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Rangamaran VR, Sankara Subramanian SH, Balachandran KRS, Gopal D. Vertical Microbial Profiling of Arabian Sea Oxygen Minimal Zone Reveals Complex Bacterial Communities and Distinct Functional Implications. MICROBIAL ECOLOGY 2023; 85:357-371. [PMID: 35195736 DOI: 10.1007/s00248-021-01952-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Arabian Sea harbours one of the largest oxygen minimal zones (OMZs) among the global oceans wherein biogeochemical cycles are regulated through dominant and complex microbial processes. The present study investigated the bacterial communities at various depths of the Arabian Sea OMZ using high-throughput sequencing of the v3-v4 hyper variable region of 16S rRNA gene. A total of 10 samples which included water samples from 8 different depths and 2 sediment samples were analyzed in this study. About 2.7 million sequences were obtained from all the samples. The sequence analysis revealed high bacterial diversity at deep waters and sediment samples and comparatively less species richness at the core OMZ depths. Number of OTUs ranged from 114 to 14441.Taxonomic assignments of the obtained OTUs showed dominant presence of Proteobacteria, Bacteriodetes, and Chloroflexi across all the samples. The identified OTUs were further affiliated to the phyla Marinimicrobia, Colwellia, Nitrospina, Tepidicaulis, Shewanella, Pseudoalteromonas, Woeseia at various depths along the water column. Correlation with abiotic factors suggested distinct variation in bacterial community composition with change in depth and dissolved oxygen (DO) levels. Predictive functional annotation based on bacterial phylotypes suggested presence of active nitrogen, sulphur, carbon, and methane metabolic cycles along the vertical transect of the studied region. Presence of nitrogen reduction bacterial group below the core OMZ depths may potentially provide insight into the expansion of OMZ region in Arabian Sea. Functional profiling further revealed presence of genes related to xenobiotic degradation in the water and sediment samples indicating a potential hotspot for bio-prospection.
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Affiliation(s)
- Vijaya Raghavan Rangamaran
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India.
| | - Sai H Sankara Subramanian
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - Karpaga Raja Sundari Balachandran
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - Dharani Gopal
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India.
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Vipindas PV, Jabir T, Rahiman KMM, Rehitha TV, Sudheesh V, Jesmi Y, Hatha AAM. Impact of anthropogenic organic matter on bacterial community distribution in the continental shelf sediments of southeastern Arabian Sea. MARINE POLLUTION BULLETIN 2022; 174:113227. [PMID: 34883441 DOI: 10.1016/j.marpolbul.2021.113227] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
The objective of this study was to understand the influence of anthropogenic organic matter on the spatial distribution microbial community in the continental shelf sediments of the Southeastern Arabian Sea (SEAS). The sediment samples were taken from the inner shelf (30 m depths) and outer shelf (100-200 m). The C:Nmolar ratio of the sediment displayed a significant variation between the inner and outer shelf and a higher terrestrial organic input in the inner shelf. Microbial community composition also showed a significant variation between the inner and outer shelf (p ≤ 0.05). Proteobacteria was the dominant phylum in the outer shelf sediments (42.5%), whereas Desulfobacterota (21.9%) was the dominant phylum in the inner shelf. Complex terrestrial organic matter degrading bacteria dominated the inner shelf, whereas oligophilic microbial community and autochthonous organic matter utilizing bacteria dominated the outer shelf. Thus the source of organic matter controlled the microbial distribution in the SEAS.
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Affiliation(s)
- P V Vipindas
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India.
| | - T Jabir
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - K M Mujeeb Rahiman
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - T V Rehitha
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - V Sudheesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - Y Jesmi
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - A A Mohamed Hatha
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India.
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3
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Long AM, Jurgensen SK, Petchel AR, Savoie ER, Brum JR. Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation. Front Microbiol 2021; 12:748961. [PMID: 34777296 PMCID: PMC8578717 DOI: 10.3389/fmicb.2021.748961] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/06/2021] [Indexed: 01/05/2023] Open
Abstract
Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.
