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Mirzaei Y, Gélinas Y. Investigating the kinetics of marine and terrestrial organic carbon incorporation and degradation in coastal bulk sediment and water settings through isotopic lenses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175279. [PMID: 39117203 DOI: 10.1016/j.scitotenv.2024.175279] [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: 01/15/2024] [Revised: 07/17/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Coastal sediments are the main deposition center for allochthonous and autochthonous organic carbon (OC). The discharge of terrestrial biomass, anthropogenic activities, oceanic primary productivity, and natural events contribute to this carbon pool. The OC buried in sediments undergoes alteration through physical, biological and chemical processes, becoming progressively refractory and more likely to be preserved on geological time scales. However, little is known about the rate of bulk OC alteration post weathering and bloom. We incubated coastal sediment slurries with isotopically distinct spikes of C4 corn leaves and cultured phytoplankton, individually and in 1:1 mixture. OC isotopic values and concentrations were probed at different time points to track degradation and incorporation in solid and liquid phases. Both amendments were composed of fresh OC with a high proportion of labile biochemicals (e.g. polysaccharides and proteins). Despite the small differences in their lability, corn leaves were incorporated into the sediments at a slower rate compared to phytoplankton. Following combined spiking of the terrestrial and marine amendments, no sign of synergistic effects was observed in system's response. Despite sediment sensitivity to OC input and the rapid alterations in its properties within the initial days of incubation, swiftly transitioning to a state of minimal change is indicative of a relatively stable system that retained the isotopic imprint of the OC spike for a long time (> 32 days). This isotopic remanence is likely due to heterotrophic bacteria that degrade OC to synthesize their biomass (food stock for successive generations) and incorporate its stable isotope characteristics. Hence, our work sheds light on the kinetics of biogeochemical changes, and recovery time of the system for returning to its pre-perturbation state.
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Affiliation(s)
- Yeganeh Mirzaei
- Geotop and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B-1R6, Canada.
| | - Yves Gélinas
- Geotop and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B-1R6, Canada
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2
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Cheng S, Meng F, Wang Y, Zhang J, Zhang L. The potential linkage between sediment oxygen demand and microbes and its contribution to the dissolved oxygen depletion in the Gan River. Front Microbiol 2024; 15:1413447. [PMID: 39144217 PMCID: PMC11322766 DOI: 10.3389/fmicb.2024.1413447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
The role of sediment oxygen demand (SOD) in causing dissolved oxygen (DO) depletion is widely acknowledged, with previous studies mainly focusing on chemical and biological SOD separately. However, the relationship between the putative functions of sediment microbes and SOD, and their impact on DO depletion in overlying water, remains unclear. In this study, DO depletion was observed in the downstream of the Gan River during the summer. Sediments were sampled from three downstream sites (YZ, Down1, and Down2) and one upstream site (CK) as a control. Aquatic physicochemical parameters and SOD levels were measured, and microbial functions were inferred from taxonomic genes through analyses of the 16S rRNA gene. The results showed that DO depletion sites exhibited a higher SOD rate compared to CK. The microbial community structure was influenced by the spatial variation of Proteobacteria, Chloroflexi, and Bacteroidota, with total organic carbon (TOC) content acting as a significant environmental driver. A negative correlation was observed between microbial diversity and DO concentration (p < 0.05). Aerobic microbes were more abundant in DO depletion sites, particularly Proteobacteria. Microbes involved in various biogeochemical cycles, such as carbon (methane oxidation, methanotrophs, and methylotrophs), nitrogen (nitrification and denitrification), sulfur (sulfide and sulfur compound oxidation), and manganese cycles (manganese oxidation), exhibited higher abundance in DO depletion sites, except for the iron cycle (iron oxidation). These processes were negatively correlated with DO concentration and positively with SOD (p < 0.05). Overall, the results highlight that aerobic bacteria's metabolic processes consume oxygen, increasing the SOD rate and contributing to DO depletion in the overlying water. Additionally, the study underscores the importance of targeting the removal of in situ microbial molecular mechanisms associated with toxic H2S and CH4 to support reoxygenation efforts in rehabilitating DO depletion sites in the Gan River, aiding in identifying factors controlling DO consumption and offering practical value for the river's restoration and management.
