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Li H, Jiang M, Li P, Xu Z, Jiang P, Chen L, Gin KYH, He Y. Picocyanobacterial-bacterial interactions sustain cyanobacterial blooms in nutrient-limited aquatic environments. ENVIRONMENTAL RESEARCH 2024; 260:119508. [PMID: 38945511 DOI: 10.1016/j.envres.2024.119508] [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: 03/06/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
Cyanobacterial blooms (CBs) and concomitant water quality issues in oligotrophic/mesotrophic waters have been recently reported, challenging the conventional understanding that CBs are primarily caused by eutrophication. To elucidate the underlying mechanism of CBs in nutrition-deficient waters, the changes in Chlorophyll a (Chl-a), cyanobacterial-bacterial community composition, and certain microbial function in Qingcaosha Reservoir, the global largest tidal estuary storage reservoir, were analyzed systematically and comprehensively after its pilot run (2011-2019) in this study. Although the water quality was improved and stabilized, more frequent occurrences of bloom level of Chl-a (>20 μg L-1) in warm seasons were observed during recent years. The meteorological changes (CO2, sunshine duration, radiation, precipitation, evaporation, and relative humidity), water quality variations (pH, total organic carbon content, dissolved oxygen, and turbidity), accumulated sediments as an endogenous source, as well as unique estuarine conditions collectively facilitated picocyanobacterial-bacterial coexistence and community functional changes in this reservoir. A stable and tight co-occurrence pattern was established between dominant cyanobacteria (Synechococcus, Cyanobium, Planktothrix, Chroococcidiopsis, and Prochlorothrix) and certain heterotrophic bacteria (Proteobacteria, Actinobacteria, and Bacteroidetes), which contributed to the remineralization of organic matter for cyanobacteria utilization. The relative abundance of chemoorganoheterotrophs and bacteria related to nitrogen transformation (Paracoccus, Rhodoplanes, Nitrosomonas, and Zoogloea) increased, promoting the emergence of CBs in nutrient-limited conditions through enhanced nutrient recycling. In environments with limited nutrients, the interaction between photosynthetic autotrophic microorganisms and heterotrophic bacteria appears to be non-competitive. Instead, they adopt complementary roles within their ecological niche over long-term succession, mutually benefiting from this association. This long-term study confirmed that enhanced nutrient cycling, facilitated by cyanobacterial-bacterial symbiosis following long-term succession, could promote CBs in oligotrophic aquatic environments devoid of external nutrient inputs. This study advances understanding of the mechanisms that trigger and sustain CBs under nutritional constraints, contributing to developing more effective mitigation strategies, ensuring water safety, and maintaining ecological balance.
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Affiliation(s)
- Huimin Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Mengqi Jiang
- Center for Ecological Research, Kyoto University, Shiga, 520-2113, Japan
| | - Peng Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Zheng Xu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Peng Jiang
- Department of Industrial Engineering and Management, Sichuan University, Chengdu, 610064, PR China
| | - Lei Chen
- Shanghai National Engineering Research Center of Urban Water Resources Co., Ltd., Shanghai, 200082, PR China
| | - Karina Yew-Hoong Gin
- National University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, Singapore, 138602, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, PR China.
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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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Charalampous G, Kormas KA, Antoniou E, Kalogerakis N, Gontikaki E. Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea). Curr Microbiol 2024; 81:381. [PMID: 39340560 DOI: 10.1007/s00284-024-03906-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024]
Abstract
Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.
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Affiliation(s)
- Georgia Charalampous
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece.
- Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Eleftheria Antoniou
- School of Mineral Resources Engineering, Technical University of Crete, Chania, Greece
| | - Nicolas Kalogerakis
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece
- Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Evangelia Gontikaki
- Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
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Gopalakrishnappa C, Li Z, Kuehn S. Environmental modulators of algae-bacteria interactions at scale. Cell Syst 2024; 15:838-853.e13. [PMID: 39236710 PMCID: PMC11412779 DOI: 10.1016/j.cels.2024.08.002] [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: 04/03/2023] [Revised: 11/29/2023] [Accepted: 08/07/2024] [Indexed: 09/07/2024]
Abstract
Interactions between photosynthetic and heterotrophic microbes play a key role in global primary production. Understanding phototroph-heterotroph interactions remains challenging because these microbes reside in chemically complex environments. Here, we leverage a massively parallel droplet microfluidic platform that enables us to interrogate interactions between photosynthetic algae and heterotrophic bacteria in >100,000 communities across ∼525 environmental conditions with varying pH, carbon availability, and phosphorus availability. By developing a statistical framework to dissect interactions in this complex dataset, we reveal that the dependence of algae-bacteria interactions on nutrient availability is strongly modulated by pH and buffering capacity. Furthermore, we show that the chemical identity of the available organic carbon source controls how pH, buffering capacity, and nutrient availability modulate algae-bacteria interactions. Our study reveals the previously underappreciated role of pH in modulating phototroph-heterotroph interactions and provides a framework for thinking about interactions between phototrophs and heterotrophs in more natural contexts.
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Affiliation(s)
| | - Zeqian Li
- Department of Physics, The University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA; Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Seppe Kuehn
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA; Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA; National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL 60637, USA; Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA.
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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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Stiffler AK, Hesketh-Best PJ, Varona NS, Zagame A, Wallace BA, Lapointe BE, Silveira CB. Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses. MICROBIOME 2024; 12:143. [PMID: 39090708 PMCID: PMC11295528 DOI: 10.1186/s40168-024-01860-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/19/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND Symbioses between primary producers and bacteria are crucial for nutrient exchange that fosters host growth and niche adaptation. Yet, how viruses that infect bacteria (phages) influence these bacteria-eukaryote interactions is still largely unknown. Here, we investigate the role of viruses on the genomic diversity and functional adaptations of bacteria associated with pelagic sargassum. This brown alga has dramatically increased its distribution range in the Atlantic in the past decade and is predicted to continue expanding, imposing severe impacts on coastal ecosystems, economies, and human health. RESULTS We reconstructed 73 bacterial and 3963 viral metagenome-assembled genomes (bMAGs and vMAGs, respectively) from coastal Sargassum natans VIII and surrounding seawater. S. natans VIII bMAGs were enriched in prophages compared to seawater (28% and 0.02%, respectively). Rhodobacterales and Synechococcus bMAGs, abundant members of the S. natans VIII microbiome, were shared between the algae and seawater but were associated with distinct phages in each environment. Genes related to biofilm formation and quorum sensing were enriched in S. natans VIII phages, indicating their potential to influence algal association in their bacterial hosts. In-vitro assays with a bacterial community harvested from sargassum surface biofilms and depleted of free viruses demonstrated that these bacteria are protected from lytic infection by seawater viruses but contain intact and inducible prophages. These bacteria form thicker biofilms when growing on sargassum-supplemented seawater compared to seawater controls, and phage induction using mitomycin C was associated with a significant decrease in biofilm formation. The induced metagenomes were enriched in genomic sequences classified as temperate viruses compared to uninduced controls. CONCLUSIONS Our data shows that prophages contribute to the flexible genomes of S. natans VIII-associated bacteria. These prophages encode genes with symbiotic functions, and their induction decreases biofilm formation, an essential capacity for flexible symbioses between bacteria and the alga. These results indicate that prophage acquisition and induction contribute to genomic and functional diversification during sargassum-bacteria symbioses, with potential implications for algae growth. Video Abstract.
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Affiliation(s)
| | - Poppy J Hesketh-Best
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Natascha S Varona
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Ashley Zagame
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Bailey A Wallace
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Brian E Lapointe
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, 34946, USA
| | - Cynthia B Silveira
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, 33149, USA.
