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Jiao N, Luo T, Chen Q, Zhao Z, Xiao X, Liu J, Jian Z, Xie S, Thomas H, Herndl GJ, Benner R, Gonsior M, Chen F, Cai WJ, Robinson C. The microbial carbon pump and climate change. Nat Rev Microbiol 2024; 22:408-419. [PMID: 38491185 DOI: 10.1038/s41579-024-01018-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 03/18/2024]
Abstract
The ocean has been a regulator of climate change throughout the history of Earth. One key mechanism is the mediation of the carbon reservoir by refractory dissolved organic carbon (RDOC), which can either be stored in the water column for centuries or released back into the atmosphere as CO2 depending on the conditions. The RDOC is produced through a myriad of microbial metabolic and ecological processes known as the microbial carbon pump (MCP). Here, we review recent research advances in processes related to the MCP, including the distribution patterns and molecular composition of RDOC, links between the complexity of RDOC compounds and microbial diversity, MCP-driven carbon cycles across time and space, and responses of the MCP to a changing climate. We identify knowledge gaps and future research directions in the role of the MCP, particularly as a key component in integrated approaches combining the mechanisms of the biological and abiotic carbon pumps for ocean negative carbon emissions.
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Affiliation(s)
- Nianzhi Jiao
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China.
| | - Tingwei Luo
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Quanrui Chen
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Zhao Zhao
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Xilin Xiao
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Jihua Liu
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Zhimin Jian
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Shucheng Xie
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Helmuth Thomas
- Institute of Carbon Cycles, Helmholtz-Zentrum Hereon, Geesthacht, Germany
- Institut für Chemie und Biologie des Meeres (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Ronald Benner
- Department of Biological Sciences, School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC, USA
| | - Micheal Gonsior
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD, USA
| | - Feng Chen
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Wei-Jun Cai
- School of Marine Science and Policy, University of Delaware, Newark, DE, USA
| | - Carol Robinson
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China.
- Centre for Ocean and Atmospheric Sciences (COAS), School of Environmental Sciences, University of East Anglia, Norwich, UK.
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Zhou C, Gao Q, Tigabu M, Wang S, Cao S, Yu Y. Continuous planting of Chinese fir monocultures significantly influences dissolved organic matter content and microbial assembly processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171943. [PMID: 38527546 DOI: 10.1016/j.scitotenv.2024.171943] [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: 12/04/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024]
Abstract
Monoculture plantations in China, characterized by the continuous cultivation of a single species, pose challenges to timber accumulation and understory biodiversity, raising concerns about sustainability. This study investigated the impact of continuous monoculture plantings of Chinese fir (Cunninghamia lanceolata [Lamb.] Hook.) on soil properties, dissolved organic matter (DOM), and microorganisms over multiple generations. Soil samples from first to fourth-generation plantations were analyzed for basic chemical properties, DOM composition using Fourier transform ion cyclotron resonance mass spectrometry, and microorganisms via high-throughput sequencing. Results revealed a significant decline in nitrate nitrogen content with successive rotations, accompanied by an increase in easily degradable compounds like carbohydrates, aliphatic/proteins, tannins, Carbon, Hydrogen, Oxygen and Nitrogen- (CHON) and Carbon, Hydrogen, Oxygen and Sulfur- (CHOS) containing compounds. However, the recalcitrant compounds, such as lignin and carboxyl-rich alicyclic molecules (CRAMs), condensed aromatics and Carbon, Hydrogen and Oxygen- (CHO) containing compounds decreased. Microorganism diversity, abundance, and structure decreased with successive plantations, affecting the ecological niche breadth of fungal communities. Bacterial communities were strongly influenced by DOM composition, particularly lignin/CRAMs and tannins. Continuous monoculture led to reduced soil nitrate, lignin/CRAMs, and compromised soil quality, altering chemical properties and DOM composition, influencing microbial community assembly. This shift increased easily degraded DOM, accelerating soil carbon and nitrogen cycling, ultimately reducing soil carbon sequestration. From environmental point of view, the study emphasizes the importance of sustainable soil management practices in continuous monoculture systems. Particularly the findings offer valuable insights for addressing challenges associated with monoculture plantations and promoting long-term ecological sustainability.
