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Kachiprath B, Solomon S, Gopi J, Jayachandran PR, Thajudeen J, Sarasan M, Mohan AS, Puthumana J, Chaithanya ER, Philip R. Exploring bacterial diversity in Arctic fjord sediments: a 16S rRNA-based metabarcoding portrait. Braz J Microbiol 2024; 55:499-513. [PMID: 38175355 PMCID: PMC10920534 DOI: 10.1007/s42770-023-01217-6] [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: 07/21/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
The frosty polar environment houses diverse habitats mostly driven by psychrophilic and psychrotolerant microbes. Along with traditional cultivation methods, next-generation sequencing technologies have become common for exploring microbial communities from various extreme environments. Investigations on glaciers, ice sheets, ponds, lakes, etc. have revealed the existence of numerous microorganisms while details of microbial communities in the Arctic fjords remain incomplete. The current study focuses on understanding the bacterial diversity in two Arctic fjord sediments employing the 16S rRNA gene metabarcoding and its comparison with previous studies from various Arctic habitats. The study revealed that Proteobacteria was the dominant phylum from both the fjord samples followed by Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Chloroflexi and Chlamydiae. A significant proportion of unclassified reads derived from bacteria was also detected. Psychrobacter, Pseudomonas, Acinetobacter, Aeromonas, Photobacterium, Flavobacterium, Gramella and Shewanella were the major genera in both the fjord sediments. The above findings were confirmed by the comparative analysis of fjord metadata with the previously reported (secondary metadata) Arctic samples. This study demonstrated the potential of 16S rRNA gene metabarcoding in resolving bacterial composition and diversity thereby providing new in situ insights into Arctic fjord systems.
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Affiliation(s)
- Bhavya Kachiprath
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Solly Solomon
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
- Fishery Survey of India, Cochin Zonal Base, Kochangadi Road, Kochi, Kerala, 682005, India
| | - Jayanath Gopi
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - P R Jayachandran
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - Jabir Thajudeen
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403804, India
| | - Manomi Sarasan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Anjali S Mohan
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Jayesh Puthumana
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - E R Chaithanya
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Rosamma Philip
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India.
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Yang SH, Park MJ, Oh HM, Park YJ, Kwon KK. Flavivirga spongiicola sp. nov. and Flavivirga abyssicola sp. nov., Isolated from Marine Environments. J Microbiol 2024; 62:11-19. [PMID: 38319586 DOI: 10.1007/s12275-023-00102-z] [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: 11/12/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 02/07/2024]
Abstract
Two novel Gram-stain-negative, strictly-aerobic, rod-shaped (1.2 ± 3.4 μm × 0.3 ± 0.7 μm), and non-motile marine bacterial species, designated MEBiC05379T and MEBiC07777T, were isolated from a marine sponge Pseudaxinella sp. in Gangneung City and deep-sea sediments of the Ulleung basin in the East Sea of Korea, respectively. The 16S rRNA gene sequence analysis revealed high levels of similarities between these strains and members of the genus Flavivirga (97.0-98.4% sequence identities). Both novel strains revealed as mesophilic, neutrophilic in pH and slightly halophilic. Similar to those of other Flavivirga members, the primary cellular fatty acids of both strains were iso-C15:0, iso-C15:1 G, iso-C15:03-OH, and iso-C17:0 3-OH, with MEBiC05379T and MEBiC07777T containing relatively higher proportions of C12:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c). In both taxa, the major isoprenoid quinone was MK-6. The DNA G + C contents of MEBiC05379T and MEBiC07777T genomes were 32.62 and 32.46 mol%, respectively. Compared to other members of Flavivirga, both strains exhibited similar DNA G + C ratio and fatty acids pattern, yet enzyme expression and carbon sources utilization pattern were different. Genomes of the genus Flavivirga showed enzyme preferences to fucoidan and sulfated galactans. Considering the monophyly rule, AAI values delineate the genus Flavivirga from adjacent genera calculated to be 76.0-78.7%. Based on the phenotypic, genomic and biochemical data, strains for MEBiC05379T and MEBiC07777T thus represent two novel species in the genus Flavivirga, for which the names Flavivirga spongiicola sp. nov. (MEBiC05379T [= KCTC 92527 T = JCM 16662 T]), and Flavivirga abyssicola sp. nov. (MEBiC07777T [= KCTC 92563 T = JCM 36477 T]) are proposed.
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Affiliation(s)
- Sung-Hyun Yang
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea
| | - Mi-Jeong Park
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea
| | - Hyun-Myung Oh
- Institute of Liberal Arts Education, Pukyong National University, Busan, 48547, Republic of Korea
| | - Yeong-Jun Park
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea.
- KIOST School, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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Yu X, Gao X, Shang L, Wang X, Jiao Y, Zhang XH, Shi X. Spatial and temporal change determined co-occurrence networks stability and community assembly processes of epipelagic seawater microbial community in the Nordic Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160321. [PMID: 36414066 DOI: 10.1016/j.scitotenv.2022.160321] [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: 09/02/2022] [Revised: 10/27/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
The Nordic Sea has a vital impact on the global climate change, occupies a significant status in the physical oceanography research, on account of its intersection of complex ocean currents. To explore the influence of seasonal and spatial heterogeneity in its epipelagic seawater on the microbial community structure, a total of 54 seawater samples from 18 stations and 3 water layers (0 m, 50 m, 100 m) were collected in the summer of 2017 and the autumn of 2018 from the Norwegian Sea, the Greenland Sea and the vicinity of Jan Mayen Island in the Nordic Sea. Alpha- and Beta- diversity analysis showed that significant differences were found between characteristic bacterial groups in detached or mixed currents of corresponding seasons, as endemic OTUs with seasonal and ocean current characteristics which revealed the existence of spatiotemporal patterns of microbial communities in the Nordic Sea. Moreover, co-occurrence networks were conducted to show different degree of complexity and stability of microbial community response to spatiotemporal dynamic changes. Furthermore, the flow and collision between ocean currents do have an impact on the community assembly processes by affecting the migration and dispersal of microbial communities. This study reflects the response of microbial communities to the spatiotemporal dynamics and reveals the microbial community assembly mechanisms under complex hydrological condition represented in the Nordic Sea.
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Affiliation(s)
- Xiaowen Yu
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, 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
| | - Xueyu Gao
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, 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
| | - Li Shang
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, 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
| | - Xiaoyu Wang
- Frontier Science Center for Deep Ocean Multispheres and Earth System (FDOMES), Physical Oceanography Laboratory, Ocean University of China, Qingdao 266071, PR China
| | - Yutian Jiao
- Frontier Science Center for Deep Ocean Multispheres and Earth System (FDOMES), Physical Oceanography Laboratory, Ocean University of China, Qingdao 266071, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, 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
| | - Xiaochong Shi
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, 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.
