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Wietz M, Engel A, Ramondenc S, Niwano M, von Appen WJ, Priest T, von Jackowski A, Metfies K, Bienhold C, Boetius A. The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone. Environ Microbiol 2024; 26:e16568. [PMID: 38268397 DOI: 10.1111/1462-2920.16568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015-2019; 5-100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anja Engel
- Biological Oceanography, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Simon Ramondenc
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matomo Niwano
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Anabel von Jackowski
- Biological Oceanography, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Zhang G, Lou M, Xu J, Li Y, Zhou J, Guo H, Qu G, Wang T, Jia H, Zhu L. Molecular insights into microbial transformation of bioaerosol-derived dissolved organic matter discharged from wastewater treatment plant. ENVIRONMENT INTERNATIONAL 2024; 183:108404. [PMID: 38154320 DOI: 10.1016/j.envint.2023.108404] [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: 10/01/2023] [Revised: 12/05/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Wastewater treatment plants (WWTP) are important sources of aerosol-derived dissolved organic matter (ADOM) which may threaten human health via the respiratory system. In this study, aerosols were sampled from a typical WWTP to explore the chemical molecular diversity, molecular ecological network, and potential toxicities of the ADOM in the aerosols. The high fluorescence index (>1.9) and biological index (0.66-1.17) indicated the strong autogenous microbial source characteristics of the ADOM in the WWTP. DOM and microbes in the wastewater were aerosolized due to strong agitation and bubbling in the treatment processes, and contributed to 74 % and 75 %, respectively, of the ADOM and microbes in the aerosols. The ADOM was mainly composed of CHO and CHOS accounting for 35 % and 29 % of the total number of molecules, respectively, with lignin-like (69 %) as the major constituent. 49 % of the ADOM transformations were thermodynamically limited, and intragroup transformations were easier than intergroup transformations. Bacteria in the aerosols involved in ADOM transformations exhibited both cooperative and divergent behaviors and tended to transform carbohydrate-like and amino sugar/protein-like into recalcitrant lignin-like. The microbial compositions were affected by atmosphere temperature and humidity indirectly by modulating the properties of ADOM. Tannin-like, lignin-like, and unsaturated hydrocarbon-like molecules in the ADOM were primary toxicity contributors, facilitating the expression of inflammatory factors IL-β (2.2-5.4 folds), TNF-α (3.5-7.0 folds), and IL-6 (3.5-11.2 folds), respectively.
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Affiliation(s)
- Guodong Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Mingxuan Lou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Jiamin Xu
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Yutong Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Jian Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - He Guo
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Guangzhou Qu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Lingyan Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China; College of Environmental Science and Engineering, Nankai University, Tianjin 300385, China.
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Câmara Dos Reis M, Romac S, Le Gall F, Marie D, Frada MJ, Koplovitz G, Cariou T, Henry N, de Vargas C, Jeanthon C. Exploring the phycosphere of Emiliania huxleyi: From bloom dynamics to microbiome assembly experiments. Mol Ecol 2023; 32:6507-6522. [PMID: 36541038 DOI: 10.1111/mec.16829] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 10/11/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. The structure and selection of prokaryotic communities associated with the most abundant coccolithophore and bloom-forming species, Emiliania huxleyi, are still poorly known. In this study, we assessed the diversity of bacterial communities associated with an E. huxleyi bloom in the Celtic Sea (Eastern North Atlantic), exposed axenic E. huxleyi cultures to prokaryotic communities derived from bloom and non-bloom conditions, and followed the dynamics of their microbiome composition over one year. Bloom-associated prokaryotic communities were dominated by SAR11, Marine group II Euryarchaeota and Rhodobacterales and contained substantial proportions of known indicators of phytoplankton bloom demises such as Flavobacteriaceae and Pseudoalteromonadaceae. The taxonomic richness of bacteria derived from natural communities associated with axenic E. huxleyi rapidly shifted and then stabilized over time. The succession of microorganisms recruited from the environment was consistently dependent on the composition of the initial bacterioplankton community. Phycosphere-associated communities derived from the E. huxleyi bloom were highly similar to one another, suggesting deterministic processes, whereas cultures from non-bloom conditions show an effect of stochasticity. Overall, this work sheds new light on the importance of the initial inoculum composition in microbiome recruitment and elucidates the temporal dynamics of its composition and long-term stability.
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Affiliation(s)
- Mariana Câmara Dos Reis
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Sarah Romac
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Florence Le Gall
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Dominique Marie
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Miguel J Frada
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil Koplovitz
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Thierry Cariou
- Sorbonne Université, Centre National de la Recherche Scientifique, FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Nicolas Henry
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Christian Jeanthon
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
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Sheng M, Chen S, Liu CQ, Fu Q, Zhang D, Hu W, Deng J, Wu L, Li P, Yan Z, Zhu YG, Fu P. Spatial and molecular variations in forest topsoil dissolved organic matter as revealed by FT-ICR mass spectrometry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165099. [PMID: 37379928 DOI: 10.1016/j.scitotenv.2023.165099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/01/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023]
Abstract
Forest soils cover about 30 % of the Earth's land surface and play a fundamental role in the global cycle of organic matter. Dissolved organic matter (DOM), the largest active pool of terrestrial carbon, is essential for soil development, microbial metabolism and nutrient cycling. However, forest soil DOM is a highly complex mixture of tens of thousands of individual compounds, which is largely composed of organic matter from primary producers, residues from microbial process and the corresponding chemical reactions. Therefore, we need a detailed picture of molecular composition in forest soil, especially the pattern of large-scale spatial distribution, which can help us understand the role of DOM in the carbon cycle. To explore the spatial and molecular variations of DOM in forest soil, we choose six major forest reserves located in different latitudes ranging in China, which were investigated by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). Results show that aromatic-like molecules are preferentially enriched in DOM at high latitude forest soils, while aliphatic/peptide-like, carbohydrate-like, and unsaturated hydrocarbon molecules are preferentially enriched in DOM at low latitude forest soils, besides, lignin-like compounds account for the highest proportion in all forest soil DOM. High latitude forest soils have higher aromatic equivalents and aromatic indices than low latitude forest soils, which suggest that organic matter at higher latitude forest soils preferentially contain plant-derived ingredients and are refractory to degradation while microbially derived carbon is dominant in organic matter at low latitudes. Besides, we found that CHO and CHON compounds make up the majority in all forest soil samples. Finally, we visualized the complexity and diversity of soil organic matter molecules through network analysis. Our study provides a molecular-level understanding of forest soil organic matter at large scales, which may contribute to the conservation and utilization of forest resources.