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Affiliation(s)
- Andrew M. Long
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States
| | | | | | | | - Jennifer R. Brum
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States
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Sachithanandam V, Saravanane N, Chandrasekar K, Karthick P, Lalitha P, Sai Elangovan S, Sudhakar M. Microbial diversity from the continental shelf regions of the Eastern Arabian Sea: A metagenomic approach. Saudi J Biol Sci 2020; 27:2065-2075. [PMID: 32714031 PMCID: PMC7376189 DOI: 10.1016/j.sjbs.2020.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 06/02/2020] [Accepted: 06/06/2020] [Indexed: 01/15/2023] Open
Abstract
The marine microbiome is a complex and least-understood habitat, which play a significant role in global biogeochemical cycles. The present study reported the culture-independent assessment of microbial diversity from the Arabian Sea (AS) sediments (from Gujarat to Malabar; at 30 m depth) by using metagenome sequence analysis. Our results elucidated that bacterial communities in the Malabar coastal region are highly diverse than the Gujarat coast. Moreover, Statistical analysis (Spearman rank correlation) showed a significant correlation co-efficient value (r = P < 0.001) between microbial communities and physicochemical parameters (salinity and dissolved oxygen) in the water column. A total of 39 bacterial phyla were recorded from the eastern side of AS, of which six phyla Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Firmicutes, and Planctomycetes were found to be the most dominant group. The most dominant genus from Valapad region (Malabar Coast) was found to be Halomonas sp., while other regions were dominated with Psychrobacter pulmonis. The subsequent Principal Coordinate Analysis (PCoA) showed 99.53% variance, which suggests that, highly distinct microbial communities at Valapad (Malabar Coast) sampling location than other sites. Moreover, the microbial metabolic activity analysis revealed the important functions of microbial communities in the AS are hydrocarbon degradation, polymer degradation, nutrient oxidation and sulphate reduction (biodegradation process). Further extended studies are needed to be carried out for better understanding the functional diversity of microbial communities from the marine sediments.
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Affiliation(s)
- V Sachithanandam
- Department of Ocean Studies and Marine Biology, Pondicherry University, Andaman Campus, Port Blair 744 112, India.,National Centre for Sustainable Coastal Management, Ministry of Environment, Forest & Climate Change, Chennai 600 025, India
| | - N Saravanane
- Centre for Marine Living Resources & Ecology, Ministry of Earth Sciences, Government of India, Kochi 682 037, India
| | - K Chandrasekar
- Centre for Marine Living Resources & Ecology, Ministry of Earth Sciences, Government of India, Kochi 682 037, India
| | - P Karthick
- Department of Ocean Studies and Marine Biology, Pondicherry University, Andaman Campus, Port Blair 744 112, India
| | - P Lalitha
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest & Climate Change, Chennai 600 025, India
| | - S Sai Elangovan
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Goa, India
| | - M Sudhakar
- Centre for Marine Living Resources & Ecology, Ministry of Earth Sciences, Government of India, Kochi 682 037, India
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Fernandes GL, Shenoy BD, Damare SR. Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing. Front Microbiol 2020; 10:3153. [PMID: 32038585 PMCID: PMC6985565 DOI: 10.3389/fmicb.2019.03153] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 12/30/2019] [Indexed: 11/13/2022] Open
Abstract
The Indian Ocean harbors oxygen minimum zones (OMZs) in the Arabian Sea and Bay of Bengal, with dissolved oxygen < 20 μM, located at the mid-depths of the water column. Till date, high-throughput sequence-data on depth-wise distribution of prokaryotic communities have rarely been reported from these OMZs. The present study aimed to characterize the prokaryotic diversity inhabiting Arabian Sea Time Series (ASTS) and India's Idea 2 (II2) in the Arabian Sea, and Bay of Bengal Time Series (BoBTS) in the Bay of Bengal OMZs based on amplicon sequencing of 16S rRNA gene regions, along six sampled depths in the water column. High prokaryotic richness was observed in the Arabian Sea and Bay of Bengal samples. Operational taxonomic units (OTUs) in the range of 1249-3298 were identified, wherein, less prokaryotic diversity was observed at surface and within oxygen minimum depths. At phylum level, most OTUs were affiliated to Bacteroidetes, Chloroflexi, Cyanobacteria, Marinimicrobia, Planctomycetes, and Proteobacteria. Prokaryotic community differed between ASTS, II2 and BoBTS locations along varying physicochemical conditions. Predictive functional profiling of the bacterial communities suggested the involvement of abundant microbes in nitrogen and sulfur metabolism pathways. Bacterial isolates belonging to genera from the clades, δ-Proteobacteria and γ-Proteobacteria, described previously for their participation in biogeochemical cycling of N-and-S in the OMZs were reported from deoxygenated waters of both the basins. Bacteria involved in anammox such as Candidatus Scalindua were found to be relatively high at ASTS and II2 locations in the Arabian Sea. Further studies are required to ascertain the role of abundant bacteria along the dynamic oceanographic processes in the OMZs.
