1
|
Chen C, Yin G, Hou L, Jiang Y, Sun D, Liang X, Han P, Zheng Y, Liu M. Reclamation of tidal flats to paddy soils reshuffles the soil microbiomes along a 53-year reclamation chronosequence: Evidence from assembly processes, co-occurrence patterns and multifunctionality. ENVIRONMENT INTERNATIONAL 2023; 179:108151. [PMID: 37603994 DOI: 10.1016/j.envint.2023.108151] [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: 05/19/2023] [Revised: 07/17/2023] [Accepted: 08/13/2023] [Indexed: 08/23/2023]
Abstract
Coastal soil microbiomes play a key role in coastal ecosystem functioning and are intensely threatened by land reclamation. However, the impacts of coastal reclamation on soil microbial communities, particularly on their assembly processes, co-occurrence patterns, and the multiple soil functions they support, remain poorly understood. This impedes our capability to comprehensively evaluate the impacts of coastal reclamation on soil microbiomes and to restore coastal ecosystem functions degraded by reclamation. Here, we investigated the temporal dynamics of bacterial and fungal communities, community assembly processes, co-occurrence patterns, and ecosystem multifunctionality along a 53-year chronosequence of paddy soil following reclamation from tidal flats. Reclamation of tidal flats to paddy soils resulted in decreased β-diversity, increased homogeneous selection, and decreased network complexity and robustness of both bacterial and fungal communities, but caused contrasting α-diversity response patterns of them. Reclamation of tidal flats to paddy soils also decreased the multifunctionality of coastal ecosystems, which was largely associated with the fungal network complexity and α-diversity. Collectively, this work demonstrates that coastal reclamation strongly reshaped the soil microbiomes at the level of assembly mechanisms, interaction patterns, and functionality level, and highlights that soil fungal community complexity should be considered as a key factor in restoring coastal ecosystem functions deteriorated by land reclamation.
Collapse
Affiliation(s)
- Cheng Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yinghui Jiang
- School of Geography and Environment, Jiangxi Normal University, Nanchang, 330022 Jiangxi, China
| | - Dongyao Sun
- School of Geography Science and Geomatics Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China.
| |
Collapse
|
2
|
Wu K, Liu Y, Liao X, Yang X, Chen Z, Mo L, Zhong S, Zhang X. Fungal Diversity and Its Relationship with Environmental Factors in Coastal Sediments from Guangdong, China. J Fungi (Basel) 2023; 9:jof9010101. [PMID: 36675922 PMCID: PMC9866456 DOI: 10.3390/jof9010101] [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: 12/27/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
As one core of the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), Guangdong is facing some serious coastal environmental problems. Fungi are more vulnerable to changes in coastal environments than bacteria and archaea. This study investigated the fungal diversity and composition by high-throughput sequencing and detected basic parameters of seven environmental factors (temperature, dissolved oxygen, pH, salinity, total organic carbon, total nitrogen, and total phosphorus) at 11 sites. A total of 2056 fungal operational taxonomic units (OTUs) belonging to 147 genera in 6 phyla were recovered; Archaeorhizomyces (17.5%) and Aspergillus (14.19%) were the most dominant genera. Interestingly, a total of 14 genera represented the first reports of coastal fungi in this study. Furthermore, there were nine genera of fungi that were significantly correlated with environmental factors. FUNGuild analysis indicated that saprotrophs and pathogens were the two trophic types with the highest proportions. Saprotrophs were significantly correlated with total organic carbon (TOC), total nitrogen (TN), and total phosphorus (TP), while pathogens were significantly correlated with pH. This study provides new scientific data for the study of the diversity and composition of fungal communities in coastal ecosystems.