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Affiliation(s)
- Ming Sheng
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Shuang Chen
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
| | - Qinglong Fu
- School of Environment Studies, China University of Geosciences, Wuhan 430074, China
| | - Donghuan Zhang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Wei Hu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Junjun Deng
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Libin Wu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Ping Li
- LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China
| | - Zhifeng Yan
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Pingqing Fu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
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Shen J, Liang Z, Kuzyakov Y, Li W, He Y, Wang C, Xiao Y, Chen K, Sun G, Lei Y. Dissolved organic matter defines microbial communities during initial soil formation after deglaciation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163171. [PMID: 37001675 DOI: 10.1016/j.scitotenv.2023.163171] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/22/2023] [Accepted: 03/26/2023] [Indexed: 05/13/2023]
Abstract
Ecosystem succession and pedogenesis reshuffle the composition and turnover of dissolved organic matter (DOM) and its interactions with soil microbiome. The changes of these connections are especially intensive during initial pedogenesis, e.g. in young post-glacial areas. The temporal succession and vertical development of DOM effects on microbial community structure remains elusive. Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS), high-throughput sequencing, and molecular ecological networks, we characterized the molecular diversity of water-extractable DOM and identified its links to microbial communities in soil profiles along deglaciation chronosequence (12, 30, 40, 52, 80, and 120 years) in the southeastern Tibetan Plateau. Low-molecular-weight compound content decreased, whereas the mid- and high-molecular-weight compounds increased with succession age and soil depth. This was confirmed by the increase in double bond equivalents and averaged oxygen-to‑carbon ratios (O/C), and decrease in hydrogen-to‑carbon ratios (H/C), which reflect DOM accumulation and stabilization. Microbial community succession shifted towards the dominance of oligotrophic Acidobacteria and saprophytic Mortierellomycota, reflecting the increase of stable DOM components (H/C < 1.5 and wider O/C). Less DOM-bacterial positive networks during the succession reduced specialization of labile DOM production (such as lipid- and protein-like compounds), whereas more DOM-fungal negative networks increased specialization of stable DOM decomposition (such as tannin- and condensed aromatic-like compounds). Consequently, DOM stability is not intrinsic during initial pedogenesis: stable DOM compounds remain after fast bacterial utilization of labile DOM compounds, whereas fungi decompose slowly the remaining DOM pools.
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Affiliation(s)
- Jie Shen
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Ziyan Liang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yakov Kuzyakov
- Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia; Institute of Environmental Sciences, Kazan Federal University, 420049 Kazan, Russia
| | - Weitao Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Yuting He
- Chengdu Popularization of Agricultural Technique Station, Chengdu 610041, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Xiao
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Ke Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Geng Sun
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Yanbao Lei
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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Aqueous Geochemical Controls on the Sestonic Microbial Community in Lakes Michigan and Superior. Microorganisms 2023; 11:microorganisms11020504. [PMID: 36838469 PMCID: PMC9963676 DOI: 10.3390/microorganisms11020504] [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: 12/13/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 02/19/2023] Open
Abstract
Despite being the largest freshwater lake system in the world, relatively little is known about the sestonic microbial community structure in the Laurentian Great Lakes. The goal of this research was to better understand this ecosystem using high-throughput sequencing of microbial communities as a function of water depth at six locations in the westernmost Great Lakes of Superior and Michigan. The water column was characterized by gradients in temperature, dissolved oxygen (DO), pH, and other physicochemical parameters with depth. Mean nitrate concentrations were 32 μmol/L, with only slight variation within and between the lakes, and with depth. Mean available phosphorus was 0.07 μmol/L, resulting in relatively large N:P ratios (97:1) indicative of P limitation. Abundances of the phyla Actinobacteria, Bacteroidetes, Cyanobacteria, Thaumarchaeota, and Verrucomicrobia differed significantly among the Lakes. Candidatus Nitrosopumilus was present in greater abundance in Lake Superior compared to Lake Michigan, suggesting the importance of ammonia-oxidating archaea in water column N cycling in Lake Superior. The Shannon diversity index was negatively correlated with pH, temperature, and salinity, and positively correlated with DO, latitude, and N2 saturation. Results of this study suggest that DO, pH, temperature, and salinity were major drivers shaping the community composition in the Great Lakes.
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Heinrichs ME, Heyerhoff B, Arslan-Gatz BS, Seidel M, Niggemann J, Engelen B. Deciphering the Virus Signal Within the Marine Dissolved Organic Matter Pool. Front Microbiol 2022; 13:863686. [PMID: 35694303 PMCID: PMC9184803 DOI: 10.3389/fmicb.2022.863686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are ubiquitously distributed in the marine environment, influencing microbial population dynamics and biogeochemical cycles on a large scale. Due to their small size, they fall into the oceanographic size-class definition of dissolved organic matter (DOM; <0.7 μm). The purpose of our study was to investigate if there is a detectable imprint of virus particles in natural DOM following standard sample preparation and molecular analysis routines using ultrahigh-resolution mass spectrometry (FT-ICR-MS). Therefore, we tested if a molecular signature deriving from virus particles can be detected in the DOM fingerprint of a bacterial culture upon prophage induction and of seawater containing the natural microbial community. Interestingly, the virus-mediated lysate of the infected bacterial culture differed from the cell material of a physically disrupted control culture in its molecular composition. Overall, a small subset of DOM compounds correlated significantly with virus abundances in the bacterial culture setup, accounting for <1% of the detected molecular formulae and <2% of the total signal intensity of the DOM dataset. These were phosphorus- and nitrogen-containing compounds and they were partially also detected in DOM samples from other studies that included high virus abundances. While some of these formulae matched with typical biomolecules that are constituents of viruses, others matched with bacterial cell wall components. Thus, the identified DOM molecular formulae were probably not solely derived from virus particles but were partially also derived from processes such as the virus-mediated bacterial cell lysis. Our results indicate that a virus-derived DOM signature is part of the natural DOM and barely detectable within the analytical window of ultrahigh-resolution mass spectrometry when a high natural background is present.
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Affiliation(s)
- Mara E. Heinrichs
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Benedikt Heyerhoff
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Berin S. Arslan-Gatz
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Michael Seidel
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Jutta Niggemann
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Bert Engelen
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
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Zhang Y, Heal KV, Shi M, Chen W, Zhou C. Decreasing molecular diversity of soil dissolved organic matter related to microbial community along an alpine elevation gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151823. [PMID: 34808163 DOI: 10.1016/j.scitotenv.2021.151823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Characterization of soil dissolved organic matter (DOM) and understanding of the interactions between soil microbial communities and DOM molecules along elevation gradients in alpine ecosystems are still limited. To unravel these interactions and how they change along alpine elevation gradients, we sampled topsoil in the Sygera Mountains (Tibet, China) at elevations between 3800 and 4600 m. The molecular characteristics of soil DOM were determined using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soil microbial composition was identified by high-throughput sequencing. Among the seven components of DOM, the lignins/CRAM (carboxyl-rich alicyclic molecules)-like structure dominated at all elevations, followed by tannins, while the relative abundance of unstable substances, including lipids, aliphatic/protein, and carbohydrates, was lower. As elevation increased, the molecular diversity, degree of oxidation, aromaticity, and unsaturation of soil DOM decreased. The abundance and diversity of soil bacteria and fungi also generally decreased with elevation. Both bacteria and fungi play an important role in the degradation of DOM molecules, but bacteria appear to have greater degradation ability. Among them, Proteobacteria and Bacteroidetes mainly promote the degradation of lignins/CRAM-like structure molecules, while Basidiomycota mainly degrade more unstable substrates. Co-occurrence network analysis revealed complex correlations between specific microbial groups and DOM molecules. Our results suggest that more active cycling of soil DOM could occur in alpine ecosystems due to climate warming, as the result of increased vegetation productivity and litter input in response to rising temperature promoting the relative abundance of microbial groups capable of degrading lignins/CRAM-like structures in soil DOM.
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Affiliation(s)
- Yanlin Zhang
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China
| | - Kate V Heal
- School of GeoSciences, The University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, UK
| | - Mengjie Shi
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China
| | - Wenxin Chen
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China
| | - Chuifan Zhou
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China.