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Zhang T, Li J, Wang N, Wang H, Yu L. Metagenomic analysis reveals microbiome and resistome in the seawater and sediments of Kongsfjorden (Svalbard, High Arctic). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151937. [PMID: 34838907 DOI: 10.1016/j.scitotenv.2021.151937] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/02/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Kongsfjorden in the high Arctic, a typical Arctic fjord, experienced long-time input of nutrients and pollutants from the remote and local resources, providing a platform for characterizing the diversity and distribution of antibiotic resistance genes (ARGs). However, the microbiome and antibiotic resistome in this pristine marine system have not been well documented. The present study aimed to characterize the diversity and distribution of bacterial communities and associated ARGs in seawater (12 samples) and sediments (13 samples) of Kongsfjorden via metagenomic analysis. In terms of both bacterial community compositions and ARG profiles, the seawater was significantly distinct from sediment. Only 29 ARG subtypes were detected in the Arctic seawater and sediments. Furthermore, three geochemical factors (i.e., longitude, depth, and PO43-) greatly influenced the bacterial communities in sediment samples, while longitude, depth, and latitude were crucial geochemical factors influencing the ARG profiles in sediment samples. Procrustes analysis revealed a significant correlation between bacterial community compositions and ARG profiles in seawater and sediment samples. Further analysis revealed the metagenome-assembled genomes (MAGs) with ARG subtypes. Overall, our study provides insights into the microbiome and resistome in a pristine Arctic fjord, thereby providing vital information for environmental management.
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Affiliation(s)
- Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China.
| | - Jun Li
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Nengfei Wang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, PR China
| | - Hao Wang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Liyan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China.
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Begmatov S, Savvichev AS, Kadnikov VV, Beletsky AV, Rusanov II, Klyuvitkin AA, Novichkova EA, Mardanov AV, Pimenov NV, Ravin NV. Microbial Communities Involved in Methane, Sulfur, and Nitrogen Cycling in the Sediments of the Barents Sea. Microorganisms 2021; 9:2362. [PMID: 34835487 PMCID: PMC8625253 DOI: 10.3390/microorganisms9112362] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
A combination of physicochemical and radiotracer analysis, high-throughput sequencing of the 16S rRNA, and particulate methane monooxygenase subunit A (pmoA) genes was used to link a microbial community profile with methane, sulfur, and nitrogen cycling processes. The objects of study were surface sediments sampled at five stations in the northern part of the Barents Sea. The methane content in the upper layers (0-5 cm) ranged from 0.2 to 2.4 µM and increased with depth (16-19 cm) to 9.5 µM. The rate of methane oxidation in the oxic upper layers varied from 2 to 23 nmol CH4 L-1 day-1 and decreased to 0.3 nmol L-1 day-1 in the anoxic zone at a depth of 16-19 cm. Sulfate reduction rates were much higher, from 0.3 to 2.8 µmol L-1 day-1. In the surface sediments, ammonia-oxidizing Nitrosopumilaceae were abundant; the subsequent oxidation of nitrite to nitrate can be carried out by Nitrospira sp. Aerobic methane oxidation could be performed by uncultured deep-sea cluster 3 of gamma-proteobacterial methanotrophs. Undetectable low levels of methanogenesis were consistent with a near complete absence of methanogens. Anaerobic methane oxidation in the deeper sediments was likely performed by ANME-2a-2b and ANME-2c archaea in consortium with sulfate-reducing Desulfobacterota. Sulfide can be oxidized by nitrate-reducing Sulfurovum sp. Thus, the sulfur cycle was linked with the anaerobic oxidation of methane and the nitrogen cycle, which included the oxidation of ammonium to nitrate in the oxic zone and denitrification coupled to the oxidation of sulfide in the deeper sediments. Methane concentrations and rates of microbial biogeochemical processes in sediments in the northern part of the Barents Sea were noticeably higher than in oligotrophic areas of the Arctic Ocean, indicating that an increase in methane concentration significantly activates microbial processes.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Alexander S. Savvichev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Igor I. Rusanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
| | - Alexey A. Klyuvitkin
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.K.); (E.A.N.)
| | - Ekaterina A. Novichkova
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.K.); (E.A.N.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Nikolai V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
- Il’ichev Pacific Institute of Oceanology, Far East Branch of the Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
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Bacterial community structure and functional profiling of high Arctic fjord sediments. World J Microbiol Biotechnol 2021; 37:133. [PMID: 34255189 DOI: 10.1007/s11274-021-03098-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/23/2021] [Indexed: 10/20/2022]
Abstract
Kongsfjorden, an Arctic fjord is significantly affected by the glacier melt and Atlantification, both the processes driven by accelerated warming in the Arctic. This has lead to changes in primary production, carbon pool and microbial communities, especially that in the sediment. In this study, we have examined the bacterial community structure of surface (0-2 cm) and subsurface (3-9 cm) sediments of Kongsfjorden using the high throughput sequencing analysis. Results revealed that bacterial community structure of Kongsfjorden sediments were dominated by phylum Proteobacteria followed by Bacteroidetes and Epsilonbacteraeota. While α- and γ-Proteobacterial class were dominant in surface sediments; δ-Proteobacteria were found to be predominant in subsurface sediments. The bacterial community structure in the surface and subsurface sediments showed significant variations (p ≤ 0.05). Total organic carbon could be one of the major parameters controlling the bacterial diversity in the surface and subsurface sediments. Functional prediction analysis indicated that the bacterial community could be involved in the degradation of complex organic compounds such as glycans, glycosaminoglycans, polycyclic aromatic hydrocarbons and also in the biosynthesis of secondary metabolites.
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Maturana-Martínez C, Fernández C, González HE, Galand PE. Different Active Microbial Communities in Two Contrasted Subantarctic Fjords. Front Microbiol 2021; 12:620220. [PMID: 34248861 PMCID: PMC8264266 DOI: 10.3389/fmicb.2021.620220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/25/2021] [Indexed: 12/02/2022] Open
Abstract
Microorganisms play a crucial role in biogeochemical processes affecting the primary production and biogeochemical cycles of the ocean. In subpolar areas, the increment of the water temperature induced by climate change could lead to changes in the structure and activity of planktonic microbial communities. To understand how the structure of the microbial community in Chilean Patagonian fjords could be affected by climate change, we analyzed the composition of the prokaryotic community (bacteria-archaea) in two fjords (Pia and Yendegaia) with contrasting morphological and hydrological features. We targeted both the standing stock (16S rRNA genes) and the active fraction (16S rRNA transcripts) of the microbial communities during two consecutive austral winters. Our results showed that in both fjords, the active community had higher diversity and stronger biogeographic patterns when compared to the standing stock. Members of the Alpha-, Gamma-, and Deltaproteobacteria followed by archaea from the Marine Group I (Thaumarchaeota) dominated the active communities in both fjords. However, in Pia fjord, which has a marine-terminating glacier, the composition of the microbial community was directly influenced by the freshwater discharges from the adjacent glacier, and indirectly by a possible upwelling phenomenon that could bring deep sea bacteria such as SAR202 to the surface layer. In turn, in the Yendegaia, which has a land-terminating glacier, microbial communities were more similar to the ones described in oceanic waters. Furthermore, in Yendegaia fjord, inter-annual differences in the taxonomic composition and diversity of the microbial community were observed. In conclusion, Yendegaia fjord, without glacier calving, represents a fjord type that will likely be more common under future climate scenarios. Our results showing distinct Yendegaia communities, with for example more potential nitrogen-fixing microorganisms (Planctomycetes), indicate that as a result of climate change, changing planktonic communities could potentially impact biogeochemical processes and nutrient sources in subantarctic fjords.