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Zhao N, Liu F, Dong W, Yu J, Halverson LJ, Xie B. Quantitative proteomics insights into Chlamydomonas reinhardtii thermal tolerance enhancement by a mutualistic interaction with Sinorhizobium meliloti. Microbiol Spectr 2024; 12:e0021924. [PMID: 39012118 DOI: 10.1128/spectrum.00219-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/21/2024] [Indexed: 07/17/2024] Open
Abstract
Interactions between photosynthetic microalgae and bacteria impact the physiology of both partners, which influence the fitness and ecological trajectories of each partner in an environmental context-dependent manner. Thermal tolerance of Chlamydomonas reinhardtii can be enhanced through a mutualistic interaction with vitamin B12 (cobalamin)-producing Sinorhizobium meliloti. Here, we used label-free quantitative proteomics to reveal the metabolic networks altered by the interaction under normal and high temperatures. We created a scenario where the growth of Sinorhizobium requires carbon provided by Chlamydomonas for growth in co-cultures, and survival of Chlamydomonas under high temperatures relies on cobalamin and possibly other metabolites produced by Sinorhizobium. Differential abundance analysis identified proteins produced by each partner in co-cultures compared to mono-cultures at each temperature. Proteins involved in cobalamin production by Sinorhizobium increased in the presence of Chlamydomonas under elevated temperatures, whereas in Chlamydomonas, there was an increase in cobalamin-dependent methionine synthase and certain proteins associated with methylation reactions. Co-cultivation and heat stress strongly modulated the central metabolism of both partners as well as various transporters that could facilitate nutrient cross-utilization. Co-cultivation modulated expression of various components of two- or one-component signal transduction systems, transcriptional activators/regulators, or sigma factors, suggesting complex regulatory networks modulate the interaction in a temperature-dependent manner. Notably, heat and general stress-response and antioxidant proteins were upregulated in co-cultures, suggesting that the interaction is inherently stressful to each partner despite the benefits of mutualism. Our results shed insight into the metabolic tradeoffs required for mutualism and how metabolic networks are modulated by elevated temperature. IMPORTANCE Photosynthetic microalgae are key primary producers in aquatic ecosystems, playing an important role in the global carbon cycle. Nearly every alga lives in association with a diverse community of microorganisms that influence each other and their metabolic activities or survival. One chemical produced by bacteria that influence algae is vitamin B12, an enzyme cofactor used for a variety of metabolic functions. The alga Chlamydomonas reinhardtii benefits from vitamin B12 produced by Sinorhizobium meliloti by producing the amino acid methionine under high temperatures which are required for Chlamydomonas thermotolerance. Yet, our understanding of this interaction under normal and stressful temperatures is poor. Here, we used quantitative proteomics to identify differentially expressed proteins to reveal metabolic adjustments made by Chlamydomonas and Sinorhizobium that could facilitate this mutualism. These findings will enhance our understanding of how photosynthetic algae and their associated microbiomes will respond as global temperatures increase.
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Affiliation(s)
- Na Zhao
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
- Translational Medicine Research Center, Guizhou Medical University, Guiyang, China
| | - Fei Liu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Wenxiu Dong
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Jie Yu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Larry J Halverson
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Bo Xie
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
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Angulo-Cánovas E, Bartual A, López-Igual R, Luque I, Radzinski NP, Shilova I, Anjur-Dietrich M, García-Jurado G, Úbeda B, González-Reyes JA, Díez J, Chisholm SW, García-Fernández JM, del Carmen Muñoz-Marín M. Direct interaction between marine cyanobacteria mediated by nanotubes. SCIENCE ADVANCES 2024; 10:eadj1539. [PMID: 38781331 PMCID: PMC11114229 DOI: 10.1126/sciadv.adj1539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Microbial associations and interactions drive and regulate nutrient fluxes in the ocean. However, physical contact between cells of marine cyanobacteria has not been studied thus far. Here, we show a mechanism of direct interaction between the marine cyanobacteria Prochlorococcus and Synechococcus, the intercellular membrane nanotubes. We present evidence of inter- and intra-genus exchange of cytoplasmic material between neighboring and distant cells of cyanobacteria mediated by nanotubes. We visualized and measured these structures in xenic and axenic cultures and in natural samples. We show that nanotubes are produced between living cells, suggesting that this is a relevant system of exchange material in vivo. The discovery of nanotubes acting as exchange bridges in the most abundant photosynthetic organisms in the ocean may have important implications for their interactions with other organisms and their population dynamics.
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Affiliation(s)
- Elisa Angulo-Cánovas
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - Ana Bartual
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Rocío López-Igual
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Nikolai P. Radzinski
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Maya Anjur-Dietrich
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gema García-Jurado
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Bárbara Úbeda
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - José Antonio González-Reyes
- Departamento de Biología Celular, Fisiología e Inmunología, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - María del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
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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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10
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Ma C, Peng C, Fu L, Ren C, Liu X, Liu Z, Qin S, Zhong Z. Phycosphere bacterial disturbance of Saccharina japonica caused by white rot disease relates to seawater nutrients. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:37245-37255. [PMID: 38767795 DOI: 10.1007/s11356-024-33707-x] [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: 09/17/2023] [Accepted: 05/13/2024] [Indexed: 05/22/2024]
Abstract
In mid-November 2021, there were large areas of white rot disease on cultivated Saccharina japonica in Rongcheng City, China, and diseases were undetected on Sargassum horneri and Porphyra yezoensis. The disturbance direction of bacterial community in the phycosphere after disease outbreak and the relationship with seawater nutrients remain unclear. Here, in situ studies of bacterial community in the non-diseased and diseased areas (Shawo and Dongchu islands) and seawater nutrient levels were carried out. 16S rRNA sequencing showed that the bacterial richness of the studied seaweeds increased in the diseased area. Only in S. japonica, Algitalea outcompeted abundant primary bacteria with probiotic relationships to the host of the non-diseased area, and dominated in the diseased area (17.6% of the total abundance). Nitrogen and phosphorus levels in seawater were 57.8% and 19.6% higher in the non-diseased area than those in the diseased area, respectively, and were strongly correlated with the phycosphere bacteria at the family level of S. japonica. There was no difference in potential pathogenicity between the two areas, while positive signal communications decreased, and nitrogen cycle, chemoheterotrophy, and cellulolysis increased in the diseased area compared to the non-diseased area. Overall, white rot disease caused a structural disturbance in phycosphere bacterial community of S. japonica that related to seawater nutrient levels. Enriched degraders and altered bacterial community functions may exacerbate the disease. This evaluation will provide information for white rot disease management to prevent and mitigate the occurrence of S. japonica outbreaks.
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Affiliation(s)
- Chen Ma
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, 570228, Hainan, China
| | - Chengxiang Peng
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
| | - Longwen Fu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
| | - Chenggang Ren
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
| | - Xintian Liu
- Weihai Oceanic Development Research Institute, Weihai, 264200, Shandong, China
| | - Zhengyi Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
| | - Zhihai Zhong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China.
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11
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Haavisto V, Landry Z, Pontrelli S. High-throughput profiling of metabolic responses to exogenous nutrients in Synechocystis sp. PCC 6803. mSystems 2024; 9:e0022724. [PMID: 38534128 PMCID: PMC11019784 DOI: 10.1128/msystems.00227-24] [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: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
Cyanobacteria fix carbon dioxide and release carbon-containing compounds into the wider ecosystem, yet they are sensitive to small metabolites that may impact their growth and physiology. Several cyanobacteria can grow mixotrophically, but we currently lack a molecular understanding of how specific nutrients may alter the compounds they release, limiting our knowledge of how environmental factors might impact primary producers and the ecosystems they support. In this study, we develop a high-throughput phytoplankton culturing platform and identify how the model cyanobacterium Synechocystis sp. PCC 6803 responds to nutrient supplementation. We assess growth responses to 32 nutrients at two concentrations, identifying 15 that are utilized mixotrophically. Seven nutrient sources significantly enhance growth, while 19 elicit negative growth responses at one or both concentrations. High-throughput exometabolomics indicates that oxidative stress limits Synechocystis' growth but may be alleviated by antioxidant metabolites. Furthermore, glucose and valine induce strong changes in metabolite exudation in a possible effort to correct pathway imbalances or maintain intracellular elemental ratios. This study sheds light on the flexibility and limits of cyanobacterial physiology and metabolism, as well as how primary production and trophic food webs may be modulated by exogenous nutrients.IMPORTANCECyanobacteria capture and release carbon compounds to fuel microbial food webs, yet we lack a comprehensive understanding of how external nutrients modify their behavior and what they produce. We developed a high throughput culturing platform to evaluate how the model cyanobacterium Synechocystis sp. PCC 6803 responds to a broad panel of externally supplied nutrients. We found that growth may be enhanced by metabolites that protect against oxidative stress, and growth and exudate profiles are altered by metabolites that interfere with central carbon metabolism and elemental ratios. This work contributes a holistic perspective of the versatile response of Synechocystis to externally supplied nutrients, which may alter carbon flux into the wider ecosystem.