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Affiliation(s)
- Chuifan Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Qianian Gao
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mulualem Tigabu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuzhen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Sheng Cao
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanchun Yu
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
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Wu C, Zhao Y, Geng Y, Shi K, Zhou S. Characterizing the regional distribution, interaction with microorganisms, and sources of dissolved organic matter for summer rainfall: Insights from spectroscopy, community structure, and back-trajectory analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172086. [PMID: 38556025 DOI: 10.1016/j.scitotenv.2024.172086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Dissolved organic matter (DOM) in rainfall participates in many biogeochemical cycles in aquatic environments and affects biological activities in water bodies. Revealing the characteristics of rainfall DOM could broaden our understanding of the carbon cycle. Therefore, the distribution characteristics and response mechanisms of DOM to microorganisms were investigated in different regions of Hebei. The results indicated that the water quality of the northern region was worse than that of the middle and southern regions. The two protein like components (C1, C2) and one humic like component (C3) were obtained; at high molecular weight (MW), the fluorescence intensity is high in the northern region (0.03 ± 0.02 R.U.), while at low MW, the fluorescence intensity is highest in the southern region (0.50 ± 0.18 R.U.). Furthermore, C2 is significantly positively correlated with C1 (P < 0.01), while C2 is significantly negatively correlated with C3 (P < 0.05) was observed. The spectral index results indicated that rainfall DOM exhibited low humification and highly autochthonous characteristics. The southern region obtained higher richness and diversity of microbial species than northern region (P < 0.05). The community exhibits significant spatiotemporal differences, and the Acinetobacter, Enterobacter, and Massilia, were dominant genus. Redundancy and network analyses showed that the effects of C1, C2, and nitrate on microorganisms increased with decreasing MW, while low MW exhibited a more complex network between DOM and microorganisms than high MW. Meanwhile, C1, C2 had a large total effect on β-diversity and function through structural equation modeling. The backward trajectory model indicates that the sources of air masses are from the northwest, local area, and sea in the northern, middle, and southern regions, respectively. This study broadened the understanding of the composition of summer rainfall DOM and its interactions with microorganisms during rainfall.
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Affiliation(s)
- Chenbin Wu
- Pollution Prevention Biotechnology Laboratory of Hebei Province, School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, PR China
| | - Yuting Zhao
- Pollution Prevention Biotechnology Laboratory of Hebei Province, School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, PR China
| | - Yuting Geng
- Pollution Prevention Biotechnology Laboratory of Hebei Province, School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, PR China
| | - Kun Shi
- School of Civil Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, PR China
| | - Shilei Zhou
- Pollution Prevention Biotechnology Laboratory of Hebei Province, School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, PR China; School of Civil Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, PR China.
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Shi W, Lin K, Zhao Y, Li Z, Zhou T. Toward a comprehensive understanding of alicyclic compounds: Bio-effects perspective and deep learning approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168927. [PMID: 38042202 DOI: 10.1016/j.scitotenv.2023.168927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/17/2023] [Accepted: 11/25/2023] [Indexed: 12/04/2023]
Abstract
The escalating use of alicyclic compounds in modern industrial production has led to a rapid increase of these substances in the environment, posing significant health hazards. Addressing this challenge necessitates a comprehensive understanding of these compounds, which can be achieved through the deep learning approach. Graph neural networks (GNN) known for its' extraordinary ability to process graph data with rich relationships, have been employed in various molecular prediction tasks. In this study, alicyclic molecules screened from PCBA, Toxcast and Tox21 are made as general bioactivity and biological targets' activity prediction datasets. GNN-based models are trained on the two datasets, while the Attentive FP and PAGTN achieve best performance individually. In addition, alicyclic carbon atoms make the greatest contribution to biological activity, which indicate that the alicycle structures have significant impact on the carbon atoms' contribution. Moreover, there are terrific number of active molecules in other public datasets, indicates that alicyclic compounds deserve more attention in POPs control. This study uncovered deeper structural-activity relationships within these compounds, offering new perspectives and methodologies for academic research in the field.
