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Yang Q, Ling J, Zhang Y, Zhou W, Wei Z, Li J, Zhang Y, Dong J, Qian P. Microbial nitrogen removal in reef-building corals: A light-sensitive process. CHEMOSPHERE 2024; 359:142394. [PMID: 38777199 DOI: 10.1016/j.chemosphere.2024.142394] [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: 12/18/2023] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Scleractinian corals are the main framework-building groups in tropical coral reefs. In the coral holobiont, nitrogen-cycling mediated by microbes is fundamental for sustaining the coral reef ecosystems. However, little direct evidence characterizing the activities of microbial nitrogen removal via complete denitrification and anaerobic ammonium oxidation (anammox) in stony corals has been presented. In this study, multiple incubation experiments using 15N-tracer were conducted to identify and characterize N2 production by denitrification and anammox in the stony coral Pocillopora damicornis. The rates of denitrification and anammox were recorded up to 0.765 ± 0.162 and 0.078 ± 0.009 nmol N2 cm-2 h-1 respectively. Denitrification contributed the majority (∼90%) of N2 production by microbial nitrogen removal in stony corals. The microbial nitrogen removal activities showed diel rhythms, which might correspond to photosynthetic oxygen production. The N2 production rates of anammox and denitrification increased with incubation time. To the authors' knowledge, this study is the first to confirm and characterize the activities of complete denitrification and anammox in stony corals via stable isotope techniques. This study extends the understanding on nitrogen-cycling in coral reefs and how it participates in corals' resilience to environmental stressors.
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Affiliation(s)
- Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China; Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhangliang Wei
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yanying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Ocean School, Yantai University, Yantai, China.
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; Tropical Marine Biological Research Station in Hainan, CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, China; Shantou Marine Plants Experiment Station, Chinese Academy of Sciences, Shantou, China.
| | - Peiyuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China; Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
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Messer LF, Bourne DG, Robbins SJ, Clay M, Bell SC, McIlroy SJ, Tyson GW. A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience. Nat Commun 2024; 15:2902. [PMID: 38575584 PMCID: PMC10995205 DOI: 10.1038/s41467-024-46905-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.
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Affiliation(s)
- Lauren F Messer
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia.
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Megan Clay
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia
| | - Sara C Bell
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia.
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3
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Shoguchi E, Kawachi M, Shinzato C, Beedessee G. Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13238. [PMID: 38444256 PMCID: PMC10915500 DOI: 10.1111/1758-2229.13238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024]
Abstract
Bacterial-algal interactions strongly influence marine ecosystems. Bacterial communities in cultured dinoflagellates of the family Symbiodiniaceae have been characterized by metagenomics. However, little is known about whole-genome analysis of marine bacteria associated with these dinoflagellates. We performed in silico analysis of four bacterial genomes from cultures of four dinoflagellates of the genera Symbiodinium, Breviolum, Cladocopium and Durusdinium. Comparative analysis showed that the former three contain the alphaproteobacterial family Parvibaculaceae and that the Durusdinium culture includes the family Sphingomonadaceae. There were no large genomic reductions in the alphaproteobacteria with genome sizes of 2.9-3.9 Mb, implying they are not obligate intracellular bacteria. Genomic annotations of three Parvibaculaceae detected the gene for diacetylchitobiose deacetylase (Dac), which may be involved in the degradation of dinoflagellate cell surfaces. They also had metabolic genes for dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen (N) cycle and cobalamin (vitamin B12 ) biosynthetic genes in the salvage pathway. Those three characters were not found in the Sphingomonadaceae genome. Predicted biosynthetic gene clusters for secondary metabolites indicated that the Parvibaculaceae likely produce the same secondary metabolites. Our study suggests that the Parvibaculaceae is a major resident of Symbiodiniaceae cultures with antibiotics.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem StudiesNational Institute for Environmental StudiesTsukubaJapan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of TokyoKashiwaJapan
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Present address:
Faculty of Health & Life SciencesNorthumbria UniversityNewcastle upon TyneUK
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4
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Chen C, Ai J, Chen L, Li Y, Tang X, Li J. Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22494-22506. [PMID: 38407711 DOI: 10.1007/s11356-024-32587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
Aha Lake artificial reservoir wetland, Niangniang Mountain karst mountain wetland, and Caohai plateau lake wetland are typical karst wetlands in Guizhou Province with unique topography and geomorphic features. They were selected as research objects in this study to explore microorganisms and functional genes in nitrogen metabolism adopting macro-genome sequencing technology. It was found that Proteobacteria, Actinobacteria, and Acidobacteria were the dominant phyla in nitrogen metabolism in these three wetlands, similar to previous studies. However, at the genus level, there was a significant difference, with the dominant bacteria being Bradyrhizobium, Methylocystis, and Anaeromyxobacter. Six nitrogen metabolism pathways, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction, assimilatory nitrate reduction, and complete nitrification, comammox, were revealed, but anaerobic ammonia oxidation genes were not detected. Nitrogen metabolism microorganisms and pathways were more affected by SOM, pH, NO3-, and EC in karst wetlands. This study further discussed microorganisms and functions of nitrogen metabolism in karst wetlands, which was of great significance to nitrogen cycles of karst wetland ecosystems.