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Affiliation(s)
- Shoutao Cheng
- Country School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Fansheng Meng
- Research Center of Environmental Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yeyao Wang
- Country School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
- China National Environmental Monitoring Center, Beijing, China
| | - Jiasheng Zhang
- Research Center of Environmental Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Lingsong Zhang
- Research Center of Environmental Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing, China
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Kim JW, Kim HG, Kim H, Hawkins SJ, Seo IS, Oh CW. Spatial distribution of meiofaunal and macrofaunal assemblages in the tidal flats of the southern Korean coast in relation to natural and anthropogenic impacts. MARINE POLLUTION BULLETIN 2023; 194:115377. [PMID: 37579707 DOI: 10.1016/j.marpolbul.2023.115377] [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: 06/13/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023]
Abstract
We investigated the spatial variability of macrofaunal and meiofaunal assemblages in intertidal flats on the southern coast of Korea. Abiotic and biotic samples were collected at five stations. The species richness, density, and composition of the assemblages differed significantly among stations. Nematoda and Annelida were the most dominant meiofaunal and macrofaunal taxa, respectively, although taxon dominance differed among stations. Distance-based linear models showed that sediment-related variables and heavy metals were the main environmental factors determining the spatial variability of the assemblages. Macrofauna had only sediment-related variables and heavy metals as major environmental factors, but meiofauna were also influenced by other environmental factors such as sea surface temperature, dissolved oxygen-related variables, and salinity. This study can provide basic ecological data for understanding the spatial distribution of macro-meiofaunal assemblages and aid in the development of marine environmental management strategies on the western south coast of Korea.
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Affiliation(s)
- Jeong Won Kim
- Department of Industry 4.0 Convergence Bionics Engineering, The Graduate School, Pukyong National University, Busan, Republic of Korea; Ocean Climate Response & Ecosystem Research Department, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Hyeong-Gi Kim
- Department of Marine Environmental Science, College of Natural Science, Chungnam National University, Daejeon, Republic of Korea.
| | - Hyein Kim
- Department of Marine Environmental Science, College of Natural Science, Chungnam National University, Daejeon, Republic of Korea
| | - Stephen John Hawkins
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, UK; Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth L1 2PB, United Kingdom
| | - In-Soo Seo
- Korea Benthos Research Center, Co. Ltd. Busan, Republic of Korea
| | - Chul-Woong Oh
- Department of Marine Biology, College of Fisheries Sciences, Pukyong National University, Busan, Republic of Korea.
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Deldicq N, Mermillod-Blondin F, Bouchet VMP. Sediment reworking of intertidal sediments by the benthic foraminifera Haynesina germanica: the importance of motion behaviour and densities. Proc Biol Sci 2023; 290:20230193. [PMID: 36883274 PMCID: PMC9993050 DOI: 10.1098/rspb.2023.0193] [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: 01/24/2023] [Accepted: 02/13/2023] [Indexed: 03/09/2023] Open
Abstract
This study aimed to describe for the first time the vertical motion behaviour of the intertidal foraminifera Haynesina germanica and its contribution to bioturbation. Its infaunal behaviour leads to the creation of a one-end tube within the first centimetre of sediment. In addition, a vertical trail following behaviour was described for the first time in foraminifera, which may be linked to the sustainability of the biogenic sedimentary structures. As a consequence, H. germanica produces a vertical transport of both mud and fine sediment fractions similarly to the sediment reworking mode reported for gallery-diffusor benthic species. This finding allows us to refine the bioturbating mode of H. germanica, previously classified as surficial biodiffusor. Furthermore, sediment reworking intensity appeared to be dependent on the foraminiferal density. H. germanica would adapt its motion behaviour to deal with the intra-specific competition for food and space that may occur when density increases. Consequently, this behavioural modification would affect both the species and the individual contribution to sediment reworking processes. In fine, sediment reworking in H. germanica may further contribute to the bioirrigation of intertidal sediments, which has implications for oxygen availability in sediments and on aerobic microbial processes involved in carbon and nutrient cycling at the sediment-water interface.
