.1038/s41564-023-01342-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, USulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, US. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of US. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.
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Affiliation(s)
- Massimiliano Molari
- Max Planck Institute for Marine Microbiology, Bremen, Germany. .,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
| | | | - Rafael Laso-Pérez
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
| | - Stefano Scilipoti
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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30
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Mimura M, Koizumi Y, Wada M, Ichijo T, Uchii K, Nasu M. Microbial Water Quality Assessment of Private Wells Using 16S rRNA Gene Amplicon Sequencing with a Nanopore Sequencer. Biol Pharm Bull 2023; 46:263-271. [PMID: 36724954 DOI: 10.1248/bpb.b22-00690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Private wells are used daily worldwide as convenient household water sources. In Japan, where water supply coverage is high, well water is occasionally used for non-potable purposes, such as irrigation and watering. Currently, the main microbiological test of well water is designed to detect Escherichia coli, which is an indicator of fecal contamination, using culture methods. Water use such as watering generates bioaerosols, which may cause airborne infection. However, many causative bacteria of aerosol-derived infections, such as Legionella spp., are difficult to detect using culture methods. Thus, more comprehensive modern assessment is desirable for securing the microbiological quality of well water. Here, the bacterial community structure of five private wells located in different environments was examined using the rapid and portable MinION sequencer, which enabled us to identify bacteria to the species level based on full-length 16S ribosomal RNA (rRNA) gene sequences. The results revealed the differences in the bacterial community structures of water samples from the five wells and detected Legionella pneumophila and Aeromonas hydrophila as new candidate microbial indicators. The comprehensive analysis method used in this study successfully detected bacteria causing opportunistic infections, which are difficult to detect by conventional methods. This approach is expected to be routinely applied in the future as a highly accurate method for assessing the microbiological quality of private well water.
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Affiliation(s)
- Mayumi Mimura
- Environmental Health Section, Osaka Institute of Public Health.,Graduate School of Pharmaceutical Sciences, Osaka Ohtani University
| | - Yoshihiko Koizumi
- Environmental Health Section, Osaka Institute of Public Health.,Graduate School of Pharmaceutical Sciences, Osaka Ohtani University
| | - Masashi Wada
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture
| | - Tomoaki Ichijo
- Faculty of Health and Nutrition, Osaka Shoin Women's University.,Graduate School of Human Sciences, Osaka Shoin Women's University
| | | | - Masao Nasu
- Graduate School of Pharmaceutical Sciences, Osaka Ohtani University
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31
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Li Y, Liu Y, Feng L, Zhang L. A review: Manganese-driven bioprocess for simultaneous removal of nitrogen and organic contaminants from polluted waters. CHEMOSPHERE 2023; 314:137655. [PMID: 36603680 DOI: 10.1016/j.chemosphere.2022.137655] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/26/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Water pollutants, such as nitrate and organics have received much attention for their harms to ecological environment and human health. The redox transformation between Mn(Ⅱ) and Mn(Ⅳ) for nitrogen and organics removal have been recognized for a long time. Mn(Ⅱ) can act as inorganic electron donor to drive autotrophic denitrification so as to realize simultaneous removal of Mn(Ⅱ), nitrate and organic pollutants. Mn oxides (MnOx) also play an important role in the adsorption and degradation of some organic contaminants and they can change or create new oxidation pathways in the nitrogen cycle. Herein, this paper provides a comprehensive review of nitrogen and organic contaminants removal pathways through applying Mn(Ⅱ) or MnOx as forerunners. The main current knowledge, developments and applications, pollutants removal efficiency, as well as microbiology and biochemistry mechanisms are summarized. Also reviewed the effects of factors such as the carbon source, the environmental factors and operation conditions have on the process. Research gaps and application potential are further proposed and discussed. Overall, Mn-based biotechnology towards advanced wastewater treatment has a promising prospect, which can achieve simultaneous removal of nitrogen and organic contaminants, and minimize sludge production.