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Affiliation(s)
- Wenjie Shi
- The State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Kunsen Lin
- The State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Youcai Zhao
- The State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, 1515 North Zhongshan Rd. (No. 2), Shanghai 200092, PR China
| | - Zongsheng Li
- The State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Tao Zhou
- The State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, 1515 North Zhongshan Rd. (No. 2), Shanghai 200092, PR China.
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Liu S, Hu R, Strong PJ, Saleem M, Zhou Z, Luo Z, Wu Y, He Z, Wang C. Vertical connectivity of microbiome and metabolome reveals depth-dependent variations across a deep cold-seep water column. ENVIRONMENTAL RESEARCH 2023; 239:117310. [PMID: 37805181 DOI: 10.1016/j.envres.2023.117310] [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: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Deciphering the vertical connectivity of oceanic microbiome and metabolome is crucial for understanding the carbon sequestration and achieving the carbon neutrality. However, we lack a systematic view of the interplay among particle transport, microbial community, and metabolic trait across depths. Through integrating the biogeochemical, microbial, and metabolic characteristics of a deep cold-seep water column (∼1989 m), we find the altered connectivity of microbial community and dissolved organic matter (DOM) across depths. Both the microbial communities (bacteria and protists) and DOM show a clear compositional connectivity from surface to the depth of 1000 m, highlighting the controls of sinking particle over microbial connectivity from the epipelagic to mesopelagic zone. However, due to the biological migration and ocean mixing, the fecal-associated bacteria and protistan consumers unexpectedly emerge and the degradation index of DOM substantially alters around 1000-1200 m. Collectively, we unveil the significance of multi-faceted particle dispersion, which supports the connectivity and variability of deep ocean microbial communities.
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Affiliation(s)
- Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - P J Strong
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Yongjie Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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Xu H, Xiao Q, Dai Y, Chen D, Zhang C, Jiang Y, Xie J. Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data. MICROBIAL ECOLOGY 2023; 86:3043-3056. [PMID: 37831075 DOI: 10.1007/s00248-023-02307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.
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Affiliation(s)
- Hongxiang Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qiong Xiao
- Institute of Karst Geology, CAGS, Key Laboratory on Karst Dynamics, MNR & Guangxi, Guilin, 541004, China
| | - Yongdong Dai
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Dexin Chen
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Cheng Zhang
- Institute of Karst Geology, CAGS, Key Laboratory on Karst Dynamics, MNR & Guangxi, Guilin, 541004, China.
| | - Yongjun Jiang
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing, 400715, China.
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China.
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing, 400715, China.
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Chen X, Cai R, Zhuo X, Chen Q, He C, Sun J, Zhang Y, Zheng Q, Shi Q, Jiao N. Niche differentiation of microbial community shapes vertical distribution of recalcitrant dissolved organic matter in deep-sea sediments. ENVIRONMENT INTERNATIONAL 2023; 178:108080. [PMID: 37429058 DOI: 10.1016/j.envint.2023.108080] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023]
Abstract
Sedimentary organic matter provides carbon substrates and energy sources for microorganisms, which drive benthic biogeochemical processes and in turn modify the quantity and quality of dissolved organic matter (DOM). However, the molecular composition and distribution of DOM and its interactions with microbes in deep-sea sediments remain poorly understood. Here, molecular composition of DOM and its relationship with microbes were analyzed in samples collected from two sediment cores (∼40 cm below the sea floor), at depths of 1157 and 2253 m from the South China Sea. Results show that niche differentiation was observed on a fine scale in different sediment layers, with Proteobacteria and Nitrososphaeria dominating the shallow sediments (0-6 cm) and Chloroflexi and Bathyarchaeia prevailing in deeper sediments (6-40 cm), indicating correspondence of microbial community composition with both geographical isolation and the availability of organic matter. An intimate link between the DOM composition and microbial community further indicates that, microbial mineralization of fresh organic matter in the shallow layer potentially resulted in the accumulation of recalcitrant DOM (RDOM), while relatively low abundance of RDOM was linked to anaerobic microbial utilization in deeper sediment layers. In addition, higher RDOM abundance in the overlying water, as compared to that in the surface sediment, suggests that sediment might be a source of deep-sea RDOM. These results emphasize the close relation between the distribution of sediment DOM and different microbial community, laying a foundation for understanding the complex dynamics of RDOM in deep-sea sediment and water column.