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Affiliation(s)
- Noémie Deldicq
- LOG, Laboratoire d'Océanologie et de Géosciences, University Lille, CNRS, University Littoral Côte d'Opale, UMR 8187, Station Marine de Wimereux, Lille 59000, France
| | - Florian Mermillod-Blondin
- University of Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne 69622, France
| | - Vincent M. P. Bouchet
- LOG, Laboratoire d'Océanologie et de Géosciences, University Lille, CNRS, University Littoral Côte d'Opale, UMR 8187, Station Marine de Wimereux, Lille 59000, France
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Orio A, Heimbrand Y, Limburg K. Deoxygenation impacts on Baltic Sea cod: Dramatic declines in ecosystem services of an iconic keystone predator. AMBIO 2022; 51:626-637. [PMID: 34075555 PMCID: PMC8800964 DOI: 10.1007/s13280-021-01572-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/07/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The intensified expansion of the Baltic Sea's hypoxic zone has been proposed as one reason for the current poor status of cod (Gadus morhua) in the Baltic Sea, with repercussions throughout the food web and on ecosystem services. We examined the links between increased hypoxic areas and the decline in maximum length of Baltic cod, a demographic proxy for services generation. We analysed the effect of different predictors on maximum length of Baltic cod during 1978-2014 using a generalized additive model. The extent of minimally suitable areas for cod (oxygen concentration ≥ 1 ml l-1) is the most important predictor of decreased cod maximum length. We also show, with simulations, the potential for Baltic cod to increase its maximum length if hypoxic areal extent is reduced to levels comparable to the beginning of the 1990s. We discuss our findings in relation to ecosystem services affected by the decrease of cod maximum length.
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Affiliation(s)
- Alessandro Orio
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Turistgatan 5, 453 30 Lysekil, Sweden
| | - Yvette Heimbrand
- Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Skolgatan 6, 742 42 Öregrund, Sweden
| | - Karin Limburg
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Turistgatan 5, 453 30 Lysekil, Sweden
- College of Environmental Science and Forestry, State University of New York, Syracuse, NY USA
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Dan SF, Li S, Yang B, Cui D, Ning Z, Huang H, Zhou J, Yang J. Influence of sedimentary organic matter sources on the distribution characteristics and preservation status of organic carbon, nitrogen, phosphorus, and biogenic silica in the Daya Bay, northern South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:146899. [PMID: 33865127 DOI: 10.1016/j.scitotenv.2021.146899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Surface sediment samples were collected from Daya Bay in October 2018, and analyzed for total organic carbon (OC), total nitrogen (TN) and their stable isotopes (δ13C and δ15N), total phosphorus (TP), biogenic silica (BSi), sediment textures and specific surface area (SSA). The primary objective was to evaluate the influence of mariculture/aquaculture on the distribution characteristics of organic matter (OM), and preservation status of OC, TN, TP, and BSi in sediments. The average δ13C and δ15N values, and OC/TN ratios were -21.27‰, 6.74‰, and 8.90, respectively. Monte Carlo simulation results revealed that mariculture/aquaculture biodeposits accounted for >40% of the buried OM at sites where the breeding rafts and cages are located, whereas marine OM increased gradually to the open sea. Terrestrial OM was generally low accounting for 17% by average. The contents and distribution characteristics of biogenic elements were more influenced by mariculture/aquaculture and primary productivity than sediment textures. Lower OC/SSA (0.3-1.2 mg OC/m2), TN/SSA (~0.05-0.18 mg TN/m2), and TP/SSA (0.02-0.04 mg TP/m2) loadings indicated that increased sequestration of labile OM in a coastal bay could contribute to significant degradation of recalcitrant OM in sediments with significant loss of P relative to OC. Nitrogen contamination in surface sediments was due to increased injection of aquaculture biodeposits, and may pose a detrimental effect on the ecological sustainability of the bay. Higher BSi/SSA loadings (0.9-1.7 mg BSi/m2) revealed that BSi was more preserved, and that BSi-based proxy could be used for paleo-productivity studies. However, such preservation may induce adverse dissolved silicate limitation in a bay perturbed by eutrophication. Fine-grained sediments (clay and silt) accounted for >77% of the sediment texture types with higher SSA, and while controlling the contents of biogenic elements under given depositional conditions were not the main determining factors of OC, TN, TP, and BSi preservation.