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Affiliation(s)
- Yingying Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yongze Liu
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Li Feng
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Liqiu Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
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32
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Lozada M, Diéguez MC, García PE, Dionisi HM. Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159392. [PMID: 36240919 DOI: 10.1016/j.scitotenv.2022.159392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Kelp forests, among the most productive ecosystems on Earth, cover large areas of the South Atlantic coast. Sediment heterotrophic bacteria have a pivotal role in the degradation of kelp biomass, however, the response of sediment microbial communities to periodic kelp biomass inputs is mostly unknown. Here, we show that kelp biomass induced rapid changes in overlying water chemistry and shifts in sediment microbial communities, which differed in the experimental systems containing Macrocystis pyrifera (M) and Undaria pinnatifida (U) with sediments of the respective regions. We observed results compatible with the degradation of labile, high molecular weight compounds into smaller and more refractory compounds towards the end of the incubations. The capability of microbial communities to degrade alginate, the major component of kelp cell walls, significantly increased with respect to controls after kelp biomass addition (Absorbance at 235 nm 1.2 ± 0.3 and 1.0 ± 0.2 for M and U, respectively, controls <0.2, t = 4 days). Shifts in microbial community structure (based on 16S rRNA gene amplicon sequencing) were tightly related to the kelp treatment and, to a lesser extent, to the sediment provenance (Principal Coordinates Analysis, 80 % of variation explained in the first two axes). Dissolved oxygen, pH, salinity, alginolytic potential, Absorbance at 235 and 600 nm, total N, total C, and SUVA index correlated significantly with community structure. Differentially abundant populations between kelp-amended treatments and controls included members of the Flavobacteriia class (Algibacter and Polaribacter), and Gammaproteobacteria (Psychromonas and Marinomonas), among others. Metagenomes of M and U-amended sediments contained sequences from 18 of the 19 enzyme families related to alginate or fucoidan degradation. Specific taxonomic groups were associated with enzyme classes targeting different substrates, suggesting niche differentiation. This work expands our knowledge on the patterns of microbial assemblages from intertidal sediments in response to kelp biomass inputs.
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Affiliation(s)
- Mariana Lozada
- Laboratorio de Microbiología Ambiental (CESIMAR-CONICET/IBIOMAR-CONICET), Puerto Madryn, Argentina.
| | - María C Diéguez
- Grupo de Ecología de Sistemas Acuáticos a Escala de Paisaje (GESAP, INIBIOMA-CONICET-UNComa), Bariloche, Argentina
| | - Patricia E García
- Grupo de Ecología de Sistemas Acuáticos a Escala de Paisaje (GESAP, INIBIOMA-CONICET-UNComa), Bariloche, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental (CESIMAR-CONICET/IBIOMAR-CONICET), Puerto Madryn, Argentina
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33
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Vineis JH, Bulseco AN, Bowen JL. Microbial chemolithoautotrophs are abundant in salt marsh sediment following long-term experimental nitrate enrichment. FEMS Microbiol Lett 2023; 370:fnad082. [PMID: 37541957 DOI: 10.1093/femsle/fnad082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
Long-term anthropogenic nitrate (NO3-) enrichment is a serious threat to many coastal systems. Nitrate reduction coupled with the oxidation of reduced forms of sulfur is conducted by chemolithoautotrophic microbial populations in a process that decreases nitrogen (N) pollution. However, little is known about the diversity and distribution of microbes capable of carbon fixation within salt marsh sediment and how they respond to long-term NO3- loading. We used genome-resolved metagenomics to characterize the distribution, phylogenetic relationships, and adaptations important to microbial communities within NO3--enriched sediment. We found NO3- reducing sulfur oxidizers became dominant members of the microbial community throughout the top 25 cm of the sediment following long-term NO3- enrichment. We also found that most of the chemolithoautotrophic genomes recovered contained striking metabolic versatility, including the potential for complete denitrification and evidence of mixotrophy. Phylogenetic reconstruction indicated that similar carbon fixation strategies and metabolic versatility can be found in several phylogenetic groups, but the genomes recovered here represent novel organisms. Our results suggest that the role of chemolithoautotrophy within NO3--enriched salt marsh sediments may be quantitatively more important for retaining carbon and filtering NO3- than previously indicated and further inquiry is needed to explicitly measure their contribution to carbon turnover and removal of N pollution.
