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Mazzoni C, Piacentini A, Di Bella L, Aldega L, Perinelli C, Conte AM, Ingrassia M, Ruspandini T, Bonfanti A, Caraba B, Falese FG, Chiocci FL, Fazi S. Carbonate precipitation and phosphate trapping by microbialite isolates from an alkaline insular lake (Bagno dell'Acqua, Pantelleria Island, Italy). Front Microbiol 2024; 15:1391968. [PMID: 38841062 PMCID: PMC11150794 DOI: 10.3389/fmicb.2024.1391968] [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: 02/26/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
The Bagno dell'Acqua lake is characterized by CO2 emissions, alkaline waters (pH = 9) and Eh values which indicate strongly oxidizing conditions. A typical feature of the lake is the presence of actively growing microbialites rich in calcium carbonates and silica precipitates. Mineralogy, petrography and morphology analyses of the microbialites were coupled with the analysis of the microbial community, combining molecular and cultivation approaches. The DNA sequencing revealed distinct patterns of microbial diversity, showing pronounced differences between emerged and submerged microbialite, with the upper layer of emerged samples exhibiting the most distinctive composition, both in terms of prokaryotes and eukaryotes. In particular, the most representative phyla in the microbial community were Proteobacteria, Actinobacteriota, and Bacteroidota, while Cyanobacteria were present only with an average of 5%, with the highest concentration in the submerged intermediate layer (12%). The role of microorganisms in carbonate mineral formation was clearly demonstrated as most of the isolates were able to precipitate calcium carbonate and five of them were characterized at molecular level. Interestingly, when microbial isolates were cultivated only in filtered water, the precipitation of hazenite was observed (up to 85%), opening new prospective in P (phosphate) recovery from P depleted environments.
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Affiliation(s)
- Cristina Mazzoni
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
- Water Research Institute, National Research Council (IRSA-CNR), Montelibretti, Rome, Italy
| | - Agnese Piacentini
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
- Water Research Institute, National Research Council (IRSA-CNR), Montelibretti, Rome, Italy
| | - Letizia Di Bella
- Department of Earth Sciences, Sapienza University of Rome, Rome, Italy
| | - Luca Aldega
- Department of Earth Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Aida Maria Conte
- Institute of Environmental Geology and Geoengineering, National Research Council (IGAG-CNR), Department of Earth Sciences, Sapienza University of Rome, Rome, Italy
| | - Michela Ingrassia
- Institute of Environmental Geology and Geoengineering, National Research Council (IGAG-CNR), Department of Earth Sciences, Sapienza University of Rome, Rome, Italy
| | - Tania Ruspandini
- Department of Earth Sciences, Sapienza University of Rome, Rome, Italy
| | - Andrea Bonfanti
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
| | - Benedetta Caraba
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
| | - Francesco Giuseppe Falese
- Institute of Environmental Geology and Geoengineering, National Research Council (IGAG-CNR), Department of Earth Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Stefano Fazi
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
- Water Research Institute, National Research Council (IRSA-CNR), Montelibretti, Rome, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
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Zhao J, Nair S, Zhang Z, Wang Z, Jiao N, Zhang Y. Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments. THE ISME JOURNAL 2024; 18:wrae083. [PMID: 38709876 PMCID: PMC11126160 DOI: 10.1093/ismejo/wrae083] [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: 01/01/2024] [Revised: 03/23/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g. deep-sea and hadal zones), indicating that macroalgal virospheres, despite being closest to us, are among the least understood. These viruses potentially maintain microbiome equilibrium critical for kelp health via lytic-lysogenic infections and the expression of folate biosynthesis genes. In-situ kelp mesocosm cultivation and metagenomic mining revealed that kelp holobiont profoundly reshaped surrounding seawater and sediment virus-prokaryote pairings through changing surrounding environmental conditions and virus-host migrations. Some kelp epiphytic viruses could even infect sediment autochthonous bacteria after deposition. Moreover, the presence of ample viral auxiliary metabolic genes for kelp polysaccharide (e.g. laminarin) degradation underscores the underappreciated viral metabolic influence on macroalgal carbon cycling. This study provides key insights into understanding the previously overlooked ecological significance of viruses within macroalgal holobionts and the macroalgae-prokaryotes-virus tripartite relationship.