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Affiliation(s)
- Claudia Maturana-Martínez
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France.,Centro de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes and Universidad Austral de Chile, Valdivia, Chile
| | - Camila Fernández
- Centro de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes and Universidad Austral de Chile, Valdivia, Chile.,Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, Banyuls-sur-Mer, France.,Departamento de Oceanografía and Centro de Investigación Oceanográfica COPAS Sur-Austral, Universidad de Concepción, Concepción, Chile
| | - Humberto E González
- Centro de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes and Universidad Austral de Chile, Valdivia, Chile
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France
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Thomas FA, Mohan M, Krishnan KP. Bacterial diversity and their metabolic profiles in the sedimentary environments of Ny-Ålesund, Arctic. Antonie van Leeuwenhoek 2021; 114:1339-1360. [PMID: 34148162 DOI: 10.1007/s10482-021-01604-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/01/2021] [Indexed: 11/26/2022]
Abstract
Sedimentary environments in the Arctic are known to harbor diverse microbial communities playing a crucial role in the remineralization of organic matter and associated biogeochemical cycles. In this study, we used a combination of culture-dependent and culture-independent approaches to understanding the bacterial community composition associated with the sediments of a terrestrial versus fjord system in the Svalbard Arctic. Community-level metabolic profiling and growth response of retrieved bacterial isolates towards different carbon substrates at varying temperatures were also studied to assess the metabolic response of communities and isolates in the system. Bacterial species belonging to Cryobacterium and Psychrobacter dominated the terrestrial and fjord sediment retrievable fraction. Amplicon sequencing analysis revealed higher bacterial diversity in the terrestrial sediments (Shannon index; 8.135 and 7.935) as compared to the fjord sediments (4.5-5.37). Phylum Proteobacteria and Bacteroidetes dominated both terrestrial and fjord sediments. Phylum Verrucomicrobia and Cyanobacteria were abundant in terrestrial sediments while Epsilonbacteraeota and Fusobacteriia dominated the fjord sediments. Significant differences were observed in the carbon substrate utilization profiles between the terrestrial and fjord sediments at both 4 °C and 20 °C incubations (p < 0.005). Utilization of N-acetyl-D-glucosamine, D-mannitol and Tween-80 by the sediment communities and bacterial isolates from both systems, irrespective of their temperature incubations implies the affinity of bacteria for such substrates as energy sources and for their survival in cold environments. Our results suggest the ability of sediment bacterial communities to adjust their substrate utilization profiles according to condition changes in the ecosystems and are found to be less influenced by their phylogenetic relatedness.
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Affiliation(s)
- Femi Anna Thomas
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama, Goa, 403804, India
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Taleigao Plateau Goa, 403206, India
| | - Mahesh Mohan
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, Kerala, 686560, India
| | - K P Krishnan
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama, Goa, 403804, India.
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Tikhonova EN, Kadnikov VV, Rusanov II, Beletsky AV, Zakharova EE, Samylina OS, Ravin NV, Pimenov NV. Methane-Oxidizing Activity and Phylogenetic Diversity of Aerobic Methanotrophs in the Laptev Sea Upper Sediment Horizons. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Zeng Y, Luo W, Li H, Yu Y. High diversity of planktonic prokaryotes in Arctic Kongsfjorden seawaters in summer 2015. Polar Biol 2021. [DOI: 10.1007/s00300-020-02791-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy). Microorganisms 2020; 8:microorganisms8060936. [PMID: 32580393 PMCID: PMC7356649 DOI: 10.3390/microorganisms8060936] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 02/06/2023] Open
Abstract
Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.
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Thomas FA, Sinha RK, Krishnan KP. Bacterial community structure of a glacio-marine system in the Arctic (Ny-Ålesund, Svalbard). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:135264. [PMID: 31848061 DOI: 10.1016/j.scitotenv.2019.135264] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 06/10/2023]
Abstract
The bacterial community composition of a valley glacier in Svalbard, its pro-glacial channels, and the associated downstream fjord ecosystem was investigated so as to figure out the degree to which downslope transport of microbes from the glacier systems along a hydrological continuum impose an effect on the patterns of diversity in the fjord system. A combination of culture based and high-throughput amplicon sequencing approach was followed which resulted in significant variation (R = 0.873, p = 0.001) in the bacterial community structure between these ecosystems. Dominance of sequences belonging to class β-Proteobacteria was seen in the glacier snow, ice and melt waters (MW) while a relatively higher abundance of OTUs belonging to α-Proteobacteria and Verrucomicrobiae demarcated the fjord waters. Similarity percentage (SIMPER) analysis of the Operational Taxonomic Units (OTUs) showed that OTU 1,105,280 (9.15%) and OTU 331 (6.5%) belonging to Burkholderiaceae (β-proteobacteria) and OTU 101,660 (5.76%) and OTU 520 (5.07%) belonging to Rhodobacteraceae (α-proteobacteria) contributed maximum to the overall dissimilarity between the sampling sites. The bacterial community from the MWs were found to be true signatures of the glacier ecosystem while the Kongsfjorden bacterial fraction mostly represented heterotrophic marine taxa influenced by warm Atlantic waters and presence of organic matter. Significant presence of unknown taxa in the MWs suggests the need to study such unexplored, transient niches for a better understanding of the associated microbial processes. Among the various environmental parameters measured, nutrients (NO3- and SiO42-) were found to exhibit strong association with the MW bacterial community while temperature, trace metals, Cl- and SO42- ions were found to influence the fjord bacterial community. The significant differences in the bacterial community composition between the glacier and the fjord ecosystem suggest the unique nature of these systems which in turn is influenced by the associated environmental parameters.
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Affiliation(s)
- Femi Anna Thomas
- National Centre for Polar and Ocean Research, Headland Sada, Vasco da Gama, Goa 403804, India; School of Earth, Ocean and Atmospheric Sciences, Goa University, Taleigao Plateau Goa 403206, India
| | - Rupesh Kumar Sinha
- National Centre for Polar and Ocean Research, Headland Sada, Vasco da Gama, Goa 403804, India
| | - K P Krishnan
- National Centre for Polar and Ocean Research, Headland Sada, Vasco da Gama, Goa 403804, India.
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13
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Latitudinal Distributions and Controls of Bacterial Community Composition during the Summer of 2017 in Western Arctic Surface Waters (from the Bering Strait to the Chukchi Borderland). Sci Rep 2019; 9:16822. [PMID: 31727995 PMCID: PMC6856522 DOI: 10.1038/s41598-019-53427-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/27/2019] [Indexed: 11/30/2022] Open
Abstract
The western Arctic Ocean is experiencing some of the most rapid environmental changes in the Arctic. However, little is known about the microbial community response to these changes. Employing observations from the summer of 2017, this study investigated latitudinal variations in bacterial community composition in surface waters between the Bering Strait and Chukchi Borderland and the factors driving the changes. Results indicate three distinctive communities. Southern Chukchi bacterial communities are associated with nutrient rich conditions, including genera such as Sulfitobacter, whereas the northern Chukchi bacterial community is dominated by SAR clades, Flavobacterium, Paraglaciecola, and Polaribacter genera associated with low nutrients and sea ice conditions. The frontal region, located on the boundary between the southern and northern Chukchi, is a transition zone with intermediate physical and biogeochemical properties; however, bacterial communities differed markedly from those found to the north and south. In the transition zone, Sphingomonas, with as yet undetermined ecological characteristics, are relatively abundant. Latitudinal distributions in bacterial community composition are mainly attributed to physical and biogeochemical characteristics, suggesting that these communities are susceptible to Arctic environmental changes. These findings provide a foundation to improve understanding of bacterial community variations in response to a rapidly changing Arctic Ocean.