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Affiliation(s)
- Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
| | - Ashley N Bulseco
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
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34
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Ding S, Henkel JV, Hopmans EC, Bale NJ, Koenen M, Villanueva L, Sinninghe Damsté JS. Changes in the membrane lipid composition of a Sulfurimonas species depend on the electron acceptor used for sulfur oxidation. ISME COMMUNICATIONS 2022; 2:121. [PMID: 37938789 PMCID: PMC9789136 DOI: 10.1038/s43705-022-00207-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 11/09/2023]
Abstract
Sulfurimonas species are among the most abundant sulfur-oxidizing bacteria in the marine environment. They are capable of using different electron acceptors, this metabolic flexibility is favorable for their niche adaptation in redoxclines. When oxygen is depleted, most Sulfurimonas spp. (e.g., Sulfurimonas gotlandica) use nitrate ([Formula: see text]) as an electron acceptor to oxidize sulfur, including sulfide (HS-), S0 and thiosulfate, for energy production. Candidatus Sulfurimonas marisnigri SoZ1 and Candidatus Sulfurimonas baltica GD2, recently isolated from the redoxclines of the Black Sea and Baltic Sea respectively, have been shown to use manganese dioxide (MnO2) rather than [Formula: see text] for sulfur oxidation. The use of different electron acceptors is also dependent on differences in the electron transport chains embedded in the cellular membrane, therefore changes in the membrane, including its lipid composition, are expected but are so far unexplored. Here, we used untargeted lipidomic analysis to reveal changes in the composition of the lipidomes of three representative Sulfurimonas species grown using either [Formula: see text] and MnO2. We found that all Sulfurimonas spp. produce a series of novel phosphatidyldiazoalkyl-diacylglycerol lipids. Ca. Sulfurimonas baltica GD2 adapts its membrane lipid composition depending on the electron acceptors it utilizes for growth and survival. When carrying out MnO2-dependent sulfur oxidation, the novel phosphatidyldiazoalkyl-diacylglycerol headgroup comprises shorter alkyl moieties than when sulfur oxidation is [Formula: see text]-dependent. This is the first report of membrane lipid adaptation when an organism is grown with different electron acceptors. We suggest novel diazoalkyl lipids have the potential to be used as a biomarker for different conditions in redox-stratified systems.
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Affiliation(s)
- Su Ding
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands.
| | - Jan V Henkel
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Ellen C Hopmans
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Nicole J Bale
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Michel Koenen
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Laura Villanueva
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
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35
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Vasquez-Cardenas D, Hidalgo-Martinez S, Hulst L, Thorleifsdottir T, Helgason GV, Eiriksson T, Geelhoed JS, Agustsson T, Moodley L, Meysman FJR. Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria. Front Microbiol 2022; 13:1034401. [PMID: 36620049 PMCID: PMC9814725 DOI: 10.3389/fmicb.2022.1034401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Fish farming in sea cages is a growing component of the global food industry. A prominent ecosystem impact of this industry is the increase in the downward flux of organic matter, which stimulates anaerobic mineralization and sulfide production in underlying sediments. When free sulfide is released to the overlying water, this can have a toxic effect on local marine ecosystems. The microbially-mediated process of sulfide oxidation has the potential to be an important natural mitigation and prevention strategy that has not been studied in fish farm sediments. We examined the microbial community composition (DNA-based 16S rRNA gene) underneath two active fish farms on the Southwestern coast of Iceland and performed laboratory incubations of resident sediment. Field observations confirmed the strong geochemical impact of fish farming on the sediment (up to 150 m away from cages). Sulfide accumulation was evidenced under the cages congruent with a higher supply of degradable organic matter from the cages. Phylogenetically diverse microbes capable of sulfide detoxification were present in the field sediment as well as in lab incubations, including cable bacteria (Candidatus Electrothrix), which display a unique metabolism based on long-distance electron transport. Microsensor profiling revealed that the activity of cable bacteria did not exert a dominant impact on the geochemistry of fish farm sediment at the time of sampling. However, laboratory incubations that mimic the recovery process during fallowing, revealed successful enrichment of cable bacteria within weeks, with concomitant high sulfur-oxidizing activity. Overall our results give insight into the role of microbially-mediated sulfide detoxification in aquaculture impacted sediments.
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Affiliation(s)
- Diana Vasquez-Cardenas
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium,*Correspondence: Diana Vasquez-Cardenas,
| | | | - Lucas Hulst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | | | | | | | | | | | - Leon Moodley
- NORCE Norwegian Research Centre, Randaberg, Norway
| | - Filip J. R. Meysman
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium
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36
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Impact of high Fe-concentrations on microbial community structure and dissolved organics in hydrothermal plumes: an experimental study. Sci Rep 2022; 12:20723. [PMID: 36456707 PMCID: PMC9715565 DOI: 10.1038/s41598-022-25320-0] [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: 08/09/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Iron (Fe) is an essential trace element for life. In the ocean, Fe can be exceptionally scarce and thus biolimiting or extremely enriched causing microbial stress. The ability of hydrothermal plume microbes to counteract unfavorable Fe-concentrations up to 10 mM is investigated through experiments. While Campylobacterota (Sulfurimonas) are prominent in a diverse community at low to intermediate Fe-concentrations, the highest 10 mM Fe-level is phylogenetically less diverse and dominated by the SUP05 clade (Gammaproteobacteria), a species known to be genetically well equipped to strive in high-Fe environments. In all incubations, Fe-binding ligands were produced in excess of the corresponding Fe-concentration level, possibly facilitating biological Fe-uptake in low-Fe incubations and detoxification in high-Fe incubations. The diversity of Fe-containing formulae among dissolved organics (SPE-DOM) decreased with increasing Fe-concentration, which may reflect toxic conditions of the high-Fe treatments. A DOM-derived degradation index (IDEG) points to a degradation magnitude (microbial activity) that decreases with Fe and/or selective Fe-DOM coagulation. Our results show that some hydrothermal microbes (especially Gammaproteobacteria) have the capacity to thrive even at unfavorably high Fe-concentrations. These ligand-producing microbes could hence play a key role in keeping Fe in solution, particularly in environments, where Fe precipitation dominates and toxic conditions prevail.