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Affiliation(s)
- Solomon Felix Dan
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China
| | - Shengyong Li
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou 510300, China
| | - Bin Yang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China.
| | - Dongyang Cui
- Key Laboratory of Urban Land Resources Monitoring and Simulation, Ministry of Natural Resources, Shenzhen 518000, China
| | - Zhiming Ning
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China
| | - Haifang Huang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China
| | - Jiaodi Zhou
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China
| | - Jian Yang
- Research Center for Coastal Environment Engineering Technology of Shandong Province, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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7
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Abstract
Cyanophages are viruses that target cyanobacteria and directly control their abundance via viral lysis. Cyanobacteria are known to cause large blooms in water bodies, substantially contributing to oxygen depletion in bottom waters resulting in areas called dead zones. Up to 20% of prokaryotic organisms in the oceans are estimated to die every day due to viral infection and lysis. Viruses can therefore alter microbial diversity, community structure, and biogeochemical processes driven by these organisms. Cyanophages are viruses that infect and lyse cyanobacterial cells, adding bioavailable carbon and nutrients into the environment. Cyanobacteria are photosynthesizing bacteria, with some species capable of N2 fixation, which are known to form large blooms as well as resistant resting cells known as akinetes. Here, we investigated cyanophage diversity and community structure plus cyanobacteria in dead zone sediments. We sampled surface sediments and sequenced DNA and RNA, along an oxygen gradient—representing oxic, hypoxic, and anoxic conditions—in one of the world’s largest dead zones located in the Baltic Sea. Cyanophages were detected at all stations and, based on partial genome contigs, had a higher alpha diversity and different beta diversity in the hypoxic-anoxic sediments, suggesting that cyanobacteria in dead zone sediments and/or environmental conditions select for specific cyanophages. Some of these cyanophages can infect cyanobacteria with potential consequences for gene expression related to their photosystem and phosphate regulation. Top cyanobacterial genera detected in the anoxic sediment included Dolichospermum/Anabaena, Synechococcus, and Cyanobium. RNA transcripts classified to cyanobacteria were associated with numerous pathways, including anaerobic carbon metabolism and N2 fixation. Cyanobacterial blooms are known to fuel oxygen-depleted ecosystems with phosphorus (so-called internal loading), and our cyanophage data indicate the potential for viral lysis of cyanobacteria which might explain the high nutrient turnover in these environments. IMPORTANCE Cyanophages are viruses that target cyanobacteria and directly control their abundance via viral lysis. Cyanobacteria are known to cause large blooms in water bodies, substantially contributing to oxygen depletion in bottom waters resulting in areas called dead zones. Our knowledge of cyanophages in dead zones is very scarce, and so far, no studies have assembled partial cyanophage genomes and investigated their associated cyanobacteria in these dark and anoxic sediments. Here, we present the first study using DNA and RNA sequencing to investigate in situ diversity of cyanophages and cyanobacteria in dead zones. Our study shows that dead zone sediments contain different cyanophages compared to oxic sediments and suggest that these viruses are able to affect cyanobacterial photosystem and phosphate regulation. Furthermore, cyanophage-controlled lysis of cyanobacteria might also increase the turnover of carbon, phosphorus, and nitrogen in these oxygen-free environments at the bottom of the sea.
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Broman E, Motwani NH, Bonaglia S, Landberg T, Nascimento FJA, Sjöling S. Denitrification responses to increasing cadmium exposure in Baltic Sea sediments. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 217:105328. [PMID: 31629202 DOI: 10.1016/j.aquatox.2019.105328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
Benthic ecosystems have come under intense pressure, due to eutrophication-driven oxygen decline and industrial metal contamination. One of the most toxic metals is Cadmium (Cd), which is lethal to many aquatic organisms already at low concentrations. Denitrification by facultative anaerobic microorganisms is an essential process to transform, but also to remove, excess nitrate in eutrophied systems. Cd has been shown to decrease denitrification and sequester free sulfide, which is available when oxygen is scarce and generally inhibits complete denitrification (i.e. N2O to N2). In polluted sediments, an interaction between oxygen and Cd may influence denitrification and this relationship has not been studied. For example, in the Baltic Sea some sediments are double exposed to both Cd and hypoxia. In this study, we examined how the double exposure of Cd and fluctuations in oxygen affects denitrification in Baltic Sea sediment. Results show that oxygen largely regulated N2O and N2 production after 21 days of exposure to Cd (ranging from 0 to 500 μg/L, 5 different treatments, measured by the isotope pairing technique (IPT)). In the high Cd treatment (500 μg/L) the variation in N2 production increased compared to the other treatments. Increases in N2 production are suggested to be an effect of 1) enhanced nitrification that increases NO3- availability thus stimulating denitrification, and 2) Cd successfully sequestrating sulfide (yielding CdS), which allows for full denitrification to N2. The in situ field sediment contained initially high Cd concentrations in the pore water (∼10 μg/L) and microbial communities might already have been adapted to metal stress, making the effect of low Cd levels negligible. Here we show that high levels of cadmium pollution might increase N2 production and influence nitrogen cycling in marine sediments.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden; Baltic Sea Centre, Stockholm University, Stockholm, 106 91, Sweden.