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9
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Cheng H, Yuan M, Tang L, Shen Y, Yu Q, Li S. Integrated microbiology and metabolomics analysis reveal responses of soil microorganisms and metabolic functions to phosphorus fertilizer on semiarid farm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152878. [PMID: 34998744 DOI: 10.1016/j.scitotenv.2021.152878] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 05/13/2023]
Abstract
Localized fertilization of phosphorus has potential benefits in achieving higher crop productivity and nutrient use efficiency, but the underlying biological mechanisms of interactions between soil microorganisms and related metabolic cycle remain largely to be recognized. Here, we combined microbiology with non-target metabolomics to explore how P fertilizer levels and fertilization patterns affect wheat soil microbial communities and metabolic functions based on high-throughput sequencing and UPLC-MS/MS platforms. The results showed P fertilizer decreased the diversity of bacterial 16S rRNA genes and fungal ITS genes, and it did significantly change both soil bacterial and fungal overall community structures and compositions. The P levels and patterns also interfered with complexity of soil bacterial and fungal symbiosis networks. Moreover, metabolomics analysis showed that P fertilizer significantly changed soil metabolite spectrum, and the differential metabolites were significantly enriched to 7 main metabolic pathways, such as arginine and proline metabolism, biosynthesis of plant hormones, amino acids, plant secondary metabolites, and alkaloids derived from ornithine. Additionally, microbes also were closely related to the accumulation of metabolites through correlation analysis. Our results indicated that localized appropriate phosphorus fertilizer plays an important role in regulating soil microbial metabolism, and their interactions in soil providing valuable information for understanding how the changed phosphorus management practices affect the complex biological processes and the adaption capacity of plants to environments.
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Affiliation(s)
- Hongyan Cheng
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China; College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Minshu Yuan
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Liang Tang
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China; College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Yufang Shen
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China; College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
| | - Qiang Yu
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China
| | - Shiqing Li
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China
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10
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Mai Y, Peng S, Lai Z, Wang X. Seasonal and inter-annual variability of bacterioplankton communities in the subtropical Pearl River Estuary, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:21981-21997. [PMID: 34775557 DOI: 10.1007/s11356-021-17449-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
It is widely recognized that environmental factors substantially influence on the seasonal and inter-annual variability of bacterioplankton communities, yet little is known about the seasonality of bacterioplankton communities in subtropical estuaries at longer-term time scales. Here, the bacterioplankton communities from the eight major outlets of the subtropical Pearl River Estuary were investigated across 3 years (2017-2019) using full-length 16S rRNA gene sequencing. Significant seasonal and inter-annual variation was observed in bacterioplankton community compositions across the 3 years (p < 0.05). In addition, the inferred functional composition of the communities varied with seasons, although not significantly, suggesting that functional redundancy existed among communities and across seasons that could help to cope with environmental changes. Five evaluated environmental parameters (temperature, salinity, pH, total dissolved solids (TDS), total phosphorus (TP)) were significantly correlated with community composition variation, while only three environmental parameters (temperature, pH, and TDS) were correlated with variation in inferred functional composition. Moreover, community composition tracked the seasonal temperature gradients, indicating that temperature was a key environmental factor that affected bacterioplankton community's variation along with seasonal succession patterns. Gammaproteobacteria and Alphaproteobacteria were the most dominant classes in the surface waters of Pearl River Estuary, and their members exhibited divergent responses to temperature changes, while several taxa within these group could be indicators of low and high temperatures that are associated with seasonal changes. These results strengthen our understanding of bacterioplankton community variation in association with temperature-dependent seasonal changes in subtropical estuarine ecosystems.
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Affiliation(s)
- Yongzhan Mai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Songyao Peng
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Zini Lai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
- Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510070, China.
| | - Xuesong Wang
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, 100 Xianlie Middle Road, 510070, China.
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11
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Montero P, Gutiérrez MH, Daneri G, Jacob B. The Effect of Salmon Food-Derived DOM and Glacial Melting on Activity and Diversity of Free-Living Bacterioplankton in Chilean Patagonian Fjords. Front Microbiol 2022; 12:772900. [PMID: 35087485 PMCID: PMC8787161 DOI: 10.3389/fmicb.2021.772900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/07/2021] [Indexed: 11/17/2022] Open
Abstract
Fjord ecosystems cycle and export significant amounts of carbon and appear to be extremely sensitive to climate change and anthropogenic perturbations. To identify patterns of microbial responses to ongoing natural and human-derived changes in the fjords of Chilean Patagonia, we examined the effect of organic enrichment associated with salmon aquaculture and freshening produced by glacial melting on bacterial production (BP), extracellular enzymatic activity (EEA), and community diversity of free-living bacterioplankton. We assayed the effects of salmon food-derived dissolved organic matter (SF-DOM) and meltwaters through microcosm experiments containing waters from Puyuhuapi Fjord and the proglacial fjords of the Southern Patagonia Icefield, respectively. Rates of BP and EEA were 2 times higher in the presence of SF-DOM than in controls, whereas the addition of autochthonous organic matter derived from diatoms (D-DOM) resulted in rates of BP and EEA similar to those measured in the controls. The addition of SF-DOM also reduced species richness and abundance of a significant fraction of the representative taxa of bacterioplankton of Puyuhuapi Fjord. In the proglacial fjords, bacterioplankton diversity was reduced in areas more heavily influenced by meltwaters and was accompanied by moderate positive changes in BP and EEA. Our findings strongly suggest that SF-DOM is highly reactive, promoting enhanced rates of microbial activity while could be influencing the diversity of bacterioplankton communities in Patagonian fjords with a strong salmon farming activity. These findings challenge the traditional view of phytoplankton production as the primary source of labile DOM that fuels heterotrophic activity in coastal ecosystems impacted by anthropogenic organic enrichment. Given the intensive local production of salmon, we analyze the significance of this emerging source of rich "allochthonous" organic substrates for autotrophic/heterotrophic balance, carbon exportation, and hypoxia in Patagonian fjords. The effect of human DOM enrichment can be enhanced in proglacial fjords, where progressive glacial melting exerts additional selective pressure on bacterioplankton diversity.