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Affiliation(s)
- Genevieve L Fernandes
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, India.,Department of Microbiology, Goa University, Taleigao, India
| | | | - Samir R Damare
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, India
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Gomes J, Khandeparker R, Meena RM, Ramaiah N. Bacterial Community Composition Markedly Altered by Coastal Hypoxia. Indian J Microbiol 2019; 59:200-208. [PMID: 31031435 DOI: 10.1007/s12088-019-00790-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/28/2019] [Indexed: 11/26/2022] Open
Abstract
Monsoonal upwelling along south and central west coast of India leads to intense biological productivity. As a consequence of excess organic matter production following upwelling during June-October and low dissolved oxygen in the upwelled waters, denitrification occurs in the near shore waters. Implicitly, these processes ought to bring alterations in microbial communities. Therefore, diversity and community structure of bacteria from subsurface layers of a tropical region experiencing intense seasonal lows of oxygen were analyzed through sequencing of 16S rRNA gene clones. The overall diversity was more during hypoxic period of Fall intermonsoon (FIM, October) compared either to Spring intermonsoon (SIM, March) or summer monsoon (SuM, June) months. As many as 14 lineages of bacterial domains: Gammaproteobacteria (37%), Alphaproteobacteria (21%), Cyanobacteria (20%), Deltaproteobacteria (3%), Firmicutes (3%), Betaproteobacteria (2%), Acidobacteria (2%), Actinobacteria (7%), Marinimicrobia (2%), Bacteroidetes (1%), Verrucomicrobia (1%), Planctomycetes (0.4%), Chloroflexi (0.2%) and Omnitrophica bacterium (0.2%), were recognized from our coastal location. Notably, sequences of Planctomycetes, Chloroflexi and Omnitrophica bacterium were found exclusively during FIM. A generally higher representation of sequences of Betaproteobacteria during SuM and of Actinobacteria and Firmicutes during SIM was discernible. This study is thus useful to recognize that microbial community might undergo strong temporal shifts in the monsoon affected tropical coastal ecosystems.
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Affiliation(s)
- Jasmine Gomes
- Microbial Ecology Laboratory, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
| | - Rakhee Khandeparker
- Microbial Ecology Laboratory, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
| | - Ram Murti Meena
- Microbial Ecology Laboratory, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
| | - N Ramaiah
- Microbial Ecology Laboratory, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
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Farha AK, TR T, Purushothaman A, Salam JA, Hatha AM. Phylogenetic diversity and biotechnological potentials of marine bacteria from continental slope of eastern Arabian Sea. J Genet Eng Biotechnol 2018; 16:253-258. [PMID: 30733732 PMCID: PMC6353758 DOI: 10.1016/j.jgeb.2018.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 06/05/2018] [Accepted: 06/20/2018] [Indexed: 11/28/2022]
Abstract
Marine environments are substantially untapped source for the isolation of bacteria with the capacity to produce various extracellular hydrolytic enzymes, which have important ecological roles and promising biotechnological applications. Hydrolases constitute a class of enzymes widely distributed in nature from bacteria to higher eukaryotes. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. A number of marine hydrolases have been described, including amylases, lipases and proteases, which are being used extensively for biotechnological applications. The present study was carried out to isolate marine bacteria from continental slope sediments of the eastern Arabian Sea and explore their biotechnological potential. Among the 119 isolates screened, producers of amylases (15%), caseinases (40%), cellulases (40%), gelatinases (60%), lipases (26%), ligninases (33%), phytase (11%) and Malachite Green dye degraders (16%) were detected. Phylogenetic analysis based on 16S rRNA gene sequencing showed that predominant marine sediment bacteria possessing more than four enzymatic activities belonged to the phyla Firmicutes and Proteobacteria, was assigned to the genera Bacillus, Planococcus, Staphylococcus, Chryseomicrobium, Exiguobacterium and Halomonas. Biodegradation of the dye Malachite Green using the liquid decolorization assay showed that both the individual cultures (Bacillus vietnamensis, Planococcus maritimus and Bacillus pumilus) and their consortium were able to decolorize more than 70% of dye within 24 h of incubation. This is the first report on diversity and extracellular hydrolytic enzymatic activities and bioremediation properties of bacteria from continental slope sediment of eastern Arabian Sea.