| | - Nisha H Motwani
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, 141 89, Sweden
| | - Stefano Bonaglia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden; Department of Biology, University of Southern Denmark, Odense, 5230, Denmark
| | - Tommy Landberg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden; Baltic Sea Centre, Stockholm University, Stockholm, 106 91, Sweden
| | - Sara Sjöling
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, 141 89, Sweden
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Pan Z, Gao QF, Dong SL, Wang F, Li HD, Zhao K, Jiang XY. Effects of abalone (Haliotis discus hannai Ino) and kelp (Saccharina japonica) mariculture on sources, distribution, and preservation of sedimentary organic carbon in Ailian Bay, China: Identified by coupling stable isotopes (δ 13C and δ 15N) with C/N ratio analyses. MARINE POLLUTION BULLETIN 2019; 141:387-397. [PMID: 30955748 DOI: 10.1016/j.marpolbul.2019.02.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/23/2019] [Accepted: 02/23/2019] [Indexed: 06/09/2023]
Abstract
To investigate the effects of mariculture on the sources, distribution and preservation of sedimentary organic carbon (SOC), sediments from an mariculture area in Ailian Bay, China, and a control area were analyzed for grain size composition, total organic carbon (TOC), total nitrogen (TN), carbon/nitrogen (C/N) ratio, and stable carbon and nitrogen isotopic composition (δ13C and δ15N). The sedimentary type of sediments in study area was clay silt. TOC, TN, C/N, δ13C, and δ15N ranged from 0.58 to 1.21%, 0.06-0.17%, 6.29-9.82, -23.20 to -18.50‰, and 6.17-7.38‰, respectively, and followed similar spatial patterns. TOC, TN and δ13C were higher in mariculture area than in control area. Biodeposit and kelp OC contributions greater of SOC in mariculture area than the control area (biodeposits: 20.10 ± 4.84 to 6.2 ± 1.3%; kelp: 15.3 ± 6.63 to 5.2 ± 0.84%). Overall, mariculture activities significantly influence the sources, distribution and preservation of SOC.
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Affiliation(s)
- Zhe Pan
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266100, China
| | - Qin-Feng Gao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266100, China.
| | - Shuang-Lin Dong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266100, China
| | - Fang Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266100, China
| | - Hai-Dong Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266100, China
| | - Kun Zhao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266100, China
| | - Xu-Yang Jiang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266100, China
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10
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Anthropogenic disturbance keeps the coastal seafloor biogeochemistry in a transient state. Sci Rep 2018; 8:5582. [PMID: 29615805 PMCID: PMC5883055 DOI: 10.1038/s41598-018-23925-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/22/2018] [Indexed: 11/08/2022] Open
Abstract
Coastal sediments and continental shelves play a crucial role in global biogeochemistry, as they form the prime site of organic carbon burial. Bottom trawling and dredging are known to increasingly impact the coastal seafloor through relocation and homogenisation of sediments, yet little is known about the effects of such anthropogenic sediment reworking on the overall cycling of carbon and other elements within the coastal seafloor. Here, we document the transient recovery of the seafloor biogeochemistry after an in situ disturbance. Evidence from pore-water data and model simulations reveal a short-term increase in the overall carbon mineralisation rate, as well as a longer-term shift in the redox pathways of organic matter mineralisation, favouring organoclastic sulphate reduction over methane formation. This data suggests that anthropogenic sediment reworking could have a sizeable impact on the carbon cycle in cohesive sediments on continental shelves. This imprint will increase in the near future, along with the growing economic exploitation of the coastal ocean.