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Affiliation(s)
- Paulina Montero
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Coyhaique, Chile
- Center for Oceanographic Research COPAS Sur-Austral and COPAS COASTAL, Universidad de Concepción, Concepción, Chile
| | - Marcelo H. Gutiérrez
- Center for Oceanographic Research COPAS Sur-Austral and COPAS COASTAL, Universidad de Concepción, Concepción, Chile
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Giovanni Daneri
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Coyhaique, Chile
- Center for Oceanographic Research COPAS Sur-Austral and COPAS COASTAL, Universidad de Concepción, Concepción, Chile
| | - Bárbara Jacob
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Coyhaique, Chile
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12
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Chen H, Kong W, Shi Q, Wang F, He C, Wu J, Lin Q, Zhang X, Zhu Y, Liang C, Luo Y. Patterns and drivers of the degradability of dissolved organic matter in dryland soils on the Tibetan Plateau. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hao Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research Chinese Academy of Sciences Beijing China
- School of Agriculture Sun Yat‐sen University Guangzhou China
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Chinese Academy of Sciences Beijing China
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research Chinese Academy of Sciences Beijing China
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Chinese Academy of Sciences Beijing China
- College of Resources and Environment University of Chinese Academy of Sciences Beijing China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing China University of Petroleum Beijing China
| | - Fei Wang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research Chinese Academy of Sciences Beijing China
- College of Resources and Environment University of Chinese Academy of Sciences Beijing China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing China University of Petroleum Beijing China
| | - Jianshuang Wu
- Institute of Environment and Sustainable Development in Agriculture Chinese Academy of Agricultural Sciences Beijing China
- Key Laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China
| | - Qimei Lin
- College of Land Science and Technology China Agricultural University Beijing China
| | - Xianzhou Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China
| | - Yong‐Guan Zhu
- Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Chao Liang
- Institute of Applied Ecology Chinese Academy of Sciences Shenyang China
| | - Yu Luo
- Key Laboratory of Agricultural Resources and Environment Zhejiang University Hangzhou China
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13
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Wietz M, Bienhold C, Metfies K, Torres-Valdés S, von Appen WJ, Salter I, Boetius A. The polar night shift: seasonal dynamics and drivers of Arctic Ocean microbiomes revealed by autonomous sampling. ISME COMMUNICATIONS 2021; 1:76. [PMID: 37938651 PMCID: PMC9723606 DOI: 10.1038/s43705-021-00074-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 06/15/2023]
Abstract
The Arctic Ocean features extreme seasonal differences in daylight, temperature, ice cover, and mixed layer depth. However, the diversity and ecology of microbes across these contrasting environmental conditions remain enigmatic. Here, using autonomous samplers and sensors deployed at two mooring sites, we portray an annual cycle of microbial diversity, nutrient concentrations and physical oceanography in the major hydrographic regimes of the Fram Strait. The ice-free West Spitsbergen Current displayed a marked separation into a productive summer (dominated by diatoms and carbohydrate-degrading bacteria) and regenerative winter state (dominated by heterotrophic Syndiniales, radiolarians, chemoautotrophic bacteria, and archaea). The autumn post-bloom with maximal nutrient depletion featured Coscinodiscophyceae, Rhodobacteraceae (e.g. Amylibacter) and the SAR116 clade. Winter replenishment of nitrate, silicate and phosphate, linked to vertical mixing and a unique microbiome that included Magnetospiraceae and Dadabacteriales, fueled the following phytoplankton bloom. The spring-summer succession of Phaeocystis, Grammonema and Thalassiosira coincided with ephemeral peaks of Aurantivirga, Formosa, Polaribacter and NS lineages, indicating metabolic relationships. In the East Greenland Current, deeper sampling depth, ice cover and polar water masses concurred with weaker seasonality and a stronger heterotrophic signature. The ice-related winter microbiome comprised Bacillaria, Naviculales, Polarella, Chrysophyceae and Flavobacterium ASVs. Low ice cover and advection of Atlantic Water coincided with diminished abundances of chemoautotrophic bacteria while others such as Phaeocystis increased, suggesting that Atlantification alters microbiome structure and eventually the biological carbon pump. These insights promote the understanding of microbial seasonality and polar night ecology in the Arctic Ocean, a region severely affected by climate change.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Sinhué Torres-Valdés
- Marine BioGeoScience, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Ian Salter
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faroe Marine Research Institute, Tórshavn, Faroe Islands
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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14
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Mayerhofer MM, Eigemann F, Lackner C, Hoffmann J, Hellweger FL. Dynamic carbon flux network of a diverse marine microbial community. ISME COMMUNICATIONS 2021; 1:50. [PMID: 37938646 PMCID: PMC9723560 DOI: 10.1038/s43705-021-00055-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 08/19/2021] [Accepted: 09/10/2021] [Indexed: 11/09/2023]
Abstract
The functioning of microbial ecosystems has important consequences from global climate to human health, but quantitative mechanistic understanding remains elusive. The components of microbial ecosystems can now be observed at high resolution, but interactions still have to be inferred e.g., a time-series may show a bloom of bacteria X followed by virus Y suggesting they interact. Existing inference approaches are mostly empirical, like correlation networks, which are not mechanistically constrained and do not provide quantitative mass fluxes, and thus have limited utility. We developed an inference method, where a mechanistic model with hundreds of species and thousands of parameters is calibrated to time series data. The large scale, nonlinearity and feedbacks pose a challenging optimization problem, which is overcome using a novel procedure that mimics natural speciation or diversification e.g., stepwise increase of bacteria species. The method allows for curation using species-level information from e.g., physiological experiments or genome sequences. The product is a mass-balancing, mechanistically-constrained, quantitative representation of the ecosystem. We apply the method to characterize phytoplankton-heterotrophic bacteria interactions via dissolved organic matter in a marine system. The resulting model predicts quantitative fluxes for each interaction and time point (e.g., 0.16 µmolC/L/d of chrysolaminarin to Polaribacter on April 16, 2009). At the system level, the flux network shows a strong correlation between the abundance of bacteria species and their carbon flux during blooms, with copiotrophs being relatively more important than oligotrophs. However, oligotrophs, like SAR11, are unexpectedly high carbon processors for weeks into blooms, due to their higher biomass. The fraction of exudates (vs. grazing/death products) in the DOM pool decreases during blooms, and they are preferentially consumed by oligotrophs. In addition, functional similarity of phytoplankton i.e., what they produce, decouples their association with heterotrophs. The methodology is applicable to other microbial ecosystems, like human microbiome or wastewater treatment plants.
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Affiliation(s)
| | - Falk Eigemann
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - Carsten Lackner
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - Jutta Hoffmann
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - Ferdi L Hellweger
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany.
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15
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Ji Y, Zhang Z, Zhuang Y, Liao R, Zhou Z, Chen S. Molecular-level variation of dissolved organic matter and microbial structure of produced water during its early storage in Fuling shale gas field, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:38361-38373. [PMID: 33733405 DOI: 10.1007/s11356-021-13228-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Shale gas-produced water (PW), the waste fluid generated during gas production, contains a large number of organic contaminants and high salinity matrix. Previous studies generally focused on the end-of-pipe treatment of the PW and ignored the early collection process. In this study, the transformation of the molecular composition and microbial community structure of the PW in the transportation and storage process (i.e., from the gas-liquid separator to the storage tank) were investigated. As the PW was transported from the gas-liquid separator to the portable storage tank, the dissolved organic matter (DOM) showed greater saturation, less oxidation, and lower polarity. DOMs with high O/C and low H/C ratios (numbers of oxygen and hydrogen divided by numbers of carbon) were eliminated, which may be due to precipitation or adsorption by the solids suspended in the PW. The values of double-bond equivalent (DBE), DBE/C (DBE divided by the number of carbon), and aromatic index (AI) decreased, likely because of the microbial degradation of aromatic compounds. The PW in the gas-liquid separator presented a lower biodiversity than that in the storage tank. The microbial community in the storage tank showed the coexistence of anaerobes and aerobes. Genera related to biocorrosion and souring were detected in the two facilities, thus indicating the necessity of more efficient anticorrosion strategies. This study helps to enhance the understanding of the environmental behavior of PW during shale gas collection and provides a scientific reference for the design and formulation of efficient transportation and storage strategies to prevent and control the environmental risk of shale gas-derived PW.