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Affiliation(s)
- Vilhelmiina Haavisto
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Zachary Landry
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
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12
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Kratzl F, Urban M, Pandhal J, Shi M, Meng C, Kleigrewe K, Kremling A, Pflüger-Grau K. Pseudomonas putida as saviour for troubled Synechococcus elongatus in a synthetic co-culture - interaction studies based on a multi-OMICs approach. Commun Biol 2024; 7:452. [PMID: 38609451 PMCID: PMC11014904 DOI: 10.1038/s42003-024-06098-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
In their natural habitats, microbes rarely exist in isolation; instead, they thrive in consortia, where various interactions occur. In this study, a defined synthetic co-culture of the cyanobacterium S. elongatus cscB, which supplies sucrose to the heterotrophic P. putida cscRABY, is investigated to identify potential interactions. Initial experiments reveal a remarkable growth-promoting effect of the heterotrophic partner on the cyanobacterium, resulting in an up to 80% increase in the growth rate and enhanced photosynthetic capacity. Vice versa, the presence of the cyanobacterium has a neutral effect on P. putida cscRABY, highlighting the resilience of pseudomonads against stress and their potential as co-culture partners. Next, a suitable reference process reinforcing the growth-promoting effect is established in a parallel photobioreactor system, which sets the basis for the analysis of the co-culture at the transcriptome, proteome, and metabolome levels. In addition to several moderate changes, including alterations in the metabolism and stress response in both microbes, this comprehensive multi-OMICs approach strongly hints towards the exchange of further molecules beyond the unidirectional feeding with sucrose. Taken together, these findings provide valuable insights into the complex dynamics between both co-culture partners, indicating multi-level interactions, which can be employed for further streamlining of the co-cultivation system.
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Affiliation(s)
- Franziska Kratzl
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Marlene Urban
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Mengxun Shi
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas Kremling
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Katharina Pflüger-Grau
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany.
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13
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Cai L, Li H, Deng J, Zhou R, Zeng Q. Biological interactions with Prochlorococcus: implications for the marine carbon cycle. Trends Microbiol 2024; 32:280-291. [PMID: 37722980 DOI: 10.1016/j.tim.2023.08.011] [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: 04/29/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023]
Abstract
The unicellular picocyanobacterium Prochlorococcus is the most abundant photoautotroph and contributes substantially to global CO2 fixation. In the vast euphotic zones of the open ocean, Prochlorococcus converts CO2 into organic compounds and supports diverse organisms, forming an intricate network of interactions that regulate the magnitude of carbon cycling and storage in the ocean. An understanding of the biological interactions with Prochlorococcus is critical for accurately estimating the contributions of Prochlorococcus and interacting organisms to the marine carbon cycle. This review synthesizes the primary production contributed by Prochlorococcus in the global ocean. We outline recent progress on the interactions of Prochlorococcus with heterotrophic bacteria, phages, and grazers that multifacetedly determine Prochlorococcus carbon production and fate. We discuss that climate change might affect the biological interactions with Prochlorococcus and thus the marine carbon cycle.
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Affiliation(s)
- Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China
| | - Junwei Deng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ruiqian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China; Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong, China.
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14
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Shi M, Evans CA, McQuillan JL, Noirel J, Pandhal J. LFQRatio: A Normalization Method to Decipher Quantitative Proteome Changes in Microbial Coculture Systems. J Proteome Res 2024; 23:999-1013. [PMID: 38354288 PMCID: PMC10913063 DOI: 10.1021/acs.jproteome.3c00714] [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: 10/30/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The value of synthetic microbial communities in biotechnology is gaining traction due to their ability to undertake more complex metabolic tasks than monocultures. However, a thorough understanding of strain interactions, productivity, and stability is often required to optimize growth and scale up cultivation. Quantitative proteomics can provide valuable insights into how microbial strains adapt to changing conditions in biomanufacturing. However, current workflows and methodologies are not suitable for simple artificial coculture systems where strain ratios are dynamic. Here, we established a workflow for coculture proteomics using an exemplar system containing two members, Azotobacter vinelandii and Synechococcus elongatus. Factors affecting the quantitative accuracy of coculture proteomics were investigated, including peptide physicochemical characteristics such as molecular weight, isoelectric point, hydrophobicity, and dynamic range as well as factors relating to protein identification such as varying proteome size and shared peptides between species. Different quantification methods based on spectral counts and intensity were evaluated at the protein and cell level. We propose a new normalization method, named "LFQRatio", to reflect the relative contributions of two distinct cell types emerging from cell ratio changes during cocultivation. LFQRatio can be applied to real coculture proteomics experiments, providing accurate insights into quantitative proteome changes in each strain.
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Affiliation(s)
- Mengxun Shi
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Caroline A. Evans
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Josie L. McQuillan
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Josselin Noirel
- GBCM
Laboratory (EA7528), Conservatoire National des Arts et Métiers, HESAM Université, 2 rue Conté, Paris 75003, France
| | - Jagroop Pandhal
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
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15
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Eigemann F, Tait K, Temperton B, Hellweger FL. Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption. THE ISME JOURNAL 2024; 18:wrae103. [PMID: 38861418 PMCID: PMC11217553 DOI: 10.1093/ismejo/wrae103] [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: 04/24/2024] [Revised: 05/18/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Molecular observational tools are useful for characterizing the composition and genetic endowment of microbial communities but cannot measure fluxes, which are critical for the understanding of ecosystems. To overcome these limitations, we used a mechanistic inference approach to estimate dissolved organic carbon (DOC) production and consumption by phytoplankton operational taxonomic units and heterotrophic prokaryotic amplicon sequence variants and inferred carbon fluxes between members of this microbial community from Western English Channel time-series data. Our analyses focused on phytoplankton spring and summer blooms, as well as bacteria summer blooms. In spring blooms, phytoplankton DOC production exceeds heterotrophic prokaryotic consumption, but in bacterial summer blooms heterotrophic prokaryotes consume three times more DOC than produced by the phytoplankton. This mismatch is compensated by heterotrophic prokaryotic DOC release by death, presumably from viral lysis. In both types of summer blooms, large amounts of the DOC liberated by heterotrophic prokaryotes are reused through internal recycling, with fluxes between different heterotrophic prokaryotes being at the same level as those between phytoplankton and heterotrophic prokaryotes. In context, internal recycling accounts for approximately 75% and 30% of the estimated net primary production (0.16 vs 0.22 and 0.08 vs 0.29 μmol l-1 d-1) in bacteria and phytoplankton summer blooms, respectively, and thus represents a major component of the Western English Channel carbon cycle. We have concluded that internal recycling compensates for mismatches between phytoplankton DOC production and heterotrophic prokaryotic consumption, and we encourage future analyses on aquatic carbon cycles to investigate fluxes between heterotrophic prokaryotes, specifically internal recycling.