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Affiliation(s)
- Arakkaveettil Kabeer Farha
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi, Kerala 682016, India
| | - Thasneem TR
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi, Kerala 682016, India
| | | | - Jaseetha Abdul Salam
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi, Kerala 682016, India
| | - Abdulla Mohamed Hatha
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kochi, Kerala 682016, India
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Johny TK, Saidumohamed BE, Sasidharan RS, Bhat SG. Inferences of gut bacterial diversity from next-generation sequencing of 16S rDNA in deep sea blind ray - Benthobatis moresbyi. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.egg.2018.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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An exploration of microbial and associated functional diversity in the OMZ and non-OMZ areas in the Bay of Bengal. J Biosci 2018. [DOI: 10.1007/s12038-018-9781-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Hua G, Cheng Y, Kong J, Li M, Zhao Z. High-throughput sequencing analysis of bacterial community spatiotemporal distribution in response to clogging in vertical flow constructed wetlands. BIORESOURCE TECHNOLOGY 2018; 248:104-112. [PMID: 28734588 DOI: 10.1016/j.biortech.2017.07.061] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 05/27/2023]
Abstract
The aim of this study was to characterize bacterial communities in vertical flow constructed wetlands (VFCWs) using Illumina high-throughput sequencing. The bacterial communities developed lower richness and diversity in response to clogging. Bacterial diversity did not overtly decrease with depth. A variety of bacterial phyla were found in VFCWs' bacterial communities, including Bacteroidetes, Actinobacteria and Acidobacteria, among which Proteobacteria was dominant. At the genus level, a spatiotemporal variation was illustrated in the diversity and structure of bacterial communities. Clustering analysis of bacterial composition in the operational taxonomic units (OTUs) at the phylum and genus levels had a consistent trend, namely, that bacterial communities were more similar at similar column depths.
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Affiliation(s)
- Guofen Hua
- College of Water Conservancy and Hydroelectric Power, Hohai University, Nanjing 210098, PR China.
| | - Ying Cheng
- College of Water Conservancy and Hydroelectric Power, Hohai University, Nanjing 210098, PR China
| | - Jun Kong
- College of Harbour, Coastal and Offshore Engineering, Hohai University, Nanjing 210098, PR China
| | - Man Li
- College of Water Conservancy and Hydroelectric Power, Hohai University, Nanjing 210098, PR China
| | - Zhongwei Zhao
- College of Harbour, Coastal and Offshore Engineering, Hohai University, Nanjing 210098, PR China
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Broman E, Sachpazidou V, Pinhassi J, Dopson M. Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism. Front Microbiol 2017; 8:2453. [PMID: 29312168 PMCID: PMC5733055 DOI: 10.3389/fmicb.2017.02453] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/27/2017] [Indexed: 01/24/2023] Open
Abstract
The Baltic Sea has undergone severe eutrophication during the last century, resulting in increased algal blooms and the development of hypoxic bottom waters. In this study, we sampled oxygen deficient sediment cores from a Baltic Sea coastal bay and exposed the bottom water including the sediment surface to oxygen shifts via artificial addition of air during laboratory incubation. Surface sediment (top 1 cm) from the replicate cores were sliced in the field as well as throughout the laboratory incubations and chemical parameters were analyzed along with high throughput sequencing of community DNA and RNA. After oxygenation, dissolved iron decreased in the water overlying the sediment while inorganic sulfur compounds (thiosulfate and tetrathionate) increased when the water was kept anoxic. Oxygenation of the sediment also maintained RNA transcripts attributed to sulfide and sulfur oxidation as well as nitrogen fixation in the sediment surface. Based on 16S rRNA gene and metatranscriptomic analyses it was found that oxygenation of the sediment surface caused a bloom of the Epsilonproteobacteria genus Arcobacter. In addition, the formation of a thick white film was observed that was likely filamentous zero-valent sulfur produced by the Arcobacter spp. Based on these results, sulfur cycling and nitrogen fixation that were evident in the field samples were ongoing during re-oxygenation of the sediment. These processes potentially added organic nitrogen to the system and facilitated the re-establishment of micro- and macroorganism communities in the benthic zone.