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Affiliation(s)
- Yufei Ji
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoji Zhang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Yiling Zhuang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rugang Liao
- Sinopec Chongqing Fuling Shale Gas Exploration & Development Co. Ltd., Chongqing, 408014, China
| | - Zejun Zhou
- Sinopec Chongqing Fuling Shale Gas Exploration & Development Co. Ltd., Chongqing, 408014, China
| | - Shaohua Chen
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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16
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Lian J, Zheng X, Zhuo X, Chen YL, He C, Zheng Q, Lin TH, Sun J, Guo W, Shi Q, Jiao N, Cai R. Microbial transformation of distinct exogenous substrates into analogous composition of recalcitrant dissolved organic matter. Environ Microbiol 2021; 23:2389-2403. [PMID: 33559211 DOI: 10.1111/1462-2920.15426] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 01/24/2021] [Accepted: 02/04/2021] [Indexed: 01/02/2023]
Abstract
Oceanic dissolved organic matter (DOM) comprises a complex molecular mixture which is typically refractory and homogenous in the deep layers of the ocean. Though the refractory nature of deep-sea DOM is increasingly attributed to microbial metabolism, it remains unexplored whether ubiquitous microbial metabolism of distinct carbon substrates could lead to similar molecular composition of refractory DOM. Here, we conducted microbial incubation experiments using four typically bioavailable substrates (L-alanine, trehalose, sediment DOM extract, and diatom lysate) to investigate how exogenous substrates are transformed by a natural microbial assemblage. The results showed that although each-substrate-amendment induced different changes in the initial microbial assemblage and the amended substrates were almost depleted after 90 days of dark incubation, the bacterial community compositions became similar in all incubations on day 90. Correspondingly, revealed by ultra-high resolution mass spectrometry, molecular composition of DOM in all incubations became compositionally consistent with recalcitrant DOM and similar toward that of DOM from the deep-sea. These results indicate that while the composition of natural microbial communities can shift with substrate exposures, long-term microbial transformation of distinct substrates can ultimately lead to a similar refractory DOM composition. These findings provide an explanation for the homogeneous and refractory features of deep-sea DOM.
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Affiliation(s)
- Jie Lian
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, WE, 6708, Netherlands
| | - Xiaoxuan Zheng
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Xiaocun Zhuo
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Beijing, 102249, China
| | - Yi-Lung Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Beijing, 102249, China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361005, China
| | - Ta-Hui Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361005, China
| | - Weidong Guo
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Beijing, 102249, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361005, China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361005, China
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17
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Li X, Yao S, Bian Y, Jiang X, Song Y. The combination of biochar and plant roots improves soil bacterial adaptation to PAH stress: Insights from soil enzymes, microbiome, and metabolome. JOURNAL OF HAZARDOUS MATERIALS 2020; 400:123227. [PMID: 32585520 DOI: 10.1016/j.jhazmat.2020.123227] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 05/05/2023]
Abstract
Polycyclic aromatic hydrocarbon (PAH) contamination in agricultural soils poses serious stress to the soil microbiome. With the broad application of biochar, however, the co-effects of biochar and plant roots on the bacterial responses to PAH stress remain unclear. Here, the effects of biochar and the rhizosphere on bacterial community structure and functions were analyzed by coupling enzyme activity tests, high-throughput sequencing, and soil metabolomics. The contents of available nutrients and dissolved organic carbon, enzyme activities, and carbon metabolism functions were improved by biochar and plant roots. With the combined effects of biochar and plant roots, sucrose and starch metabolism was mainly impacted, and the soil metabolite diversity decreased. There was a strong co-occurrence network among soil properties, bacterial members, and metabolites in the biochar-amended and rhizosphere soils, favoring bacterial resistance to PAH stress, and consequently, PAH removal. In light of the above results, we suggest that biochar application can efficiently improve bacterial functions in rhizosphere soil, and our results facilitate the development of in situ remediation programs in soil contaminated with PAHs.
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Affiliation(s)
- Xiaona Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shi Yao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongrong Bian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China.
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18
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Goto S, Tada Y, Suzuki K, Yamashita Y. Evaluation of the Production of Dissolved Organic Matter by Three Marine Bacterial Strains. Front Microbiol 2020; 11:584419. [PMID: 33178167 PMCID: PMC7593260 DOI: 10.3389/fmicb.2020.584419] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 11/17/2022] Open
Abstract
A large part of marine dissolved organic matter (DOM) is considered to be recalcitrant DOM (RDOM) produced by marine bacteria. However, it is still unclear whether differences in bacterial species and/or physiology control the efficiency of RDOM production. Here, batch culture experiments with glucose as the sole carbon source were carried out using three model marine bacterial strains, namely, Alteromonas macleodii (Alt), Vibrio splendidus (Vib), and Phaeobacter gallaeciensis (Pha). Dissolved organic carbon (DOC) concentrations drastically decreased during the exponential growth phases of these bacteria due to the consumption of glucose. The efficiency of bacterial DOC production at the end of incubation was largely different among the strains and was higher for Vib (20%) than for the other two strains (Alt, 4%; Pha, 6%). All strains produced fluorescent DOM (FDOM), including humic-like FDOM which is considered as recalcitrant component in the ocean, even though the composition of bacterial FDOM was also different among the strains. The efficiency of humic-like FDOM production during the exponential growth phase was different among the bacterial strains; that is, Pha produced humic-like FDOM efficiently compared with the other two species. The efficiency of humic-like FDOM production with mineralization of organic matter was lower during the exponential growth phase than during the stationary phase of Alt and Pha. Four processes for the production of bacterially derived recalcitrant humic-like FDOM are suggested from this study: (1) production during active growing (in all strains), (2) production with the reutilization of bacterial DOM (Alt), (3) production with the consumption of cellular materials (Pha), and (4) release from lysis (Vib). Our results suggest that bacterial species and physiology can regulate RDOM production and accumulation in the ocean.
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Affiliation(s)
- Shuji Goto
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Yuya Tada
- National Institute for Minamata Disease, Minamata, Japan
| | - Koji Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan.,Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Youhei Yamashita
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan.,Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
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19
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Carter-Gates M, Balestreri C, Thorpe SE, Cottier F, Baylay A, Bibby TS, Moore CM, Schroeder DC. Implications of increasing Atlantic influence for Arctic microbial community structure. Sci Rep 2020; 10:19262. [PMID: 33159130 PMCID: PMC7648788 DOI: 10.1038/s41598-020-76293-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Increasing influence of Atlantic water in the Arctic Ocean has the potential to significantly impact regional water temperature and salinity. Here we use a rDNA barcoding approach to reveal how microbial communities are partitioned into distinct assemblages across a gradient of Atlantic-Polar Water influence in the Norwegian Sea. Data suggest that temperate adapted bacteria may replace cold water taxa under a future scenario of increasing Atlantic influence, but the eukaryote response is more complex. Some abundant eukaryotic cold water taxa could persist, while less abundant eukaryotic taxa may be replaced by warmer adapted temperate species. Furthermore, within lineages, different taxa display evidence of increased relative abundance in reaction to favourable conditions and we observed that rare microbial taxa are sample site rather than region specific. Our findings have significant implications for the vulnerability of polar associated community assemblages, which may change, impacting the ecosystem services they provide, under predicted increases of Atlantic mixing and warming within the Arctic region.
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Affiliation(s)
- Michael Carter-Gates
- Cellular and Molecular Department, The Marine Biological Association of the UK, Plymouth, PL1 2PB, UK
| | - Cecilia Balestreri
- Cellular and Molecular Department, The Marine Biological Association of the UK, Plymouth, PL1 2PB, UK
| | | | - Finlo Cottier
- Scottish Association for Marine Science, Oban, PA37 1QA, Argyll, UK.,Department of Arctic and Marine Biology, University of Tromsø - The Arctic University of Norway, 9037, Tromsø, Norway
| | - Alison Baylay
- Ocean and Earth Sciences, University of Southampton, Southampton, SO14 3ZH, UK
| | - Thomas S Bibby
- Ocean and Earth Sciences, University of Southampton, Southampton, SO14 3ZH, UK
| | - C Mark Moore
- Ocean and Earth Sciences, University of Southampton, Southampton, SO14 3ZH, UK
| | - Declan C Schroeder
- Cellular and Molecular Department, The Marine Biological Association of the UK, Plymouth, PL1 2PB, UK. .,Veterinary Population Medicine, The University of Minnesota, St Paul, MN, 55108, USA. .,School of Biological Sciences, University of Reading, Reading, RG6 6AH, UK.