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Affiliation(s)
- Falk Eigemann
- Water Quality Engineering, Technical University of Berlin, 10623 Berlin, Germany
| | - Karen Tait
- Plymouth Marine Laboratory, PL1 Plymouth, United Kingdom
| | - Ben Temperton
- Faculty of Health and Life Sciences, University of Exeter, EX2 Exeter, United Kingdom
| | - Ferdi L Hellweger
- Water Quality Engineering, Technical University of Berlin, 10623 Berlin, Germany
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16
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Li W, Baliu-Rodriguez D, Premathilaka SH, Thenuwara SI, Kimbrel JA, Samo TJ, Ramon C, Kiledal EA, Rivera SR, Kharbush J, Isailovic D, Weber PK, Dick GJ, Mayali X. Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures. THE ISME JOURNAL 2024; 18:wrae082. [PMID: 38718148 PMCID: PMC11126159 DOI: 10.1093/ismejo/wrae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/01/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis cause worldwide public and ecosystem health concerns. The response of Microcystis growth and toxin production to new and recycled nitrogen (N) inputs and the impact of heterotrophic bacteria in the Microcystis phycosphere on these processes are not well understood. Here, using microbiome transplant experiments, cyanotoxin analysis, and nanometer-scale stable isotope probing to measure N incorporation and exchange at single cell resolution, we monitored the growth, cyanotoxin production, and microbiome community structure of several Microcystis strains grown on amino acids or proteins as the sole N source. We demonstrate that the type of organic N available shaped the microbial community associated with Microcystis, and external organic N input led to decreased bacterial colonization of Microcystis colonies. Our data also suggest that certain Microcystis strains could directly uptake amino acids, but with lower rates than heterotrophic bacteria. Toxin analysis showed that biomass-specific microcystin production was not impacted by N source (i.e. nitrate, amino acids, or protein) but rather by total N availability. Single-cell isotope incorporation revealed that some bacterial communities competed with Microcystis for organic N, but other communities promoted increased N uptake by Microcystis, likely through ammonification or organic N modification. Our laboratory culture data suggest that organic N input could support Microcystis blooms and toxin production in nature, and Microcystis-associated microbial communities likely play critical roles in this process by influencing cyanobacterial succession through either decreasing (via competition) or increasing (via biotransformation) N availability, especially under inorganic N scarcity.
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Affiliation(s)
- Wei Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - David Baliu-Rodriguez
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States
| | - Sanduni H Premathilaka
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States
| | - Sharmila I Thenuwara
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Erik Anders Kiledal
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48104, United States
| | - Sara R Rivera
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48104, United States
| | - Jenan Kharbush
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48104, United States
| | - Dragan Isailovic
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48104, United States
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI 48104, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
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17
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Potekhin A, Plotnikov AO, Gogoleva N, Sonntag B. Editorial: Microbial associations formed and hosted by protists, algae, and fungi. Front Microbiol 2024; 14:1341058. [PMID: 38249461 PMCID: PMC10799554 DOI: 10.3389/fmicb.2023.1341058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024] Open
Affiliation(s)
- Alexey Potekhin
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Andrey O. Plotnikov
- Institute for Cellular and Intracellular Symbiosis of the UrB RAS, Orenburg Federal Research Center, Orenburg, Russia
| | - Natalia Gogoleva
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Laboratory of Environmental Metagenomics, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
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18
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Goyal A, Flamholz AI, Petroff AP, Murugan A. Closed ecosystems extract energy through self-organized nutrient cycles. Proc Natl Acad Sci U S A 2023; 120:e2309387120. [PMID: 38127977 PMCID: PMC10756307 DOI: 10.1073/pnas.2309387120] [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: 06/04/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023] Open
Abstract
Our planet is a self-sustaining ecosystem powered by light energy from the sun, but roughly closed to matter. Many ecosystems on Earth are also approximately closed to matter and recycle nutrients by self-organizing stable nutrient cycles, e.g., microbial mats, lakes, open ocean gyres. However, existing ecological models do not exhibit the self-organization and dynamical stability widely observed in such planetary-scale ecosystems. Here, we advance a conceptual model that explains the self-organization, stability, and emergent features of closed microbial ecosystems. Our model incorporates the bioenergetics of metabolism into an ecological framework. By studying this model, we uncover a crucial thermodynamic feedback loop that enables metabolically diverse communities to almost always stabilize nutrient cycles. Surprisingly, highly diverse communities self-organize to extract [Formula: see text]10[Formula: see text] of the maximum extractable energy, or [Formula: see text]100 fold more than randomized communities. Further, with increasing diversity, distinct ecosystems show strongly correlated fluxes through nutrient cycles. However, as the driving force from light increases, the fluxes of nutrient cycles become more variable and species-dependent. Our results highlight that self-organization promotes the efficiency and stability of complex ecosystems at extracting energy from the environment, even in the absence of any centralized coordination.
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Affiliation(s)
- Akshit Goyal
- Department of Physics, Massachusetts Insitute of Technology, Cambridge, MA02139
| | - Avi I. Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA91125
| | | | - Arvind Murugan
- Department of Physics, University of Chicago, Chicago, IL60637
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19
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Wang X, Teng Y, Wang X, Xu Y, Li R, Sun Y, Dai S, Hu W, Wang H, Li Y, Fang Y, Luo Y. Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation. THE ISME JOURNAL 2023; 17:2169-2181. [PMID: 37775536 PMCID: PMC10689768 DOI: 10.1038/s41396-023-01522-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS - 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of the Chinese Academy of Sciences, 100049, Beijing, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Ran Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yi Sun
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Shixiang Dai
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenbo Hu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Hongzhe Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanning Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan Fang
- University of the Chinese Academy of Sciences, 100049, Beijing, China
- Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
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20
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Kong L, Feng Y, Du W, Zheng R, Sun J, Rong K, Sun W, Liu S. Cross-Feeding between Filamentous Cyanobacteria and Symbiotic Bacteria Favors Rapid Photogranulation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16953-16963. [PMID: 37886803 DOI: 10.1021/acs.est.3c04867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Photogranules are dense algal-bacterial aggregates used in aeration-free and carbon-negative wastewater treatment, wherein filamentous cyanobacteria (FC) are essential components. However, little is known about the functional role of symbiotic bacteria in photogranulation. Herein, we combined cyanobacterial isolation, reactor operation, and multiomics analysis to investigate the cyanobacterial-bacterial interaction during photogranulation. The addition of FC to the inoculated sludge achieved a 1.4-fold higher granule size than the control, and the aggregation capacity of FC-dominant photogranules was closely related to the extracellular polysaccharide (PS) concentration (R = 0.86). Importantly, we found that cross-feeding between FC and symbiotic bacteria for macromolecular PS synthesis is at the heart of photogranulation and substantially enhanced the granular stability. Chloroflexi-affiliated bacteria intertwined with FC throughout the photogranules and promoted PS biosynthesis using the partial nucleotide sugars produced by FC. Proteobacteria-affiliated bacteria were spatially close to FC, and highly expressed genes for vitamin B1 and B12 synthesis, contributing the necessary cofactors to promote FC proliferation. In addition, Bacteroidetes-affiliated bacteria degraded FC-derived carbohydrates and influenced granules development. Our metabolic characterization identified the functional role of symbiotic bacteria of FC during photogranulation and shed light on the critical cyanobacterial-bacterial interactions in photogranules from the viewpoint of cross-feeding.
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Affiliation(s)
- Lingrui Kong
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Yiming Feng
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Wenran Du
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ru Zheng
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Jingqi Sun
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Kaiyu Rong
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Weiling Sun
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Sitong Liu
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
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21
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Pan M, Wang Y, Krömer JO, Zhu X, Lin MKTH, Angelidaki I. A Coculture of Photoautotrophs and Hydrolytic Heterotrophs Enables Efficient Upcycling of Starch from Wastewater toward Biomass-Derived Products: Synergistic Interactions Impacting Metabolism of the Consortium. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15523-15532. [PMID: 37792456 DOI: 10.1021/acs.est.3c05321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Even with particular interest in sustainable development, due to the limited types of bioavailable carbon sources that could support heterotrophic/mixotrophic growth, microalgae-derived products still suffer from inconsistent yield and high costs. This study demonstrates a successful cocultivation of the photoautotroph Chlorella vulgaris with a hydrolytic-enzyme-abundant heterotroph, Saccharomycopsis fibuligera, enabling efficient starch upcycling from water/wastewater toward enhancing microalgae-dominant biomass and lipid production. The enzymatic activities of S. fibuligera contributed to the hydrolysis of starch into glucose, generating a 7-fold higher biomass through mixotrophic/heterotrophic growth of C. vulgaris. Further, scanning transmission electron microscopy (STEM) and quantitative analysis suggested a significantly induced accumulation of lipids in C. vulgaris. Results of meta-transcriptomics revealed the critical regulatory role of illumination in interaction shifting. Gene expression for glycolysis and lipid biosynthesis of C. vulgaris were highly activated during dark periods. Meanwhile, during illumination periods, genes coding for glucoamylase and the sulfur-related activities in S. fibuligera were significantly upregulated, leading to induced starch hydrolysis and potential increased competition for sulfur utilization, respectively. This study indicates that hydrolytic organisms could collaborate to make starch bioavailable for nonhydrolytic microalgae, thus broadening the substrate spectrum and making starch a novel biotechnological feedstock for microalgae-derived products, e.g., biofuels or single-cell protein.