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37
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Nguyen PM, Arslan M, Kappelmeyer U, Mäusezahl I, Wiessner A, Müller JA. Spatial characterization of microbial sulfur cycling in horizontal-flow constructed wetland models. CHEMOSPHERE 2022; 309:136605. [PMID: 36179921 DOI: 10.1016/j.chemosphere.2022.136605] [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: 07/11/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Constructed wetlands (CWs) are a cost-effective technology for wastewater treatment in which plant-microorganism relationships play a key role in transforming pollutants. However, there is little knowledge about the spatial organization of microbial metabolic processes in CWs. Here we show the structuring of microbial transformation of inorganic sulfur compounds (ISCs) in two horizontal subsurface-flow CW models fed with sulfate-rich artificial wastewater. One model was fully planted with Juncus effusus, while the other was planted only in the middle to investigate further the influence of the plant on ISC transformations. Chemical analyses revealed that sulfate reduction and re-oxidation of sulfide/sulfur occurred simultaneously along the flow paths, with net reduction at the beginning of the CWs, where organic carbon from the influent was still present, and predominant re-oxidation in the downstream sections. Porewater ISC concentrations hardly differed between the two CWs. However, analysis of the bacterial communities showed that sulfur cycling in the fully planted CW was much higher. Total bacterial abundances were about 50 times and 3-4 orders of magnitude higher in the rhizoplane than in porewater and on gravel, respectively, as quantified by qPCR determination of the 16S rRNA gene. Sequencing of 16S rRNA gene amplicons revealed that bacterial communities on the roots and in the porewater differed substantially, apparently a consequence of the fluxes of oxygen and exudates from the roots. Furthermore, we observed partitioning of ISC transforming bacteria into different niches of the CWs. The results of the chemical and microbial analyses collectively support that extensive sulfur cycling occurred in the rhizospheres of the CW models. The study is relevant to the treatment of sulfur-containing wastewater and the elucidation of microbial communities involved in biogeochemical activities to improve water quality.
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Affiliation(s)
- Phuong Minh Nguyen
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Department of Environmental Technology, Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, Viet Nam
| | - Muhammad Arslan
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Uwe Kappelmeyer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ines Mäusezahl
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Arndt Wiessner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jochen A Müller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
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38
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Zhao L, Shao H, Zhang L, Panno SV, Kelly WR, Lin TY, Liu WT, Flynn TM, Berger P. Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA. Environ Microbiol 2022; 24:6112-6127. [PMID: 36222141 PMCID: PMC10099389 DOI: 10.1111/1462-2920.16241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 10/10/2022] [Indexed: 01/12/2023]
Abstract
Saline springs within the Illinois Basin result from the discharge of deep-seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%-94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.
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Affiliation(s)
- Linduo Zhao
- Illinois Sustainable Technology Center, Illinois, USA.,Illinois State Water Survey, Illinois, USA
| | - Hongbo Shao
- Illinois State Geology Survey, Illinois, USA
| | - Li Zhang
- Illinois Sustainable Technology Center, Illinois, USA
| | | | | | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Theodore M Flynn
- California Department of Water Resources, West Sacramento, California, USA
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Wang Z, Wang S, Lai Q, Wei S, Jiang L, Shao Z. Sulfurimonas marina sp. nov., an obligately chemolithoautotrophic, sulphur-oxidizing bacterium isolated from a deep-sea sediment sample from the South China Sea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel marine bacterium, designated strain B2T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were observed to be Gram-stain negative, motile and rod shaped with a single polar flagellum. B2T could grow at 10–45 °C (optimum, 35 °C), pH 4.5–9.0 (optimum, pH 7.0) and in the presence of 1.0–8.0 % (w/v) NaCl (optimum, 3.0%). The isolate grew chemolithoautotrophically with sulphide, elemental sulphur and thiosulphate as electron donors, carbon dioxide as the sole carbon source, and molecular oxygen as the sole electron acceptor. Molecular hydrogen did not support growth. The predominant fatty acids of B2T were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that B2T represented a member of the genus
Sulfurimonas
, with the highest similarity to the 16S rRNA gene sequences of
Sulfurimonas indica
NW8NT (95.9 %),
Sulfurimonas crateris
SN118T (95.7 %),
Sulfurimonas xiamenensis
1-1NT (95.6 %) and
Sulfurimonas paralvinellae
GO25T (95.4 %). Sequence similarities to other members of the genus
Sulfurimonas
were less than 95.0 %. In addition, the average nucleotide identity (ANI) value and digital DNA–DNA hybridization (dDDH) estimate between B2T and
S. indica
NW8NT were 73.0 and 23.7 %, respectively. The size of the complete genome of B2T is 22 61 034 bp, with a DNA G+C content of 36.0 mol %. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain B2T represent a novel species of the genus
Sulfurimonas
, for which the name Sulfurimonas marina sp. nov. is proposed, with the type strain B2T (=MCCC 1A14515T=KCTC 15852T).