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11
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Danovaro R, Corinaldesi C, Dell'Anno A, Rastelli E. Potential impact of global climate change on benthic deep-sea microbes. FEMS Microbiol Lett 2018; 364:4553516. [PMID: 29045616 DOI: 10.1093/femsle/fnx214] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/12/2017] [Indexed: 11/12/2022] Open
Abstract
Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models.
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Affiliation(s)
- Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Eugenio Rastelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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12
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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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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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Danovaro R, Dell’Anno A, Corinaldesi C, Rastelli E, Cavicchioli R, Krupovic M, Noble RT, Nunoura T, Prangishvili D. Virus-mediated archaeal hecatomb in the deep seafloor. SCIENCE ADVANCES 2016; 2:e1600492. [PMID: 27757416 PMCID: PMC5061471 DOI: 10.1126/sciadv.1600492] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/11/2016] [Indexed: 05/12/2023]
Abstract
Viruses are the most abundant biological entities in the world's oceans, and they play a crucial role in global biogeochemical cycles. In deep-sea ecosystems, archaea and bacteria drive major nutrient cycles, and viruses are largely responsible for their mortality, thereby exerting important controls on microbial dynamics. However, the relative impact of viruses on archaea compared to bacteria is unknown, limiting our understanding of the factors controlling the functioning of marine systems at a global scale. We evaluate the selectivity of viral infections by using several independent approaches, including an innovative molecular method based on the quantification of archaeal versus bacterial genes released by viral lysis. We provide evidence that, in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria. We also found that, within deep-sea benthic archaea, the impact of viruses was mainly directed at members of specific clades of Marine Group I Thaumarchaeota. Although archaea represent, on average, ~12% of the total cell abundance in the top 50 cm of sediment, virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally. Our results indicate that viral infection represents a key mechanism controlling the turnover of archaea in surface deep-sea sediments. We conclude that interactions between archaea and their viruses might play a profound, previously underestimated role in the functioning of deep-sea ecosystems and in global biogeochemical cycles.
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Affiliation(s)
- Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- Corresponding author.
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, Ancona 60131, Italy
| | - Eugenio Rastelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mart Krupovic
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris 75015, France
| | - Rachel T. Noble
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC 28557, USA
| | - Takuro Nunoura
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka 237-0061, Japan
| | - David Prangishvili
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris 75015, France
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Abstract
To better understand the origin, evolution, and extent of life, we seek to determine the minimum flux of energy needed for organisms to remain viable. Despite the difficulties associated with direct measurement of the power limits for life, it is possible to use existing data and models to constrain the minimum flux of energy required to sustain microorganisms. Here, a we apply a bioenergetic model to a well characterized marine sedimentary environment in order to quantify the amount of power organisms use in an ultralow-energy setting. In particular, we show a direct link between power consumption in this environment and the amount of biomass (cells cm-3) found in it. The power supply resulting from the aerobic degradation of particular organic carbon (POC) at IODP Site U1370 in the South Pacific Gyre is between ∼10-12 and 10-16 W cm-3. The rates of POC degradation are calculated using a continuum model while Gibbs energies have been computed using geochemical data describing the sediment as a function of depth. Although laboratory-determined values of maintenance power do a poor job of representing the amount of biomass in U1370 sediments, the number of cells per cm-3 can be well-captured using a maintenance power, 190 zW cell-1, two orders of magnitude lower than the lowest value reported in the literature. In addition, we have combined cell counts and calculated power supplies to determine that, on average, the microorganisms at Site U1370 require 50–3500 zW cell-1, with most values under ∼300 zW cell-1. Furthermore, we carried out an analysis of the absolute minimum power requirement for a single cell to remain viable to be on the order of 1 zW cell-1.