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Affiliation(s)
- Chen Chen
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Jia Ai
- Ecological and Environmental Monitoring Center, Guizhou, 558013, Qiannan, China
| | - Li Chen
- College of Civil Engineering, Chongqing Vocational Institute of Engineering, Chongqing, 402260, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China.
| | - Xin Tang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
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5
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Chen Y, Lin Y, Zhu J, Zhou J, Lin H, Fu Y, Zhou Y. Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions. Front Microbiol 2024; 15:1323160. [PMID: 38500581 PMCID: PMC10945327 DOI: 10.3389/fmicb.2024.1323160] [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: 10/17/2023] [Accepted: 02/12/2024] [Indexed: 03/20/2024] Open
Abstract
The acceleration of the nitrogen cycle and the nitrogen excess observed in some coastal waters has increased interest into understanding the biochemical and molecular basis of nitrogen metabolism in various microorganisms. To investigate nitrogen metabolism of a novel heterotrophic nitrification and aerobic denitrification bacterium Klebsiella aerogenes strain (B23) under nitrogen-rich conditions, we conducted physiological and transcriptomic high-throughput sequencing analyses on strain B23 cultured on potassium nitrate-free or potassium nitrate-rich media. Overall, K. aerogenes B23 assimilated 82.47% of the nitrate present into cellular nitrogen. Further, 1,195 differentially expressed genes were observed between K. aerogenes B23 cultured on potassium nitrate-free media and those cultured on potassium nitrate-rich media. Gene annotation and metabolic pathway analysis of the transcriptome were performed using a series of bioinformatics tools, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Non-Redundant Protein Database annotation. Accordingly, the nitrogen metabolism pathway of K. aerogenes B23 was analyzed; overall, 39 genes were determined to be involved in this pathway. Differential expression analysis of the genes involved in the nitrogen metabolism pathway demonstrated that, compared to the control, FNR, NarK/14945, fdx, gshA, proB, proA, gapA, argH, artQ, artJ, artM, ArgR, GAT1, prmB, pyrG, glnS, and Ca1 were significantly upregulated in the nitrogen-treated K. aerogenes B23; these genes have been established to be involved in the regulation of nitrate, arginine, glutamate, and ammonia assimilation. Further, norV, norR, and narI were also upregulated in nitrogen-treated K. aerogenes B23; these genes are involved in the regulation of NO metabolism. These differential expression results are important for understanding the regulation process of key nitrogen metabolism enzyme genes in K. aerogenes B23. Therefore, this study establishes a solid foundation for further research into the expression regulation patterns of nitrogen metabolism-associated genes in K. aerogenes B23 under nitrogen-rich conditions; moreover, this research provides essential insight into how K. aerogenes B23 utilizes nutritional elements.
