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Schiksnis C, Xu M, Saito MA, McIlvin M, Moran D, Bian X, John SG, Zheng Q, Yang N, Fu F, Hutchins DA. Proteomics analysis reveals differential acclimation of coastal and oceanic Synechococcus to climate warming and iron limitation. Front Microbiol 2024; 15:1323499. [PMID: 38444803 PMCID: PMC10912551 DOI: 10.3389/fmicb.2024.1323499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024] Open
Abstract
In many oceanic regions, anthropogenic warming will coincide with iron (Fe) limitation. Interactive effects between warming and Fe limitation on phytoplankton physiology and biochemical function are likely, as temperature and Fe availability affect many of the same essential cellular pathways. However, we lack a clear understanding of how globally significant phytoplankton such as the picocyanobacteria Synechococcus will respond to these co-occurring stressors, and what underlying molecular mechanisms will drive this response. Moreover, ecotype-specific adaptations can lead to nuanced differences in responses between strains. In this study, Synechococcus isolates YX04-1 (oceanic) and XM-24 (coastal) from the South China Sea were acclimated to Fe limitation at two temperatures, and their physiological and proteomic responses were compared. Both strains exhibited reduced growth due to warming and Fe limitation. However, coastal XM-24 maintained relatively higher growth rates in response to warming under replete Fe, while its growth was notably more compromised under Fe limitation at both temperatures compared with YX04-1. In response to concurrent heat and Fe stress, oceanic YX04-1 was better able to adjust its photosynthetic proteins and minimize the generation of reactive oxygen species while reducing proteome Fe demand. Its intricate proteomic response likely enabled oceanic YX04-1 to mitigate some of the negative impact of warming on its growth during Fe limitation. Our study highlights how ecologically-shaped adaptations in Synechococcus strains even from proximate oceanic regions can lead to differing physiological and proteomic responses to these climate stressors.
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Affiliation(s)
- Cara Schiksnis
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Min Xu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Mak A. Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Matthew McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Dawn Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Xiaopeng Bian
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Seth G. John
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Nina Yang
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
- Marine Policy Center, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Feixue Fu
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - David A. Hutchins
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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Reji L, Darnajoux R, Zhang X. A genomic view of environmental and life history controls on microbial nitrogen acquisition strategies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13220. [PMID: 38057292 PMCID: PMC10866080 DOI: 10.1111/1758-2229.13220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/15/2023] [Indexed: 12/08/2023]
Abstract
Microorganisms have evolved diverse strategies to acquire the vital element nitrogen (N) from the environment. Ecological and physiological controls on the distribution of these strategies among microbes remain unclear. In this study, we examine the distribution of 10 major N acquisition strategies in taxonomically and metabolically diverse microbial genomes, including those from the Genomic Catalogue of Earth's Microbiomes dataset. We utilize a marker gene-based approach to assess relationships between N acquisition strategy prevalence and microbial life history strategies. Our results underscore energetic costs of assimilation as a broad control on strategy distribution. The most prevalent strategies are the uptake of ammonium and simple amino acids, which have relatively low energetic costs, while energy-intensive biological nitrogen fixation is the least common. Deviations from the energy-based framework include the higher-than-expected prevalence of the assimilatory pathway for chitin, a large organic polymer. Energy availability is also important, with aerobic chemoorganotrophs and oxygenic phototrophs notably possessing ~2-fold higher numbers of total strategies compared to anaerobic microbes. Environmental controls are evidenced by the enrichment of inorganic N assimilation strategies among free-living taxa compared to host-associated taxa. Physiological constraints such as pathway incompatibility add complexity to N acquisition strategy distributions. Finally, we discuss the necessity for microbially-relevant spatiotemporal environmental metadata for improving mechanistic and prediction-oriented analyses of genomic data.