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Affiliation(s)
- Elias Broman
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Varvara Sachpazidou
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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12
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Broman E, Sjöstedt J, Pinhassi J, Dopson M. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism. MICROBIOME 2017; 5:96. [PMID: 28793929 PMCID: PMC5549381 DOI: 10.1186/s40168-017-0311-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/18/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface. RESULTS Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation. CONCLUSIONS These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.
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Affiliation(s)
- Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Johanna Sjöstedt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Present address: Department of Biology/Aquatic ecology, Lund University, Sölvesgatan 37, 223 62 Lund, Sweden
- Present address: Centre for Ocean Life, Institute for Aquatic Resources, Technical University of Denmark, 2900 Charlottenlund, Denmark
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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Cao Q, Wang H, Chen X, Wang R, Liu J. Composition and distribution of microbial communities in natural river wetlands and corresponding constructed wetlands. ECOLOGICAL ENGINEERING 2017; 98:40-48. [DOI: 10.1016/j.ecoleng.2016.10.063] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
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14
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Anas A, Nilayangod C, Jasmin C, Vinothkumar S, Parameswaran PS, Nair S. Diversity and bioactive potentials of culturable heterotrophic bacteria from the surficial sediments of the Arabian Sea. 3 Biotech 2016; 6:238. [PMID: 28330310 PMCID: PMC5106401 DOI: 10.1007/s13205-016-0556-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/19/2016] [Indexed: 11/28/2022] Open
Abstract
Marine sediments accommodate plethora of diverse microorganisms with varying ecological functions. In the present study, we isolated bacteria from surficial sediments of south east Arabian Sea (AS) and evaluated their bioactive potentials. A total of 131 isolates belonging to the phylum: γ-Proteobacteria (63%), Bacillales (34%) and Micrococcaceae (3%) were isolated. Among these, about 40% of the isolates showed the presence of secondary metabolite biosynthetic genes such as PKS or NRPS or both. Organic extracts of nearly 50% of these organisms were cytotoxic to human breast cancer MCF-7 cells and were bactericidal to human pathogens, Escherichia coli and Pseudomonas sp., while 20–30% of them were bactericidal to Vibrio sp. and Staphylococcus sp. too. In all, 8 isolates, belonging to Pseudomonas spp., Bacillus sp. and/or Lysinibacillus sp. displayed high level of bactericidal/cytotoxic properties. The study proposes AS sediment as a rich source for microorganisms with prospective bioactive molecules.
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Affiliation(s)
- Abdulaziz Anas
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India.
| | - Charulatha Nilayangod
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - C Jasmin
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - Saradavey Vinothkumar
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - P S Parameswaran
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - Shanta Nair
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
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15
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Stamps BW, Lyles CN, Suflita JM, Masoner JR, Cozzarelli IM, Kolpin DW, Stevenson BS. Municipal Solid Waste Landfills Harbor Distinct Microbiomes. Front Microbiol 2016; 7:534. [PMID: 27148222 PMCID: PMC4837139 DOI: 10.3389/fmicb.2016.00534] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/31/2016] [Indexed: 11/16/2022] Open
Abstract
Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.