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Affiliation(s)
- Zhaodi Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Shiping Wei
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
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Deng YF, Zan FX, Huang H, Wu D, Tang WT, Chen GH. Coupling sulfur-based denitrification with anammox for effective and stable nitrogen removal: A review. WATER RESEARCH 2022; 224:119051. [PMID: 36113234 DOI: 10.1016/j.watres.2022.119051] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/15/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Anoxic ammonium oxidation (anammox) is an energy-efficient nitrogen removal process for wastewater treatment. However, the unstable nitrite supply and residual nitrate in the anammox process have limited its wide application. Recent studies have proven coupling of sulfur-based denitrification with anammox (SDA) can achieve an effective nitrogen removal, owing to stable provision of substrate nitrite from the sulfur-based denitrification, thus making its process control more efficient in comparison with that of partial nitrification and anammox process. Meanwhile, the anammox-produced nitrate can be eliminated through sulfur-based denitrification, thereby enhancing SDA's overall nitrogen removal efficiency. Nonetheless, this process is governed by a complex microbial system that involves both complicated sulfur and nitrogen metabolisms as well as multiple interactions among sulfur-oxidising bacteria and anammox bacteria. A comprehensive understanding of the principles of the SDA process is the key to facilitating the development and application of this novel process. Hence, this review is conducted to systematically summarise various findings on the SDA process, including its associated biochemistry, biokinetic reactions, reactor performance, and application. The dominant functional bacteria and microbial interactions in the SDA process are further discussed. Finally, the advantages, challenges, and future research perspectives of SDA are outlined. Overall, this work gives an in-depth insight into the coupling mechanism of SDA and its potential application in biological nitrogen removal.
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Affiliation(s)
- Yang-Fan Deng
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China
| | - Fei-Xiang Zan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Huang
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China
| | - Di Wu
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Center for Environmental and Energy Research, Ghent University Global Campus, Republic of Korea
| | - Wen-Tao Tang
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China.
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Smrhova T, Jani K, Pajer P, Kapinusova G, Vylita T, Suman J, Strejcek M, Uhlik O. Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis. ENVIRONMENTAL MICROBIOME 2022; 17:48. [PMID: 36089611 PMCID: PMC9465906 DOI: 10.1186/s40793-022-00440-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/26/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs may host phylogenetically novel microorganisms with potential use in biotechnology. With this hypothesis in mind, we examined the microbial composition of four thermal springs of the world-renowned spa town of Karlovy Vary (Carlsbad), Czechia, which differ in their temperature and chemical composition. RESULTS Microbial profiling using 16S rRNA gene sequencing revealed the presence of phylogenetically novel taxa at various taxonomic levels, spanning from genera to phyla. Many sequences belonged to novel classes within the phyla Hydrothermae, Altiarchaeota, Verrucomicrobia, and TA06. Cultivation-based methods employing oligotrophic media resulted in the isolation of 44 unique bacterial isolates. These include strains that withstand concentrations of up to 12% NaClw/v in cultivation media or survive a temperature of 100 °C, as well as hitherto uncultured bacterial species belonging to the genera Thermomonas, Paenibacillus, and Cellulomonas. These isolates harbored stress response genes that allow them to thrive in the extreme environment of thermal springs. CONCLUSIONS Our study is the first to analyze the overall microbial community composition of the renowned Karlovy Vary thermal springs. We provide insight into yet another level of uniqueness of these springs. In addition to their unique health benefits and cultural significance, we demonstrate that these springs harbor phylogenetically distinct microorganisms with unusual life strategies. Our findings open up avenues for future research with the promise of a deeper understanding of the metabolic potential of these microorganisms.