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20
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Dang H. Grand Challenges in Microbe-Driven Marine Carbon Cycling Research. Front Microbiol 2020; 11:1039. [PMID: 32655507 PMCID: PMC7324536 DOI: 10.3389/fmicb.2020.01039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/27/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Frontiers Science Center for Ocean Carbon Sink and Climate Change, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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21
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Käse L, Kraberg AC, Metfies K, Neuhaus S, Sprong PAA, Fuchs BM, Boersma M, Wiltshire KH. Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea. JOURNAL OF PLANKTON RESEARCH 2020; 42:305-319. [PMID: 32494090 PMCID: PMC7252501 DOI: 10.1093/plankt/fbaa017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 05/22/2023]
Abstract
The dynamics of diatoms and dinoflagellates have been monitored for many decades at the Helgoland Roads Long-Term Ecological Research site and are relatively well understood. In contrast, small-sized eukaryotic microbes and their community changes are still much more elusive, mainly due to their small size and uniform morphology, which makes them difficult to identify microscopically. By using next-generation sequencing, we wanted to shed light on the Helgoland planktonic community dynamics, including nano- and picoplankton, during a spring bloom. We took samples from March to May 2016 and sequenced the V4 region of the 18S rDNA. Our results showed that mixotrophic and heterotrophic taxa were more abundant than autotrophic diatoms. Dinoflagellates dominated the sequence assemblage, and several small-sized eukaryotic microbes like Haptophyta, Choanoflagellata, Marine Stramenopiles and Syndiniales were identified. A diverse background community including taxa from all size classes was present during the whole sampling period. Five phases with several communities were distinguished. The fastest changes in community composition took place in phase 3, while the communities from phases 1 to 5 were more similar to each other despite contrasting environmental conditions. Synergy effects of next-generation sequencing and traditional methods may be exploited in future long-term observations.
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Affiliation(s)
- Laura Käse
- ALFRED-WEGENER-INSTITUT, HELMHOLTZ-ZENTRUM FüR POLAR- UND MEERESFORSCHUNG, BIOLOGISCHE ANSTALT HELGOLAND, 27498 HELGOLAND, Germany
- CORRESPONDING AUTHOR:
| | - Alexandra C Kraberg
- ALFRED-WEGENER-INSTITUT, HELMHOLTZ-ZENTRUM FüR POLAR- UND MEERESFORSCHUNG, 27570 BREMERHAVEN, Germany
| | - Katja Metfies
- ALFRED-WEGENER-INSTITUT, HELMHOLTZ-ZENTRUM FüR POLAR- UND MEERESFORSCHUNG, 27570 BREMERHAVEN, Germany
- HELMHOLTZ-INSTITUT FüR FUNKTIONELLE MARINE BIODIVERSITäT, 26129 OLDENBURG, Germany
| | - Stefan Neuhaus
- ALFRED-WEGENER-INSTITUT, HELMHOLTZ-ZENTRUM FüR POLAR- UND MEERESFORSCHUNG, 27570 BREMERHAVEN, Germany
| | - Pim A A Sprong
- ALFRED-WEGENER-INSTITUT, HELMHOLTZ-ZENTRUM FüR POLAR- UND MEERESFORSCHUNG, 27570 BREMERHAVEN, Germany
| | - Bernhard M Fuchs
- DEPARTMENT OF MOLECULAR ECOLOGY, MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY, 28359 BREMEN, Germany
| | - Maarten Boersma
- ALFRED-WEGENER-INSTITUT, HELMHOLTZ-ZENTRUM FüR POLAR- UND MEERESFORSCHUNG, BIOLOGISCHE ANSTALT HELGOLAND, 27498 HELGOLAND, Germany
- UNIVERSITY OF BREMEN, 28359 BREMEN, Germany
| | - Karen H Wiltshire
- ALFRED-WEGENER-INSTITUT, HELMHOLTZ-ZENTRUM FüR POLAR- UND MEERESFORSCHUNG, BIOLOGISCHE ANSTALT HELGOLAND, 27498 HELGOLAND, Germany
- ALFRED-WEGENER-INSTITUT, HELMHOLTZ-ZENTRUM FüR POLAR- UND MEERESFORSCHUNG, WADDEN SEA STATION, 25992 LIST AUF SYLT, Germany
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22
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Ávila MP, Brandão LPM, Brighenti LS, Tonetta D, Reis MP, Stæhr PA, Asmala E, Amado AM, Barbosa FAR, Bezerra-Neto JF, Nascimento AMA. Linking shifts in bacterial community with changes in dissolved organic matter pool in a tropical lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:990-1003. [PMID: 30981171 DOI: 10.1016/j.scitotenv.2019.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/15/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Bacterioplankton communities have a pivotal role in the global carbon cycle. Still the interaction between microbial community and dissolved organic matter (DOM) in freshwater ecosystems remains poorly understood. Here, we report results from a 12-day mesocosm study performed in the epilimnion of a tropical lake, in which inorganic nutrients and allochthonous DOM were supplemented under full light and shading. Although the production of autochthonous DOM triggered by nutrient addition was the dominant driver of changes in bacterial community structure, temporal covariations between DOM optical proxies and bacterial community structure revealed a strong influence of community shifts on DOM fate. Community shifts were coupled to a successional stepwise alteration of the DOM pool, with different fractions being selectively consumed by specific taxa. Typical freshwater clades as Limnohabitans and Sporichthyaceae were associated with consumption of low molecular weight carbon, whereas Gammaproteobacteria and Flavobacteria utilized higher molecular weight carbon, indicating differences in DOM preference among clades. Importantly, Verrucomicrobiaceae were important in the turnover of freshly produced autochthonous DOM, ultimately affecting light availability and dissolved organic carbon concentrations. Our findings suggest that taxonomically defined bacterial assemblages play definite roles when influencing DOM fate, either by changing specific fractions of the DOM pool or by regulating light availability and DOC levels.