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Affiliation(s)
- Minmin Pan
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, UFZ, Leipzig 04318, Germany
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby DK-2899, Denmark
| | - Yiru Wang
- German Center for Neurodegenerative Diseases (DZNE), Bonn 53127, Germany
| | - Jens O Krömer
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, UFZ, Leipzig 04318, Germany
| | - Xinyu Zhu
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby DK-2899, Denmark
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Marie Karen Tracy Hong Lin
- National Center for Nanofabrication and Characterization, Technical University of Denmark, Lyngby DK-2899, Denmark
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby DK-2899, Denmark
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22
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Gilbert L, Jeanniard-du-Dot T, Authier M, Chouvelon T, Spitz J. Composition of cetacean communities worldwide shapes their contribution to ocean nutrient cycling. Nat Commun 2023; 14:5823. [PMID: 37726276 PMCID: PMC10509247 DOI: 10.1038/s41467-023-41532-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023] Open
Abstract
Defecation by large whales is known to fertilise oceans with nutrients, stimulating phytoplankton and ecosystem productivity. However, our current understanding of these processes is limited to a few species, nutrients and ecosystems. Here, we investigate the role of cetacean communities in the worldwide biological cycling of two major nutrients and six trace nutrients. We show that cetaceans release more nutrients in mesotrophic to eutrophic temperate waters than in oligotrophic tropical waters, mirroring patterns of ecosystem productivity. The released nutrient cocktails also vary geographically, driven by the composition of cetacean communities. The roles of small cetaceans, deep diving cetaceans and baleen whales differ quantitatively and functionally, with contributions of small cetaceans and deep divers exceeding those of large whales in some areas. The functional diversity of cetacean communities expands beyond their role as top predators to include their role as active nutrient vectors, which might be equally important to local ecosystem dynamics.
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Affiliation(s)
- Lola Gilbert
- Centre for Biological Studies of Chizé, UMR 7372 La Rochelle University - CNRS, La Rochelle, France
- Pelagis Observatory, UAR 3462 La Rochelle University - CNRS, La Rochelle, France
| | | | - Matthieu Authier
- Pelagis Observatory, UAR 3462 La Rochelle University - CNRS, La Rochelle, France
| | - Tiphaine Chouvelon
- Pelagis Observatory, UAR 3462 La Rochelle University - CNRS, La Rochelle, France
- Ifremer, Chemical Contamination of Marine Ecosystems Unit, Nantes, France
| | - Jérôme Spitz
- Centre for Biological Studies of Chizé, UMR 7372 La Rochelle University - CNRS, La Rochelle, France.
- Pelagis Observatory, UAR 3462 La Rochelle University - CNRS, La Rochelle, France.
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23
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Mayali X, Samo TJ, Kimbrel JA, Morris MM, Rolison K, Swink C, Ramon C, Kim YM, Munoz-Munoz N, Nicora C, Purvine S, Lipton M, Stuart RK, Weber PK. Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum. Nat Commun 2023; 14:5642. [PMID: 37704622 PMCID: PMC10499878 DOI: 10.1038/s41467-023-41179-9] [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: 07/07/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.
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Affiliation(s)
- Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jeff A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Megan M Morris
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kristina Rolison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Courtney Swink
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Nathalie Munoz-Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Sam Purvine
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mary Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Rhona K Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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24
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Xue X, Su X, Zhou L, Ji J, Qin Z, Liu J, Li K, Wang H, Wang Z. Antibiotic-Induced Recruitment of Specific Algae-Associated Microbiome Enhances the Adaptability of Chlorella vulgaris to Antibiotic Stress and Incidence of Antibiotic Resistance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13336-13345. [PMID: 37642958 DOI: 10.1021/acs.est.3c02801] [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] [Indexed: 08/31/2023]
Abstract
Insights into the symbiotic relation between eukaryotic hosts and their microbiome lift the curtain on the crucial roles of microbes in host fitness, behavior, and ecology. However, it remains unclear whether and how abiotic stress shapes the microbiome and further affects host adaptability. This study first investigated the effect of antibiotic exposure on behavior across varying algae taxa at the community level. Chlorophyta, in particular Chlorella vulgaris, exhibited remarkable adaptability to antibiotic stress, leading to their dominance in phytoplankton communities. Accordingly, we isolated C. vulgaris strains and compared the growth of axenic and nonaxenic ones under antibiotic conditions. The positive roles of antibiotics in algal growth were apparent only in the presence of bacteria. Results of 16S rRNA sequencing further revealed that antibiotic challenges resulted in the recruitment of specific bacterial consortia in the phycosphere, whose functions were tightly linked to the host growth promotion and adaptability enhancement. In addition, the algal phycosphere was characterized with 47-fold higher enrichment capability of antibiotic resistance genes (ARGs) than the surrounding water. Under antibiotic stress, specific ARG profiles were recruited in C. vulgaris phycosphere, presumably driven by the specific assembly of bacterial consortia and mobile genetic elements induced by antibiotics. Moreover, the antibiotics even enhanced the dissemination potential of the bacteria carrying ARGs from the algal phycosphere to broader environmental niches. Overall, this study provides an in-depth understanding into the potential functional significance of antibiotic-mediated recruitment of specific algae-associated bacteria for algae adaptability and ARG proliferation in antibiotic-polluted waters.
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Affiliation(s)
- Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoyue Su
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linjun Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiaqi Ji
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ziwei Qin
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jialin Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiqi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - He Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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25
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Li C, Zheng H, Li H, Liu L, Wang J, Ni J. Synthetic Light-Driven Consortia for Carbon-Negative Biosynthesis. Chembiochem 2023; 24:e202300122. [PMID: 37401840 DOI: 10.1002/cbic.202300122] [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: 02/27/2023] [Revised: 05/07/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
Synthetic light-driven consortia composed of phototrophs and heterotrophs have attracted increasing attention owing to their potential to be used in sustainable biotechnology. In recent years, synthetic phototrophic consortia have been used to produce bulk chemicals, biofuels, and other valuable bioproducts. In addition, autotrophic-heterotrophic symbiosis systems have potential applications in wastewater treatment, bioremediation, and as a method for phytoplankton bloom control. Here, we discuss progress made on the biosynthesis of phototrophic microbial consortia. In addition, strategies for optimizing the synthetic light-driven consortia are summarized. Moreover, we highlight current challenges and future research directions for the development of robust and controllable synthetic light-driven consortia.