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Affiliation(s)
- Tereza Smrhova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Kunal Jani
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czech Republic
| | - Gabriela Kapinusova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Tomas Vylita
- Institute of Balneology and Spa Sciences, Karlovy Vary, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
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42
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Kojima H, Kato Y, Watanabe T, Fukui M. Sulfurimonas aquatica sp. nov., a sulfur-oxidizing bacterium isolated from water of a brackish lake. Arch Microbiol 2022; 204:559. [PMID: 35976522 DOI: 10.1007/s00203-022-03167-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/26/2022]
Abstract
A novel chemolithoautotrophic bacterium, strain H1576T, was isolated from water of a brackish lake. Strain H1576T grew aerobically on inorganic sulfur compounds. Hydrogen gas did not support autotrophic growth, and heterotrophic growth was not observed. Cells were rod shaped, motile, 1.5-2.7 μm in length and 0.6-0.7 μm in width. Growth was observed at 3-22 °C with an optimum growth temperature of 13-15 °C. The pH range for growth was 6.0-7.4 with an optimum pH of 6.6-6.8. Major fatty acids were summed feature 3 (C16: 1ω7c and/or C16: 1ω6c). The complete genome of strain H1576T consists of a circular chromosome and a plasmid, with total length of 2.8 Mbp and G+C content of 46.4 mol%. Phylogenetic analyses indicated that strain H1576T belongs to the genus Sulfurimonas but distinct from representatives of existing species. On the basis of genomic and phenotypic characteristics, a new species named Sulfurimonas aquatica sp. nov. is proposed with the type strain of strain H1576T (= BCRC 81254T = JCM 35004T).
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Affiliation(s)
- Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan.
| | - Yukako Kato
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
| | - Tomohiro Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
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Savvichev AS, Kulakova AA, Krasnova ED, Voronov DA, Kadnikov VV, Beletskii AV, Kozyaeva VV, Rusanov II, Letarova MA, Veslopolova EF, Belenkova VV, Demidenko NA, Gorlenko VM. Microbial Community of a Marine Meromictic Trough (Biofilter Bay) in the Kandalaksha Bay, White Sea. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722100940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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44
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Lu L, He Y, Peng C, Wen X, Ye Y, Ren D, Tang Y, Zhu D. Dispersal of antibiotic resistance genes in an agricultural influenced multi-branch river network. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154739. [PMID: 35331763 DOI: 10.1016/j.scitotenv.2022.154739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Rivers in agricultural regions serve as an important sink for livestock and poultry farm runoff, fertilizer runoff, and country living sewage, which could bring antibiotic resistance genes (ARGs) contaminations. However, the diversity and distribution of ARGs has not been well documented in the agricultural influenced river. Here, the diversity of ARGs, and their relationship with biochemical factors were determined in the surface water in an agricultural region of the Jialing River and its five rural branches. The 218 unique ARGs encoding resistance to eight major antibiotic classes have been detected using high-throughput quantitative PCR. The branches of the river had a remarkably higher abundance of ARGs than the mainstream. The aminoglycoside, beta_Lactamase, MLSB, and Multidrug resistance genes were significantly enriched in the branches compared to the mainstream. Compared with the mainstream, the ARGs profiles in the branches showed obvious higher spatial variability. Significant correlation between ARGs profiles and bacterial community structures were observed, and network analysis further showed that the ARGs were associated with their potential hosts, such as Ottowia and Novosphingobium. Redundancy discrimination analysis revealed that Cu content has a significant contribution to the increase of ARGs in the river. The microbial diversity index was negatively correlated with the abundance of the ARGs. These results provide evidence for the enrichment of ARGs in the agricultural influenced river and branches due to the joint influence of chemical and microbial variables.
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Affiliation(s)
- Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yan He
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Xingyue Wen
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yuqiu Ye
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dong Ren
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yun Tang
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dong Zhu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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45
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Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep. Appl Environ Microbiol 2022; 88:e0210921. [PMID: 35604226 DOI: 10.1128/aem.02109-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b ("Candidatus Methanocomedenaceae") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. IMPORTANCE Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.