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14
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Cao S, Zhang F, He J, Ji Z, Zhou Q. Water masses influence bacterioplankton community structure in summer Kongsfjorden. Extremophiles 2019; 24:107-120. [PMID: 31679078 DOI: 10.1007/s00792-019-01139-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/08/2019] [Indexed: 10/25/2022]
Abstract
To ascertain the saying "Everything is everywhere, but the environment selects", it was imperative to find out the main factor influencing bacterioplankton composition at genus level of Kongsfjorden where was influenced both by glacier melting water and Atlantic water. Thus, bacterioplankton diversity was investigated using pyrosequencing. In addition, nutrients, chlorophyll a, in situ temperature and salinity were measured. There were seventeen of 33 identified genera with relative abundance > 0.1%. Redundancy analysis showed that 73.02% of bacterioplankton community variance could be explained by environmental parameters. Furthermore, most of the abundant genera demonstrated significant correlation with environment parameters revealed by correlation analysis. Moreover, phosphate, nitrate and Chl a concentration, and the abundance of top nine identified genera varied with water mass significantly as shown by analysis of variance. Our results supported the notion that environmental factors, especially water mass had significant effect on bacterioplankton distribution at genus level. Considering the high sensitivity to environmental change and low error rate in identification, bacterioplankton at genus level could be potential bio-markers for monitoring environmental changes.
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Affiliation(s)
- Shunan Cao
- Key Laboratory for Polar Science SOA, Polar Research Institute of China, No. 451 JinQiao Road, Pudong Avenue, Shanghai, 200136, China
| | - Fang Zhang
- Key Laboratory for Polar Science SOA, Polar Research Institute of China, No. 451 JinQiao Road, Pudong Avenue, Shanghai, 200136, China
| | - Jianfeng He
- Key Laboratory for Polar Science SOA, Polar Research Institute of China, No. 451 JinQiao Road, Pudong Avenue, Shanghai, 200136, China.
| | - Zhongqiang Ji
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Qiming Zhou
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin, 150080, China.,ChosenMed Technology (Beijing) Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
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15
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Effects of Vertical Water Mass Segregation on Bacterial Community Structure in the Beaufort Sea. Microorganisms 2019; 7:microorganisms7100385. [PMID: 31554216 PMCID: PMC6843845 DOI: 10.3390/microorganisms7100385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 11/16/2022] Open
Abstract
The Arctic Ocean is one of the least well-studied marine microbial ecosystems. Its low-temperature and low-salinity conditions are expected to result in distinct bacterial communities, in comparison to lower latitude oceans. However, this is an ocean currently in flux, with climate change exerting pronounced effects on sea-ice coverage and freshwater inputs. How such changes will affect this ecosystem are poorly constrained. In this study, we characterized the bacterial community compositions at different depths in both coastal, freshwater-influenced, and pelagic, sea-ice-covered locations in the Beaufort Sea in the western Canadian Arctic Ocean. The environmental factors controlling the bacterial community composition and diversity were investigated. Alphaproteobacteria dominated the bacterial communities in samples from all depths and stations. The Pelagibacterales and Rhodobacterales groups were the predominant taxonomic representatives within the Alphaproteobacteria. Bacterial communities in coastal and offshore samples differed significantly, and vertical water mass segregation was the controlling factor of community composition among the offshore samples, regardless of the taxonomic level considered. These data provide an important baseline view of the bacterial community in this ocean system that will be of value for future studies investigating possible changes in the Arctic Ocean in response to global change and/or anthropogenic disturbance.
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16
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Zeng YX, Qiao ZY. Diversity of Dimethylsulfoniopropionate Degradation Genes Reveals the Significance of Marine Roseobacter Clade in Sulfur Metabolism in Coastal Areas of Antarctic Maxwell Bay. Curr Microbiol 2019; 76:967-974. [DOI: 10.1007/s00284-019-01709-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/21/2019] [Indexed: 11/24/2022]
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17
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Bacterial community pattern along the sediment seafloor of the Arctic fjorden (Kongsfjorden, Svalbard). Antonie van Leeuwenhoek 2019; 112:1121-1136. [PMID: 30783849 DOI: 10.1007/s10482-019-01245-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
Abstract
The Arctic region has been the focus of increasing attention as an ecosystem that is highly sensitive to changes associated with global warming. Although it was assumed to be vulnerable to changes in climate, a limited number of studies have been conducted on the surface sediment bacteria of Arctic fjorden. This study assessed the diversity and distribution pattern of bacterial communities in eight marine sediments along the seafloor in a high Arctic fjorden (Kongsfjorden, Svalbard). A total of 822 operational taxonomic units (OTUs) were identified by Illumina MiSeq sequencing, targeting the V3-V4 hypervariable regions of the 16S rRNA gene. In these surface marine sediments, more than half of the sequences belonged to the phylum Proteobacteria, followed by Bacteroidetes, Verrucomicrobia, Actinobacteria, Chloroflexi and Lentisphaerae. The bacterial genera Marinicella, Desulfobulbus, Lutimonas, Sulfurovum and clade SEEP-SRB4 were dominant in all samples. Analysis of similarity indicated that bacterial communities were significantly different among the inner, central and outer basins (r2 = 0.5, P = 0.03 < 0.05). Canonical correspondence analysis and permutation tests revealed that location depth (r2 = 0.87, P < 0.01), temperature (r2 = 0.88, P < 0.01) and salinity (r2 = 0.88, P < 0.05) were the most significant factors that correlated with the bacterial communities in the sediments. 28 differentially abundant taxonomic clades in the inner and outer basin with an LDA score higher than 2.0 were found by the LEfSe method. The Spearman correlation heat map revealed different degrees of correlation between most major OTUs and environmental factors, while some clades have an inverse correlation with environmental factors. The spatial patterns of bacterial communities along the Kongsfjorden may offer insight into the ecological responses of prokaryotes to climate change in the Arctic ecosystem, which makes it necessary to continue with monitoring.
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18
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Fernández-Gómez B, Díez B, Polz MF, Arroyo JI, Alfaro FD, Marchandon G, Sanhueza C, Farías L, Trefault N, Marquet PA, Molina-Montenegro MA, Sylvander P, Snoeijs-Leijonmalm P. Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 °N. THE ISME JOURNAL 2019; 13:316-333. [PMID: 30228379 PMCID: PMC6331608 DOI: 10.1038/s41396-018-0268-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/11/2018] [Accepted: 07/24/2018] [Indexed: 01/13/2023]
Abstract
Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
- INTA-Universidad de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile.