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Affiliation(s)
- Xiaoxia Chen
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Ruanhong Cai
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China.
| | - Xiaocun Zhuo
- State Key Laboratory of Heavy Oil Processing, Research Centre for Geomicrobial Resources and Application, China University of Petroleum, Beijing 102249, China
| | - Quanrui Chen
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, Research Centre for Geomicrobial Resources and Application, China University of Petroleum, Beijing 102249, China
| | - Jia Sun
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Qiang Zheng
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, Research Centre for Geomicrobial Resources and Application, China University of Petroleum, Beijing 102249, China
| | - Nianzhi Jiao
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China; Carbon Neutral Innovation Research Center, Xiamen University, Xiamen 361005, China.
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Nathani NM, Mootapally C, Sharma P, Solomon S, Kumar R, Fulke AB, Kumar M. Microbial machinery dealing diverse aromatic compounds: Decoded from pelagic sediment ecogenomics in the gulfs of Kathiawar Peninsula and Arabian Sea. ENVIRONMENTAL RESEARCH 2023; 225:115603. [PMID: 36863652 DOI: 10.1016/j.envres.2023.115603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/16/2023] [Accepted: 02/28/2023] [Indexed: 05/25/2023]
Abstract
Aromatic hydrocarbons are persistent pollutants in aquatic systems as endocrine disruptors, significantly impacting natural ecosystems and human health. Microbes perform as natural bioremediators to remove and regulate aromatic hydrocarbons in the marine ecosystem. The present study focuses upon the comparative diversity and abundance of various hydrocarbon-degrading enzymes and their pathways from deep sediments along the Gulf of Kathiawar Peninsula and Arabian Sea, India. The elucidation of large number of degradation pathways in the study area under the presence of a wide range of pollutants whose fate needs to be addressed. Sediment core samples were collected, and the whole microbiome was sequenced. Analysis of the predicted ORFs (open reading frames) against the AromaDeg database revealed 2946 aromatic hydrocarbon-degrading enzyme sequences. Statistical analysis portrayed that the Gulfs were more diverse in degradation pathways compared to the open sea, with the Gulf of Kutch being more prosperous and more diverse than the Gulf of Cambay. The vast majority of the annotated ORFs belonged to groups of dioxygenases that included catechol, gentisate, and benzene dioxygenases, along with Rieske (2Fe-2S) and vicinal oxygen chelate (VOC) family proteins. From the sampling sites, only 960 of the total predicted genes were given taxonomic annotations, which mention the presence of many under-explored marine microorganism-derived hydrocarbon degrading genes and pathways. Through the present study, we tried to unveil the array of catabolic pathways of aromatic hydrocarbon degradation and genes from a marine ecosystem that upholds economic and ecological significance in India. Thus, this study provides vast opportunities and strategies for microbial resource recovery in marine ecosystems, which can be investigated to explore aromatic hydrocarbon degradation and their potential mechanisms under various oxic or anoxic environments. Future studies should focus on aromatic hydrocarbon degradation by considering degradation pathways, biochemical analysis, enzymatic, metabolic, and genetic systems, and regulations.