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Wang X, Xie GJ, Tian N, Dang CC, Cai C, Ding J, Liu BF, Xing DF, Ren NQ, Wang Q. Anaerobic microbial manganese oxidation and reduction: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153513. [PMID: 35101498 DOI: 10.1016/j.scitotenv.2022.153513] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Manganese is a vital heavy metal abundant in terrestrial and aquatic environments. Anaerobic manganese redox reactions mediated by microorganisms have been recognized for a long time, which promote elements mobility and bioavailability in the environment. Biological anaerobic redox of manganese serves two reactions, including Mn(II) oxidation and Mn(IV) reduction. This review provides a comprehensive analysis of manganese redox cycles in the environment, closely related to greenhouse gas mitigation, the fate of nutrients, microbial bioremediation, and global biogeochemical cycle, including nitrogen, sulfur, and carbon. The oxidation and reduction of manganese occur cyclically and simultaneously in the environment. Anaerobic reduction of Mn(IV) receives electrons from methane, ammonium and sulfide, while Mn(II) can function as an electron source for manganese-oxidizing microorganisms for autotrophic denitrification and photosynthesis. The anaerobic redox transition between Mn(II) and Mn(IV) promotes a dynamic biogeochemical cycle coupled to microorganisms in water, soil and sediment environments. The discussion of reaction mechanisms, microorganism diversity, environmental influence bioremediation and application identify the research gaps for future investigation, which provides promising opportunities for further development of biotechnological applications to remediate contaminated environments.
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Affiliation(s)
- Xuan Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Ning Tian
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chen Cai
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Chaudhary DK, Kim KH, Lee M, Kim H, Hong Y. Insights into Bacterial Community Structure and Metabolic Diversity of Mercury-Contaminated Sediments from Hyeongsan River, Pohang, South Korea. Curr Microbiol 2022; 79:156. [PMID: 35397046 DOI: 10.1007/s00284-022-02847-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Abstract
This study investigated the bacterial community structure and metabolic diversity and their relationship with Hg and other environmental variables in sediments collected from different locations (HSR-1-HSR-6) in the Hyeongsan River estuary in South Korea. The results showed that the highest total mercury (THg) and methylmercury (MeHg) concentrations were in HSR-2, with values of 4585.3 µg/kg and 13.4 µg/kg, respectively. The lowest THg (31.9 µg/kg) and MeHg (0.1 µg/kg) concentrations were found in HSR-1. Sulfate and organic matter (OM) were more influential environmental variables, revealing a positive association with THg and MeHg and negatively affecting bacterial and metabolic diversities. Bacterial and metabolic diversities were also negatively impacted by the THg and MeHg concentrations. Proteobacteria and Bacteroidetes were abundantly distributed in all the sediments. The dominance of Proteobacteria was upscaled in all the heavily Hg-contaminated sites (HSR-2-HSR-6), and it was the only phylum that showed a significant positive correlation with THg, MeHg, and OM. The genera Sulfurovum and Sulfurimonas were abundantly observed in sites with high Hg contamination, whereas Congregibacter, Gaetbulibacter, Ilumatobacter, Methylotenera, Nevskia, and Sediminibacter were only detected in low Hg-contaminated sites (HSR-1). The community-level physiological profile data showed the highest (1.0) average well color development (AWCD) value in HSR-1 and the lowest (0.45) AWCD value in HSR-2. Overall, these results demonstrated the inhibitory effects of THg, MeHg, and other environmental variables on microbial communities and metabolic diversity. These findings broaden the current knowledge on the dynamics of bacterial and metabolic diversities in Hg-contaminated sediments and might be useful in the management of Hg pollution.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Kyung Hee Kim
- Water Environmental Engineering Research Division, National Institute of Environmental Research, Hwangyong-ro 42, Seogu, Incheon, 22689, Republic of Korea
| | - Mikyung Lee
- Water Environmental Engineering Research Division, National Institute of Environmental Research, Hwangyong-ro 42, Seogu, Incheon, 22689, Republic of Korea
| | - Hwansuk Kim
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Yongseok Hong
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
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48
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Zhai X, Cao W, Zhang Y, Ju P, Chen J, Duan J, Sun C. Study on the Bacterial Communities of the Biofilms on Titanium, Aluminum, and Copper Alloys at 5,772 m Undersea in Yap Trench. Front Microbiol 2022; 13:831984. [PMID: 35369519 PMCID: PMC8973411 DOI: 10.3389/fmicb.2022.831984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Biofilms formed on metal surfaces strongly affect metallic instruments serving in marine environments. However, due to sampling difficulty, less has been known about the bacterial communities of the biofilm on metallic surfaces in hadal environments, so the failure process of these deep-sea metallic instruments influenced by microbial communities could be hardly predicted. In this research, seven alloys, including titanium, aluminum, and copper alloys, were exposed in Yap Trench hadal environment for 1 year. Thus, the communities of the biofilms formed on metallic surfaces at 5,772 m undersea in Yap Trench were initially reported in previous studies. Then, 16S rRNA gene sequencing was performed to visualize the in situ bacterial communities of the biofilms formed on titanium, aluminum, and copper alloys at 5,772 m undersea in Yap Trench. It was found that Proteobacteria was the dominant phylum in all samples, but distinct genera were discovered on various alloys. The titanium alloy provided a suitable substrate for a mutualistic symbiotic biofilm with abundant bacterial richness. Aluminum alloys without copper components showed the least bacterial richness and formed a cold-adapted and oligotrophic-adapted biofilm containing the genera Sulfurimonas and PS1 Clade, while copper-present alloys showed relatively high bacterial richness with copper-resistant or even copper-utilizing biofilms constituting the genera Stenotrophomonas, Burkholderia-Caballeronia-Paraburkholderia, and Achromobacter on the surfaces. Furthermore, among all the element components contained in alloys investigated in this research, copper element showed the strongest influences on the composition and function of microbial communities in the biofilms formed on various metallic surfaces.
