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Liu B, Zheng Y, Wang X, Qi L, Zhou J, An Z, Wu L, Chen F, Lin Z, Yin G, Dong H, Li X, Liang X, Han P, Liu M, Hou L. Active dark carbon fixation evidenced by 14C isotope assimilation and metagenomic data across the estuarine-coastal continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169833. [PMID: 38190922 DOI: 10.1016/j.scitotenv.2023.169833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
Estuaries, as important land-ocean transitional zones across the Earth's surface, are hotspots of microbially driven dark carbon fixation (DCF), yet understanding of DCF process remains limited across the estuarine-coastal continuum. This study explored DCF activities and associated chemoautotrophs along the estuarine and coastal environmental gradients, using radiocarbon labelling and molecular techniques. Significantly higher DCF rates were observed at middle- and high-salinity regions (0.65-2.31 and 0.66-2.82 mmol C m-2 d-1, respectively), compared to low-salinity zone (0.07-0.19 mmol C m-2 d-1). Metagenomic analysis revealed relatively stable DCF pathways along the estuarine-coastal continuum, primarily dominated by Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway. Nevertheless, chemoautotrophic communities driving DCF exhibited significant spatial variations. It is worth noting that although CBB cycle played an important role in DCF in estuarine sediments, WL pathway might play a more significant role, which has not been previously recognized. Overall, this study highlights that DCF activities coincide with the genetic potential of chemoautotrophy and the availability of reductive substrates across the estuarine-coastal continuum, and provides an important scientific basis for accurate quantitative assessment of global estuarine carbon sink.
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Affiliation(s)
- Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Xinyu Wang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhirui An
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li Wu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhuke Lin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
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Hiralal A, Geelhoed JS, Hidalgo-Martinez S, Smets B, van Dijk JR, Meysman FJR. Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads. Microb Genom 2024; 10:001197. [PMID: 38376381 PMCID: PMC10926707 DOI: 10.1099/mgen.0.001197] [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: 11/13/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.
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Affiliation(s)
- Anwar Hiralal
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | | | - Bent Smets
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | - Filip J. R. Meysman
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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Vuillemin A. Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia. Front Microbiol 2023; 14:1101902. [PMID: 36846760 PMCID: PMC9950273 DOI: 10.3389/fmicb.2023.1101902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.
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Vasquez-Cardenas D, Hidalgo-Martinez S, Hulst L, Thorleifsdottir T, Helgason GV, Eiriksson T, Geelhoed JS, Agustsson T, Moodley L, Meysman FJR. Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria. Front Microbiol 2022; 13:1034401. [PMID: 36620049 PMCID: PMC9814725 DOI: 10.3389/fmicb.2022.1034401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Fish farming in sea cages is a growing component of the global food industry. A prominent ecosystem impact of this industry is the increase in the downward flux of organic matter, which stimulates anaerobic mineralization and sulfide production in underlying sediments. When free sulfide is released to the overlying water, this can have a toxic effect on local marine ecosystems. The microbially-mediated process of sulfide oxidation has the potential to be an important natural mitigation and prevention strategy that has not been studied in fish farm sediments. We examined the microbial community composition (DNA-based 16S rRNA gene) underneath two active fish farms on the Southwestern coast of Iceland and performed laboratory incubations of resident sediment. Field observations confirmed the strong geochemical impact of fish farming on the sediment (up to 150 m away from cages). Sulfide accumulation was evidenced under the cages congruent with a higher supply of degradable organic matter from the cages. Phylogenetically diverse microbes capable of sulfide detoxification were present in the field sediment as well as in lab incubations, including cable bacteria (Candidatus Electrothrix), which display a unique metabolism based on long-distance electron transport. Microsensor profiling revealed that the activity of cable bacteria did not exert a dominant impact on the geochemistry of fish farm sediment at the time of sampling. However, laboratory incubations that mimic the recovery process during fallowing, revealed successful enrichment of cable bacteria within weeks, with concomitant high sulfur-oxidizing activity. Overall our results give insight into the role of microbially-mediated sulfide detoxification in aquaculture impacted sediments.
