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Wang X, Sun T, Yan S, Chen S, Zhang Y. Sediment microbial community characteristics in sea cucumber restocking area. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106233. [PMID: 37866200 DOI: 10.1016/j.marenvres.2023.106233] [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: 07/08/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Variations of microbial species and functional composition in coastal sediment are usually taken as the results of the provision of supplementary nutrients affected by human activities. However, responses of microbiome stability to restocking biological resources remain less understood in coastal benthic systems without nutrient supplements. Here, combined with metagenomics and microbiome co-occurrence networks, the composition, function, and community stability of microbes were evaluated in a coastal area where sea cucumbers (Apostichopus japonicus) restocked after six months. Also, the physicochemical characteristics of sediments and bottom water were analyzed. We found the total organic carbon, total nitrogen, and total phosphorus of sediment did not change significantly in the restocking area after six months, whereas the concentration of dissolved inorganic nitrogen in bottom water increased significantly. Moreover, the relative abundance of Nitrospina at the class level was increased significantly in the restocking area. Also, enzymes related to nitrate reduction and nitrous oxide reductase were increased in the restocking area. Of note, stock enhancement of sea cucumbers altered associations between bacteria rather than their composition. The elimination of negative associations and reduction of the potential keystone taxa in the restocking area indicated destabilized bacterial communities. Our work may contribute to elucidating the response of microbial stability to stock enhancement. This finding also suggests that microbial community stability can be considered as an indicator of ecological risk under the influence of stock enhancement.
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Affiliation(s)
- Xiaoling Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Tao Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Shengjun Yan
- National Marine Environmental Monitoring Center, Dalian, 116021, China
| | - Shangyi Chen
- Comprehensive Administrative Law Enforcement Bureau, Qingdao, 266011, China
| | - Yue Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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Li T, Li Y, Zhang X, Yuan J, Guo J, Wang P, Wei G, Chen C. Distinct response patterns of bacterial communities in Ag- and ZnO-rGO nanocomposite-amended silt loam soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:151270. [PMID: 34756902 DOI: 10.1016/j.scitotenv.2021.151270] [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: 08/09/2021] [Revised: 09/26/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
The widespread application of metal-based nanoparticle (MNPs)/reduced graphene oxide (rGO) composites inevitably leads to their release into soils. However, we lack a detailed understanding of the bacterial community response to MNPs-rGO exposure in farmland soils. Here, we conducted a soil microcosm experiment to analyze the potential impact of MNPs-rGO on bacterial communities in two field soils via high-throughput sequencing. The change in alpha diversity of bacterial communities was more susceptible to Ag-rGO and ZnO-rGO treatments than CuO-rGO. In both soils, MNPs-rGO significantly changed the bacterial community structure even at a low dose (1 mg kg-1). The bacterial community structure was most strongly affected by Ag-rGO at 30 days, but the greatest changes occurred in ZnO-rGO at 60 days. The differences in soil properties could shape bacterial communities to MNPs-rGO exposure. Distance-based redundancy analysis and functional annotation of prokaryotic taxa showed that some bacterial species associated with nitrogen cycling were greatly influenced by Ag-rGO and ZnO-rGO exposure. In sum, Ag-rGO and ZnO-rGO may potentially affect bacterial communities and nitrogen turnover under long-term realistic field exposure. These findings present a perspective on the response of bacterial communities to MNPs-rGO and provide a fundamental basis for estimating the ecological behavior of MNPs-rGO.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Yuhua Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Xike Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Jiawei Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Junkang Guo
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an 710021, Shaanxi, PR China
| | - Pan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
| | - Chun Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
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Zafeiropoulos H, Paragkamian S, Ninidakis S, Pavlopoulos GA, Jensen LJ, Pafilis E. PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. Microorganisms 2022; 10:microorganisms10020293. [PMID: 35208748 PMCID: PMC8879827 DOI: 10.3390/microorganisms10020293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO’s capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes.
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Affiliation(s)
- Haris Zafeiropoulos
- Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013 Heraklion, Crete, Greece; (H.Z.); (S.P.)
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, P.O. Box 2214, 71003 Heraklion, Crete, Greece;
| | - Savvas Paragkamian
- Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013 Heraklion, Crete, Greece; (H.Z.); (S.P.)
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, P.O. Box 2214, 71003 Heraklion, Crete, Greece;
| | - Stelios Ninidakis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, P.O. Box 2214, 71003 Heraklion, Crete, Greece;
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece;
- Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, P.O. Box 2214, 71003 Heraklion, Crete, Greece;
- Correspondence: or ; Tel.: +30-2810-337748
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Phylogenetic and Phenogenetic Diversity of Synechococcus along a Yellow Sea Section Reveal Its Environmental Dependent Distribution and Co-Occurrence Microbial Pattern. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9091018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Synechococcus is a dominant genus of the coastal phytoplankton with an effective contribution to primary productivity. Here, the phylogenetic and phenogenetic composition of Synechococcus in the coastal Yellow Sea was addressed by sequencing marker gene methods. Meanwhile, its co-occurrence pattern with bacterial and eukaryotic microbes was further investigated based on the construction of networks. The result revealed that Synechococcus abundance ranged from 9.8 × 102 cells mL−1 to 1.6 × 105 cells mL−1, which was significantly correlated to sampling depth and nutrient contents of nitrite, ammonia, and dissolved silicon. A total of eight Synechococcus phylogenetic lineages were detected, of which clade III was dominant in most of the samples. Meanwhile, clade I increased along the water column and even reached a maximum value of 76.13% at 20 m of station B. Phenogenetically, Synechococcus PT3 was always the predominant pigment type across the whole study zone. Only salinity was significantly correlated to the phenogenetic constitution. The networks revealed that Synechococcus co-occurred with 159 prokaryotes, as well as 102 eukaryotes including such possible grazers as Gymnodinium clades and Alveolata. Potential function prediction further showed that microbes co-occurring with Synechococcus were associated with diverse element cycles, but the exact mechanism needed further experimentation to verify. This research promotes exploring regularity in the genomic composition and niche position of Synechococcus in the coastal ecosystem and is significant to further discuss its potential participation in materials circulation and bottom-up effects in microbial food webs.
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