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Chen W, Park YK, Studená L, Bell D, Hapeta P, Fu J, Nixon PJ, Ledesma-Amaro R. Synthetic, marine, light-driven, autotroph-heterotroph co-culture system for sustainable β-caryophyllene production. BIORESOURCE TECHNOLOGY 2024; 410:131232. [PMID: 39117247 DOI: 10.1016/j.biortech.2024.131232] [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: 05/26/2024] [Revised: 07/27/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
Applying low-cost substrate is critical for sustainable bioproduction. Co-culture of phototrophic and heterotrophic microorganisms can be a promising solution as they can use CO2 and light as feedstock. This study aimed to create a light-driven consortium using a marine cyanobacterium Synechococcus sp. PCC 7002 and an industrial yeast Yarrowia lipolytica. First, the cyanobacterium was engineered to accumulate and secrete sucrose by regulating the expression of genes involved in sucrose biosynthesis and transport, resulting in 4.0 g/L of sucrose secretion. Then, Yarrowia lipolytica was engineered to efficiently use sucrose and produce β-caryophyllene that has various industrial applications. Then, co- and sequential-culture were optimized with different induction conditions and media compositions. A maximum β-caryophyllene yield of 14.1 mg/L was obtained from the co-culture. This study successfully established an artificial light-driven consortium based on a marine cyanobacterium and Y. lipolytica, and provides a foundation for sustainable bioproduction from CO2 and light through co-culture systems.
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Affiliation(s)
- Wenchao Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China; Department of Bioengineering, Bezos Centre for Sustainable Protein, Microbial Food Hub and Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Young-Kyoung Park
- Department of Bioengineering, Bezos Centre for Sustainable Protein, Microbial Food Hub and Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK; Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Lucie Studená
- Department of Bioengineering, Bezos Centre for Sustainable Protein, Microbial Food Hub and Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - David Bell
- SynbiCITE Innovation and Knowledge Centre, Imperial College London, London SW7 2AZ, UK
| | - Piotr Hapeta
- Department of Bioengineering, Bezos Centre for Sustainable Protein, Microbial Food Hub and Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Jing Fu
- Department of Bioengineering, Bezos Centre for Sustainable Protein, Microbial Food Hub and Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Peter J Nixon
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Bezos Centre for Sustainable Protein, Microbial Food Hub and Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK.
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2
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Su G, Guo Z, Hu Y, Zheng Q, Zopfi J, Lehmann MF, Jiao N. Tidal control on aerobic methane oxidation and mitigation of methane emissions from coastal mangrove sediments. ENVIRONMENTAL RESEARCH 2024; 263:120049. [PMID: 39322055 DOI: 10.1016/j.envres.2024.120049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 09/20/2024] [Accepted: 09/21/2024] [Indexed: 09/27/2024]
Abstract
Mangrove forests represent important sources of methane, partly thwarting their ecosystem function as an efficient atmospheric carbon dioxide sink. Many studies have focused on the spatial and temporal variability of methane emissions from mangrove ecosystems, yet little is known about the microbial and physical controls on the release of biogenic methane from tidally influenced mangrove sediments. Here, we show that aerobic methane oxidation is a key microbial process that effectively reduces methane emissions from mangrove sediments. We further demonstrate clear links between the tidal cycle and fluctuations in methane fluxes, with contrasting methane emission rates under different tidal amplitudes. Our data suggest that both the microbial methane oxidation activity and pressure-induced advective transport modulated methane fluxes in the mangrove sediments. Methane oxidation activity is limited by the availability of oxygen in the surface sediments, which in turn is controlled by tidal dynamics, further highlighting the interactive physico-biogeochemical controls on biological methane fluxes. Although we found some molecular evidence for anaerobic methanotrophs in the deeper sediments, anaerobic methane oxidation seems to play only a minor role in the mangrove sediments, with potential rates being two orders of magnitude lower than those of aerobic methane oxidation. Our findings confirmed the importance of surface sediments as biological barrier for methane. Specifically, when sediments were exposed to the air, methane consumption increased by ∼227%, and the methane flux was reduced by ∼62%, compared to inundated conditions. Our data demonstrate how tides can orchestrate the daily rhythm of methane consumption and production within mangrove sediments, thus explaining the temporal variability of methane emissions in the tidally influenced coastal mangrove systems.
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Affiliation(s)
- Guangyi Su
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences and Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, China.
| | - Zhenli Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences and Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, China
| | - Yuxing Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences and Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences and Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, China
| | - Jakob Zopfi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Moritz F Lehmann
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences and Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, China.
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3
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Li H, Chen H, He X, Lu Y, Gao H, Song H, Cheng S. Enhancing the nitrogen removal of anammox sludge by setting up novel redox mediators-mediated anammox process. CHEMOSPHERE 2024; 365:143360. [PMID: 39303793 DOI: 10.1016/j.chemosphere.2024.143360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Revised: 09/09/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Anaerobic ammonium oxidizing (anammox) bacteria have been proven weak-electroactive. However, the impact of exogenous anthraquinone-2,6-disulfonate (AQDS) on the anammox activity, although it usually plays essential roles in the life activities of many other electroactive microorganisms, is still unknown. Therefore, this study further explored the influences of AQDS on the anammox activity and the interaction mechanism with anammox bacteria, as well as the behaviors of NH4+, NO2-, and NO3-. The results showed that exogenous AQDS increased the ammonium and total nitrogen removal rates by 12.8% and 10.7%, respectively. Interestingly, the conversion from NO2- to NO3- was significantly reduced after adding AQDS, resulting in a 40.1% reduction in NO3- production of anammox process. In this study, we found for the first time that anammox bacteria could not only carry out the conventional anammox process but also perform a weak redox mediator-mediated anammox process, which could achieve the 1:1 consumption of NH4+ and NO2-. The redox mediator-mediated anammox process was related to an endogenous redox mediator (ERM) synthesized and secreted by anammox bacteria, whose redox midpoint potential was around -0.26 V (vs. Ag/AgCl). After adding AQDS, not only the ERM-mediated anammox process was enhanced, but also two novel redox mediator-mediated anammox processes were introduced, including the AQDS-mediated anammox process and ERM-AQDS-mediated anammox process. These three redox mediator-mediated anammox processes significantly improved the nitrogen removal performance of anammox bacteria and reduced energy consumption. These findings will help reduce the dependence of anammox technology on NO2-, reduce the cost of subsequent treatment of NO3-, and provide new visions for optimizing and applying anammox technology.
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Affiliation(s)
- Huahua Li
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Hua Chen
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xinyuan He
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Yi Lu
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
| | - Shaoan Cheng
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou, 310027, China.
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Abate R, Oon YL, Oon YS, Bi Y, Mi W, Song G, Gao Y. Diverse interactions between bacteria and microalgae: A review for enhancing harmful algal bloom mitigation and biomass processing efficiency. Heliyon 2024; 10:e36503. [PMID: 39286093 PMCID: PMC11402748 DOI: 10.1016/j.heliyon.2024.e36503] [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: 02/16/2024] [Revised: 08/15/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024] Open
Abstract
The interactions between bacteria and microalgae play pivotal roles in resource allocation, biomass accumulation, nutrient recycling, and species succession in aquatic systems, offering ample opportunities to solve several social problems. The escalating threat of harmful algal blooms (HABs) in the aquatic environment and the lack of cheap and eco-friendly algal-biomass processing methods have been among the main problems, demanding efficient and sustainable solutions. In light of this, the application of algicidal bacteria to control HABs and enhance algal biomass processing has been promoted in the past few decades as potentially suitable mechanisms to solve those problems. Hence, this comprehensive review aims to explore the diverse interaction modes between bacteria and microalgae, ranging from synergistic to antagonistic, and presents up-to-date information and in-depth analysis of their potential biotechnological applications, particularly in controlling HABs and enhancing microalgal biomass processing. For instance, several studies revealed that algicidal bacteria can effectively inhibit the growth of Microcystis aeruginosa, a notorious freshwater HAB species, with an antialgal efficiency of 24.87 %-98.8 %. The review begins with an overview of the mechanisms behind algae-bacteria interactions, including the environmental factors influencing these dynamics and their broader implications for aquatic ecosystems. It then provides a detailed analysis of the role of algicidal bacteria in controlling harmful algal blooms, as well as their role in bioflocculation and the pretreatment of microalgal biomass. Additionally, the review identifies and discusses the constraints and challenges in the biotechnological application of these interactions. By exploring the strategic use of algicidal bacteria, this review not only underscores their importance in maintaining aquatic environmental health but also in enhancing biomass processing efficiency. It offers valuable insights into future research avenues and the potential scalability of these applications, both in situ and at an industrial level.
