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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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Hwang K, Choe H, Kim KM. Complete genome of Polaribacter huanghezhanensis KCTC 32516 T isolated from glaciomarine fjord sediment of Svalbard. Mar Genomics 2023; 72:101068. [PMID: 38008528 DOI: 10.1016/j.margen.2023.101068] [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: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 11/28/2023]
Abstract
Polaribacter huanghezhanensis KCTC 32516T is an aerobic, non-flagellated, Gram-negative, orange-colony-forming bacterium that was isolated from the surficial glaciomarine sediment of inner basin of Kongsfjorden, Svalbard. The sampling site is characterized by a sedimentation of organic depleted lithogenous particles from the nearby glaciers, resulting in reduction of organic matter concentration. In order to understand microbial adaptation to the oligotrophic environment, we here sequenced the complete genome of the P. huanghezhanensis KCTC 32516T. The genome consists of 2,587,874 bp (G + C content of 31.5%) with a single chromosome, 2391 protein-coding genes, 39 tRNAs, and 2 rRNA operons. Our comparative analysis revealed that the P. huanghezhanensis possess the smallest genome in fifteen Polaribacter species with genome. The streamlined genome of this species, required less resource in replication, could evolved by the nutrient deficiency in surrounding environment. Simultaneously, the 15 KOs involved in amino acid biosynthesis and anaplerotic carbon fixation is uniquely absent in the P. huanghezhanensis. In addition, although the advantage of small genome, other 15 KOs involved in resource recycling and stress resistance is uniquely present in sequenced genome. This result demonstrates that the sequenced genome serves as a valuable model for further studies aimed at elucidating the molecular mechanisms associated with adaptation to oligotrophic habitat.
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Affiliation(s)
- Kyuin Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea.
| | - Hanna Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup 56212, Republic of Korea
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
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Najafpour B, Pinto PIS, Canario AVM, Power DM. Quantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genus‐specific primers. Microbiologyopen 2022; 11:e1274. [PMID: 35765179 PMCID: PMC9055463 DOI: 10.1002/mbo3.1274] [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: 01/28/2022] [Accepted: 03/05/2022] [Indexed: 12/03/2022] Open
Abstract
The goal of this study was to design genus‐specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon‐based sequencing of the 16S rRNA gene in fish‐related samples and surrounding water. Efficient genus‐specific primers were designed for 11 bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus‐specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus‐specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus‐specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus‐specific primers are proposed as rapid and cost‐effective tools to evaluate the most abundant bacterial genera in fish‐related or potentially other metagenomics samples.
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Affiliation(s)
- Babak Najafpour
- Centro de Ciências do Mar (CCMAR/CIMAR) Universidade do Algarve Faro Portugal
| | - Patricia I. S. Pinto
- Centro de Ciências do Mar (CCMAR/CIMAR) Universidade do Algarve Faro Portugal
- International Center for Marine Studies Shanghai Ocean University Shanghai China
| | - A. V. M. Canario
- Centro de Ciências do Mar (CCMAR/CIMAR) Universidade do Algarve Faro Portugal
- International Center for Marine Studies Shanghai Ocean University Shanghai China
| | - Deborah M. Power
- Centro de Ciências do Mar (CCMAR/CIMAR) Universidade do Algarve Faro Portugal
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