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Affiliation(s)
- Blake W Stamps
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | - Christopher N Lyles
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | | | | | | | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
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16
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Ye Q, Wu Y, Zhu Z, Wang X, Li Z, Zhang J. Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea. Microbiologyopen 2016; 5:323-39. [PMID: 26817579 PMCID: PMC4831476 DOI: 10.1002/mbo3.330] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 11/05/2015] [Accepted: 11/24/2015] [Indexed: 11/30/2022] Open
Abstract
Changjiang (Yangtze River) Estuary has experienced severe hypoxia since the 1950s. In order to investigate potential ecological functions of key microorganisms in relation to hypoxia, we performed 16S rRNA‐based Illumina Miseq sequencing to explore the bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea (ECS). The results showed that numerous Proteobacteria‐affiliated sequences in the sediments of the inner continental shelf were related to both sulfate‐reducing and sulfur‐oxidizing bacteria, suggesting an active sulfur cycle in this area. Many sequences retrieved from the hypoxic zone were also related to Planctomycetes from two marine upwelling systems, which may be involved in the initial breakdown of sulfated heteropolysaccharides. Bacteroidetes, which is expected to degrade high‐molecular‐weight organic matter, was abundant in all the studied stations except for station A8, which was the deepest and possessed the largest grain size. In addition, dissolved organic carbon, water depth, percentage ratio of clay to silt, salinity, and sedimentary grain size were environmental effectors that shaped the sedimentary microbial community structure. Our results showed that putative Gammaproteobacteria‐affiliated sulfur‐oxidizing bacteria may not only detoxify hydrogen sulfide produced by sulfate‐reducing prokaryotes, but also serve as the primary producers in the marine sediments. Specific groups of aerobic Bacteroidetes and Planctomycetes participated in degrading organic matter, which might contribute to the oxygen depletion in the hypoxic zones.
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Affiliation(s)
- Qi Ye
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Ying Wu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Zhuoyi Zhu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Xiaona Wang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Zhongqiao Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
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17
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Wang N, Ding LJ, Xu HJ, Li HB, Su JQ, Zhu YG. Variability in responses of bacterial communities and nitrogen oxide emission to urea fertilization among various flooded paddy soils. FEMS Microbiol Ecol 2015; 91:fiv013. [DOI: 10.1093/femsec/fiv013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2015] [Indexed: 11/12/2022] Open
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18
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Chan Y, Li A, Gopalakrishnan S, Shin PKS, Wu RSS, Pointing SB, Chiu JMY. Interactive effects of hypoxia and polybrominated diphenyl ethers (PBDEs) on microbial community assembly in surface marine sediments. MARINE POLLUTION BULLETIN 2014; 85:400-409. [PMID: 24878302 DOI: 10.1016/j.marpolbul.2014.04.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 06/03/2023]
Abstract
Hypoxia alters the oxidation-reduction balance and the biogeochemical processes in sediments, but little is known about its impacts on the microbial community that is responsible for such processes. In this study, we investigated the effects of hypoxia and the ubiquitously dispersed flame-retardant BDE47 on the bacterial communities in marine surface sediments during a 28-days microcosm experiment. Both hypoxia and BDE47 alone significantly altered the bacterial community and reduced the species and genetic diversity. UniFrac analysis revealed that BDE47 selected certain bacterial species and resulted in major community shifts, whereas hypoxia changed the relative abundances of taxa, suggesting slower but nonetheless significant community shifts. These two stressors targeted mostly different taxa, but they both favored Bacteroidetes and suppressed Gammaproteobacteria. Importantly, the impacts of BDE47 on bacterial communities were different under hypoxic and normoxic conditions, highlighting the need to consider risk assessments for BDE47 in a broader context of interaction with hypoxia.
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Affiliation(s)
- Yuki Chan
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong; Auckland University of Technology, School of Applied Sciences, Institute for Applied Ecology New Zealand, Private Bag 92006, Auckland 1142, New Zealand
| | - Amy Li
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | | | - Paul K S Shin
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Rudolf S S Wu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Stephen B Pointing
- Auckland University of Technology, School of Applied Sciences, Institute for Applied Ecology New Zealand, Private Bag 92006, Auckland 1142, New Zealand
| | - Jill M Y Chiu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong.
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19
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The ecological roles of bacterial populations in the surface sediments of coastal lagoon environments in Japan as revealed by quantification and qualification of 16S rDNA. World J Microbiol Biotechnol 2012; 29:759-74. [PMID: 23264132 DOI: 10.1007/s11274-012-1231-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
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