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Handler ER, Andersen SDJ, Gradinger R, McGovern M, Vader A, Poste AE. Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat. FEMS Microbiol Ecol 2024; 100:fiad162. [PMID: 38111220 PMCID: PMC10799726 DOI: 10.1093/femsec/fiad162] [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: 02/27/2023] [Revised: 10/26/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.
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Affiliation(s)
- Eleanor R Handler
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Sebastian D J Andersen
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Rolf Gradinger
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Maeve McGovern
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
| | - Amanda E Poste
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
- Norwegian Institute for Nature Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
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Dai W, Sun W, Fu T, Jia C, Cui H, Han Y, Shi X, Zhang XH. Marinifilum caeruleilacunae sp. nov., isolated from Yongle Blue Hole in the South China Sea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005358] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, facultatively anaerobic and non-flagellated marine bacterium, designated JC070T was isolated from the Yongle Blue Hole in the South China Sea. The temperature, pH and NaCl ranges for growth of strain JC070T were 4–37 °C (optimum, 16 °C), pH 6.0–9.0 (optimum, pH 7.0) and 1.0 –6.0% (w/v; optimum, 3.0%). The predominant isoprenoid quinone of strain JC070T was identified as menaquinone-7. The dominant fatty acids (>10%) were iso-C15:0 (59.6%) and iso-C17:0 3-OH (17.2%). The major polar lipids were aminophospholipid, aminolipid, two unknown phospholipids and two unidentified lipids. The genomic DNA G+C content was determined to be 37.0 mol%. Based on the results of polyphasic analysis, a new species, named Marinifilum caeruleilacunae sp. nov., within the genus
Marinifilum
was proposed. The type strain is JC070T (= JCM 39045T=MCCC 1K03774T).
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Affiliation(s)
- Wei Dai
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Wen Sun
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Tianyu Fu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Chao Jia
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Hongchang Cui
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Yanqiong Han
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Xiaochong Shi
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, PR China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, PR China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
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Ceron-Chafla P, García-Timermans C, de Vrieze J, Ganigué R, Boon N, Rabaey K, van Lier JB, Lindeboom REF. Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure. Biotechnol Bioeng 2022; 119:1792-1807. [PMID: 35312065 PMCID: PMC9325544 DOI: 10.1002/bit.28085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 02/08/2022] [Accepted: 03/05/2022] [Indexed: 11/11/2022]
Abstract
Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, that is, acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP; < 10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity, and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature-halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio.
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Affiliation(s)
- Pamela Ceron-Chafla
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, the Netherlands
| | - Cristina García-Timermans
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Jo de Vrieze
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium.,Division of Soil and Water Management, Department of Earth and Environmental Sciences, KU Leuven, Leuven, Belgium.,Bio- and Chemical Systems Technology, Reactor Engineering and Safety (CREaS), Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | - Ramon Ganigué
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Nico Boon
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Korneel Rabaey
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium.,Center for Advanced Process Technology for Urban Resource Recovery, Ghent, Belgium
| | - Jules B van Lier
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, the Netherlands
| | - Ralph E F Lindeboom
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, the Netherlands
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Atashgahi S. Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS Microbiol Ecol 2020; 95:5426821. [PMID: 30942854 PMCID: PMC6797604 DOI: 10.1093/femsec/fiz048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Attempts for bioremediation of toxic organohalogens resulted in the identification of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases) enzymes. RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that does not have membrane-integral domains, and a small putative membrane anchor (RdhB, encoded by rdhB) that (presumably) locates the A subunit to the outside of the cytoplasmic membrane. Recent genomic studies identified a putative rdh gene in an uncultured deltaproteobacterial genome that was not accompanied by an rdhB gene, but contained transmembrane helixes in N-terminus. Therefore, rather than having a separate membrane anchor protein, this putative RDase is likely a hybrid of RdhA and RdhB, and directly connected to the membrane with transmembrane helixes. However, functionality of the hybrid putative RDase remains unknown. Further analysis showed that the hybrid putative rdh genes are present in the genomes of pure cultures and uncultured members of Bacteriodetes and Deltaproteobacteria, but also in the genomes of the candidate divisions. The encoded hybrid putative RDases have cytoplasmic or exoplasmic C-terminus localization, and cluster phylogenetically separately from the existing RDase groups. With increasing availability of (meta)genomes, more diverse and likely novel rdh genes are expected, but questions regarding their functionality and ecological roles remain open.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Fu T, Cui H, Jia C, Sun W, Zhou S, Han Y, Liu L, Shi X, Zhang XH. Ancylomarina longa sp. nov., isolated from southern Okinawa Trough sediment and emended description of the family Marinifilaceae. Int J Syst Evol Microbiol 2020; 70:2531-2536. [PMID: 32100699 DOI: 10.1099/ijsem.0.004066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, obligately anaerobic, non-motile, non-spore-forming, long-rod-shaped and non-flagellated bacterial strain, designated T3-2 S1-CT, was isolated from a sediment sample collected at the Okinawa Trough. Phylogenetic analyses of 16S rRNA gene sequences and the whole genome revealed that strain T3-2 S1-CT was a member of the family Marinifilaceae and exhibited less than 95.1 % sequence similarities to the closely related type strains of the family Marinifilaceae. Optimal growth occurred at pH 7.0, 28 °C and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain T3-2 S1-CT was identified as menaquinone-7 (MK-7) and the predominant fatty acids (>10 %) were iso-C15 : 0 (38.9 %) and anteiso-C15 : 0 (11.6 %). The major polar lipids were one phosphatidylethanolamine, one phosphatidylmonomethylethanolamine, one aminolipids, two unidentified lipids and two unidentified phospholipids. The DNA G+C content of strain T3-2 S1-CT was 35.7 mol%. On the basis of the results of polyphasic analyses, strain T3-2 S1-CT is considered to represent a novel species of the genus Ancylomarina, for which the name Ancylomarina longa sp. nov. is proposed. The type strain is T3-2 S1-CT (=KCTC 15505T=MCCC 1K01617T).
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Affiliation(s)
- Tianyu Fu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Hongchang Cui
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Chao Jia
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Wen Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Shun Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yanqiong Han
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Lijun Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaochong Shi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China.,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China.,College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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