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Affiliation(s)
- Linta Reji
- Department of GeosciencesPrinceton UniversityPrincetonNew JerseyUSA
- High Meadows Environmental InstitutePrinceton UniversityPrincetonNew JerseyUSA
| | - Romain Darnajoux
- Department of GeosciencesPrinceton UniversityPrincetonNew JerseyUSA
| | - Xinning Zhang
- Department of GeosciencesPrinceton UniversityPrincetonNew JerseyUSA
- High Meadows Environmental InstitutePrinceton UniversityPrincetonNew JerseyUSA
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Zhang X, Xu J, Dai J, Zhang L, Feng L, Tian X, Yang Q. Taxonomic, Phylogenomic and Bioactivity Profiling of Novel Phycosphere Bacterium from Model Cyanobacterium Synechococcus elongatus PCC 7942. Mar Drugs 2024; 22:36. [PMID: 38248661 PMCID: PMC10817584 DOI: 10.3390/md22010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Phycosphere niches host rich microbial consortia that harbor dynamic algae-bacteria interactions with fundamental significance in varied natural ecosystems. Hence, culturing the uncultured microbial majority of the phycosphere microbiota is vital for deep understanding of the intricate mechanisms governing the dynamic interactions, and also to provide novel and rich microbial resources, and to discover new natural bioactive metabolites. Synechococcus elongatus PCC 7942 is a robust model cyanobacterium widely used in environment, synthesis biology, and biotechnology research. To expand the number of novel phycosphere species that were brought into culture and to discover the natural bioactivities, we presented a new yellow-pigmented bacterium named ABI-127-1, which was recovered from the phycosphere of PCC 7942, using an optimized bacterial isolation procedure. Combined polyphasic taxonomic and phylogenomic characterization was performed to confidently identify the new isolate as a potential novel species belonging to the genus Qipengyuania. The observed bioactivity of strain ABI-127-1 with promoting potential towards the growth and CO2 fixation efficiency of the host microalgae was measured. Additionally, the bacterial production of active bioflocculant exopolysaccharides was evaluated after culture optimization. Thus, these findings revealed the potential environmental and biotechnological implications of this new microalgae growth-promoting bacterium isolated from the phycosphere microenvironment.
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Affiliation(s)
- Xiaoling Zhang
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- ABI Group, Laboratory of Phycosphere Microbiology, Zhejiang Ocean University, Zhoushan 316021, China
| | - Jiaquan Xu
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
- Donghai Laboratory, Zhoushan 316022, China
| | - Jun Dai
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Lei Zhang
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
| | - Lijuan Feng
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiaoqing Tian
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Qiao Yang
- ABI Group, Laboratory of Phycosphere Microbiology, Zhejiang Ocean University, Zhoushan 316021, China
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
- Donghai Laboratory, Zhoushan 316022, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Song W, Li H, Zhou Y, Liu X, Li Y, Wang M, Li DD, Tu Q. Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms. Front Microbiol 2023; 14:1291242. [PMID: 38053549 PMCID: PMC10694361 DOI: 10.3389/fmicb.2023.1291242] [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: 09/08/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.
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Affiliation(s)
- Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Dan-dan Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
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Lin S, Li S, Ouyang T, Chen G. Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803. Int J Mol Sci 2023; 24:ijms24076606. [PMID: 37047577 PMCID: PMC10094980 DOI: 10.3390/ijms24076606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
Excess ammonium imposes toxicity and stress response in cyanobacteria. How cyanobacteria acclimate to NH4+ stress is so far poorly understood. Here, Synechocystis sp. PCC6803 S2P homolog Slr1821 was identified as the essential regulator through physiological characterization and transcriptomic analysis of its knockout mutant. The proper expression of 60% and 67% of the NH4+ activated and repressed genes, respectively, were actually Slr1821-dependent since they were abolished or reversed in ∆slr1821. Synechocystis 6803 suppressed nitrogen uptake and assimilation, ammonium integration and mobilization of other nitrogen sources upon NH4+ stress. Opposite regulation on genes for assimilation of nitrogen and carbon, such as repression of nitrogen regulatory protein PII, PII interactive protein PirC and activation of carbon acquisition regulator RcbR, demonstrated that Synechocystis 6803 coordinated regulation to maintain carbon/nitrogen homeostasis under increasing nitrogen, while functional Slr1821 was indispensable for most of this coordinated regulation. Additionally, slr1821 knockout disrupted the proper response of regulators and transporters in the ammonium-specific stimulon, and resulted in defective photosynthesis as well as compromised translational and transcriptional machinery. These results provide new insight into the coordinated regulation of nutritional fluctuation and the functional characterization of S2Ps. They also provide new targets for bioengineering cyanobacteria in bioremediation and improving ammonium tolerance in crop plants.
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Affiliation(s)
- Shiqi Lin
- School of Food Sciences and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China
| | - Shiliang Li
- School of Food Sciences and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China
| | - Tong Ouyang
- School of Food Sciences and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China
| | - Gu Chen
- School of Food Sciences and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China
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