Collapse
Affiliation(s)
- Keyue Wu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yongchun Liu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xinyu Liao
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xinyue Yang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zihui Chen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Li Mo
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Saiyi Zhong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
- Correspondence: (S.Z.); (X.Z.)
| | - Xiaoyong Zhang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (S.Z.); (X.Z.)
| |
Collapse
|
3
|
Rath S, Palit K, Das S. Variable pH and subsequent change in pCO 2 modulates the biofilm formation, synthesis of extracellular polymeric substances, and survivability of a marine bacterium Bacillus stercoris GST-03. ENVIRONMENTAL RESEARCH 2022; 214:114128. [PMID: 36007573 DOI: 10.1016/j.envres.2022.114128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/03/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Biofilm-forming bacteria adhere to the substrates and engage in the nutrient cycling process. However, environmental conditions may interrupt the biofilm formation ability, which ultimately may affect various biogeochemical cycles. The present study reports the effect of varying pH and subsequent change in pCO2 on the survivability, biofilm formation, and synthesis of extracellular polymeric substances (EPS) of a biofilm-forming marine bacterium Bacillus stercoris GST-03 isolated from the Bhitarkanika mangrove ecosystem, Odisha, India. Understanding the pH-dependent alteration in EPS constituents, and associated functional groups of a marine bacterium will provide better insight into the adaptability of the bacteria in future ocean acidification scenarios. The strain was found to tolerate and form biofilm up to pH 4, with the maximum biofilm formation at pH 6. EPS yield and the synthesis of the key components of the EPS, including carbohydrate, protein, and lipid, were found maximum at pH 6. Changes in biofilm formation patterns and various topological parameters at varying pH/pCO2 conditions were observed. A cellular chaining pattern was observed at pH 4, and maximum biofilm formation was obtained at pH 6 with biomass of 5.28582 ± 0.5372 μm3/μm2 and thickness of 9.982 ± 1.5288 μm. Structural characterization of EPS showed changes in various functional groups of constituent macromolecules with varying pH. The amorphous nature of the EPS and the changes in linkages and associated functional groups (-R2CHOR, -CH3, and -CH2) with pH variation was confirmed. EPS showed a two-step degradation with a maximum weight loss of 59.147% and thermal stability up to 480 °C at pH 6. The present work efficiently demonstrates the role of EPS in providing structural and functional stability to the biofilm in varying pH conditions. The findings will provide a better understanding of the adaptability of marine bacteria in the future effect of ocean acidification.
Collapse
Affiliation(s)
- Sonalin Rath
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Krishna Palit
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
| |
Collapse
|
4
|
Su X, Cui L, Tang Y, Wen T, Yang K, Wang Y, Zhang J, Zhu G, Yang X, Hou L, Zhu YG. Denitrification and N 2O Emission in Estuarine Sediments in Response to Ocean Acidification: From Process to Mechanism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14828-14839. [PMID: 36194569 DOI: 10.1021/acs.est.2c03550] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Global estuarine ecosystems are experiencing severe nitrogen pollution and ocean acidification (OA) simultaneously. Sedimentary denitrification is an important way of reactive nitrogen removal but at the same time leads to the emission of large amounts of nitrous oxide (N2O), a potent greenhouse gas. It is known that OA in estuarine regions could impact denitrification and N2O production; however, the underlying mechanism is still underexplored. Here, sediment incubation and pure culture experiments were conducted to explore the OA impacts on microbial denitrification and the associated N2O emissions in estuarine sediments. Under neutral (in situ) conditions, fungal N2O emission dominated in the sediment, while the bacterial and fungal sources had a similar role under acidification. This indicated that acidification decreased the sedimentary fungal denitrification and likely inhibited the activity of fungal denitrifiers. To explore molecular mechanisms, a denitrifying fungal strain of Penicillium janthinellum was isolated from the sediments. By using deuterium-labeled single-cell Raman spectroscopy and isobaric tags for relative and absolute quantitation proteomics, we found that acidification inhibited electron transfers in P. janthinellum and downregulated expressions of the proteins related to energy production and conservation. Two collaborative pathways of energy generation in the P. janthinellum were further revealed, that is, aerobic oxidative phosphorylation and TCA cycle and anoxic pyruvate fermentation. This indicated a distinct energy supply strategy from bacterial denitrification. Our study provides insights into fungi-mediated nitrogen cycle in acidifying aquatic ecosystems.