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Affiliation(s)
- Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Luciana P M Brandão
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ludmila S Brighenti
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Denise Tonetta
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
| | - Peter A Stæhr
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, Box 358, 4000 Roskilde, Denmark
| | - Eero Asmala
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, Box 358, 4000 Roskilde, Denmark; Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, 10900 Hanko, Finland
| | - André M Amado
- Limnology Laboratory, Department of Oceanography and Limnology, Universidade Federal do Rio Grande do Norte, Rio Grande do Norte, Brazil
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - José F Bezerra-Neto
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
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23
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Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: coupling of bacterial diversity and DOM chemodiversity. ISME JOURNAL 2019; 13:2551-2565. [PMID: 31227815 DOI: 10.1038/s41396-019-0449-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/27/2019] [Accepted: 05/03/2019] [Indexed: 02/01/2023]
Abstract
Picocyanobacteria make up half of the ocean's primary production, and they are subjected to frequent viral infection. Viral lysis of picocyanobacteria is a major driving force converting biologically fixed carbon into dissolved organic carbon (DOC). Viral-induced dissolved organic matter (vDOM) released from picocyanobacteria provides complex organic matter to bacterioplankton in the marine ecosystem. In order to understand how picocyanobacterial vDOM are transformed by bacteria and the impact of this process on bacterial community structure, viral lysate of picocyanobacteria was incubated with coastal seawater for 90 days. The transformation of vDOM was analyzed by ultrahigh-resolution mass spectrometry and the shift of bacterial populations analyzed using high-throughput sequencing technology. Addition of picocyanobacterial vDOM introduced abundant nitrogen components into the coastal water, which were largely degraded during the 90 days' incubation period. However, some DOM signatures were accumulated and the total assigned formulae number increased over time. In contrast to the control (no addition of vDOM), bacterial community enriched with vDOM changed markedly with increased biodiversity indices. The network analysis showed that key bacterial species formed complex relationship with vDOM components, suggesting the potential correspondence between bacterial populations and DOM molecules. We demonstrate that coastal bacterioplankton are able to quickly utilize and transform lysis products of picocyanobacteria, meanwhile, bacterial community varies with changing chemodiverisity of DOM. vDOM released from picocyanobacteria generated a complex labile DOM pool, which was converted to a rather stable DOM pool after microbial processing in the time frame of days to weeks.
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24
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Zhang B, Shan C, Hao Z, Liu J, Wu B, Pan B. Transformation of dissolved organic matter during full-scale treatment of integrated chemical wastewater: Molecular composition correlated with spectral indexes and acute toxicity. WATER RESEARCH 2019; 157:472-482. [PMID: 30981978 DOI: 10.1016/j.watres.2019.04.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/14/2019] [Accepted: 04/02/2019] [Indexed: 05/21/2023]
Abstract
As one of the key economic modes in China, chemical industry park (CIP) has made great contribution to the Chinese rapid economic growth. Concomitantly, how to effectively and safely dispose of the CIP wastewater (CIPWW) has been an unavoidable issue. Molecular transformation of dissolved organic matter (DOM) in CIPWW treatment is essential to optimize the employed process and to provide solid basis for risk evaluation of the discharged effluent as well. In this study, electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) was used to characterize the molecular transformation of DOM during full-scale treatment of integrated chemical wastewater in a centralized wastewater treatment plant (CWWTP), where the combined process follows hydrolysis/acidification (HA)-flocculation/precipitation (FP)-A2/O-membrane bioreactor (MBR)-ultrafiltration (UF)-reverse osmosis (RO). Compared to municipal wastewater, DOM in CIPWW exhibited higher unsaturation degree, lower molecular weight, and higher toxicity. In FP unit, DOM of C<24 and higher nominal oxidation state of carbon (NOSC) values was preferentially removed. The HA and anaerobic units are capable of significantly degrading DOM, resulting in great changes in molecular composition of DOM. However, the anoxic, oxic, and MBR units only lead to a slight change of the molecular formulae. The terminal units of UF and RO can remove most DOM, with the concentration of dissolved organic carbon (DOC) declining by 19.2% and 94.6% respectively. The correlation between spectral indexes and acute toxicity with the molecular formulae of DOM suggested that polyphenols and highly unsaturated phenols were positively correlated with the specific UV absorbance at 254 nm (SUVA254). In addition, both compounds (0.32 < O/C < 0.63) as well as the aliphatic ones (0.22 < O/C < 0.56) presented positive correlation with acute toxicity. Further, the pairwise correlation analysis illustrated that SUVA254, O/Cwa, double bond equivalence (DBEwa), and NOSCwa were positively correlated with each other, whereas the acute toxicity was positively correlated with humification index (HIX), O/Cwa, and DBEwa.
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Affiliation(s)
- Bingliang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Chao Shan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Research Center for Environmental Nanotechnology (ReCENT), Nanjing University, Nanjing 210023, China
| | - Zhineng Hao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Jingfu Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Bingcai Pan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Research Center for Environmental Nanotechnology (ReCENT), Nanjing University, Nanjing 210023, China.
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25
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Li XM, Chen QL, He C, Shi Q, Chen SC, Reid BJ, Zhu YG, Sun GX. Organic Carbon Amendments Affect the Chemodiversity of Soil Dissolved Organic Matter and Its Associations with Soil Microbial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:50-59. [PMID: 30485747 DOI: 10.1021/acs.est.8b04673] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The "4 per mil" initiative recognizes the pivotal role of soil in carbon resequestration. The need for evidence to substantiate the influence of agricultural practices on chemical nature of soil carbon and microbial biodiversity has become a priority. However, owing to the molecular complexity of soil dissolved organic matter (DOM), specific linkages to microbial biodiversity have eluded researchers. Here, we characterized the chemodiversity of soil DOM, assessed the variation of soil bacterial community composition (BCC), and identified specific linkages between DOM traits and BCC. Sustained organic carbon amendment significantly ( P < 0.05) increased total organic matter reservoirs, resulted in higher chemodiversity of DOM and emergence of recalcitrant moieties (H/C < 1.5). In the meantime, sustained organic carbon amendment shaped the BCC to a more eutrophic state while long-term chemical fertilization directed the BCC toward an oligotrophic state. Meanwhile, higher connectivity and complexity were observed in organic carbon amendment by DOM-BCC network analysis, indicating that soil microbes tended to have more interaction with DOM molecules after organic matter inputs. These results highlight the potential for organic carbon amendments to not only build soil carbon stocks and increase their resilience but also mediate the functional state of soil bacterial communities.
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Affiliation(s)
- Xiao-Ming Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Shuangqing Road, No. 18 , Haidian District, Beijing 100085 , People's Republic of China
- University of Chinese Academy of Sciences , Yuquan Road, No. 19A , Shijingshan District, Beijing 100049 , People's Republic of China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Jimei Road, No. 1799 , Jimei District, Xiamen 361021 , People's Republic of China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing , China University of Petroleum , 18 Fuxue Road , Changping, Beijing 102249 , China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing , China University of Petroleum , 18 Fuxue Road , Changping, Beijing 102249 , China
| | - Song-Can Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Shuangqing Road, No. 18 , Haidian District, Beijing 100085 , People's Republic of China
- University of Chinese Academy of Sciences , Yuquan Road, No. 19A , Shijingshan District, Beijing 100049 , People's Republic of China
| | - Brian J Reid
- School of Environmental Sciences , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Jimei Road, No. 1799 , Jimei District, Xiamen 361021 , People's Republic of China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Shuangqing Road, No. 18 , Haidian District, Beijing 100085 , People's Republic of China
- University of Chinese Academy of Sciences , Yuquan Road, No. 19A , Shijingshan District, Beijing 100049 , People's Republic of China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Jimei Road, No. 1799 , Jimei District, Xiamen 361021 , People's Republic of China
| | - Guo-Xin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Shuangqing Road, No. 18 , Haidian District, Beijing 100085 , People's Republic of China
- University of Chinese Academy of Sciences , Yuquan Road, No. 19A , Shijingshan District, Beijing 100049 , People's Republic of China
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26
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Li XM, Sun GX, Chen SC, Fang Z, Yuan HY, Shi Q, Zhu YG. Molecular Chemodiversity of Dissolved Organic Matter in Paddy Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:963-971. [PMID: 29301078 DOI: 10.1021/acs.est.7b00377] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Organic matter (OM), and dissolved organic matter (DOM), have a major influence upon biogeochemical processes; most significantly, the carbon cycle. To date, very few studies have examined the spatial heterogeneity of DOM in paddy soils. Thus, very little is known about the DOM molecular profiles and the key environmental factors that underpin DOM molecular chemodiversity in paddy soils. Here, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry was applied to unambiguously resolve 11 361 molecular formulas in 16 paddy soils; thereby elucidating the molecular characteristics of paddy soil DOM. Soil pH, iron complexing index (Fep/FeR) and C/N ratio were established to be key factors controlling DOM profiles. Polycyclic aromatics (derived from combustion) and polyphenols (derived from plants) increased with increasing pH, while polyphenols molecules, pyrogenic aromatics, and carboxylic compounds decreased with increasing iron complexing index. Patterns in molecular profiles indicated DOM in paddy soils to become more recalcitrant at higher soil C/N ratio and higher pH. Furthermore, plant-derived polyphenols and pyrogenic DOM were retained favorably by iron and the chemodiversity of DOM in paddy soil increased with increasing soil C/N ratios. This study provides critical information about DOM characteristics at a molecular level and will inform better global management of soil carbon in paddy soil ecosystems.