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Affiliation(s)
- Rediat Abate
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Natural and Computatinal Science, Arba Minch University, Ethiopia
| | - Yoong-Ling Oon
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Yoong-Sin Oon
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Yonghong Bi
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wujuan Mi
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gaofei Song
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yahui Gao
- School of Life Sciences, Xiamen University, Xiamen, 361102, China
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5
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Park H, Bulzu PA, Shabarova T, Kavagutti VS, Ghai R, Kasalický V, Jezberová J. Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria. MICROBIOME 2024; 12:150. [PMID: 39127705 DOI: 10.1186/s40168-024-01867-0] [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: 04/04/2024] [Accepted: 07/03/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies. RESULTS In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla. CONCLUSIONS Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. Video Abstract.
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Affiliation(s)
- Hongjae Park
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Paul-Adrian Bulzu
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Tanja Shabarova
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Vinicius S Kavagutti
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Rohit Ghai
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Vojtěch Kasalický
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jitka Jezberová
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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6
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Gan Y, Ji X, Yang R. Metagenomic profiling of antibiotic resistance genes/bacteria removal in urban water: Algal-bacterial consortium treatment system. BIORESOURCE TECHNOLOGY 2024; 404:130905. [PMID: 38801952 DOI: 10.1016/j.biortech.2024.130905] [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: 03/19/2024] [Revised: 05/12/2024] [Accepted: 05/25/2024] [Indexed: 05/29/2024]
Abstract
Antibiotic resistance genes (ARGs) have exhibited significant ecological concerns, especially in the urban water that are closely associated with human health. In this study, with presence of exogenous Chlorella vulgaris-Bacillus licheniformis consortium, most of the typical ARGs and MGEs were removed. Furthermore, the relative abundance of potential ARGs hosts has generally decreased by 1-4 orders of magnitude, revealing the role of algal-bacterial consortium in cutting the spread of ARGs in urban water. While some of ARGs such as macB increased, which may be due to the negative impact of algicidal bacteria and algal viruses in urban water on exogenous C. vulgaris and the suppression of exogenous B. licheniformis by indigenous microorganisms. A new algal-bacterial interaction might form between C. vulgaris and indigenous microorganisms. The interplay between C. vulgaris and bacteria has a significant impact on the fate of ARGs removal in urban water.
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Affiliation(s)
- Yongdi Gan
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai 201418, PR China
| | - Xiyan Ji
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai 201418, PR China.
| | - Ruzhou Yang
- Iontra Inc., 5925 E. Evans Ave, Denver, CO 80222, USA
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7
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Kim KH, Kim JM, Baek JH, Jeong SE, Kim H, Yoon HS, Jeon CO. Metabolic relationships between marine red algae and algae-associated bacteria. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:298-314. [PMID: 38827136 PMCID: PMC11136935 DOI: 10.1007/s42995-024-00227-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/28/2023] [Indexed: 06/04/2024]
Abstract
Mutualistic interactions between marine phototrophs and associated bacteria are an important strategy for their successful survival in the ocean, but little is known about their metabolic relationships. Here, bacterial communities in the algal sphere (AS) and bulk solution (BS) of nine marine red algal cultures were analyzed, and Roseibium and Phycisphaera were identified significantly more abundantly in AS than in BS. The metabolic features of Roseibium RMAR6-6 (isolated and genome-sequenced), Phycisphaera MAG 12 (obtained by metagenomic sequencing), and a marine red alga, Porphyridium purpureum CCMP1328 (from GenBank), were analyzed bioinformatically. RMAR6-6 has the genetic capability to fix nitrogen and produce B vitamins (B1, B2, B5, B6, B9, and B12), bacterioferritin, dimethylsulfoniopropionate (DMSP), and phenylacetate that may enhance algal growth, whereas MAG 12 may have a limited metabolic capability, not producing vitamins B9 and B12, DMSP, phenylacetate, and siderophores, but with the ability to produce bacitracin, possibly modulating algal microbiome. P. purpureum CCMP1328 lacks the genetic capability to fix nitrogen and produce vitamin B12, DMSP, phenylacetate, and siderophore. It was shown that the nitrogen-fixing ability of RMAR6-6 promoted the growth of P. purpureum, and DMSP reduced the oxidative stress of P. purpureum. The metabolic interactions between strain RMAR6-6 and P. purpureum CCMP1328 were also investigated by the transcriptomic analyses of their monoculture and co-culture. Taken together, potential metabolic relationships between Roseibium and P. purpureum were proposed. This study provides a better understanding of the metabolic relationships between marine algae and algae-associated bacteria for successful growth. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00227-z.
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Affiliation(s)
- Kyung Hyun Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon, 34054 Republic of Korea
| | - Jeong Min Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Hocheol Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
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Cheng S, Li H, He X, Chen H, Li L. Improving anammox activity and reactor start-up speed by using CO 2/NaHCO 3 buffer. J Environ Sci (China) 2024; 139:60-71. [PMID: 38105078 DOI: 10.1016/j.jes.2023.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/28/2023] [Accepted: 05/12/2023] [Indexed: 12/19/2023]
Abstract
Anammox bacteria grow slowly and can be affected by large pH fluctuations. Using suitable buffers could make the start-up of anammox reactors easy and rapid. In this study, the effects of three kinds of buffers on the nitrogen removal and growth characteristics of anammox sludge were investigated. Reactors with CO2/NaHCO3 buffer solution (CCBS) performed the best in nitrogen removal, while 4-(2-hydroxyerhyl)piperazine-1-ethanesulfonic acid (HEPES) and phosphate buffer solution (PBS) inhibited the anammox activity. Reactors with 50 mmol/L CCBS could start up in 20 days, showing the specific anammox activity and anammox activity of 1.01±0.10 gN/(gVSS·day) and 0.83±0.06 kgN/(m3·day), respectively. Candidatus Kuenenia was the dominant anammox bacteria, with a relative abundance of 71.8%. Notably, anammox reactors could also start quickly by using 50 mmol/L CCBS under non-strict anaerobic conditions. These findings are meaningful for the quick start-up of engineered anammox reactors and prompt enrichment of anammox bacteria.
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Affiliation(s)
- Shaoan Cheng
- State Key Laboratory of Clean Energy Utilization, College of Energy Engineering, Zhejiang University, Hangzhou 310027, China.
| | - Huahua Li
- State Key Laboratory of Clean Energy Utilization, College of Energy Engineering, Zhejiang University, Hangzhou 310027, China
| | - Xinyuan He
- State Key Laboratory of Clean Energy Utilization, College of Energy Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hua Chen
- State Key Laboratory of Clean Energy Utilization, College of Energy Engineering, Zhejiang University, Hangzhou 310027, China
| | - Longxin Li
- State Key Laboratory of Clean Energy Utilization, College of Energy Engineering, Zhejiang University, Hangzhou 310027, China
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9
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Wang YF, Xu JY, Liu ZL, Cui HL, Chen P, Cai TG, Li G, Ding LJ, Qiao M, Zhu YG, Zhu D. Biological Interactions Mediate Soil Functions by Altering Rare Microbial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5866-5877. [PMID: 38504110 DOI: 10.1021/acs.est.4c00375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Soil microbes, the main driving force of terrestrial biogeochemical cycles, facilitate soil organic matter turnover. However, the influence of the soil fauna on microbial communities remains poorly understood. We investigated soil microbiota dynamics by introducing competition and predation among fauna into two soil ecosystems with different fertilization histories. The interactions significantly affected rare microbial communities including bacteria and fungi. Predation enhanced the abundance of C/N cycle-related genes. Rare microbial communities are important drivers of soil functional gene enrichment. Key rare microbial taxa, including SM1A02, Gammaproteobacteria, and HSB_OF53-F07, were identified. Metabolomics analysis suggested that increased functional gene abundance may be due to specific microbial metabolic activity mediated by soil fauna interactions. Predation had a stronger effect on rare microbes, functional genes, and microbial metabolism compared to competition. Long-term organic fertilizer application increased the soil resistance to animal interactions. These findings provide a comprehensive understanding of microbial community dynamics under soil biological interactions, emphasizing the roles of competition and predation among soil fauna in terrestrial ecosystems.