Collapse
Affiliation(s)
- Xiaoxuan Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment; Key Laboratory of Low-Carbon Green Agriculture in Southwestern China, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing400715, China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Yijia Tang
- School of Life and Environmental Sciences, The University of Sydney, Biomedical Building (C81), Sydney, New South Wales2015, Australia
| | - Teng Wen
- School of Geography, Nanjing Normal University, Nanjing210023, China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, Nanjing210023, China
| | - Kai Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Yingmu Wang
- College of Civil Engineering, Fuzhou University, Fuzhou350116, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing210023, China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, Nanjing210023, China
| | - Guibing Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai200062, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- University of the Chinese Academy of Sciences, Beijing100049, China
| |
Collapse
|
5
|
Su X, Yang L, Yang K, Tang Y, Wen T, Wang Y, Rillig MC, Rohe L, Pan J, Li H, Zhu YG. Estuarine plastisphere as an overlooked source of N2O production. Nat Commun 2022; 13:3884. [PMID: 35794126 PMCID: PMC9259610 DOI: 10.1038/s41467-022-31584-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/22/2022] [Indexed: 12/13/2022] Open
Abstract
“Plastisphere”, microbial communities colonizing plastic debris, has sparked global concern for marine ecosystems. Microbiome inhabiting this novel human-made niche has been increasingly characterized; however, whether the plastisphere holds crucial roles in biogeochemical cycling remains largely unknown. Here we evaluate the potential of plastisphere in biotic and abiotic denitrification and nitrous oxide (N2O) production in estuaries. Biofilm formation provides anoxic conditions favoring denitrifiers. Comparing with surrounding bulk water, plastisphere exhibits a higher denitrifying activity and N2O production, suggesting an overlooked N2O source. Regardless of plastisphere and bulk water, bacterial and fungal denitrifications are the main regulators for N2O production instead of chemodenitrification. However, the contributions of bacteria and fungi in the plastisphere are different from those in bulk water, indicating a distinct N2O production pattern in the plastisphere. These findings pinpoint plastisphere as a N2O source, and provide insights into roles of the new biotope in biogeochemical cycling in the Anthropocene. The roles of marine plastisphere in global nitrogen cycling are largely unknown. Here, the authors indicate that the plastisphere could act as a potential source of N2O production, which is mainly regulated by the biotic denitrification
Collapse
|
6
|
Su X, Wen T, Wang Y, Xu J, Cui L, Zhang J, Xue X, Ding K, Tang Y, Zhu YG. Stimulation of N 2 O emission via bacterial denitrification driven by acidification in estuarine sediments. GLOBAL CHANGE BIOLOGY 2021; 27:5564-5579. [PMID: 34453365 DOI: 10.1111/gcb.15863] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 05/02/2023]
Abstract
Ocean acidification in nitrogen-enriched estuaries has raised global concerns. For decades, biotic and abiotic denitrification in estuarine sediments has been regarded as the major ways to remove reactive nitrogen, but they occur at the expense of releasing greenhouse gas nitrous oxide (N2 O). However, how these pathways respond to acidification remains poorly understood. Here we performed a N2 O isotopocules analysis coupled with respiration inhibition and molecular approaches to investigate the impacts of acidification on bacterial, fungal, and chemo-denitrification, as well as N2 O emission, in estuarine sediments through a series of anoxic incubations. Results showed that acidification stimulated N2 O release from sediments, which was mainly mediated by the activity of bacterial denitrifiers, whereas in neutral environments, N2 O production was dominated by fungi. We also found that the contribution of chemo-denitrification to N2 O production cannot be ignored, but was not significantly affected by acidification. The mechanistic investigation further demonstrated that acidification changed the keystone taxa of sedimentary denitrifiers from N2 O-reducing to N2 O-producing ones and reduced microbial electron-transfer efficiency during denitrification. These findings provide novel insights into how acidification stimulates N2 O emission and modulates its pathways in estuarine sediments, and how it may contribute to the acceleration of global climate change in the Anthropocene.
Collapse
Affiliation(s)
- Xiaoxuan Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Teng Wen
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Yingmu Wang
- College of Civil Engineering, Fuzhou University, Fuzhou, China
| | - Junshi Xu
- Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing, China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, Nanjing, China
| | - Ximei Xue
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yijia Tang
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Institute of Agriculture, Sydney, New South Wales, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of the Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|