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Affiliation(s)
- Xiao-Ming Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Shuangqing Road, No. 18, Haidian District, Beijing 100085, People's Republic of China
- University of Chinese Academy of Sciences , Yuquan Road, No. 19A, Shijingshan District, Beijing 100049, People's Republic of China
| | - Guo-Xin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Shuangqing Road, No. 18, Haidian District, Beijing 100085, People's Republic of China
| | - Song-Can Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Shuangqing Road, No. 18, Haidian District, Beijing 100085, People's Republic of China
- University of Chinese Academy of Sciences , Yuquan Road, No. 19A, Shijingshan District, Beijing 100049, People's Republic of China
| | - Zhi Fang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum , 18 Fuxue Road, Changping, Beijing 102249, China
| | - Hai-Yan Yuan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Shuangqing Road, No. 18, Haidian District, Beijing 100085, People's Republic of China
- University of Chinese Academy of Sciences , Yuquan Road, No. 19A, Shijingshan District, Beijing 100049, People's Republic of China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum , 18 Fuxue Road, Changping, Beijing 102249, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Shuangqing Road, No. 18, Haidian District, Beijing 100085, People's Republic of China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Jimei Road, No. 1799, Jimei District, Xiamen 361021, People's Republic of China
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27
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Chafee M, Fernàndez-Guerra A, Buttigieg PL, Gerdts G, Eren AM, Teeling H, Amann RI. Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME JOURNAL 2017; 12:237-252. [PMID: 29064479 PMCID: PMC5739018 DOI: 10.1038/ismej.2017.165] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 08/18/2017] [Accepted: 09/04/2017] [Indexed: 12/25/2022]
Abstract
Temperate coastal marine environments are replete with complex biotic and abiotic interactions that are amplified during spring and summer phytoplankton blooms. During these events, heterotrophic bacterioplankton respond to successional releases of dissolved organic matter as algal cells are lysed. Annual seasonal shifts in the community composition of free-living bacterioplankton follow broadly predictable patterns, but whether similar communities respond each year to bloom disturbance events remains unknown owing to a lack of data sets, employing high-frequency sampling over multiple years. We capture the fine-scale microdiversity of these events with weekly sampling using a high-resolution method to discriminate 16S ribosomal RNA gene amplicons that are >99% identical. Furthermore, we used 2 complete years of data to facilitate identification of recurrent sub-networks of co-varying microbes. We demonstrate that despite inter-annual variation in phytoplankton blooms and despite the dynamism of a coastal–oceanic transition zone, patterns of microdiversity are recurrent during both bloom and non-bloom conditions. Sub-networks of co-occurring microbes identified reveal that correlation structures between community members appear quite stable in a seasonally driven response to oligotrophic and eutrophic conditions.
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Affiliation(s)
- Meghan Chafee
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antonio Fernàndez-Guerra
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Jacobs University Bremen gGmbH, Bremen, Germany.,University of Oxford, Oxford e-Research Centre, Oxford, UK
| | - Pier Luigi Buttigieg
- HGF-MPG Bridge-Group for Deep Sea Ecology and Technology, Alfred-Wegener Institute, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Gunnar Gerdts
- Alfred-Wegener Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - A Murat Eren
- University of Chicago, Department of Medicine, Knapp Center for Biomedical Discovery, Chicago, IL, USA.,Marine Biological Laboratory, Woods Hole, MA, USA
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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28
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Hengy MH, Horton DJ, Uzarski DG, Learman DR. Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI. PeerJ 2017; 5:e3937. [PMID: 29062609 PMCID: PMC5647861 DOI: 10.7717/peerj.3937] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/26/2017] [Indexed: 11/20/2022] Open
Abstract
Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island.
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Affiliation(s)
- Miranda H Hengy
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, United States of America
| | - Dean J Horton
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, United States of America
| | - Donald G Uzarski
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, United States of America
| | - Deric R Learman
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, United States of America
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Li Y, Harir M, Uhl J, Kanawati B, Lucio M, Smirnov KS, Koch BP, Schmitt-Kopplin P, Hertkorn N. How representative are dissolved organic matter (DOM) extracts? A comprehensive study of sorbent selectivity for DOM isolation. WATER RESEARCH 2017; 116:316-323. [PMID: 28359043 DOI: 10.1016/j.watres.2017.03.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 06/07/2023]
Abstract
Solid phase extraction (SPE) has become a widespread method for isolating dissolved organic matter (DOM) of diverse origin such as fresh and marine waters. This study investigated the DOM extraction selectivity of 24 commercially available SPE sorbents under identical conditions (pH = 2, methanol elution) on the example of Suwannee River (SR) water and North Sea (NS) water by using DOC analysis and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Proton nuclear magnetic resonance (1H NMR) spectroscopy was employed to assess leaching behavior, and HLB sorbent was found to leach substantially, among others. Variable DOC recoveries observed for SR DOM and NS DOM were primarily caused by the respective molecular composition, with subordinated and heterogeneous contributions of relative salinity. Scatter of average H/C and O/C elemental ratios and gross alignment in mass-edited H/C ratios according to five established coarse SPE characteristics was near identical for SR DOM and NS DOM. FTMS-based principal component analysis (PCA) provided essentially analogous alignment of SR DOM and NS DOM molecular compositions according to the five established groups of SPE classification, and corroborated the sorption-mechanism-based selectivity of DOM extraction in both cases. Evaluation of structural blanks and leaching of SPE cartridges requires NMR spectroscopy because FT-ICR mass spectrometry alone will not reveal inconspicuous displacements of continual bulk signatures caused by leaching of SPE resin constituents.
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Affiliation(s)
- Yan Li
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Mourad Harir
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technische Universität München, 85354 Freising, Germany
| | - Jenny Uhl
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Basem Kanawati
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Marianna Lucio
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Kirill S Smirnov
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Boris P Koch
- Alfred-Wegener-Institut, Helmholtz Zentrum für Polar- und Meeresforschung, Ecological Chemistry, Am Handelshafen 12, 27570 Bremerhaven, Germany; Hochschule Bremerhaven, University of Applied Sciences, An der Karlstadt 8, 27568 Bremerhaven, Germany
| | - Philippe Schmitt-Kopplin
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technische Universität München, 85354 Freising, Germany
| | - Norbert Hertkorn
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.
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