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Affiliation(s)
- Yi-Fei Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jia-Yang Xu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe-Lun Liu
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hui-Ling Cui
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Peng Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Tian-Gui Cai
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
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10
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Zhao Y, Sun T, Li Y, Yang Z, Chen J, Wang J, Yu X, Tang X, Xiao H. The host sex contributes to the endophytic bacterial community in Sargassum thunbergii and their receptacles. Front Microbiol 2024; 15:1334918. [PMID: 38559345 PMCID: PMC10978810 DOI: 10.3389/fmicb.2024.1334918] [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: 11/08/2023] [Accepted: 02/14/2024] [Indexed: 04/04/2024] Open
Abstract
Endophytic bacteria have a complex coevolutionary relationship with their host macroalgae. Dioecious macroalgae are important producers in marine ecosystems, but there is still a lack of research on how sex influences their endophytic bacteria. In this study, the endophytic bacterial communities in male and female S. thunbergii and their reproductive tissues (receptacles) were compared using culture methods and high-throughput sequencing. The endophytic bacterial communities detected by the two methods were different. Among the 78 isolated strains, the dominant phylum, genus, and species were Bacillota, Alkalihalobacillus, and Alkalihalobacillus algicola, respectively, in the algal bodies, while in the receptacles, they were Bacillota, Vibrio, and Vibrio alginolyticus. However, 24 phyla and 349 genera of endophytic bacteria were identified by high-throughput sequencing, and the dominant phylum and genus were Pseudomonadota and Sva0996_ Marine_ Group, respectively, in both the algal body and the receptacles. The two methods showed similar compositions of endophytic bacterial communities between the samples of different sexes, but the relative abundances of dominant and specific taxa were different. The high-throughput sequencing results showed more clearly that the sex of the host alga had an effect on its endophyte community assembly and a greater effect on the endophytic bacterial community in the receptacles. Moreover, most specific bacteria and predicted functional genes that differed between the samples from the males and females were related to metabolism, suggesting that metabolic differences are the main causes of sex differences in the endophytic bacterial community. Our research is the first to show that host sex contributes to the composition of endophytic bacterial communities in dioecious marine macroalgae. The results enrich the database of endophytic bacteria of dioecious marine macroalgae and pave the way for better understanding the assembly mechanism of the endophytic bacterial community of algae.
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Affiliation(s)
- Yayun Zhao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Tao Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Qingdao Branch CCCC Water Transportation Consultants Co.,LTD, Qingdao, China
| | - Yang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Shandong Marine Forecast and Hazard Mitigation Service, Qingdao, China
| | - Zhibo Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinlong Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
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11
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Zhang H, Tan Y, Zhou Y, Liu J, Xia X. Light-dark fluctuated metabolic features of diazotrophic and non-diazotrophic cyanobacteria and their coexisting bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 910:168702. [PMID: 37992836 DOI: 10.1016/j.scitotenv.2023.168702] [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: 09/06/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Cyanobacteria, the most abundant photosynthetic organisms in oceans, are tightly associated with diverse microbiota. However, the relationships between heterotrophic bacteria and cyanobacteria, particularly the diazotrophic group, are not fully understood. Here, we compared diel gene expressions of N2 fixing cyanobacteria Crocosphaera watsonii WH0003 and non-diazotrophic Synechococcus sp. RS9902 and their associated bacteria using metatranscriptomics approach. WH0003 showed significant up-regulation of O2 restriction and oxidative phosphorylation related genes at nighttime due to large carbon and energy investments for active N2 fixation. In contrast, RS9902 had higher expression for those genes at daytime. The two cyanobacteria hosted distinct bacterial communities with clear separate substrate utilization niches to reduce competition. Light-dark partitioning of nutrient acquisition among the dominant bacterial groups likely contributed to the dynamic balance for community coexistence. Moreover, particle-attached (PA) bacteria in RS9902 largely expressed glycoside hydrolases to hydrolyze complex carbohydrate compounds, while free-living (FL) bacteria priorly assimilated soluble, diffusible molecules. Spatial partitioning of nutrient acquisition between PA and FL bacteria implied that location initially influenced metabolic features of host associated bacteria. Our results advance knowledge on light-dark regulated metabolic activities of diazotrophic and non-diazotrophic cyanobacteria, and provide new insights into the coexisting strategies of different bacterial groups.
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Affiliation(s)
- Hao Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Youping Zhou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiaxing Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China..
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China..
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12
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Qu W, Zuo Y, Zhang Y, Wang J. Structure and assembly process of fungal communities in the Yangtze River Estuary. Front Microbiol 2024; 14:1220239. [PMID: 38260888 PMCID: PMC10800840 DOI: 10.3389/fmicb.2023.1220239] [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: 05/10/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Marine fungi are essential for the ecological function of estuarine ecosystems. However, limited studies have reported on the structure and assembly pattern of the fungal communities in estuaries. The purpose of this study is to reveal the structure and the ecological process of the fungal community in the Yangtze River Estuary (YRE) by using the amplicon sequencing method. Phyla of Ascomycota, Basidiomycota, and Chytridiomycota were dominant in the seawater and sediment samples from YRE. The null model analysis, community-neutral community model (NCM), and phylogenetic normalized stochasticity ratio (pNST) showed that the stochastic process dominated the assembly of fungal communities in YRE. Drift and homogeneous dispersal were the predominant stochastic processes for the fungal community assembly in seawater and sediment samples, respectively. The co-occurrence network analysis showed that fungal communities were more complex and closely connected in the sediment than in the seawater samples. Phyla Ascomycota, Basidiomycota, and Mucoromycota were the potential keystone taxa in the network. These findings demonstrated the importance of stochastic processes for the fungal community assembly, thereby widening our knowledge of the community structure and dynamics of fungi for future study and utilization in the YRE ecosystem.
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Affiliation(s)
| | | | | | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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13
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Xu H, Xiao Q, Dai Y, Chen D, Zhang C, Jiang Y, Xie J. Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data. MICROBIAL ECOLOGY 2023; 86:3043-3056. [PMID: 37831075 DOI: 10.1007/s00248-023-02307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.
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Affiliation(s)
- Hongxiang Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qiong Xiao
- Institute of Karst Geology, CAGS, Key Laboratory on Karst Dynamics, MNR & Guangxi, Guilin, 541004, China
| | - Yongdong Dai
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Dexin Chen
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Cheng Zhang
- Institute of Karst Geology, CAGS, Key Laboratory on Karst Dynamics, MNR & Guangxi, Guilin, 541004, China.
| | - Yongjun Jiang
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing, 400715, China.
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China.
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing, 400715, China.
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14
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Ascandari A, Aminu S, Safdi NEH, El Allali A, Daoud R. A bibliometric analysis of the global impact of metaproteomics research. Front Microbiol 2023; 14:1217727. [PMID: 37476667 PMCID: PMC10354264 DOI: 10.3389/fmicb.2023.1217727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
Background Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated. Methods Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores. Results A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1. Conclusion The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.
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Affiliation(s)
- AbdulAziz Ascandari
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Suleiman Aminu
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Nour El Houda Safdi
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid Daoud
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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15
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Determinants of Total and Active Microbial Communities Associated with Cyanobacterial Aggregates in a Eutrophic Lake. mSystems 2023; 8:e0099222. [PMID: 36927063 PMCID: PMC10134853 DOI: 10.1128/msystems.00992-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Cyanobacterial aggregates (CAs) comprised of photosynthetic and phycospheric microorganisms are often the cause of cyanobacterial blooms in eutrophic freshwater lakes. Although phylogenetic diversity in CAs has been extensively studied, much less was understood about the activity status of microorganisms inside CAs and determinants of their activities. In this study, the 16S rRNA gene (rDNA)-based total communities within CAs in Lake Taihu of China were analyzed over a period of 6 months during the bloom season; the 16S rRNA-based active communities during daytime, nighttime, and under anoxic conditions were also profiled. Synchronous turnover of both cyanobacterial and phycospheric communities was observed, suggesting the presence of close interactions. The rRNA/rDNA ratio-based relative activities of individual taxa were predominantly determined by their rDNA-based relative abundances. In particular, high-abundance taxa demonstrated comparatively lower activities, whereas low-abundance taxa were generally more active. In comparison, hydrophysicochemical factors as well as diurnal and redox conditions showed much less impact on relative activities of microbial taxa within CAs. Nonetheless, total and active communities exhibited differences in community assembly processes, the former of which were almost exclusively controlled by homogeneous selection during daytime and under anoxia. Taken together, the results from this study provide novel insights into the relationships among microbial activities, community structure, and environmental conditions and highlight the importance of further exploring the regulatory mechanisms of microbial activities at the community level. IMPORTANCE Cyanobacterial aggregates are important mediators of biogeochemical cycles in eutrophic lakes during cyanobacterial blooms, yet regulators of microbial activities within them are not well understood. This study revealed rDNA-based abundances strongly affected the relative activities of microbial taxa within Microcystis aggregates, as well as trade-off effects between microbial abundances and activities. Environmental conditions further improved the levels of relative activities and affected community assembly mechanisms in phycospheric communities. The relationships among microbial activities, abundances, and environmental conditions improve our understanding of the regulatory mechanisms of microbial activities in cyanobacterial aggregates and also provide a novel clue for studying determinants of microbial activities in other ecosystems.