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Affiliation(s)
- Diana Vasquez-Cardenas
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium,*Correspondence: Diana Vasquez-Cardenas,
| | | | - Lucas Hulst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | | | | | | | | | | | - Leon Moodley
- NORCE Norwegian Research Centre, Randaberg, Norway
| | - Filip J. R. Meysman
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium
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5
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Zhao L, Shao H, Zhang L, Panno SV, Kelly WR, Lin TY, Liu WT, Flynn TM, Berger P. Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA. Environ Microbiol 2022; 24:6112-6127. [PMID: 36222141 PMCID: PMC10099389 DOI: 10.1111/1462-2920.16241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 10/10/2022] [Indexed: 01/12/2023]
Abstract
Saline springs within the Illinois Basin result from the discharge of deep-seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%-94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.
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Affiliation(s)
- Linduo Zhao
- Illinois Sustainable Technology Center, Illinois, USA.,Illinois State Water Survey, Illinois, USA
| | - Hongbo Shao
- Illinois State Geology Survey, Illinois, USA
| | - Li Zhang
- Illinois Sustainable Technology Center, Illinois, USA
| | | | | | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Theodore M Flynn
- California Department of Water Resources, West Sacramento, California, USA
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Zhou XQ, Qu XM, Yang Z, Zhao J, Hao YY, Feng J, Huang Q, Liu YR. Increased water inputs fuel microbial mercury methylation in upland soils. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129578. [PMID: 35853337 DOI: 10.1016/j.jhazmat.2022.129578] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/28/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Mercury (Hg) can be converted to neurotoxic methylmercury (MeHg) by certain microbes typically in anaerobic environments, threatening human health due to its bioaccumulation in food webs. However, it is unclear whether and how Hg can be methylated in legacy aerobic uplands with increasing water. Here, we conducted a series of incubation experiments to investigate the effects of increased water content on MeHg production in two typical upland soils (i.e., long-term and short-term use). Results showed that marked MeHg production occurred in water-saturated upland soils, which was strongly correlated with the proportions of significantly stimulated Hg methylating taxon (i.e., Geobacter). Elevated temperature further enhanced MeHg production by blooming proportions of typical Hg methylators (i.e., Clostridium, Acetonema, and Geobacter). Water saturation could also enhance microbial Hg methylation by facilitating microbial syntrophy between non-Hg methylators and Hg methylators. Taken together, the present work suggests that uplands could turn into a potential MeHg reservoir in response to water inputs resulting from rainfall or anthropogenic irrigation.
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Affiliation(s)
- Xin-Quan Zhou
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Min Qu
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziming Yang
- Department of Chemistry, Oakland University, Rochester, MI 48309, United States
| | - Jiating Zhao
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Yun-Yun Hao
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiao Feng
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
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Liu B, Hou L, Zheng Y, Zhang Z, Tang X, Mao T, Du J, Bi Q, Dong H, Yin G, Han P, Liang X, Liu M. Dark carbon fixation in intertidal sediments: Controlling factors and driving microorganisms. WATER RESEARCH 2022; 216:118381. [PMID: 35381430 DOI: 10.1016/j.watres.2022.118381] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Dark carbon fixation (DCF) contributes approximately 0.77 Pg C y-1 to oceanic primary production and the global carbon budget. It is estimated that nearly half of the DCF in marine sediments occurs in estuarine and coastal regions, but the environmental factors controlling DCF and the microorganisms responsible for its production remain under exploration. In this study, we investigated DCF rates and the active chemoautotrophic microorganisms in intertidal sediments of the Yangtze Estuary, using 14C-labeling and DNA-stable isotope probing (DNA-SIP) techniques. The measured DCF rates ranged from 0.27 to 3.37 mmol C m-2 day-1 in intertidal surface sediments. The rates of DCF were closely related to sediment sulfide content, demonstrating that the availability of reductive substrates may be the dominant factor controlling DCF in the intertidal sediments. A significant positive correlation was also observed between the DCF rates and abundance of the cbbM gene. DNA-stable isotope probing (DNA-SIP) results further confirmed that cbbM-harboring bacteria, rather than cbbL-harboring bacteria, played a dominant role in DCF in intertidal sediments. Phylogenetic analysis showed that the predominant cbbM-harboring bacteria were affiliated with Burkholderia, including Sulfuricella denitrificans, Sulfuriferula, Acidihalobacter, Thiobacillus, and Sulfurivermis fontis. Moreover, metagenome analyses indicated that most of the potential dark-carbon-fixing bacteria detected in intertidal sediments also harbor genes for sulfur oxidation, denitrification, or dissimilatory nitrate reduction to ammonium (DNRA), indicating that these chemoautotrophic microorganisms may play important roles in coupled carbon, nitrogen, and sulfur cycles. These results shed light on the ecological importance and the underlying mechanisms of the DCF process driven by chemoautotrophic microorganisms in intertidal wetlands.