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Affiliation(s)
- Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
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26
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Baek JH, Kristyanto S, Kim JM, Han DM, Quan ZX, Jeon CO. Hoeflea algicola sp. nov. and Hoeflea ulvae sp. nov., isolated from phycosphere of marine algae. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755148 DOI: 10.1099/ijsem.0.006058] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Two Gram-negative, moderately halophilic, and motile rod bacteria, strains G2-23T and J2-29T, showing catalase- and oxidase-positive activities were isolated from species of the marine algae Chondrus and Ulva, respectively. Both strains optimally grew at 30 °C, pH 7.0 and 2% (w/v) NaCl. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. Strain G2-23T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c/ω6c) as major cellular fatty acids, and phosphatidylethanolamine (PE), phosphatidyl-N-monomethylethanolamine (PME), phosphatidylglycerol (PG), diphosphatidylglycerol and an unidentified phospholipid (PL) as major polar lipids. Strain J2-29T contained summed feature 8, C18 : 1 ω7c 11-methyl and C16 : 0 as major cellular fatty acids and PE, PME, PG and PL as major polar lipids. The genomic DNA G+C contents of strains G2-23T and J2-29T were 59.5 and 62.2 mol%, respectively. Both strains shared 97.9 % 16S rRNA gene sequence similarity, 79.8 % average nucleotide identity (ANI) and 22.8 % digital DNA-DNA hybridization (dDDH) values, indicating that they represent different species. Phylogenetic and phylogenomic analyses by 16S rRNA gene and genome sequences, respectively, revealed that strains G2-23T and J2-29T formed different phylogenic lineages within the genus Hoeflea. ANI and dDDH values between strains G2-23T and J2-29T and other Hoeflea type strains were less than 79.0 and 22.1% and 80.5 and 23.3 %, respectively, suggesting that they represent novel species of the genus Hoeflea. In summary, based on their phenotypic, chemotaxonomic and molecular properties, strains G2-23T and J2-29T represent two different novel species of the genus Hoeflea, for which the names Hoeflea algicola sp. nov. (G2-23T=KACC 22714T=JCM 35548T) and Hoeflea ulvae sp. nov. (J2-29T=KACC 22715T=JCM 35549T), respectively, are proposed.
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Affiliation(s)
- Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sylvia Kristyanto
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jeong Min Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Zhe-Xue Quan
- School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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27
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Le Reun N, Bramucci A, Ajani P, Khalil A, Raina JB, Seymour JR. Temporal variability in the growth-enhancing effects of different bacteria within the microbiome of the diatom Actinocyclus sp. Front Microbiol 2023; 14:1230349. [PMID: 37608955 PMCID: PMC10440540 DOI: 10.3389/fmicb.2023.1230349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/18/2023] [Indexed: 08/24/2023] Open
Abstract
Reciprocal metabolite exchanges between diatoms and bacteria can enhance the growth of both partners and therefore fundamentally influence aquatic ecosystem productivity. Here, we examined the growth-promoting capabilities of 15 different bacterial isolates from the bacterial community associated with the marine diatom Actinocyclus sp. and investigated the magnitude and timing of their effect on the growth of this diatom. In the presence of its microbiome, Actinocyclus sp. growth was significantly enhanced relative to axenic cultures. Co-culture with each of the 15 bacterial isolates examined here (seven Rhodobacteraceae, four Vibrionaceae, two Pseudoalteromonadaceae, one Oceanospirillaceae and one Alteromonadaceae) increased the growth of the diatom host, with four isolates inducing rates of growth that were similar to those delivered by the diatom's full microbiome. However, the timing and duration of this effect differed between the different bacteria tested. Indeed, one Rhodobacteraceae and one Alteromonadaceae enhanced Actinocyclus sp. cell numbers between days 0-6 after co-incubation, five other Rhodobacteraceae promoted diatom cell numbers the most between days 8-12, whilst four Vibrionaceae, one Oceanospirillaceae and one Rhodobacteraceae enhanced Actinocyclus sp. cell abundance between days 14-16. These results are indicative of a succession of the growth-enhancing effects delivered by diverse bacteria throughout the Actinocyclus sp. life cycle, which will likely deliver sustained growth benefits to the diatom when its full microbiome is present.
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Affiliation(s)
- Nine Le Reun
- Climate Change Cluster, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Anna Bramucci
- Climate Change Cluster, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Penelope Ajani
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Abeeha Khalil
- Climate Change Cluster, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Justin R. Seymour
- Climate Change Cluster, University of Technology Sydney (UTS), Sydney, NSW, Australia
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28
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Eigemann F, Rahav E, Grossart HP, Aharonovich D, Voss M, Sher D. Phytoplankton Producer Species and Transformation of Released Compounds over Time Define Bacterial Communities following Phytoplankton Dissolved Organic Matter Pulses. Appl Environ Microbiol 2023; 89:e0053923. [PMID: 37409944 PMCID: PMC10370336 DOI: 10.1128/aem.00539-23] [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: 03/31/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Phytoplankton-bacterium interactions are mediated, in part, by phytoplankton-released dissolved organic matter (DOMp). Two factors that shape the bacterial community accompanying phytoplankton are (i) the phytoplankton producer species, defining the initial composition of released DOMp, and (ii) the DOMp transformation over time. We added phytoplankton DOMp from the diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus marinus MIT9312 to natural bacterial communities from the eastern Mediterranean and determined the bacterial responses over a time course of 72 h in terms of cell numbers, bacterial production, alkaline phosphatase activity, and changes in active bacterial community composition based on rRNA amplicon sequencing. Both DOMp types were demonstrated to serve the bacterial community as carbon and, potentially, phosphorus sources. Bacterial communities in diatom-derived DOM treatments maintained higher Shannon diversities throughout the experiment and yielded higher bacterial production and lower alkaline phosphatase activity compared to cyanobacterium-derived DOM after 24 h of incubation (but not after 48 and 72 h), indicating greater bacterial usability of diatom-derived DOM. Bacterial communities significantly differed between DOMp types as well as between different incubation times, pointing to a certain bacterial specificity for the DOMp producer as well as a successive utilization of phytoplankton DOM by different bacterial taxa over time. The highest differences in bacterial community composition with DOMp types occurred shortly after DOMp additions, suggesting a high specificity toward highly bioavailable DOMp compounds. We conclude that phytoplankton-associated bacterial communities are strongly shaped by the phytoplankton producer as well as the transformation of its released DOMp over time. IMPORTANCE Phytoplankton-bacterium interactions influence biogeochemical cycles of global importance. Phytoplankton photosynthetically fix carbon dioxide and subsequently release the synthesized compounds as dissolved organic matter (DOMp), which becomes processed and recycled by heterotrophic bacteria. Yet the importance of phytoplankton producers in combination with the time-dependent transformation of DOMp compounds on the accompanying bacterial community has not been explored in detail. The diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus marinus MIT9312 belong to globally important phytoplankton genera, and our study revealed that DOMp of both species was selectively incorporated by the bacterial community. The producer species had the highest impact shortly after DOMp appropriation, and its effect diminished over time. Our results improve the understanding of the dynamics of organic matter produced by phytoplankton in the oceans as it is utilized and modified by cooccurring bacteria.
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Affiliation(s)
- Falk Eigemann
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
- Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Potsdam University, Potsdam, Germany
| | | | - Maren Voss
- Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Daniel Sher
- Leon H. Charney School of Marine Sciences, University Haifa, Israel
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29
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Hao YY, Liu HW, Zhao J, Feng J, Hao X, Huang Q, Gu B, Liu YR. Plastispheres as hotspots of microbially-driven methylmercury production in paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131699. [PMID: 37270960 DOI: 10.1016/j.jhazmat.2023.131699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/09/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
Microplastics (MPs) as emerging contaminants have accumulated extensively in agricultural ecosystems and are known to exert important effects on biogeochemical processes. However, how MPs in paddy soils influence the conversion of mercury (Hg) to neurotoxic methylmercury (MeHg) remains poorly understood. Here, we evaluated the effects of MPs on Hg methylation and associated microbial communities in microcosms using two typical paddy soils in China (i.e., yellow and red soils). Results showed that the addition of MPs significantly increased MeHg production in both soils, which could be related to higher Hg methylation potential in the plastisphere than in the bulk soil. We found significant divergences in the community composition of Hg methylators between the plastisphere and the bulk soil. In addition, the plastisphere had higher proportions of Geobacterales in the yellow soil and Methanomicrobia in the red soil compared with the bulk soil, respectively; and plastisphere also had more densely connected microbial groups between non-Hg methylators and Hg methylators. These microbiota in the plastisphere are different from those in the bulk soil, which could partially account for their distinct MeHg production ability. Our findings suggest plastisphere as a unique biotope for MeHg production and provide new insights into the environment risks of MP accumulation in agricultural soils.