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16
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Liu L, Chen X, Ye J, Ma X, Han Y, He Y, Tang K. Sulfoquinovose is a widespread organosulfur substrate for Roseobacter clade bacteria in the ocean. THE ISME JOURNAL 2023; 17:393-405. [PMID: 36593260 PMCID: PMC9938184 DOI: 10.1038/s41396-022-01353-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 01/03/2023]
Abstract
Sulfoquinovose (SQ) is one of the most abundant organosulfur compounds in the biosphere, and its biosynthesis and degradation can represent an important contribution to the sulfur cycle. To data, in marine environments, the microorganisms capable of metabolising SQ have remained unidentified and the sources of SQ are still uncertain. Herein, the marine Roseobacter clade bacteria (RCB) Dinoroseobacter shibae DFL 12 and Roseobacter denitrificans OCh 114 were found to grow using SQ as the sole source of carbon and energy. In the presence of SQ, we identified a set of highly up-regulated proteins encoded by gene clusters in these two organisms, of which four homologues to proteins in the SQ monooxygenase pathway of Agrobacterium fabrum C58 may confer the ability to metabolise SQ to these marine bacteria. The sulfite released from SQ desulfonation by FMN-dependent SQ monooxygenase (SmoC) may provide bacteria with reduced sulfur for assimilation, while proteins associated with sulfite production via assimilatory sulfate reduction were significantly down-regulated. Such SQ catabolic genes are restricted to a limited number of phylogenetically diverse bacterial taxa with the predominate genera belonging to the Roseobacter clade (Roseobacteraceae). Moreover, transcript analysis of Tara Oceans project and coastal Bohai Sea samples provided additional evidence for SQ metabolism by RCB. SQ was found to be widely distributed in marine phytoplankton and cyanobacteria with variable intracellular concentrations ranging from micromolar to millimolar levels, and the amounts of SQ on particulate organic matter in field samples were, on average, lower than that of dimethylsulfoniopropionate (DMSP) by one order of magnitude. Together, the phototroph-derived SQ actively metabolised by RCB represents a previously unidentified link in the marine sulfur cycle.
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Affiliation(s)
- Le Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jianing Ye
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Xiaoyi Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Yu Han
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Yajie He
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
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17
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Weissberg O, Aharonovich D, Sher D. Phototroph-heterotroph interactions during growth and long-term starvation across Prochlorococcus and Alteromonas diversity. THE ISME JOURNAL 2023; 17:227-237. [PMID: 36335212 PMCID: PMC9860064 DOI: 10.1038/s41396-022-01330-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/02/2022] [Accepted: 10/05/2022] [Indexed: 11/08/2022]
Abstract
Due to their potential impact on ecosystems and biogeochemistry, microbial interactions, such as those between phytoplankton and bacteria, have been studied intensively using specific model organisms. Yet, to what extent interactions differ between closely related organisms, or how these interactions change over time, or culture conditions, remains unclear. Here, we characterize the interactions between five strains each of two globally abundant marine microorganisms, Prochlorococcus (phototroph) and Alteromonas (heterotroph), from the first encounter between individual strains and over more than a year of repeated cycles of exponential growth and long-term nitrogen starvation. Prochlorococcus-Alteromonas interactions had little effect on traditional growth parameters such as Prochlorococcus growth rate, maximal fluorescence, or lag phase, affecting primarily the dynamics of culture decline, which we interpret as representing cell mortality and lysis. The shape of the Prochlorococcus decline curve and the carrying capacity of the co-cultures were determined by the phototroph and not the heterotroph strains involved. Comparing various mathematical models of culture mortality suggests that Prochlorococcus death rate increases over time in mono-cultures but decreases in co-cultures, with cells potentially becoming more resistant to stress. Our results demonstrate intra-species differences in ecologically relevant co-culture outcomes. These include the recycling efficiency of N and whether the interactions are mutually synergistic or competitive. They also highlight the information-rich growth and death curves as a useful readout of the interaction phenotype.
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Affiliation(s)
- Osnat Weissberg
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
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18
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Xu L, Chen Y, Wang Z, Zhang Y, He Y, Zhang A, Chen H, Xue G. Discovering dominant ammonia assimilation: Implication for high-strength nitrogen removal in full scale biological treatment of landfill leachate. CHEMOSPHERE 2023; 312:137256. [PMID: 36395888 DOI: 10.1016/j.chemosphere.2022.137256] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Landfill leachate containing high-strength nitrogen is generated in domestic waste landfilling. The integration of anoxic and aerobic process (AO) based on nitrification and denitrification, has been a mainstream process of biological nitrogen removal (BNR). But the high-strength organics as well as aerobic effluent reflux might change the biochemical environment designed and operated as AO. In view of the nitrogen balance in a full scale landfill leachate treatment plant with two-stage AO, we found that approximately 90% removal of total nitrogen (TN) and ammonia (NH4+-N) focused on primary anoxic and aerobic stage. Meanwhile, the less nitrate and nitrite in the aerobic effluent were incapable of sustaining denitrification or anaerobic ammonia oxidation (anammox). The high reflux flow from aerobic to anoxic process enabled the similar microbial community and functional genes in anoxic and aerobic process units. However, the functional genes involving ammonia assimilation in all process units showcased the highest abundance compared to those correlated with other BNR pathways, including nitrification and denitrification, assimilatory and dissimilatory nitrate reduction, nitrogen fixation and anammox. The ammonia assimilation dominated the removals of TN and NH4+-N, rather than other BNR mechanism. The insight of dominant ammonia assimilation is favorable for illustrating the authentic BNR mechanism of landfill leachate in AO, thereby guiding the optimization of engineering design and operation.
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Affiliation(s)
- Lei Xu
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yuting Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Zheng Wang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yu Zhang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yueling He
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Ai Zhang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Hong Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Gang Xue
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200000, China.
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19
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Halary S, Duperron S, Demay J, Duval C, Hamlaoui S, Piquet B, Reinhardt A, Bernard C, Marie B. Metagenome-Based Exploration of Bacterial Communities Associated with Cyanobacteria Strains Isolated from Thermal Muds. Microorganisms 2022; 10:2337. [PMID: 36557590 PMCID: PMC9785279 DOI: 10.3390/microorganisms10122337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Cyanobacteria constitute a pioneer colonizer of specific environments for whom settlement in new biotopes precedes the establishment of composite microbial consortia. Some heterotrophic bacteria constitute cyanobacterial partners that are considered as their cyanosphere, being potentially involved in mutualistic relationships through the exchange and recycling of key nutrients and the sharing of common goods. Several non-axenic cyanobacterial strains have been recently isolated, along with their associated cyanospheres, from the thermal mud of Balaruc-les-Bains (France) and the biofilms of the retention basin where they develop. The community structure and relationships among the members of the isolated cyanobacterial strains were characterized using a metagenomic approach combined with taxonomic and microscopic descriptions of the microbial consortia. The results provided insights into the potential role and metabolic capabilities of the microorganisms of thermal mud-associated cyanobacterial biofilms. Thus, the physical proximity, host-specificity, and genetic potential functions advocate for their complementarity between cyanobacteria and their associated microbiota. Besides these findings, our results also highlighted the great influence of the reference protein database chosen for performing functional annotation of the metagenomes from organisms of the cyanosphere and the difficulty of selecting one unique database that appropriately covers both autotroph and heterotroph metabolic specificities.
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Affiliation(s)
- Sébastien Halary
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Sébastien Duperron
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Justine Demay
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
- Thermes de Balaruc-Les-Bains, 1 rue du Mont Saint-Clair BP 45, 34540 Balaruc-Les-Bains, France
| | - Charlotte Duval
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Sahima Hamlaoui
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Bérénice Piquet
- Electron Microscopy Platform, Muséum National d’Histoire Naturelle, CP 39, 12 rue Buffon, CEDEX 05, 75231 Paris, France
| | - Anita Reinhardt
- Thermes de Balaruc-Les-Bains, 1 rue du Mont Saint-Clair BP 45, 34540 Balaruc-Les-Bains, France
| | - Cécile Bernard
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
| | - Benjamin Marie
- UMR 7245, CNRS/MNHN, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), équipe “Cyanobactéries, Cyanotoxines et Environnement”, 12 rue Buffon-CP 39, CEDEX 05, 75231 Paris, France
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20
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Pestana CJ, Santos AA, Capelo-Neto J, Melo VMM, Reis KC, Oliveira S, Rogers R, Pacheco ABF, Hui J, Skillen NC, Barros MUG, Edwards C, Azevedo SMFO, Robertson PKJ, Irvine JTS, Lawton LA. Suppressing cyanobacterial dominance by UV-LED TiO 2-photocatalysis in a drinking water reservoir: A mesocosm study. WATER RESEARCH 2022; 226:119299. [PMID: 36323220 DOI: 10.1016/j.watres.2022.119299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Cyanobacteria and their toxic secondary metabolites present challenges for water treatment globally. In this study we have assessed TiO2 immobilized onto recycled foamed glass beads by a facile calcination method, combined in treatment units with 365 nm UV-LEDs. The treatment system was deployed in mesocosms within a eutrophic Brazilian drinking water reservoir. The treatment units were deployed for 7 days and suppressed cyanobacterial abundance by 85% while at the same time enhancing other water quality parameters; turbidity and transparency improved by 40 and 81% respectively. Genomic analysis of the microbiota in the treated mesocosms revealed that the composition of the cyanobacterial community was affected and the abundance of Bacteroidetes and Proteobacteria increased during cyanobacterial suppression. The effect of the treatment on zooplankton and other eukaryotes was also monitored. The abundance of zooplankton decreased while Chrysophyte and Alveolata loadings increased. The results of this proof-of-concept study demonstrate the potential for full-scale, in-reservoir application of advanced oxidation processes as complementary water treatment processes.