- Center for Climate and Resilience Research, Concepción, Chile.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - José Ignacio Arroyo
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Germán Marchandon
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Cynthia Sanhueza
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Laura Farías
- Center for Climate and Resilience Research, Concepción, Chile
- Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Pablo A Marquet
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Marco A Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Universidad Católica del Norte, Coquimbo, Chile
| | - Peter Sylvander
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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19
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Liao L, Liu C, Zeng Y, Zhao B, Zhang J, Chen B. Multipartite genomes and the sRNome in response to temperature stress of an Arctic Pseudoalteromonas fuliginea BSW20308. Environ Microbiol 2018; 21:272-285. [PMID: 30362272 DOI: 10.1111/1462-2920.14455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 11/28/2022]
Abstract
Little is known about the survival and effect of rapid climate warming on Pseudoalteromonas in the Arctic, although it is abundant and important in this ecosystem. Here, we investigated a cold-adapted Pseudoalteromonas fuliginea BSW20308 from the Arctic Ocean, from the genome to its transcriptomic responses towards temperature changes. It contained two circular chromosomes, with the second chromosome probably evolved from an ancestral plasmid. The evolution of multipartite genomes may be advantageous for its survival under changing environments. RNA-seq analysis revealed the extensive involvement of sRNome in response to temperature stress for the first time, especially tmRNA and a novel Pf1 sRNA strongly induced under heat stress. The present study makes significant contributions towards the understanding of Pseudoalteromonas in two aspects: the genome structure and evolution of its two chromosomes, and the important discovery of the sRNome in response to temperature stress.
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Affiliation(s)
- Li Liao
- SOA Key Laboratory for Polar Science, Division of Polar Biological Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yinxin Zeng
- SOA Key Laboratory for Polar Science, Division of Polar Biological Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
| | - Bin Zhao
- SOA Key Laboratory for Polar Science, Division of Polar Biological Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.,School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jin Zhang
- SOA Key Laboratory for Polar Science, Division of Polar Biological Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Division of Polar Biological Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
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20
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Yoon J, Yasumoto-Hirose M, Kasai H. Seonamhaeicola acroporae sp. nov., a marine species of the family Flavobacteriaceae isolated from the hard coral Acropora formosa. Arch Microbiol 2018; 201:499-504. [PMID: 30386885 DOI: 10.1007/s00203-018-1589-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 12/01/2022]
Abstract
A novel marine flavobacterial species, designated 3KA7-17T, was isolated from the hard coral Acropora formosa D. collected in Japan. The strain was pale-orange pigmented, Gram-stain negative, strictly aerobic, coccus shaped, and non-motile. Preliminary analysis based on the 16S rRNA gene sequence revealed an affiliation with the family Flavobacteriaceae of the phylum Bacteroidetes, and it had the greatest sequence similarity (96.0%) to Seonamhaeicola algicola Gy8T. The DNA G + C content was 34.3 mol%. MK-6 was the major menaquinone, with iso-C15:1 H and/or C13:0 3-OH (24.3%), iso-C15:0 (19.5%), iso-C15:0 3-OH (14.2%), and iso-C17:0 3-OH (15.9%) as the main (> 10%) cellular fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids, and two unidentified lipids. Based on distinct phylogenetic and phenotypic evidence, the strain represents a novel species of the genus Seonamhaeicola, for which the name Seonamhaeicola acroporae sp. nov. is proposed and the type strain is 3KA7-17T (= KCTC 62713T = NBRC 113410T).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu, 42601, Republic of Korea.
| | - Mina Yasumoto-Hirose
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate, 026-0001, Japan.,Tropical Technology Plus, 12-75 Suzaki, Uruma, Okinawa, 904-2234, Japan
| | - Hiroaki Kasai
- Marine Biosciences Kamaishi Research Laboratory, Kitasato University, 160-4 Utou, Okirai, Sanriku-cho, Ofunato, Iwate, 022-0101, Japan
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21
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Description of Lacinutrix salivirga sp. nov., a marine member of the family Flavobacteriaceae isolated from seawater. Arch Microbiol 2018; 200:1159-1165. [PMID: 29872888 DOI: 10.1007/s00203-018-1533-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/05/2018] [Accepted: 05/28/2018] [Indexed: 10/14/2022]
Abstract
A novel marine bacterium, designated KMU-57T, was isolated from seawater collected from the Republic of Korea, and it was characterized using polyphasic taxonomic methods. Strain KMU-57T was Gram-stain-negative, strictly aerobic, rod-shaped, motile and dark-yellow-pigmented. Comparative analysis based on the 16S rRNA gene sequence showed the affiliation of the isolate with members of the family Flavobacteriaceae of the phylum Bacteroidetes, and it had the greatest sequence similarity (97.6%) to Lacinutrix jangbogonensis PAMC 27137T. The DNA-DNA relatedness value between strain KMU-57T and L. jangbogonensis PAMC 27137T was 37.8 ± 2.2%. The DNA G + C content of strain KMU-57T was 29.9 mol%; MK-6 was the major menaquinone with; iso-C15:1 G (18.6%) and C16:1 ω7c and/or C16:1 ω6c (15.8%) as the major (> 10%) cellular fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, three unidentified aminolipids, and five unidentified lipids. The strain represents a novel species of the genus Lacinutrix for which the name Lacinutrix salivirga sp. nov. is proposed. The type strain of L. salivirga sp. nov. is KMU-57T (= KCTC 52878T = NBRC 112845T).
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22
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Ribicic D, Netzer R, Winkler A, Brakstad OG. Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures. MARINE POLLUTION BULLETIN 2018; 129:308-317. [PMID: 29680553 DOI: 10.1016/j.marpolbul.2018.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/09/2018] [Accepted: 02/12/2018] [Indexed: 05/20/2023]
Abstract
Biodegradation of chemically dispersed oil at low temperature (0-2 °C) was compared in natural seawater from Arctic (Svalbard) and a temperate (Norway) fjords. The oil was premixed with a dispersant (Corexit 9500) and small-droplet oil dispersions prepared. Faster biotransformation of n-alkanes in the Arctic than in the temperate seawater were associated with the initially higher abundance of the alkane-degrading genus Oleispira in the Arctic than the temperate seawater. Comparable transformation of aromatic hydrocarbons was further associated with the late emergences Cycloclasticus in both seawater sources. The results showed that chemically dispersed oil may be rapidly biodegraded by microbial communities in Arctic seawater. Compared to oil biodegradation studies at higher seawater temperatures, longer lag-periods were experienced here, and may be attributed to both microbial and oil properties at these low seawater temperatures.
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Affiliation(s)
- Deni Ribicic
- The Norwegian University of Science and Technology, Dept. Cancer Research and Molecular Medicine, 7491 Trondheim, Norway
| | - Roman Netzer
- SINTEF Ocean, Dept. Environmental Technology, Brattørkaia 17C, 7010 Trondheim, Norway
| | - Anika Winkler
- Bielefeld University, Centre for Biotechnology (CeBiTec), 33501 Bielefeld, Germany
| | - Odd Gunnar Brakstad
- SINTEF Ocean, Dept. Environmental Technology, Brattørkaia 17C, 7010 Trondheim, Norway.