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Affiliation(s)
- Yun-Yun Hao
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui-Wen Liu
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiating Zhao
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jiao Feng
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yu-Rong Liu
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
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30
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Westermann LM, Lidbury ID, Li CY, Wang N, Murphy AR, Aguilo Ferretjans MDM, Quareshy M, Shanmugan M, Torcello-Requena A, Silvano E, Zhang YZ, Blindauer CA, Chen Y, Scanlan DJ. Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles. SCIENCE ADVANCES 2023; 9:eadf5122. [PMID: 37126561 PMCID: PMC10132767 DOI: 10.1126/sciadv.adf5122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
In marine systems, the availability of inorganic phosphate can limit primary production leading to bacterial and phytoplankton utilization of the plethora of organic forms available. Among these are phospholipids that form the lipid bilayer of all cells as well as released extracellular vesicles. However, information on phospholipid degradation is almost nonexistent despite their relevance for biogeochemical cycling. Here, we identify complete catabolic pathways for the degradation of the common phospholipid headgroups phosphocholine (PC) and phosphorylethanolamine (PE) in marine bacteria. Using Phaeobacter sp. MED193 as a model, we provide genetic and biochemical evidence that extracellular hydrolysis of phospholipids liberates the nitrogen-containing substrates ethanolamine and choline. Transporters for ethanolamine (EtoX) and choline (BetT) are ubiquitous and highly expressed in the global ocean throughout the water column, highlighting the importance of phospholipid and especially PE catabolism in situ. Thus, catabolic activation of the ethanolamine and choline degradation pathways, subsequent to phospholipid metabolism, specifically links, and hence unites, the phosphorus, nitrogen, and carbon cycles.
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Affiliation(s)
- Linda M. Westermann
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Ian D. E. A. Lidbury
- Molecular Microbiology: Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Chun-Yang Li
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Andrew R. J. Murphy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | | | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Muralidharan Shanmugan
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | | | - Eleonora Silvano
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Yu-Zhong Zhang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | | | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - David J. Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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31
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Van Etten J, Benites LF, Stephens TG, Yoon HS, Bhattacharya D. Algae obscura: The potential of rare species as model systems. JOURNAL OF PHYCOLOGY 2023; 59:293-300. [PMID: 36764681 DOI: 10.1111/jpy.13321] [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: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 05/28/2023]
Abstract
Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Luiz Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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32
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Holderman NR, Ferrer-González FX, Glushka J, Moran MA, Edison AS. Dissolved organic metabolite extraction from high-salt media. NMR IN BIOMEDICINE 2023; 36:e4797. [PMID: 35799308 DOI: 10.1002/nbm.4797] [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: 10/25/2021] [Revised: 06/13/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
We describe considerations and strategies for developing a nuclear magnetic resonance (NMR) sample preparation method to extract low molecular weight metabolites from high-salt spent media in a model coculture system of phytoplankton and marine bacteria. Phytoplankton perform half the carbon fixation and oxygen generation on Earth. A substantial fraction of fixed carbon becomes part of a metabolite pool of small molecules known as dissolved organic matter (DOM), which are taken up by marine bacteria proximate to phytoplankton. There is an urgent need to elucidate these metabolic exchanges due to widespread anthropogenic transformations on the chemical, phenotypic, and species composition of seawater. These changes are increasing water temperature and the amount of CO2 absorbed by the ocean at energetic costs to marine microorganisms. Little is known about the metabolite-mediated, structured interactions occurring between phytoplankton and associated marine bacteria, in part because of challenges in studying high-salt solutions on various analytical platforms. NMR analysis is problematic due to the high-salt content of both natural seawater and culture media for marine microbes. High-salt concentration degrades the performance of the radio frequency coil, reduces the efficiency of some pulse sequences, limits signal-to-noise, and prolongs experimental time. The method described herein can reproducibly extract low molecular weight DOM from small-volume, high-salt cultures. It is a promising tool for elucidating metabolic flux between marine microorganisms and facilitates genetic screens of mutant microorganisms.
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Affiliation(s)
- Nicole R Holderman
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | | | - John Glushka
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
| | - Arthur S Edison
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
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33
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Chemotaxis increases metabolic exchanges between marine picophytoplankton and heterotrophic bacteria. Nat Microbiol 2023; 8:510-521. [PMID: 36759754 DOI: 10.1038/s41564-023-01327-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/09/2023] [Indexed: 02/11/2023]
Abstract
Behaviours such as chemotaxis can facilitate metabolic exchanges between phytoplankton and heterotrophic bacteria, which ultimately regulate oceanic productivity and biogeochemistry. However, numerically dominant picophytoplankton have been considered too small to be detected by chemotactic bacteria, implying that cell-cell interactions might not be possible between some of the most abundant organisms in the ocean. Here we examined how bacterial behaviour influences metabolic exchanges at the single-cell level between the ubiquitous picophytoplankton Synechococcus and the heterotrophic bacterium Marinobacter adhaerens, using bacterial mutants deficient in motility and chemotaxis. Stable-isotope tracking revealed that chemotaxis increased nitrogen and carbon uptake of both partners by up to 4.4-fold. A mathematical model following thousands of cells confirmed that short periods of exposure to small but nutrient-rich microenvironments surrounding Synechococcus cells provide a considerable competitive advantage to chemotactic bacteria. These findings reveal that transient interactions mediated by chemotaxis can underpin metabolic relationships among the ocean's most abundant microorganisms.
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34
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Jameson BD, Murdock SA, Ji Q, Stevens CJ, Grundle DS, Kim Juniper S. Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N 2O cycling. Commun Biol 2023; 6:212. [PMID: 36823449 PMCID: PMC9950131 DOI: 10.1038/s42003-023-04597-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N2O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N2O supersaturations, linking N2O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N2O yields and N2O production from denitrification. Close coupling between N2O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N2O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N2O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.
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Affiliation(s)
- Brett D Jameson
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada.
| | - Sheryl A Murdock
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
| | - Qixing Ji
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- Thrust of Earth, Ocean & Atmospheric Sciences, Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong, 511400, China
| | - Catherine J Stevens
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Damian S Grundle
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- School of Ocean Futures & School of Earth & Space Exploration, Arizona State University, Tempe, AZ, 85287-7904, USA
| | - S Kim Juniper
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Ocean Networks Canada, 2474 Arbutus Road, Victoria, BC, V8N 1V8, Canada
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35
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Effect of pressure treatment on Microcystis blooms and the subsequent succession of bacterial community. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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36
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Macey MC, Ramkissoon NK, Cogliati S, Toubes-Rodrigo M, Stephens BP, Kucukkilic-Stephens E, Schwenzer SP, Pearson VK, Preston LJ, Olsson-Francis K. Habitability and Biosignature Formation in Simulated Martian Aqueous Environments. ASTROBIOLOGY 2023; 23:144-154. [PMID: 36577028 DOI: 10.1089/ast.2021.0197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Water present on early Mars is often assumed to have been habitable. In this study, experiments were performed to investigate the habitability of well-defined putative martian fluids and to identify the accompanying potential formation of biosignatures. Simulated martian environments were developed by combining martian fluid and regolith simulants based on the chemistry of the Rocknest sand shadow at Gale Crater. The simulated chemical environment was inoculated with terrestrial anoxic sediment from the Pyefleet mudflats (United Kingdom). These enrichments were cultured for 28 days and subsequently subcultured seven times to ensure that the microbial community was solely grown on the defined, simulated chemistry. The impact of the simulated chemistries on the microbial community was assessed by cell counts and sequencing of 16S rRNA gene profiles. Associated changes to the fluid and precipitate chemistries were established by using ICP-OES, IC, FTIR, and NIR. The fluids were confirmed as habitable, with the enriched microbial community showing a reduction in abundance and diversity over multiple subcultures relating to the selection of specific metabolic groups. The final community comprised sulfate-reducing, acetogenic, and other anaerobic and fermentative bacteria. Geochemical characterization and modeling of the simulant and fluid chemistries identified clear differences between the biotic and abiotic experiments. These differences included the elimination of sulfur owing to the presence of sulfate-reducing bacteria and more general changes in pH associated with actively respiring cells that impacted the mineral assemblages formed. This study confirmed that a system simulating the fluid chemistry of Gale Crater could support a microbial community and that variation in chemistries under biotic and abiotic conditions can be used to inform future life-detection missions.