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Affiliation(s)
- Carlos J Pestana
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK.
| | - Allan A Santos
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Capelo-Neto
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Brazil
| | - Vânia M M Melo
- Department of Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Kelly C Reis
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Brazil
| | - Samylla Oliveira
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Brazil
| | - Ricardo Rogers
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana B F Pacheco
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jianing Hui
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Nathan C Skillen
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast, UK
| | - Mário U G Barros
- Ceára Water Resources Management Company (COGERH), Fortaleza, Brazil
| | - Christine Edwards
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK
| | - Sandra M F O Azevedo
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Peter K J Robertson
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast, UK
| | - John T S Irvine
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Linda A Lawton
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK
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21
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Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence. Appl Environ Microbiol 2022; 88:e0180321. [PMID: 35862730 PMCID: PMC9317899 DOI: 10.1128/aem.01803-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H2O2. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.
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22
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He C, Liu J, Wang R, Li Y, Zheng Q, Jiao F, He C, Shi Q, Xu Y, Zhang R, Thomas H, Batt J, Hill P, Lewis M, Maclntyre H, Lu L, Zhang Q, Tu Q, Shi T, Chen F, Jiao N. Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment. WATER RESEARCH 2022; 216:118281. [PMID: 35316680 DOI: 10.1016/j.watres.2022.118281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source. The DOM composition, community structure, and metabolic pathways were characterised using multi-omics approaches. The addition of diatom lysate introduced a mass of labile DOM into the incubation seawater, which led to a low degradation index (IDEG) and refractory molecular lability boundary (RMLB) on days 1 and 18. The molecular compositions of the DOM molecules in the later incubation period (from day 120 to day 220) were more similar in composition to those on day 0, suggesting a rapid turnover of phytoplankton debris by microbial communities. Taxonomically, while Alpha proteobacteria dominated during the entire incubation period, Gamma proteobacteria became more sensitive and abundant than the other bacterial groups on days 1 and 18. Recalcitrant measurements such as IDEG and RMLB were closely related to the DOM molecules, bacterial community, and Kyoto encyclopaedia of Genes and Genomes (KEGG) modules, suggesting close associations between RDOM accumulation and microbial metabolism. KEGG modules that showed strong positive correlation with CRAMs were identified using a microbial ecological network approach. The identified KEGG modules produced the substrates, such as the acetyl-CoA or 3‑hydroxy-3-methylglutaryl-CoA, which could participate in the mevalonate pathway to generate the precursor of CRAM analogues, isopentenyl-PP, suggesting a potential generation pathway of CRAM analogues in bacteria and archaea. This study revealed the potential genetic and molecular processes involved in the microbial origin of CRAM analogues, and thus indicated a vital ecological role of bacteria and archaea in RDOM production. This study also offered new perspectives on the carbon sequestration in the ocean.
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Affiliation(s)
- Changfei He
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou 510000, China.
| | - Rui Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Qiang Zheng
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Fanglue Jiao
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Rui Zhang
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Helmuth Thomas
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada; Helmholtz-Center Geesthacht, Institute for Coastal Research, Max-Planck-Strasse 1, Geesthacht d-21502, Germany
| | - John Batt
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Paul Hill
- Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Marlon Lewis
- Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Hugh Maclntyre
- Department of Oceanography, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Longfei Lu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China; Weihai Changqing Ocean Science Technology Co., Ltd., Weihai, Shandong, China
| | - Qinghua Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China; Marine Equipment Inspection & Testing Co. Ltd, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Tuo Shi
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China
| | - Feng Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Environmental Research Center, University of Maryland at Baltimore, United States
| | - Nianzhi Jiao
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Halifax, NS, B3H 4R2, Canada, Qingdao 266237, China, and Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou 510000, China
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Li D, He Y, Zheng Y, Zhang S, Zhang H, Lin L, Wang D. Metaproteomics reveals unique metabolic niches of dominant bacterial groups in response to rapid regime shifts during a mixed dinoflagellate bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153557. [PMID: 35114235 DOI: 10.1016/j.scitotenv.2022.153557] [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: 11/09/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The dynamics of bacterial composition and metabolic activity during a distinct phytoplankton bloom have been reported. However, there is limited information on the bacterial community response to drastic environmental changes caused by species succession during a mixed-species bloom. This study investigated active bacterial groups and metabolic activity during a mixed bloom formed by dinoflagellates Prorocentrum obtusidens and Karenia mikimotoi using a metaproteomic approach. Bacterial community structure and dominant bacterial groups varied rapidly with the bloom regime shifts caused by species succession. Pseudoalteromonas and Vibrio dominated the bacterial community in the P. obtusidens-dominated regime, while Alteromonas, Cytophaga-Flavobacteria-Bacteroides (CFB) group, and marine Roseobacter clade (MRC) were the major contributors in other regimes, with the most abundant taxa being Alteromonas in the K. mikimotoi-dominated regime and the CFB group in the dissipation regime. Specific metabolic niches and unique substrate specificity of different bacterial groups enabled them to dominate and thrive in different bloom regimes. High metabolic plasticity in signal response, substrate utilization, motility, and adhesion are essential for bacteria to respond to drastic bloom regime shift, and the predominance of specific bacteria under unique bloom regimes may be the result of long-term coevolution between bacteria and bloom-forming phytoplankton species.
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Affiliation(s)
- Dongxu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong 519082, China
| | - Yaohui He
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian 361102, China
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Shufeng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Hao Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.
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24
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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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25
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Wang T, Li J, Jing H, Qin S. Picocyanobacterial Synechococcus in marine ecosystem: Insights from genetic diversity, global distribution, and potential function. MARINE ENVIRONMENTAL RESEARCH 2022; 177:105622. [PMID: 35429822 DOI: 10.1016/j.marenvres.2022.105622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Marine Synechococcus, a main group of picocyanobacteria, has been ubiquitously observed across the global oceans. Synechococcus exhibits high phylogenetical and phenotypical diversity, and horizontal gene transfer makes its genetic evolution much more intricate. With the development of measurement technologies and analysis methods, the genomic information and niche partition of each Synechococcus lineage tend to be precisely described, but the global analysis is still lacking. Therefore, it is necessary to summarize existing studies and integrate published data to gain a comprehensive understanding of Synechococcus on genetic variation, niche division, and potential functions. In this review, the maximum likelihood trees are constructed based on existing sequence data, including both phylogenetic and pigmentary gene markers. The global distribution characteristics of abundance, lineages, and pigment types are concluded through pooled analysis of more than 700 samples obtained from approximately 50 scientific research cruises. The potential functions of Synechococcus are explored in element cycles and biological interactions. Future work on Synechococcus is suggested to focus on not only elucidating the nature of Synechococcus biodiversity but also demonstrating its interactions with the ecosystem by combining bioinformatics and macroscopic isotope-labeled environmental parameters.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Coastal Biology and Biological Resource Conservation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, China; CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jialin Li
- Key Laboratory of Coastal Biology and Biological Resource Conservation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resource Conservation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
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26
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Mai Z, Zeng X, Wei X, Sun C, Niu J, Yan W, Du J, Sun Y, Cheng H. Mangrove restoration promotes the anti-scouribility of the sediments by modifying inherent microbial community and extracellular polymeric substance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152369. [PMID: 34919933 DOI: 10.1016/j.scitotenv.2021.152369] [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: 10/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Coastal erosion will aggravate the loss of shorelines and threaten the safety of coastal engineering facilities. Mangrove is often considered as an efficient coastal guard; however the mechanisms involved in anti-scouribility ascribed to mangrove are still poorly understood. Thus, two artificial mangrove forests (including exotic Sonneratia apetala and native Kandelia obovata) and an unvegetated mudflat control were selected to explore the potential function of microbial extracellular polymeric substance (EPS) on the anti-scouribility of the sediments. A cohesive strength meter was used for the analysis of anti-scouribility, while a sequential extraction and 16S high-throughput sequencing were employed to evaluate the changes in EPS and microbial community driven by mangrove restoration. Principal component, redundancy, and two-matrix correlation heatmap analyses were performed for the analyses of the correlations among shear stress, EPS, microbes, and soil properties. The results showed an obvious enhancement of anti-scouribility after mangrove restoration. Compared to those of unvegetated mudflat, shear stress increased from 1.94 N/m2 to 3.26 and 4.93 N/m2 in the sediments of S. apetala and K. obovata stands, respectively. Mangrove restoration also promoted EPS content in the sediments, irrespective of EPS components and sub-fractions. Both extracellular protein and polysaccharide were found to be positively correlated with anti-scouribility. Coinciding with increased anti-scouribility and EPS, increased bacterial abundances were also detected in the sediments after mangrove restoration (especially K. obovata), whereas Proteobacteria and Bacteroides may be important and influential for EPS secretion and anti-scouribility promotion. Nevertheless, increased total organic carbon, total nitrogen and total phosphorus induced by mangrove restoration may also partially contribute to improvement of anti-scouribility. In conclusion, this is the first study to provide evidence for a link between mangrove restoration and increased EPS which improve resistance to scouring. The present study provides a novel perspective on the revealing of the function of mangrove on erosion mitigation.