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Affiliation(s)
- Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Tieqiang Mao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jinzhou Du
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Qianqian Bi
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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Sun Q, Song J, Li X, Yuan H, Ma J, Wang Q. Bacterial vertical and horizontal variability around a deep seamount in the Tropical Western Pacific Ocean. MARINE POLLUTION BULLETIN 2020; 158:111419. [PMID: 32753203 DOI: 10.1016/j.marpolbul.2020.111419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Research on bacterial communities in seamounts is still in its infancy. Spatial variability of bacterial communities was investigated around M5 seamount of the Tropical Western Pacific Ocean. Our results revealed greater variability of bacterial communities vertically than horizontally. Bacterial diversity generally increased with depths within water column and the complexity increased with the sampling depths. All stations had water mass-specific bacterial community compositions, with distinct bacterial community structure between the bottom layer (being Actinobacteria and Firmicutes-dominant) and other layers (being Alphaproteobacteria-dominant), except the deepest B2 which showed gradual transition. Major orders tended to be distributed symmetrically at bilateral sides of the seamount with more differences occurring at section B than at section A, possibly due to the westward North Equatorial Current (NEC) along section B and reverse subcurrent, as well possible upwelling. Seamount exerted certain effect on bacterial horizontal distribution in the surrounding water mainly through topography-current interaction.
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Affiliation(s)
- Qiqi Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Meta-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jinming Song
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Meta-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xuegang Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Meta-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huamao Yuan
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Meta-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Ma
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Meta-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qidong Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Meta-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Nascimento JR, Easson CG, Jurelevicius DDA, Lopez JV, Bidone ED, Sabadini-Santos E. Microbial community shift under exposure of dredged sediments from a eutrophic bay. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:539. [PMID: 32705349 DOI: 10.1007/s10661-020-08507-8] [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: 01/06/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities occur in almost every habitat. To evaluate the homeostasis disruption of in situ microbiomes, dredged sediments from Guanabara Bay-Brazil (GB) were mixed with sediments from outside of the bay (D) in three different proportions (25%, 50%, and 75%) which we called GBD25, GBD50, and GBD75. Grain size, TOC, and metals-as indicators of complex contamination-dehydrogenase (DHA) and esterase enzymes (EST)-as indicators of microbial community availability-were determined. Microbial community composition was addressed by amplifying the 16S rRNA gene for DGGE analysis and sequencing using MiSeq platform (Illumina).We applied the quality ratio index (QR) to the GB, D, and every GBD mixture to integrate geochemical parameters with our microbiome data. QR indicated high environmental risk for GB and every GBD mixture, and low risk for D. The community shifted from aerobic to anaerobic profile, consistent with the characteristics of GB. Sample D was dominated by JTB255 marine benthic group, related to low impacted areas. Milano-WF1B-44 was the most representative of GB, often found in anaerobic and sulfur enriched environments. In GBD, the denitrifying sulfur-oxidizing bacteria, Sulfurovum, was the most representative, typically found in suboxic or anoxic niches. The canonical correspondence analysis was able to explain 60% of the community composition variation and exhibit the decrease of environmental quality as the contamination increases. Physiological and taxonomic shifts of the microbial assemblage in sediments were inferred by QR, which was suitable to determine sediment risk. The study produced sufficient information to improve the dredging plan and management.