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Affiliation(s)
- Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles CA, USA
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles CA, USA ; Department of Biological Sciences, University of Southern California, Los Angeles CA, USA
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16
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Affiliation(s)
- Jack J. Middelburg
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, P.O. Box 80021, 3508 TA Utrecht, Netherlands
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Virus decomposition provides an important contribution to benthic deep-sea ecosystem functioning. Proc Natl Acad Sci U S A 2015; 112:E2014-9. [PMID: 25848024 DOI: 10.1073/pnas.1422234112] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses are key biological agents of prokaryotic mortality in the world oceans, particularly in deep-sea ecosystems where nearly all of the prokaryotic C production is transformed into organic detritus. However, the extent to which the decomposition of viral particles (i.e., organic material of viral origin) influences the functioning of benthic deep-sea ecosystems remains completely unknown. Here, using various independent approaches, we show that in deep-sea sediments an important fraction of viruses, once they are released by cell lysis, undergo fast decomposition. Virus decomposition rates in deep-sea sediments are high even at abyssal depths and are controlled primarily by the extracellular enzymatic activities that hydrolyze the proteins of the viral capsids. We estimate that on a global scale the decomposition of benthic viruses releases ∼37-50 megatons of C per year and thus represents an important source of labile organic compounds in deep-sea ecosystems. Organic material released from decomposed viruses is equivalent to 3 ± 1%, 6 ± 2%, and 12 ± 3% of the input of photosynthetically produced C, N, and P supplied through particles sinking to bathyal/abyssal sediments. Our data indicate that the decomposition of viruses provides an important, previously ignored contribution to deep-sea ecosystem functioning and has an important role in nutrient cycling within the largest ecosystem of the biosphere.
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Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments. CHROMATOGRAPHY 2014. [DOI: 10.3390/chromatography1040176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Danovaro R, Corinaldesi C, Dell'Anno A, Fuhrman JA, Middelburg JJ, Noble RT, Suttle CA. Marine viruses and global climate change. FEMS Microbiol Rev 2011; 35:993-1034. [DOI: 10.1111/j.1574-6976.2010.00258.x] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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20
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Van Frausum J, Middelburg JJ, Soetaert K, Meysman FJ. Different proxies for the reactivity of aquatic sediments towards oxygen: A model assessment. Ecol Modell 2010. [DOI: 10.1016/j.ecolmodel.2010.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Hubert C, Arnosti C, Brüchert V, Loy A, Vandieken V, Jørgensen BB. Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperature. Environ Microbiol 2010; 12:1089-104. [PMID: 20192966 DOI: 10.1111/j.1462-2920.2010.02161.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50 degrees C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0 degrees C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50 degrees C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50 degrees C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50 degrees C. Incubations with four different fluorescently labelled polysaccharides at 4 degrees C and 50 degrees C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere.
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Affiliation(s)
- Casey Hubert
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Meysman FJR, Bruers S. A thermodynamic perspective on food webs: quantifying entropy production within detrital-based ecosystems. J Theor Biol 2007; 249:124-39. [PMID: 17720204 DOI: 10.1016/j.jtbi.2007.07.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 07/17/2007] [Accepted: 07/17/2007] [Indexed: 11/15/2022]
Abstract
Because ecosystems fit so nicely the framework of a "dissipative system", a better integration of thermodynamic and ecological perspectives could benefit the quantitative analysis of ecosystems. One obstacle is that traditional food web models are solely based upon the principles of mass and energy conservation, while the theory of non-equilibrium thermodynamics principally focuses on the concept of entropy. To properly cast classical food web models within a thermodynamic framework, one requires a proper quantification of the entropy production that accompanies resource processing of the food web. Here we present such a procedure, which emphasizes a rigorous definition of thermodynamic concepts (e.g. thermodynamic gradient, disequilibrium distance, entropy production, physical environment) and their correct translation into ecological terms. Our analysis provides a generic way to assess the thermodynamic operation of a food web: all information on resource processing is condensed into a single resource processing constant. By varying this constant, one can investigate the range of possible food web behavior within a given fixed physical environment. To illustrate the concepts and methods, we apply our analysis to a very simple example ecosystem: the detrital-based food web of marine sediments. We examine whether entropy production maximization has any ecological relevance in terms of food web functioning.
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Affiliation(s)
- Filip J R Meysman
- Netherlands Institute of Ecology (NIOO-KNAW), Centre for Estuarine and Marine Ecology, Korringaweg 7, 4401 NT Yerseke, The Netherlands.
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