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Affiliation(s)
- Zhimao Mai
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xin Zeng
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xing Wei
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Cuici Sun
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jianwei Niu
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Wenwen Yan
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061,China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Jun Du
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061,China
| | - Yingting Sun
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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27
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Interaction and Assembly of Bacterial Communities in High-Latitude Coral Habitat Associated Seawater. Microorganisms 2022; 10:microorganisms10030558. [PMID: 35336132 PMCID: PMC8955259 DOI: 10.3390/microorganisms10030558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
Threatened by climate change and ocean warming, coral reef ecosystems have been shifting in geographic ranges toward a higher latitude area. The water-associated microbial communities and their potential role in primary production contribution are well studied in tropical coral reefs, but poorly defined in high-latitude coral habitats to date. In this study, amplicon sequencing of 16S rRNA and cbbL gene, co-occurrence network, and βNTI were used. The community structure of bacterial and carbon-fixation bacterial communities showed a significant difference between the center of coral, transitional, and non-coral area. Nitrite, DOC, pH, and coral coverage ratio significantly impacted the β-diversity of bacterial and carbon-fixation communities. The interaction of heterotrophs and autotrophic carbon-fixers was more complex in the bottom than in surface water. Carbon-fixers correlated with diverse heterotrophs in surface water but fewer lineages of heterotrophic taxa in the bottom. Bacterial community assembly showed an increase by deterministic process with decrease of coral coverage in bottom water, which may correlate with the gradient of nitrite and pH in the habitat. A deterministic process dominated the assembly of carbon-fixation bacterial community in surface water, while stochastic process dominated t the bottom. In conclusion, the structure and assembly of bacterial and carbon-fixer community were affected by multi-environmental variables in high-latitude coral habitat-associated seawater.
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28
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Prochlorococcus Exudate Stimulates Heterotrophic Bacterial Competition with Rival Phytoplankton for Available Nitrogen. mBio 2022; 13:e0257121. [PMID: 35012332 PMCID: PMC8749424 DOI: 10.1128/mbio.02571-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine cyanobacterium Prochlorococcus numerically dominates the phytoplankton community of the nutrient-limited open ocean, establishing itself as the most abundant photosynthetic organism on Earth. This ecological success has been attributed to lower cell quotas for limiting nutrients, superior resource acquisition, and other advantages associated with cell size reduction and genome streamlining. In this study, we tested the prediction that Prochlorococcus outcompetes its rivals for scarce nutrients and that this advantage leads to its numerical success in nutrient-limited waters. Strains of Prochlorococcus and its sister genus Synechococcus grew well in both mono- and cocultures when nutrients were replete. However, in nitrogen-limited medium, Prochlorococcus outgrew Synechococcus but only when heterotrophic bacteria were also present. In the nitrogen-limited medium, the heterotroph Alteromonas macleodii outcompeted Synechococcus for nitrogen but only if stimulated by the exudate released by Prochlorococcus or if a proxy organic carbon source was provided. Genetic analysis of Alteromonas suggested that it outcompetes Synechococcus for nitrate and/or nitrite, during which cocultured Prochlorococcus grows on ammonia or other available nitrogen species. We propose that Prochlorococcus can stimulate antagonism between heterotrophic bacteria and potential phytoplankton competitors through a metabolic cross-feeding interaction, and this stimulation could contribute to the numerical success of Prochlorococcus in nutrient-limited regions of the ocean. IMPORTANCE In nutrient-poor habitats, competition for limited resources is thought to select for organisms with an enhanced ability to scavenge nutrients and utilize them efficiently. Such adaptations characterize the cyanobacterium Prochlorococcus, the most abundant photosynthetic organism in the nutrient-limited open ocean. In this study, the competitive superiority of Prochlorococcus over a rival cyanobacterium, Synechococcus, was captured in laboratory culture. Critically, this outcome was achieved only when key aspects of the open ocean were simulated: a limited supply of nitrogen and the presence of heterotrophic bacteria. The results indicate that Prochlorococcus promotes its numerical dominance over Synechococcus by energizing the heterotroph's ability to outcompete Synechococcus for available nitrogen. This study demonstrates how interactions between trophic groups can influence interactions within trophic groups and how these interactions likely contribute to the success of the most abundant photosynthetic microorganism.
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Hua ZL, Li XQ, Zhang JY, Gu L. Removal potential of multiple perfluoroalkyl acids (PFAAs) by submerged macrophytes in aquatic environments: Tolerance of Vallisneria natans and PFAA removal in submerged macrophyte-microbiota systems. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127695. [PMID: 34775308 DOI: 10.1016/j.jhazmat.2021.127695] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Perfluoroalkyl acids (PFAAs) have emerged as a global concern in aquatic environment remediation due to their abundance, persistence, bioaccumulation, and toxicity. To comprehensively understand the removal potential of multiple PFAAs by submerged macrophytes in aquatic environments, systematic investigations into the tolerance of the typical submerged macrophyte Vallisneria natans to 12 typical PFAAs and the removal capacity to PFAAs in V. natans-microbiota systems were carried out. Results showed that although PFAAs could induce the accumulation of hydrogen peroxide and malondialdehyde, V. natans was overall resistant to multiple PFAAs with natural concentrations. Catalase is one of the main strategies of V. natans to alleviate PFAA stress. Microbiota can remove 18.10-30.84% of the PFAAs from the water column. 24.35-73.45% of PFAAs were removed from water in V. natans-microbiota systems. The uptake of plant tissues and the bioaccumulation of microbiota were proposed as the main removal processes. The removal rates were significantly correlated with the perfluorinated carbon atoms numbers (p < 0.05). PFAAs and V. natans increased the relative abundance of Betaproteobacteria, Nostocales, Microscillaceae, Sphingobacteriales, SBR1031, Chlamydiales, Phycisphaerae, Caldilineales, Rhodobacterales, and Verrucomicrobiales. The present study suggested that V. natans can be a potential species to remove multiple PFAAs in aquatic environments, and further providing insights into the PFAAs' remediation.
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Affiliation(s)
- Zu-Lin Hua
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Jiangsu 210098, PR China
| | - Xiao-Qing Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Jiangsu 210098, PR China.
| | - Jian-Yun Zhang
- Yangtze Institute for Conservation and Development, Jiangsu 210098, PR China.
| | - Li Gu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Jiangsu 210098, PR China
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Chen J, Li Y, Jing H, Zhang X, Xu Z, Xu J, Liu H. Genomic and transcriptomic evidence for the diverse adaptations of Synechococcus subclusters 5.2 and 5.3 to mesoscale eddies. THE NEW PHYTOLOGIST 2022; 233:1828-1842. [PMID: 34870848 DOI: 10.1111/nph.17903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Mesoscale eddies are ubiquitous oceanographic features that influence the metabolism and community structure of Synechococcus. However, the metabolic adaptations of this genus to eddy-associated environmental changes have rarely been studied. We recovered two high-quality Synechococcus metagenome-assembled genomes (MAGs) from eddies in the South China Sea and compared their metabolic variations using metatranscriptomic samples obtained at the same time. The two MAGs (syn-bin1 and syn-bin2) are affiliated with marine Synechococcus subclusters 5.2 (S5.2) and 5.3 (S5.3), respectively. The former exhibited a higher abundance at the surface layer, whereas the latter was more abundant in the deep euphotic layer. Further analysis indicated that syn-bin1 had a strong ability to utilize organic nutrients, which could help it to thrive in the nutrient-deprived surface water. By contrast, syn-bin2 had the genetic potential to perform chromatic acclimation, which could allow it to capture green or blue light at different depths. Additionally, transcriptomic analysis showed that syn-bin2 upregulated genes involved in the synthesis of C4 acids, photosystem II proteins, and HCO3- transporters in the deep euphotic layer, which might contribute to its predominance in low-light environments. Overall, this study expands our understanding of oceanic S5.2 and S5.3 Synechococcus by revealing their metabolic adaptations to mesoscale eddies.