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Affiliation(s)
- Xiaofan Zhai
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Wei Cao
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yimeng Zhang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Peng Ju
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- *Correspondence: Peng Ju,
| | - Juna Chen
- Navy Submarine Academy, Qingdao, China
- Juna Chen,
| | - Jizhou Duan
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chengjun Sun
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Chengjun Sun,
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Liu CC, Dong SS, Chen JB, Wang C, Ning P, Guo Y, Yang TL. MetaDecoder: a novel method for clustering metagenomic contigs. MICROBIOME 2022; 10:46. [PMID: 35272700 PMCID: PMC8908641 DOI: 10.1186/s40168-022-01237-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Clustering the metagenomic contigs into potential genomes is a key step to investigate the functional roles of microbial populations. Existing algorithms have achieved considerable success with simulated or real sequencing datasets. However, accurately classifying contigs from complex metagenomes is still a challenge. RESULTS We introduced a novel clustering algorithm, MetaDecoder, which can classify metagenomic contigs based on the frequencies of k-mers and coverages. MetaDecoder was built as a two-layer model with the first layer being a GPU-based modified Dirichlet process Gaussian mixture model (DPGMM), which controls the weight of each DPGMM cluster to avoid over-segmentation by dynamically dissolving contigs in small clusters and reassigning them to the remaining clusters. The second layer comprises a semi-supervised k-mer frequency probabilistic model and a modified Gaussian mixture model for modeling the coverage based on single copy marker genes. Benchmarks on simulated and real-world datasets demonstrated that MetaDecoder can be served as a promising approach for effectively clustering metagenomic contigs. CONCLUSIONS In conclusion, we developed the GPU-based MetaDecoder for effectively clustering metagenomic contigs and reconstructing microbial communities from microbial data. Applying MetaDecoder on both simulated and real-world datasets demonstrated that it could generate more complete clusters with lower contamination. Using MetaDecoder, we identified novel high-quality genomes and expanded the existing catalog of bacterial genomes. Video Abstract.
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Affiliation(s)
- Cong-Cong Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Chen Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Pan Ning
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi 710004 P. R. China
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50
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Hester ER, Vaksmaa A, Valè G, Monaco S, Jetten MSM, Lüke C. Effect of water management on microbial diversity and composition in an Italian rice field system. FEMS Microbiol Ecol 2022; 98:6529233. [PMID: 35170720 PMCID: PMC8924702 DOI: 10.1093/femsec/fiac018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/26/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Traditional rice cultivation consumes up to 2500 L of water per kg yield and new strategies such as the ‘Alternate Wetting and Drying’ (AWD) might be promising water-saving alternatives. However, they might have large impacts on the soil microbiology. In this study, we compared the bacterial and archaeal communities in experimental field plots, cultivated under continuously flooding (CF) and AWD management, by high-throughput sequencing of the 16S rRNA gene. We analysed alpha and beta diversity in bulk soil and on plant roots, in plots cultivated with two different rice cultivars. The strongest difference was found between soil and root communities. Beside others, the anaerobic methanotroph Methanoperedens was abundant in soil, however, we detected a considerable number of ANME-2a-2b on plant roots. Furthermore, root communities were significantly affected by the water management: Differential abundance analysis revealed the enrichment of aerobic and potentially plant-growth-promoting bacteria under AWD treatment, such as Sphingomonadaceae and Rhizobiaceae (both Alphaproteobacteria), and Bacteroidetes families. Microorganisms with an overall anaerobic lifestyle, such as various Delta- and Epsilonproteobacteria, and Firmicutes were depleted. Our study indicates that the bulk soil communities seem overall well adapted and more resistant to changes in the water treatment, whereas the root microbiota seems more vulnerable.
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Affiliation(s)
- Eric R Hester
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Giampiero Valè
- CREA - Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy.,DiSIT-Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Piazza San Eusebio 5, I-13100 Vercelli, Italy
| | - Stefano Monaco
- CREA - Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
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