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Affiliation(s)
| | | | | | | | | | | | - Yan Zhou
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
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Mannochio-Russo H, Swift SOI, Nakayama KK, Wall CB, Gentry EC, Panitchpakdi M, Caraballo-Rodriguez AM, Aron AT, Petras D, Dorrestein K, Dorrestein TK, Williams TM, Nalley EM, Altman-Kurosaki NT, Martinelli M, Kuwabara JY, Darcy JL, Bolzani VS, Wegley Kelly L, Mora C, Yew JY, Amend AS, McFall-Ngai M, Hynson NA, Dorrestein PC, Nelson CE. Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses. Commun Biol 2023; 6:896. [PMID: 37653089 PMCID: PMC10471604 DOI: 10.1038/s42003-023-05230-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/08/2023] [Indexed: 09/02/2023] Open
Abstract
The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, O'ahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.
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Affiliation(s)
- Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, 14800-060, Brazil.
| | - Sean O I Swift
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
| | - Kirsten K Nakayama
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Christopher B Wall
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
- Ecology Behavior and Evolution Section, Department of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Andrés M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Kathleen Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Taylor M Williams
- Marine Option Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Eileen M Nalley
- Hawai'i Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Noam T Altman-Kurosaki
- School of Biological Sciences, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | | | - Jeff Y Kuwabara
- Marine Option Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - John L Darcy
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Vanderlan S Bolzani
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, 14800-060, Brazil
| | - Linda Wegley Kelly
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, CA, USA
| | - Camilo Mora
- Geography, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Joanne Y Yew
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Anthony S Amend
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Margaret McFall-Ngai
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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He H, Huang J, Zhao Z, Feng W, Zheng X, Du P. Impact of clomazone on bacterial communities in two soils. Front Microbiol 2023; 14:1198808. [PMID: 37583513 PMCID: PMC10424789 DOI: 10.3389/fmicb.2023.1198808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023] Open
Abstract
Introduction Bacterial communities are important for soil functions, but the effect of clomazone on network complexity, composition, and stability is not well studied. Method In this study, two agricultural soils were used to test the impact of clomazone on bacterial communities, and the two soils were treated with three concentrations of clomazone (0, 0.8, 8, and 80 mg kg1) in an incubator. Results and discussion Bacterial network nodes, links, and average degrees were all decreased by 9-384, 648-829, and 0.703-2.429, respectively. Based on keystone nodes, the topological roles of the nodes were also influenced by clomazone. Bacterial network composition was also impacted based on the analysis of similarity (ANOSIM) and network dissimilarity. Compared with control and clomazone treatments in both soils, the ANOSIM between control and all clomazone treatments was higher than 0.6, network dissimilarities were 0.97-0.98, shared nodes were 131-260, and shared links were 12-100. The bacterial network stability was decreased by clomazone, with decreased robustness by 0.01-0.016 and increased vulnerability by 0.00023-0.00147 in both soils. There were fewer bacterial network modules preserved after clomazone treatment, and the bacterial network community functions were also impacted in both soils. Based on these results, soil bacterial species connections, modularization, and network stability were significantly impacted by clomazone.
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Affiliation(s)
- Hairong He
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jiarui Huang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zhenzhu Zhao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Weisheng Feng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiaoke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Pengqiang Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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He H, Huang J, Zhao Z, Xu H, Zheng X, Zhang C, Du P. Fungal network composition and stability in two soils impacted by trifluralin. Front Microbiol 2023; 14:1128853. [PMID: 37234547 PMCID: PMC10206129 DOI: 10.3389/fmicb.2023.1128853] [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: 12/21/2022] [Accepted: 04/10/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction The composition and stability of soil fungal network are important for soil function, but the effect of trifluralin on network complexity and stability is not well understood. Methods In this study, two agricultural soils were used to test the impact of trifluralin on a fungal network. The two soils were treated with trifluralin (0, 0.84, 8.4, and 84 mg kg-1) and kept in artificial weather boxes. Results and discussion Under the impact of trifluralin, the fungal network nodes, edges, and average degrees were increased by 6-45, 134-392, and 0.169-1.468 in the two soils, respectively; however, the average path length was decreased by 0.304-0.70 in both soils. The keystone nodes were also changed in trifluralin treatments in the two soils. In the two soils, trifluralin treatments shared 219-285 nodes and 16-27 links with control treatments, and the network dissimilarity was 0.98-0.99. These results indicated that fungal network composition was significantly influenced. After trifluralin treatment, fungal network stability was increased. Specifically, the network robustness was increased by trifluralin with 0.002-0.009, and vulnerability was decreased by trifluralin with 0.0001-0.00032 in the two soils. Fungal network community functions were also impacted by trifluralin in both soils. Trifluralin significantly impacts the fungal network.