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23
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Conte A, Papale M, Amalfitano S, Mikkonen A, Rizzo C, De Domenico E, Michaud L, Lo Giudice A. Bacterial community structure along the subtidal sandy sediment belt of a high Arctic fjord (Kongsfjorden, Svalbard Islands). THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:203-211. [PMID: 29149744 DOI: 10.1016/j.scitotenv.2017.11.077] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
Open fjords are subject to contrasting environmental conditions, owing to meltwater glacial inputs, terrestrial runoff, and marine water mass exchanges, which are exacerbated by anthropogenic and climate perturbations. Following a slope-dependent water circulation, the subtidal sandy sediment belt regulates the convergent transport of nutrients downward the fjord depths, and the effective entrapment of suspended particles and microorganisms. In this study, we aimed at testing how glacial and seawater inputs may influence the bacterial community structure of subtidal sand deposits in the Kongsfjorden. Through total and viable cell counting and an amplicon sequencing approach, we found relevant differences in bacterial community structure along the glacio-marine sampling transect. Viable and high nucleic acid content (HNA) cells represented an important fraction of the total community, generally decreasing toward the glacier front. Besides the predominance of Alpha- and Gammaproteobacteria, Bacteroidetes, Firmicutes and Parcubacteria, the bacterial community structure was likely affected by the glacial activity in the inner fjord, with the occurrence of distinctive phylotypes belonging to Gemmatimonadates, Nitrospirae, Acidobacteria, and Chloroflexi. Overall, our outcomes highlighted that exploring the bacterial community distribution and structure can provide new insights into the active role of sand deposits in coastal cold environments.
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Affiliation(s)
- Antonella Conte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Stefano Amalfitano
- Water Research Institute, National Research Council (IRSA-CNR), Monterotondo, Rome, Italy
| | - Anu Mikkonen
- Department of Biological and Environmental Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Carmen Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Emilio De Domenico
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Luigi Michaud
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Angelina Lo Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy; Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Messina, Italy.
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24
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Zeng YX, Yu Y, Li HR, Luo W. Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments As Revealed by 454 Pyrosequencing. Front Microbiol 2017; 8:2498. [PMID: 29312204 PMCID: PMC5732994 DOI: 10.3389/fmicb.2017.02498] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/30/2017] [Indexed: 11/13/2022] Open
Abstract
Fjords and continental shelves represent distinct marine ecosystems in the pan-arctic region. Kongsfjorden is a glacial fjord that is located on the west coast of Svalbard, and is influenced by both Atlantic and Arctic water masses. The Bering Sea consists of a huge continental shelf in the northeast and a deep ocean basin in the southwest, and is influenced by Pacific water. Microbial community compositions of Arctic sediment samples BJ4 from outer basin and BJ36 from inner basin of Kongsfjorden and sub-Arctic samples NEC5 from shallow shelf and DBS1 from deep basin region of the northern Bering Sea were investigated using 454 pyrosequencing of archaeal and bacterial 16S rRNA genes. Most archaeal sequences in the sediments were related to Thaumarchaeota, though Euryarchaeota were more abundant in the Arctic glacier-influencing inner basin sediment BJ36. Thaumarchaeota Group C3 was the dominant archaeal population in all samples. Proteobacteria and Bacteroidetes dominated the sediment bacterial communities. Acidobacteria and Actinobacteria were also dominant in the northern Bering Sea samples. Alphaproteobacteria and Epsilonproteobacteria were the two main classes in Kongsfjorden sediment bacterial communities while Deltaproteobacteria and Gammaproteobacteria were dominant in the northern Bering Sea sediments. Differences in the presence and abundance of other dominant archaeal and bacterial populations were observed among sediment samples. In contrast to archaeal community differences that the Arctic BJ36 archaeal community was distinct from the sub-Arctic sediments and the Arctic outer basin sediment BJ4, cluster analysis based on bacterial OTU (operational taxonomic unit) distributions indicated that the Arctic and sub-Arctic bacterial communities segregated from one another. These results suggest that the sediment archaeal and bacterial community compositions can be driven by different environmental factors. Differences in the presence and abundance of particular archaeal species (e.g., Candidatus Nitrosopumilus and Methanococcoides) or bacterial species (e.g., Sulfurimonas, Sulfurovum, and Desulfobulbaceae) involved in biogeochemical cycles were also observed among sediment samples. At the same time, despite the community variation, some phylotypes (e.g., Marinicella) were dominant in all sediments. This study indicates diverse microbial communities inhabiting pan-arctic marine sediments, and highlights potential roles for Archaea and Bacteria in global biogeochemical cycles in these environments.
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Affiliation(s)
- Yin-Xin Zeng
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai, China
| | - Yong Yu
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai, China
| | - Hui-Rong Li
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai, China
| | - Wei Luo
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai, China
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Yoon J, Yasumoto-Hirose M, Kasai H. Frondibacter mangrovi sp. nov., a member of the family Flavobacteriaceae isolated from seawater by in situ cultivation, and emended description of Frondibacter aureus. Int J Syst Evol Microbiol 2017; 67:5013-5018. [DOI: 10.1099/ijsem.0.002404] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 42601, Republic of Korea
| | - Mina Yasumoto-Hirose
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
- Present address: Tropical Technology Plus, 12-75 Suzaki, Uruma, Okinawa 904-2234, Japan
| | - Hiroaki Kasai
- School of Marine Biosciences, Kitasato University, 160-4 Utou, Okirai, Sanriku-cho, Ofunato, Iwate 022-0101, Japan
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Zeng J, Chen M, Zheng M, Hu W, Qiu Y. A potential nitrogen sink discovered in the oxygenated Chukchi Shelf waters of the Arctic. GEOCHEMICAL TRANSACTIONS 2017; 18:5. [PMID: 29086802 PMCID: PMC5607156 DOI: 10.1186/s12932-017-0043-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
The western Arctic Shelf has long been considered as an important sink of nitrogen because high primary productivity of the shelf water fuels active denitrification within the sediments, which has been recognized to account for all the nitrogen (N) removal of the Pacific water inflow. However, potentially high denitrifying activity was discovered within the oxygenated Chukchi Shelf water during our summer expedition. Based on 15N-isotope pairing incubations, we estimated denitrification rates ranging from 1.8 ± 0.4 to 75.9 ± 8.7 nmol N2 L-1 h-1. We find that the spatial pattern of denitrifying activity follows well with primary productivity, which supplies plentiful fresh organic matter, and there was a strong correlation between integrated denitrification and integrated primary productivity. Considering the active hydrodynamics over the Chukchi Shelf during summer, resuspension of benthic sediment coupled with particle-associated bacteria induces an active denitrification process in the oxic water column. We further extrapolate to the whole Chukchi Shelf and estimate an N removal flux from this cold Arctic shelf water to be 12.2 Tg-N year-1, which compensates for the difference between sediment cores incubation (~ 3 Tg-N year-1) and geochemical estimation based on N deficit relative to phosphorous (~ 16 Tg-N year-1). We infer that dynamic sediment resuspension combined with high biological productivity stimulates intensive denitrification in the water column, potentially creating a nitrogen sink over the shallow Arctic shelves that have previously been unrecognized.