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Affiliation(s)
- Jiawei Chen
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Yingdong Li
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Sanya, 572000, China
| | - Xiaodong Zhang
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518000, China
| | - Jie Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Sanya, 572000, China
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Liu C, Yan J, Huang Q, Liu H, Qiao C, Li R, Shen B, Shen Q. The addition of sawdust reduced the emission of nitrous oxide in pig manure composting by altering the bacterial community structure and functions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3733-3742. [PMID: 34392479 DOI: 10.1007/s11356-021-15786-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Although composting, a measure to dispose agricultural waste, is widely accepted and applied, specific knowledge of microbially driven effects on nitrous oxide (N2O) emissions during composting remains limited. Here, we monitored the impact of sawdust on N2O emissions during pig manure composting. The results suggested that adding sawdust to the compost improved the compost temperature and reduced N2O emissions. The addition of sawdust significantly altered the bacterial community structure and enhanced community turnover during the composting process. The addition of sawdust significantly reduced the relative abundance of denitrification and ureolysis, while increasing the relative abundance of nitrogen fixation. Specifically, adding sawdust may reduce N2O emissions by reducing the relative abundance of Salinithrix, Truepera, Azomonas, Iamia, Silanimonas, Phycisphaera, and Gp21 during the thermophilic and mature phases of the composting period.
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Affiliation(s)
- Chao Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jiao Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Qian Huang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Cece Qiao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Biao Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
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Genome Sequence of Microbacterium sp. Strain R1, Isolated from a Synechococcus Culture. Microbiol Resour Announc 2021; 10:e0054221. [PMID: 34498928 PMCID: PMC8428252 DOI: 10.1128/mra.00542-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synechococcus cultures in the laboratory are often associated with heterotrophic bacteria. Here, we report the genome sequence of the bacterium Microbacterium sp. strain R1, isolated from a culture of the estuarine Synechococcus strain CBW1107. Several secondary metabolites and transporter-related genes were identified in the genome of Microbacterium sp. strain R1.
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Draft Genome Sequences of Four Bacterial Strains of Heterotrophic Alteromonas macleodii and Marinobacter, Isolated from a Nonaxenic Culture of Two Marine Synechococcus Strains. Microbiol Resour Announc 2021; 10:10/19/e00116-21. [PMID: 33986074 PMCID: PMC8142560 DOI: 10.1128/mra.00116-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Species of the Alteromonas and Marinobacter genera are heterotrophic Gammaproteobacteria that are part of the marine microbial ecosystem. In this study, four strains were isolated from two nonaxenic Synechococcus cultures and were sequenced. Few studies of these two genera have been reported. Therefore, genomic data of Alteromonadaceae are valuable for the study of heterotroph-phototroph dynamics in marine bacterial communities.
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Han Y, Jiao N, Zhang Y, Zhang F, He C, Liang X, Cai R, Shi Q, Tang K. Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms. MICROBIOME 2021; 9:71. [PMID: 33762013 PMCID: PMC7992965 DOI: 10.1186/s40168-021-01022-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/02/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Phytoplankton blooms are frequent events in coastal areas and increase the production of organic matter that initially shapes the growth of opportunistic heterotrophic bacteria. However, it is unclear how these opportunists are involved in the transformation of dissolved organic matter (DOM) when blooms occur and the subsequent impacts on biogeochemical cycles. RESULTS We used a combination of genomic, proteomic, and metabolomic approaches to study bacterial diversity, genome traits, and metabolic responses to assess the source and lability of DOM in a spring coastal bloom of Akashiwo sanguinea. We identified molecules that significantly increased during bloom development, predominantly belonging to amino acids, dipeptides, lipids, nucleotides, and nucleosides. The opportunistic members of the bacterial genera Polaribacter, Lentibacter, and Litoricola represented a significant proportion of the free-living and particle-associated bacterial assemblages during the stationary phase of the bloom. Polaribacter marinivivus, Lentibacter algarum, and Litoricola marina were isolated and their genomes exhibited streamlining characterized by small genome size and low GC content and non-coding densities, as well as a smaller number of transporters and peptidases compared to closely related species. However, the core proteomes identified house-keeping functions, such as various substrate transporters, peptidases, motility, chemotaxis, and antioxidants, in response to bloom-derived DOM. We observed a unique metabolic signature for the three species in the utilization of multiple dissolved organic nitrogen compounds. The metabolomic data showed that amino acids and dipeptides (such as isoleucine and proline) were preferentially taken up by P. marinivivus and L. algarum, whereas nucleotides and nucleosides (such as adenosine and purine) were preferentially selected by L. marina. CONCLUSIONS The results suggest that the enriched DOM in stationary phase of phytoplankton bloom is a result of ammonium depletion. This environment drives genomic streamlining of opportunistic bacteria to exploit their preferred nitrogen-containing compounds and maintain nutrient cycling. Video abstract.
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Affiliation(s)
- Yu Han
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Fan Zhang
- Department of Molecular Virology & Microbiology, Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing, 102249, People's Republic of China
| | - Xuejiao Liang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing, 102249, People's Republic of China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
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Moreira M, Schrama D, Farinha AP, Cerqueira M, Raposo de Magalhães C, Carrilho R, Rodrigues P. Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective. Animals (Basel) 2021; 11:E125. [PMID: 33430015 PMCID: PMC7827161 DOI: 10.3390/ani11010125] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 12/22/2022] Open
Abstract
One of the main constraints in aquaculture production is farmed fish vulnerability to diseases due to husbandry practices or external factors like pollution, climate changes, or even the alterations in the dynamic of product transactions in this industry. It is though important to better understand and characterize the intervenients in the process of a disease outbreak as these lead to huge economical losses in aquaculture industries. High-throughput technologies like proteomics can be an important characterization tool especially in pathogen identification and the virulence mechanisms related to host-pathogen interactions on disease research and diagnostics that will help to control, prevent, and treat diseases in farmed fish. Proteomics important role is also maximized by its holistic approach to understanding pathogenesis processes and fish responses to external factors like stress or temperature making it one of the most promising tools for fish pathology research.
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Affiliation(s)
- Márcio Moreira
- CCMAR—Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (M.M.); (D.S.); (A.P.F.); (M.C.); (C.R.d.M.); (R.C.)
- University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
- IPMA—Portuguese Institute for the Sea and Atmosphere, EPPO—Aquaculture Research Station, Av. Parque Natural da Ria Formosa s/n, 8700-194 Olhão, Portugal
| | - Denise Schrama
- CCMAR—Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (M.M.); (D.S.); (A.P.F.); (M.C.); (C.R.d.M.); (R.C.)
- University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Ana Paula Farinha
- CCMAR—Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (M.M.); (D.S.); (A.P.F.); (M.C.); (C.R.d.M.); (R.C.)
- University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Marco Cerqueira
- CCMAR—Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (M.M.); (D.S.); (A.P.F.); (M.C.); (C.R.d.M.); (R.C.)
| | - Cláudia Raposo de Magalhães
- CCMAR—Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (M.M.); (D.S.); (A.P.F.); (M.C.); (C.R.d.M.); (R.C.)
- University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Raquel Carrilho
- CCMAR—Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (M.M.); (D.S.); (A.P.F.); (M.C.); (C.R.d.M.); (R.C.)
- University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Pedro Rodrigues
- CCMAR—Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (M.M.); (D.S.); (A.P.F.); (M.C.); (C.R.d.M.); (R.C.)
- University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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Kearney SM, Thomas E, Coe A, Chisholm SW. Microbial diversity of co-occurring heterotrophs in cultures of marine picocyanobacteria. ENVIRONMENTAL MICROBIOME 2021; 16:1. [PMID: 33902739 PMCID: PMC8067657 DOI: 10.1186/s40793-020-00370-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The cyanobacteria Prochlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; heterotrophs grow on organic carbon supplied by the photolithoautotrophs. For examining the selective pressures shaping autotroph/heterotroph interactions, we have made use of unialgal enrichment cultures of Prochlorococcus and Synechococcus maintained for hundreds to thousands of generations in the lab. We examine the diversity of heterotrophs in 74 enrichment cultures of these picocyanobacteria obtained from diverse areas of the global oceans. RESULTS Heterotroph community composition differed between clades and ecotypes of the autotrophic 'hosts' but there was significant overlap in heterotroph community composition across these cultures. Collectively, the cultures were comprised of many shared taxa, even at the genus level. Yet, observed differences in community composition were associated with time since isolation, location, depth, and methods of isolation. The majority of heterotrophs in the cultures are rare in the global ocean, but enrichment conditions favor the opportunistic outgrowth of these rare bacteria. However, we found a few examples, such as bacteria in the family Rhodobacteraceae, of heterotrophs that were ubiquitous and abundant in cultures and in the global oceans. We found their abundance in the wild is also positively correlated with that of picocyanobacteria. CONCLUSIONS Particular conditions surrounding isolation have a persistent effect on long-term culture composition, likely from bottlenecking and selection that happen during the early stages of enrichment for the picocyanobacteria. We highlight the potential for examining ecologically relevant relationships by identifying patterns of distribution of culture-enriched organisms in the global oceans.