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Affiliation(s)
- Jiulong Zhao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Shailesh Nair
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Zenghu Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zengmeng Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
| | - Yongyu Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Humphrey B, Mackenzie M, Lobitz M, Schambach JY, Lasley G, Kolker S, Ricken B, Bennett H, Williams KP, Smallwood CR, Cahill J. Biotic countermeasures that rescue Nannochloropsis gaditana from a Bacillus safensis infection. Front Microbiol 2023; 14:1271836. [PMID: 37920264 PMCID: PMC10618357 DOI: 10.3389/fmicb.2023.1271836] [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: 08/02/2023] [Accepted: 09/15/2023] [Indexed: 11/04/2023] Open
Abstract
The natural assemblage of a symbiotic bacterial microbiome (bacteriome) with microalgae in marine ecosystems is now being investigated as a means to increase algal productivity for industry. When algae are grown in open pond settings, biological contamination causes an estimated 30% loss of the algal crop. Therefore, new crop protection strategies that do not disrupt the native algal bacteriome are needed to produce reliable, high-yield algal biomass. Bacteriophages offer an unexplored solution to treat bacterial pathogenicity in algal cultures because they can eliminate a single species without affecting the bacteriome. To address this, we identified a highly virulent pathogen of the microalga Nannochloropsis gaditana, the bacterium Bacillus safensis, and demonstrated rescue of the microalgae from the pathogen using phage. 16S rRNA amplicon sequencing showed that phage treatment did not alter the composition of the bacteriome. It is widely suspected that the algal bacteriome could play a protective role against bacterial pathogens. To test this, we compared the susceptibility of a bacteriome-attenuated N. gaditana culture challenged with B. safensis to a N. gaditana culture carrying a growth-promoting bacteriome. We showed that the loss of the bacteriome increased the susceptibility of N. gaditana to the pathogen. Transplanting the microalgal bacteriome to the bacteriome-attenuated culture reconstituted the protective effect of the bacteriome. Finally, the success of phage treatment was dependent on the presence of beneficial bacteriome. This study introduces two synergistic countermeasures against bacterial pathogenicity in algal cultures and a tractable model for studying interactions between microalgae, phages, pathogens, and the algae microbiome.
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Affiliation(s)
- Brittany Humphrey
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
| | - Morgan Mackenzie
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
| | - Mia Lobitz
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
| | - Jenna Y. Schambach
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
| | - Greyson Lasley
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
| | - Stephanie Kolker
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
| | - Bryce Ricken
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
| | - Haley Bennett
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
| | - Kelly P. Williams
- Sandia National Laboratories, Department of Systems Biology, Livermore, CA, United States
| | - Chuck R. Smallwood
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
| | - Jesse Cahill
- Sandia National Laboratories, Department of Molecular and Microbiology, Albuquerque, NM, United States
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Zhang Z, Zhao H, Mou S, Nair S, Zhao J, Jiao N, Zhang Y. Phage Infection Benefits Marine Diatom Phaeodactylum tricornutum by Regulating the Associated Bacterial Community. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02045-1. [PMID: 35622094 DOI: 10.1007/s00248-022-02045-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
The interaction between marine phyto- and bacterioplankton is regulated by multiple environmental and biological factors. Among them, phages as the major regulators of bacterial mortality are considered to have important impacts on algae-associated bacteria and algae-bacteria relationship. However, little is currently known about the actual impact of phages from this perspective. Here, we revealed that phage infection improved the maximum quantum efficiency of photosystem II of Phaeodactylum tricornutum by regulating the associated bacterial community. Specifically, phage infection weakened bacterial abundance and eliminated their negative effects on the diatom. Unexpectedly, the structure of the bacterial community co-cultured with the diatom was not significantly affected, likely because the shaping effect of the diatom on the bacterial community structure can far outcompete or mask the impact of phage infection. Our results established a link between algae, bacteria, and phages, suggesting that phage infection benefits the diatom by regulating the associated bacterial community.
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Affiliation(s)
- Zenghu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hanshuang Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shanli Mou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shailesh Nair
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiulong Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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