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Affiliation(s)
- Jian Zeng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
| | - Min Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
| | - Minfang Zheng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
| | - Wangjiang Hu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
| | - Yusheng Qiu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
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Jain A, Krishnan KP. Differences in free-living and particle-associated bacterial communities and their spatial variation in Kongsfjorden, Arctic. J Basic Microbiol 2017; 57:827-838. [DOI: 10.1002/jobm.201700216] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/16/2017] [Accepted: 07/07/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Anand Jain
- Cryobiology Laboratory; National Centre for Antarctic and Ocean Research; Vasco-da-Gama, Goa India
| | - Kottekkatu P. Krishnan
- Cryobiology Laboratory; National Centre for Antarctic and Ocean Research; Vasco-da-Gama, Goa India
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Papale M, Giannarelli S, Francesconi S, Di Marco G, Mikkonen A, Conte A, Rizzo C, De Domenico E, Michaud L, Giudice AL. Enrichment, isolation and biodegradation potential of psychrotolerant polychlorinated-biphenyl degrading bacteria from the Kongsfjorden (Svalbard Islands, High Arctic Norway). MARINE POLLUTION BULLETIN 2017; 114:849-859. [PMID: 27855955 DOI: 10.1016/j.marpolbul.2016.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/04/2016] [Accepted: 11/10/2016] [Indexed: 06/06/2023]
Abstract
Persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs), have been detected in abiotic Arctic matrices: surface sediments and seawater from coastal areas in the Kongsfjorden were collected and analyzed. Levels of PCBs varied depending on the sampling site. Total PCB concentrations were between 11.63 (site C2W) and 27.69pgl-1 (site AW). These levels were comparable to those reported previously in lake sediments from the northern Svalbard. The occurrence and biodegradation potential of cold-adapted PCB-oxidizing bacteria in seawater and sediment along the fjord was also evaluated. After enrichment with biphenyl, 246 isolates were obtained with 45 of them that were able to grow in the presence of the PCB mixture Aroclor 1242, as the sole carbon source. The catabolic gene bphA was harbored by 17 isolates with affiliates to the genera Algoriphagus, Devosia and Salinibacterium that have been never reported as able to utilize PCBs, thus deserving further investigation. The total removal of Aroclor 1242 and selected PCB congeners was evaluated at 4 and 15°C for eight bphA-harboring isolates and Gelidibacter sp. DS-10. With few exceptions, tested strains showed greater efficiency at 15 than at 4°C. Isolates were able to reduce most chromatographic peaks by >50%, with some di- and trichlorobiphenyls that were quite totally removed (>90%).
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Affiliation(s)
- Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Stefania Giannarelli
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Sandro Francesconi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Gaetano Di Marco
- Istituto per i Processi Chimico Fisici, National Research Council (IPCF-CNR), Messina, Italy
| | - Anu Mikkonen
- Department of Biological and Environmental Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Antonella Conte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Carmen Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Emilio De Domenico
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Luigi Michaud
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy
| | - Angelina Lo Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Messina, Italy; Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Messina, Italy.
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Diversity of bacterial dimethylsulfoniopropionate degradation genes in surface seawater of Arctic Kongsfjorden. Sci Rep 2016; 6:33031. [PMID: 27604458 PMCID: PMC5015088 DOI: 10.1038/srep33031] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/19/2016] [Indexed: 11/08/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP), which is the major source of organic sulfur in the world's oceans, plays a significant role in the global sulfur cycle. This compound is rapidly degraded by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methylmercaptopropionate (MMPA). The diversity of genes encoding bacterial demethylation (dmdA) and DMS production (dddL and dddP) were measured in Arctic Kongsfjorden. Both dmdA and dddL genes were detected in all stations along a transect from the outer to the inner fjord, while dddP gene was only found in the outer and middle parts of the fjord. The dmdA gene was completely confined to the Roseobacter clade, while the dddL gene was confined to the genus Sulfitobacter. Although the dddP gene pool was also dominated by homologs from the Roseobacter clade, there were a few dddP genes showing close relationships to both Alphaproteobacter and Gammaproteobacter. The results of this study suggest that the Roseobacter clade may play an important role in DMSP catabolism via both demethylation and cleavage pathways in surface waters of Kongsfjorden during summer.
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Dong C, Sheng H, Wang W, Zhou H, Shao Z. Bacterial distribution pattern in the surface sediments distinctive among shelf, slope and basin across the western Arctic Ocean. Polar Biol 2016. [DOI: 10.1007/s00300-016-1970-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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31
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Mamaeva EV, Galach’yants YP, Khabudaev KV, Petrova DP, Pogodaeva TV, Khodzher TB, Zemskaya TI. Metagenomic analysis of microbial communities of the sediments of the Kara Sea shelf and the Yenisei Bay. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716020132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Yoon J, Adachi K, Kasai H. Aureisphaera salina sp. nov., a member of the family Flavobacteriaceae isolated from an ascidian. Int J Syst Evol Microbiol 2016; 66:2999-3004. [PMID: 27150454 DOI: 10.1099/ijsem.0.001132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-motile, strictly aerobic, chemoheterotrophic, pale-yellow-pigmented bacterium, designated strain A6D-50T, was isolated from an ascidian collected at Kohama Island offshore Okinawa, Japan. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (97.6 %) to Aureisphaera galaxeae 04OKA003-7T. The DNA-DNA relatedness value between strain A6D-50T and A. galaxeae 04OKA003-7T was 23.6 %. The DNA G+C content of strain A6D-50T was 40.8 mol%, MK-6 was the only menaquinone, and iso-C17 : 0 3-OH, iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) were the major (>10 %) cellular fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species of the genus Aureisphaera for which the name Aureisphaera salina sp. nov. is proposed. The type strain is A6D-50T (= KCTC 42975T=NBRC 111827T).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 42601, Republic of Korea
| | - Kyoko Adachi
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
| | - Hiroaki Kasai
- Marine Biosciences Kamaishi Research Laboratory, Kitasato University, 160-4 Utou, Okirai, Sanriku-cho, Ofunato, Iwate 022-0101, Japan
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Moreno-Pino M, De la Iglesia R, Valdivia N, Henríquez-Castilo C, Galán A, Díez B, Trefault N. Variation in coastal Antarctic microbial community composition at sub-mesoscale: spatial distance or environmental filtering? FEMS Microbiol Ecol 2016; 92:fiw088. [DOI: 10.1093/femsec/fiw088] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2016] [Indexed: 11/13/2022] Open
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34
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Phylogenetic and taxonomic analysis of Neptunitalea chrysea gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from seawater by using an in situ cultivation technique. Antonie van Leeuwenhoek 2015; 108:537-44. [DOI: 10.1007/s10482-015-0508-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/13/2015] [Indexed: 10/23/2022]
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35
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Gutiérrez MH, Galand PE, Moffat C, Pantoja S. Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord. Environ Microbiol 2015; 17:3882-97. [PMID: 25856307 DOI: 10.1111/1462-2920.12872] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 04/02/2015] [Accepted: 04/02/2015] [Indexed: 01/30/2023]
Abstract
Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.