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Affiliation(s)
- Juliana R Nascimento
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, 24020-150, Brazil.
| | - Cole G Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, 33004, USA
- Biology Department, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Diogo de A Jurelevicius
- Instituto de Microbiologia Professor Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21944-570, Brazil
| | - Jose V Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, 33004, USA
| | - Edison D Bidone
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, 24020-150, Brazil
| | - Elisamara Sabadini-Santos
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, 24020-150, Brazil
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10
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Vasquez‐Cardenas D, Meysman FJR, Boschker HTS. A Cross-System Comparison of Dark Carbon Fixation in Coastal Sediments. GLOBAL BIOGEOCHEMICAL CYCLES 2020; 34:e2019GB006298. [PMID: 32713991 PMCID: PMC7375125 DOI: 10.1029/2019gb006298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 01/09/2020] [Accepted: 01/24/2020] [Indexed: 05/22/2023]
Abstract
Dark carbon fixation (DCF) by chemoautotrophic microorganisms can sustain food webs in the seafloor by local production of organic matter independent of photosynthesis. The process has received considerable attention in deep sea systems, such as hydrothermal vents, but the regulation, depth distribution, and global importance of coastal sedimentary DCF have not been systematically investigated. Here we surveyed eight coastal sediments by means of stable isotope probing (13C-DIC) combined with bacterial biomarkers (phospholipid-derived fatty acids) and compiled additional rates from literature into a global database. DCF rates in coastal sediments range from 0.07 to 36.30 mmol C m-2 day-1, and there is a linear relation between DCF and water depth. The CO2 fixation ratio (DCF/CO2 respired) also shows a trend with water depth, decreasing from 0.09 in nearshore environments to 0.04 in continental shelf sediments. Five types of depth distributions of chemoautotrophic activity are identified based on the mode of pore water transport (advective, bioturbated, and diffusive) and the dominant pathway of microbial sulfur oxidation. Extrapolated to the global coastal ocean, we estimate a DCF rate of 0.04 to 0.06 Pg C year-1, which is less than previous estimates based on indirect measurements (0.15 Pg C year-1), but remains substantially higher than the global DCF rate at deep sea hydrothermal vents (0.001-0.002 Pg C year-1).
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Affiliation(s)
| | - Filip J. R. Meysman
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
- Department of BiologyUniversity of AntwerpAntwerpBelgium
| | - Henricus T. S. Boschker
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
- Department of BiologyUniversity of AntwerpAntwerpBelgium
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11
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Zhao Y, Liu P, Rui J, Cheng L, Wang Q, Liu X, Yuan Q. Dark carbon fixation and chemolithotrophic microbial community in surface sediments of the cascade reservoirs, Southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134316. [PMID: 31783464 DOI: 10.1016/j.scitotenv.2019.134316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/04/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Dark carbon fixation (DCF) by chemolithotrophic microbes can make considerable contribution to inorganic carbon fixation in aquatic ecosystems. However, little is known about the importance and diversity of chemolithotrophic microbes in cascade reservoir sediments. In this study, we determined the potential DCF rates of sediments of three cascade reservoirs in Wujiang River basin by carbon isotopic labeling. The results showed that the DCF rates of the surface sediments ranged from 1.5 to 14.7 mmol C m-2 d-1. The ratio of DCF to mineralization rate of sediment organic matter of surface sediment was between 11.6%~60.9%. High-throughput sequencing analysis of cbbL and cbbM genes involved in Calvin Benson Cycle indicated that cbbL-carrying CO2-assimilating bacteria included diverse functional groups, while cbbM type was mostly involved in sulfur oxidation. The sediments of Hongfeng (HF) reservoir, which has much longer hydraulic residence time (HRT) and locates in most upstream of a major tributary of Wujiang River, have substantially higher DCF rates. The cbbL and cbbM communities in HF were dominated by sulfur oxidizing bacteria, and were largely different from that in the other two reservoirs. Our results suggested that chemolithotrophy plays an important role in carbon cycling of sediments in cascade reservoir. Meanwhile, HRT and relative location of cascade reservoirs are the key control factors of both DCF and composition of autotrophic microbial communities in cascade reservoir sediments.
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Affiliation(s)
- Yuan Zhao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengfei Liu
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Junpeng Rui
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, China
| | - Qian Wang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
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12
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Cable Bacteria Take a New Breath Using Long-Distance Electricity. Trends Microbiol 2018; 26:411-422. [DOI: 10.1016/j.tim.2017.10.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022]
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13
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Mori F, Umezawa Y, Kondo R, Wada M. Effects of bottom-water hypoxia on sediment bacterial community composition in a seasonally hypoxic enclosed bay (Omura Bay, West Kyushu, Japan). FEMS Microbiol Ecol 2018; 94:4951600. [DOI: 10.1093/femsec/fiy053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 03/21/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
| | - Yu Umezawa
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Fukui 917-0003, Japan
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
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14
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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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