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Affiliation(s)
- Neelam M Nathani
- School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, 382424, Gujarat, India; Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, 364001, Gujarat, India
| | - Chandrashekar Mootapally
- School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, 382424, Gujarat, India; Department of Marine Science, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, 364001, Gujarat, India
| | - Parth Sharma
- School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, 382424, Gujarat, India
| | - Solly Solomon
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science & Technology, Kochi, 682022, Kerala, India; Cochin Base of Fishery Survey of India, Post Box 853 Kochangady, Cochin, 682005, Kerala, India
| | - Rakesh Kumar
- School of Ecology and Environment Studies, Nalanda University, Rajgir, 803116, Bihar, India
| | - Abhay B Fulke
- Microbiology Division, CSIR - National Institute of Oceanography (CSIR-NIO), Regional Centre, Andheri (West), Maharashtra, 400053, India
| | - Manish Kumar
- Sustainability Cluster, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India; Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterey, Monterrey, 64849, Nuevo Leon, Mexico.
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Zhang X, Zhang C, Liu Y, Zhang R, Li M. Non-negligible roles of archaea in coastal carbon biogeochemical cycling. Trends Microbiol 2022; 31:586-600. [PMID: 36567186 DOI: 10.1016/j.tim.2022.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 12/25/2022]
Abstract
Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO2 fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.
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Affiliation(s)
- Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Rui Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China.
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Wen Z, Shang Y, Song K, Liu G, Hou J, Lyu L, Tao H, Li S, He C, Shi Q, He D. Composition of dissolved organic matter (DOM) in lakes responds to the trophic state and phytoplankton community succession. WATER RESEARCH 2022; 224:119073. [PMID: 36113235 DOI: 10.1016/j.watres.2022.119073] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Dissolved organic matter (DOM), a heterogeneous mixture of diverse compounds with different molecular weights, is crucial for the lake carbon cycle. The properties and concentration of DOM in lakes are closely related to anthropogenic activities, terrigenous input, and phytoplankton growth. Thus, the lake's trophic state, along with the above factors, has an important effect on DOM. We determined the DOM sources and molecular composition in six lakes along a trophic gradient during and after phytoplankton bloom by combining optical techniques and the Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). CDOM pools in eutrophic lakes may be more biologically refractory than in oligotrophic and mesotrophic lakes. Molecular formulas of DOM were positively correlated with the TSI (trophic state index) value (R2 = 0.73), with the nitrogen-containing compounds (CHON) being the most abundant formulas in all studied lakes. Eutrophication modified the molecular formulas of DOM to have less CHO% and more heteroatom S-containing compounds (CHOS% and CHNOS%), and this was the synactic result of the anthropogenic perturbation and phytoplankton proliferation. In eutrophic lakes, summer DOM showed higher molecular lability than in autumn, which was related to the seasonal phytoplankton community succession. Although the phytoplankton-derived DOM is highly bioavailable, we detected a simpler and more fragile phytoplankton community ecosystem in autumn, which may be accompanied by a lower phytoplankton production and metabolic activity. Therefore, we concluded that the lake eutrophication increased the allochthonous DOM accumulation along with sewage and nutrient input, and subsequently increased its release with phytoplankton bloom. Eutrophication and phytoplankton growth are accompanied by more highly unsaturated compounds, O3S+O5S compounds, and carboxylic-rich alicyclic compounds (CRAMs), which are the biotransformation product of phytoplankton-derived DOM. Eutrophication may be a potential source of refractory DOM compounds for biodegradation and photodegradation. Our results can clarify the potential role of water organic matter in the future global carbon cycle processes, considering the increasing worldwide eutrophication of inland waters.
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Affiliation(s)
- Zhidan Wen
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yingxin Shang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Kaishan Song
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; School of Environment and Planning, Liaocheng University, Liaocheng 252000, China.
| | - Ge Liu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Junbin Hou
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lili Lyu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Hui Tao
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Sijia Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Changping District, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Changping District, Beijing 102249, China
| | - Ding He
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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