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Affiliation(s)
- Hairong He
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jiarui Huang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zhenzhu Zhao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Huifang Xu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiaoke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Changpeng Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Products Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Pengqiang Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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9
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Exploring the Potential Molecular Mechanisms of Interactions between a Probiotic Consortium and Its Coral Host. mSystems 2023; 8:e0092122. [PMID: 36688656 PMCID: PMC9948713 DOI: 10.1128/msystems.00921-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Beneficial microorganisms for corals (BMCs) have been demonstrated to be effective probiotics to alleviate bleaching and mitigate coral mortality in vivo. The selection of putative BMCs is traditionally performed manually, using an array of biochemical and molecular tests for putative BMC traits. We present a comprehensive genetic survey of BMC traits using a genome-based framework for the identification of alternative mechanisms that can be used for future in silico selection of BMC strains. We identify exclusive BMC traits associated with specific strains and propose new BMC mechanisms, such as the synthesis of glycine betaine and ectoines. Our roadmap facilitates the selection of BMC strains while increasing the array of genetic targets that can be included in the selection of putative BMC strains to be tested as coral probiotics. IMPORTANCE Probiotics are currently the main hope as a potential medicine for corals, organisms that are considered the marine "canaries of the coal mine" and that are threatened with extinction. Our experiments have proved the concept that probiotics mitigate coral bleaching and can also prevent coral mortality. Here, we present a comprehensive genetic survey of probiotic traits using a genome-based framework. The main outcomes are a roadmap that facilitates the selection of coral probiotic strains while increasing the array of mechanisms that can be included in the selection of coral probiotics.
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Tandon K, Ricci F, Costa J, Medina M, Kühl M, Blackall LL, Verbruggen H. Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera. Gigascience 2022; 12:giac127. [PMID: 36683362 PMCID: PMC9868349 DOI: 10.1093/gigascience/giac127] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/17/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023] Open
Abstract
At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.
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Affiliation(s)
- Kshitij Tandon
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Francesco Ricci
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
- Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, NSW 2052, Australia
| | - Joana Costa
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, DK-3000 Helsingør, Denmark
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
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11
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Xiang N, Rädecker N, Pogoreutz C, Cárdenas A, Meibom A, Wild C, Gärdes A, Voolstra CR. Presence of algal symbionts affects denitrifying bacterial communities in the sea anemone Aiptasia coral model. ISME COMMUNICATIONS 2022; 2:105. [PMID: 37938763 PMCID: PMC9723753 DOI: 10.1038/s43705-022-00190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2023]
Abstract
The coral-algal symbiosis is maintained by a constant and limited nitrogen availability in the holobiont. Denitrifiers, i.e., prokaryotes reducing nitrate/nitrite to dinitrogen, could contribute to maintaining the nitrogen limitation in the coral holobiont, however the effect of host and algal identity on their community is still unknown. Using the coral model Aiptasia, we quantified and characterized the denitrifier community in a full-factorial design combining two hosts (CC7 and H2) and two strains of algal symbionts of the family Symbiodiniaceae (SSA01 and SSB01). Strikingly, relative abundance of denitrifiers increased by up to 22-fold in photosymbiotic Aiptasia compared to their aposymbiotic (i.e., algal-depleted) counterparts. In line with this, while the denitrifier community in aposymbiotic Aiptasia was largely dominated by diet-associated Halomonas, we observed an increasing relative abundance of an unclassified bacterium in photosymbiotic CC7, and Ketobacter in photosymbiotic H2, respectively. Pronounced changes in denitrifier communities of Aiptasia with Symbiodinium linucheae strain SSA01 aligned with the higher photosynthetic carbon availability of these holobionts compared to Aiptasia with Breviolum minutum strain SSB01. Our results reveal that the presence of algal symbionts increases abundance and alters community structure of denitrifiers in Aiptasia. Thereby, patterns in denitrifier community likely reflect the nutritional status of aposymbiotic vs. symbiotic holobionts. Such a passive regulation of denitrifiers may contribute to maintaining the nitrogen limitation required for the functioning of the cnidarian-algal symbiosis.