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Affiliation(s)
- Sean M. Kearney
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, MA 02139 USA
| | - Elaina Thomas
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, MA 02139 USA
| | - Allison Coe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, MA 02139 USA
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, MA 02139 USA
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Dong Z, Shen X, Hao Y, Li J, Li H, Xu H, Yin L, Kuang W. Gut Microbiome: A Potential Indicator for Differential Diagnosis of Major Depressive Disorder and General Anxiety Disorder. Front Psychiatry 2021; 12:651536. [PMID: 34589003 PMCID: PMC8473618 DOI: 10.3389/fpsyt.2021.651536] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 08/19/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Major depressive disorder (MDD) and general anxiety disorder (GAD) share many common features, leading to numerous challenges in their differential diagnosis. Given the importance of the microbiota-gut-brain axis, we investigated the differences in gut microbiota between representative cases of these two diseases and sought to develop a microbiome-based approach for their differential diagnosis. Methods: We enrolled 23 patients with MDD, 21 with GAD, and 10 healthy subjects (healthy crowd, HC) in the present study. We used 16S rRNA gene-sequencing analysis to determine the microbial compositions of the gut microbiome based on Illumina Miseq and according to the standard protocol. Results: GAD showed a significant difference in microbiota richness and diversity as compared with HC. Additionally, Otu24167, Otu19140, and Otu19751 were significantly decreased in MDD relative to HC, and Otu2581 and Otu10585 were significantly increased in GAD relative to MDD. At the genus level, the abundances of Sutterella and Fusicatenibacter were significantly lower in MDD relative to HC, and the abundances of Fusicatenibacter and Christensenellaceae_R7_group were significantly lower in GAD than in HC. The abundance of Sutterella was significantly higher whereas that of Faecalibacterium was significantly lower in GAD relative to MDD. Moreover, we observed that Christensenellaceae_R7_group negatively correlated with the factor score (Limited to Hopelessness) and total score of HAMD-24 (p < 0.05), whereas Fusicatenibacter negatively correlated with FT4 (p < 0.05). Furthermore, the GAD group showed significant differences at the genus level for Faecalibacterium, which negatively correlated with PTC (p < 0.05). Conclusions: This study elucidated a unique gut-microbiome signature associated with MDD and GAD that could facilitate differential diagnosis and targeted therapy.
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Affiliation(s)
- Zaiquan Dong
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoling Shen
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China
| | - Yanni Hao
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China
| | - Jin Li
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China
| | - Haoran Li
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China
| | - Haizheng Xu
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China
| | - Li Yin
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China
| | - Weihong Kuang
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China
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Yang SH, Park MJ, Kwon KK. Oricola thermophila sp. nov., a marine bacterium isolated from tidal flat sediment and emended description of the genus Oricola Hameed et al. 2015. Int J Syst Evol Microbiol 2020; 71. [PMID: 33263513 DOI: 10.1099/ijsem.0.004574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultatively anaerobic, rod-shaped (1.8-4.4×0.5-0.7 µm) and motile marine bacterium, designated as MEBiC13590T, was isolated from tidal flat sediment sampled at Incheon City, on the west coast of the Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC13590T showed high similarity to Oricola cellulosilytica CC-AMH-0T (98.2 %), followed by Oceaniradius stylonematis StC1T (97.5 %); however, it clustered with Oricola cellulosilytica. The phylogenomic tree inferred by the up-to-date bacterial core gene set suggested that strain MEBiC13590T shared a phyletic line with Oricola cellulosilytica. Average nucleotide identity and digital DNA-DNA hybridization values (75.0 and 19.3 %, respectively) between strain MEBiC13590T and Oricola cellulosilytica CC-AMH-0T were below the respective species delineation cutoffs. Growth was observed at 22-50 °C (optimum, 45 °C), at pH 5-9 (optimum, pH 7) and with 1-6 % (optimum, 3 %) NaCl. The predominant cellular fatty acids were C16 : 0 (7.6 %), C18 : 0 (12.2 %), 11-methyl C18 : 1 ω7c (5.7 %), C19 : 0 cyclo ω6c and summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c; 38 %). The DNA G+C content was 63.5 mol%. The major respiratory quinone was Q-10. Several phenotypic characteristics such as growth temperature, oxygen requirement, enzyme activities of urease, gelatinase, lipase (C14), α-chymotrypsin, acid phosphatase, β-galactosidase, β-glucosidase etc. differentiate strain MEBiC13590T from Oricola cellulosilytica CC-AMH-0T. Based on this polyphasic taxonomic data, strain MEBiC13590T should be classified as representing a novel species in the genus Oricola for which the name Oricola thermophila sp. nov. is proposed . The type strain is MEBiC13590T (=KCCM 43313T=JCM 33661T).
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Affiliation(s)
- Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, 385, Haeyang-ro, Yeongdo-gu, Busan, Republic of Korea
| | - Mi-Jeong Park
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, 385, Haeyang-ro, Yeongdo-gu, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, 385, Haeyang-ro, Yeongdo-gu, Busan, Republic of Korea
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Varela MM, Rodríguez-Ramos T, Guerrero-Feijóo E, Nieto-Cid M. Changes in Activity and Community Composition Shape Bacterial Responses to Size-Fractionated Marine DOM. Front Microbiol 2020; 11:586148. [PMID: 33329457 PMCID: PMC7714726 DOI: 10.3389/fmicb.2020.586148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022] Open
Abstract
To study the response of bacteria to different size-fractions of naturally occurring dissolved organic matter (DOM), a natural prokaryotic community from North Atlantic mesopelagic waters (1000 m depth) was isolated and grown in (i) 0.1-μm filtered seawater (CONTROL), (ii) the low-molecular-weight (<1 kDa) DOM fraction (L-DOM), and (iii) the recombination of high- (>1 kDa) and low-molecular-weight DOM fractions (H + L-DOM), to test the potential effect of ultrafiltration on breaking the DOM size continuum. Prokaryotic abundance and leucine incorporation were consistently higher in the H + L-DOM niche than in the L-DOM and CONTROL treatments, suggesting a different interaction with each DOM fraction and the disruption of the structural DOM continuum by ultrafiltration, respectively. Rhodobacterales (Alphaproteobacteria) and Flavobacteriales (Bacteroidetes) were particularly enriched in L-DOM and closely related to the colored DOM (CDOM) fraction, indicating the tight link between these groups and changes in DOM aromaticity. Conversely, some other taxa that were rare or undetectable in the original bacterial community were enriched in the H + L-DOM treatment (e.g., Alteromonadales belonging to Gammaproteobacteria), highlighting the role of the rare biosphere as a seed bank of diversity against ecosystem disturbance. The relationship between the fluorescence of protein-like CDOM and community composition of populations in the H + L-DOM treatment suggested their preference for labile DOM. Conversely, the communities growing on the L-DOM niche were coupled to humic-like CDOM, which may indicate their ability to degrade more reworked DOM and/or the generation of refractory substrates (as by-products of the respiration processes). Most importantly, L- and/or H + L-DOM treatments stimulated the growth of unique bacterial amplicon sequence variants (ASVs), suggesting the potential of environmental selection (i.e., changes in DOM composition and availability), particularly in the light of climate change scenarios. Taken together, our results suggest that different size-fractions of DOM induced niche-specialization and differentiation of mesopelagic bacterial communities.
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Affiliation(s)
- Marta M. Varela
- Centro Oceanográfico de A Coruña, Instituto Español de Oceanografía (IEO), A Coruña, Spain
| | - Tamara Rodríguez-Ramos
- Centro Oceanográfico de A Coruña, Instituto Español de Oceanografía (IEO), A Coruña, Spain
| | - Elisa Guerrero-Feijóo
- Centro Oceanográfico de A Coruña, Instituto Español de Oceanografía (IEO), A Coruña, Spain
| | - Mar Nieto-Cid
- Centro Oceanográfico de A Coruña, Instituto Español de Oceanografía (IEO), A Coruña, Spain
- Laboratorio de Geoquímica Orgánica, Instituto de Investigaciones Marinas (CSIC), Vigo, Spain
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