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Affiliation(s)
- Marcelo H Gutiérrez
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile
| | - Pierre E Galand
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, F-66650, Banyuls sur Mer, France
| | - Carlos Moffat
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile.,Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Silvio Pantoja
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile
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36
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Aureisphaera galaxeae gen. nov., sp. nov., a marine member of the family Flavobacteriaceae isolated from the hard coral Galaxea fascicularis. Antonie van Leeuwenhoek 2015; 107:1379-86. [PMID: 25795444 DOI: 10.1007/s10482-015-0432-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 03/14/2015] [Indexed: 10/23/2022]
Abstract
A novel Gram-stain negative, spherical, non-motile, strictly aerobic, heterotrophic, yellow pigmented bacterium, designated strain 04OKA003-7(T) was isolated from the hard coral Galaxea fascicularis L. collected at Akajima, Okinawa, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (92.9 %) to Vitellibacter aestuarii JC2436(T) and Aureitalea marina S1-66(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain 04OKA003-7(T) were identified as iso-C15:0 and iso-C17:0 3-OH as defined by the MIDI system. The DNA G+C content was determined to be 41 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Aureisphaera galaxeae gen. nov., sp. nov. is proposed. The type strain of A. galaxeae is 04OKA003-7(T) (=KCTC 32993(T) = NBRC 110018(T)).
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Yoon J, Adachi K, Kasai H. Isolation and classification of a novel marine Bacteroidetes as Frondibacter aureus gen. nov., sp. nov. Antonie van Leeuwenhoek 2014; 107:321-8. [DOI: 10.1007/s10482-014-0330-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 11/04/2014] [Indexed: 11/29/2022]
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38
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Sun Z, Li G, Wang C, Jing Y, Zhu Y, Zhang S, Liu Y. Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir. Sci Rep 2014; 4:6966. [PMID: 25382138 PMCID: PMC4225533 DOI: 10.1038/srep06966] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/22/2014] [Indexed: 01/19/2023] Open
Abstract
This study demonstrates both prokaryotic and eukaryotic community structures and dominant taxonomies in different positions of the greatest estuary reservoir for drinking water source in the world in four seasons of one year using 454 pyrosequencing method with total of 312,949 16S rRNA and 374,752 18S rRNA gene fragments, including 1,652 bacteria OTUs and 1,182 fungus OTUs. During winter and spring, the community composition at the phylum level showed that microorganisms had similar structures but their quantities were different. Similarly, obvious changes at the genus level were observed among the samples taken in winter and spring between summer and fall. Microorganisms located the reservoir inlet were founded to be different from those in rear at both phylum and genus level. Air temperature had a stronger effect than sampling location on the microbial community structure. Total nitrogen and dissolved oxygen were algae-monitoring indicators during the whole year. Moreover, Bacillus was an efficient indicator during summer and autumn for bacteria OTUs.
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Affiliation(s)
- Zhen Sun
- Department of Environmental Science and Engineering, Fudan University, Handan Road, 200433, Shanghai, China
| | - Guoping Li
- Shanghai Chengtou Raw Water Limited Company, Beiai Road, 200125, Shanghai, China
| | - Chengwei Wang
- Department of Environmental Science and Engineering, Fudan University, Handan Road, 200433, Shanghai, China
| | - Yuhang Jing
- Department of Environmental Science and Engineering, Fudan University, Handan Road, 200433, Shanghai, China
| | - Yiping Zhu
- Shanghai Chengtou Raw Water Limited Company, Beiai Road, 200125, Shanghai, China
| | - Shumin Zhang
- Shanghai Chengtou Raw Water Limited Company, Beiai Road, 200125, Shanghai, China
| | - Yan Liu
- Department of Environmental Science and Engineering, Fudan University, Handan Road, 200433, Shanghai, China
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Archer SDJ, McDonald IR, Herbold CW, Cary SC. Characterisation of bacterioplankton communities in the meltwater ponds of Bratina Island, Victoria Land, Antarctica. FEMS Microbiol Ecol 2014; 89:451-64. [PMID: 24862286 DOI: 10.1111/1574-6941.12358] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 05/12/2014] [Accepted: 05/17/2014] [Indexed: 12/01/2022] Open
Abstract
A unique collection of Antarctic aquatic environments (meltwater ponds) lies in close proximity on the rock and sediment-covered undulating surface of the McMurdo Ice Shelf, near Bratina Island (Victoria Land, Antarctica). During the 2009-10 mid-austral summer, sets of discrete water samples were collected across the vertical geochemical gradients of five meltwater ponds (Egg, P70E, Legin, Salt and Orange) for geochemical and microbial community structure analysis. Bacterial DNA fingerprints (using Automated Ribosomal Intergenic Spacer Analysis) statistically clustered communities within ponds based on anosim (R = 0.766, P = 0.001); however, one highly stratified pond (Egg) had two distinct depth-related bacterial communities (R = 0.975, P = 0.008). 454 pyrosequencing at three depths within Egg also identified phylum level shifts and increased diversity with depth, Bacteroidetes being the dominant phyla in the surface sample and Proteobacteria being dominant in the bottom two depths. best analysis, which attempts to link community structure and the geochemistry of a pond, identified conductivity and pH individually, and to a lesser extent Ag(109) , NO2 and V(51) as dominant influences to the microbial community structure in these ponds. Increasing abundances of major halo-tolerant OTUs across the strong conductivity gradient reinforce it as the primary driver of community structure in this study.
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Affiliation(s)
- Stephen D J Archer
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton, New Zealand
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40
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Weisse T. Ciliates and the Rare Biosphere—Community Ecology and Population Dynamics. J Eukaryot Microbiol 2014; 61:419-33. [DOI: 10.1111/jeu.12123] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/09/2014] [Accepted: 04/09/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Thomas Weisse
- Research Institute for Limnology University of Innsbruck Mondseestraße 95310 Mondsee Austria
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41
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Diversity of bacterioplankton in coastal seawaters of Fildes Peninsula, King George Island, Antarctica. Arch Microbiol 2014; 196:137-47. [PMID: 24408126 DOI: 10.1007/s00203-013-0950-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/13/2013] [Accepted: 12/27/2013] [Indexed: 01/19/2023]
Abstract
The bacterioplankton not only serves critical functions in marine nutrient cycles, but can also serve as indicators of the marine environment. The compositions of bacterial communities in the surface seawater of Ardley Cove and Great Wall Cove were analyzed using a 16S rRNA multiplex 454 pyrosequencing approach. Similar patterns of bacterial composition were found between the two coves, in which Bacteroidetes, Alphaproteobacteria, and Gammaproteobacteria were the dominant members of the bacterioplankton communities. In addition, a large fraction of the bacterial sequence reads (on average 5.3 % per station) could not be assigned below the domain level. Compared with Ardley Cove, Great Wall Cove showed higher chlorophyll and particulate organic carbon concentrations and exhibited relatively lower bacterial richness and diversity. Inferred metabolisms of summer bacterioplankton in the two coves were characterized by chemoheterotrophy and photoheterotrophy. Results suggest that some cosmopolitan species (e.g., Polaribacter and Sulfitobacter) belonging to a few bacterial groups that usually dominate in marine bacterioplankton communities may have similar ecological functions in similar marine environments but at different geographic locations.
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