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Affiliation(s)
- Nan Xiang
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany.
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany.
| | - Nils Rädecker
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Claudia Pogoreutz
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- Center for Advanced Surface Analysis (CASA), Institute of Earth Science, University of Lausanne, 1015, Lausanne, Switzerland
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
| | - Astrid Gärdes
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Hochschule Bremerhaven, Fachbereich 1, An der Karlstadt 8, 27568, Bremerhaven, Germany
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12
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Morrow KM, Pankey MS, Lesser MP. Community structure of coral microbiomes is dependent on host morphology. MICROBIOME 2022; 10:113. [PMID: 35902906 PMCID: PMC9331152 DOI: 10.1186/s40168-022-01308-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai'i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities. RESULTS The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai'i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community. CONCLUSIONS The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral "super trait," on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. Video Abstract.
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Affiliation(s)
- Kathleen M Morrow
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
- Present address: Thomas Jefferson High School for Science and Technology, 6560 Braddock Rd, Alexandria, VA, 22312, USA
| | - M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Michael P Lesser
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
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13
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Li P, Liu J, Saleem M, Li G, Luan L, Wu M, Li Z. Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems. MICROBIOME 2022; 10:108. [PMID: 35841078 PMCID: PMC9287909 DOI: 10.1186/s40168-022-01287-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Rhizodeposits regulate rhizosphere interactions, processes, nutrient and energy flow, and plant-microbe communication and thus play a vital role in maintaining soil and plant health. However, it remains unclear whether and how alteration in belowground carbon allocation and chemodiversity of rhizodeposits influences microbiome functioning in the rhizosphere ecosystems. To address this research gap, we investigated the relationship of rhizosphere carbon allocation and chemodiversity with microbiome biodiversity and functioning during peanut (Arachis hypogaea) continuous mono-cropping. After continuously labeling plants with 13CO2, we studied the chemodiversity and composition of rhizodeposits, along with the composition and diversity of active rhizosphere microbiome using metabolomic, amplicon, and shotgun metagenomic sequencing approaches based on DNA stable-isotope probing (DNA-SIP). RESULTS Our results indicated that enrichment and depletion of rhizodeposits and active microbial taxa varied across plant growth stages and cropping durations. Specifically, a gradual decrease in the rhizosphere carbon allocation, chemodiversity, biodiversity and abundance of plant-beneficial taxa (such as Gemmatimonas, Streptomyces, Ramlibacter, and Lysobacter), and functional gene pathways (such as quorum sensing and biosynthesis of antibiotics) was observed with years of mono-cropping. We detected significant and strong correlations between rhizodeposits and rhizosphere microbiome biodiversity and functioning, though these were regulated by different ecological processes. For instance, rhizodeposits and active bacterial communities were mainly governed by deterministic and stochastic processes, respectively. Overall, the reduction in carbon deposition and chemodiversity during peanut continuous mono-cropping tended to suppress microbial biodiversity and its functions in the rhizosphere ecosystem. CONCLUSIONS Our results, for the first time, provide the evidence underlying the mechanism of rhizosphere microbiome malfunctioning in mono-cropped systems. Our study opens new avenues to deeply disentangle the complex plant-microbe interactions from the perspective of rhizodeposits chemodiversity and composition and will serve to guide future microbiome research for improving the functioning and services of soil ecosystems. Video abstract.
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Affiliation(s)
- Pengfa Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jia Liu
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104 USA
| | - Guilong Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
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