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Affiliation(s)
- Michael C Macey
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Nisha K Ramkissoon
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Simone Cogliati
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Mario Toubes-Rodrigo
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Ben P Stephens
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Ezgi Kucukkilic-Stephens
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Susanne P Schwenzer
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Victoria K Pearson
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Louisa J Preston
- Mullard Space Science Laboratory, Department of Space and Climate Physics, University College London, London, United Kingdom
| | - Karen Olsson-Francis
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
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37
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Zhou L, Liu W, Duan H, Dong H, Li J, Zhang S, Zhang J, Ding S, Xu T, Guo B. Improved effects of combined application of nitrogen-fixing bacteria Azotobacter beijerinckii and microalgae Chlorella pyrenoidosa on wheat growth and saline-alkali soil quality. CHEMOSPHERE 2023; 313:137409. [PMID: 36457265 DOI: 10.1016/j.chemosphere.2022.137409] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/05/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Soil salinization seriously affects crop yield and soil productivity. The application of bacteria and microalgae has been considered as a promising strategy to alleviate soil salinization. However, the effect of bacteria-microalgae symbiosis on saline-alkali land is still unclear. This study evaluated the effects of Azotobacter beijerinckii, Chlorella pyrenoidosa, and their combined application on the wheat growth and saline-alkali soil improvement. The results showed that, among all the treatments, A. beijerinckii + live C. pyrenoidosa combined inoculation group (BA) had the best effect on increasing wheat plant biomass, improving salt tolerance, and improving soil fertility. The dry weight of wheat plant in the BA group increased by 66.7%, 17.4%, and 35.0%, respectively, compared with the control group (CK), A. beijerinckii inoculation group (B), and live C. pyrenoidosa inoculation group (A). The total nitrogen content of wheat plant in the BA group increased by 69.5%, 76.7%, and 71.1%, compared with the CK, B, and A group. The proline content of wheat plant in the BA group was 100% higher than that in the CK group. The N/P ratio and K/Na ratio of wheat plant increased by 157% and 12.9% in the BA group compared with the CK group, respectively, which was more conducive to alleviating nitrogen limitation and salt stress. The A. beijerinckii + live C. pyrenoidosa inoculation treatment better reduced soil pH and improved the availability of phosphorus in soil. This study illustrated the comprehensive application prospects of bacteria-microalgae interactions on wheat growth promotion and soil improvement in saline-alkali land, and provided a new effective strategy for improving saline-alkali soil quality and increasing crop productivity.
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Affiliation(s)
- Lixiu Zhou
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China; Faculty of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Wei Liu
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China; Faculty of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Huijie Duan
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China; Faculty of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Haiwen Dong
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China; Faculty of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Jingchao Li
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China; Faculty of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Shuxi Zhang
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China; Faculty of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Jing Zhang
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China
| | - Shigang Ding
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China
| | - Tongtong Xu
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China; Faculty of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Beibei Guo
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan 250014, China
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38
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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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39
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Moreno-Cabezuelo JÁ, Gómez-Baena G, Díez J, García-Fernández JM. Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus. Microbiol Spectr 2023; 11:e0327522. [PMID: 36722960 PMCID: PMC10100731 DOI: 10.1128/spectrum.03275-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/29/2022] [Indexed: 02/02/2023] Open
Abstract
We compared changes induced by the addition of 100 nM and 5 mM glucose on the proteome and metabolome complements in Synechococcus sp. strains WH8102, WH7803, and BL107 and Prochlorococcus sp. strains MED4, SS120, and MIT9313, grown either under standard light conditions or in darkness. Our results suggested that glucose is metabolized by these cyanobacteria, using primarily the oxidative pentoses and Calvin pathways, while no proof was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the effects of glucose availability, both between genera and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. We found evidence for fermentation in Prochlorococcus sp. strain SS120 and Synechococcus sp. strain WH8102 after 5 mM glucose addition. Our results additionally suggested that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness. Furthermore, the KaiB and KaiC proteins were also affected in Synechococcus sp. WH8102, pointing to a direct link between glucose assimilation and circadian rhythms in marine cyanobacteria. In conclusion, our study provides a wide overview on the metabolic effects induced by glucose availability in representative strains of the diverse marine picocyanobacteria, providing further evidence for the importance of mixotrophy in marine picocyanobacteria. IMPORTANCE Glucose uptake by marine picocyanobacteria has been previously described and strongly suggests they are mixotrophic organisms (capable of using energy from the sun to make organic matter, but also to directly use organic matter from the environment when available). However, a detailed analysis of the effects of glucose addition on the proteome and metabolome of these microorganisms had not been carried out. Here, we analyzed three Prochlorococcus sp. and three Synechococcus sp. strains which were representative of several marine picocyanobacterial clades. We observed differential features in the effects of glucose availability, depending on both the genus and strain; our study illuminated the strategies utilized by these organisms to metabolize glucose and showed unexpected links to other pathways, such as circadian regulation. Furthermore, we found glucose addition had profound effects in the microbiome, favoring the growth of coexisting heterotrophic bacteria.
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Affiliation(s)
- José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
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40
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Qu T, Zhao X, Guan C, Hou C, Chen J, Zhong Y, Lin Z, Xu Y, Tang X, Wang Y. Structure-Function Covariation of Phycospheric Microorganisms Associated with the Typical Cross-Regional Harmful Macroalgal Bloom. Appl Environ Microbiol 2023; 89:e0181522. [PMID: 36533927 PMCID: PMC9888261 DOI: 10.1128/aem.01815-22] [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: 10/25/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
Unravelling the structure-function variation of phycospheric microorganisms and its ecological correlation with harmful macroalgal blooms (HMBs) is a challenging research topic that remains unclear in the natural dynamic process of HMBs. During the world's largest green tide bloom, causative macroalgae Ulva prolifera experienced dramatic changes in growth state and environmental conditions, providing ideal scenarios for this investment. Here, we assess the phycospheric physicochemical characteristics, the algal host's biology, the phycospheric bacterial constitutive patterns, and the functional potential during the U. prolifera green tide. Our results indicated that (i) variation in the phycosphere nutrient structure was closely related to the growth state of U. prolifera; (ii) stochastic processes govern phycospheric bacterial assembly, and the contribution of deterministic processes to assembly varied among phycospheric seawater bacteria and epiphytic bacteria; (iii) phycospheric seawater bacteria and epiphytic bacteria exhibited significant heterogeneity variation patterns in community composition, structure, and metabolic potential; and (iv) phycospheric bacteria with carbon or nitrogen metabolic functions potentially influenced the nutrient utilization of U. prolifera. Furthermore, the keystone genera play a decisive role in the structure-function covariation of phycospheric bacterial communities. Our study reveals complex interactions and linkages among environment-algae-bacterial communities which existed in the macroalgal phycosphere and highlights the fact that phycospheric microorganisms are closely related to the fate of the HMBs represented by the green tide. IMPORTANCE Harmful macroalgal blooms represented by green tides have become a worldwide marine ecological problem. Unraveling the structure-function variation of phycospheric microorganisms and their ecological correlation with HMBs is challenging. This issue is still unclear in the natural dynamics of HMBs. Here, we revealed the complex interactions and linkages among environment-algae-bacterial communities in the phycosphere of the green macroalgae Ulva prolifera, which causes the world's largest green tides. Our study provides new ideas to increase our understanding of the variation patterns of macroalgal phycospheric bacterial communities and the formation mechanisms and ecological effects of green tides and highlights the importance of phycospheric microorganisms as a robust tool to help understand the fate of HMBs.
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Affiliation(s)
- Tongfei Qu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinyu Zhao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chen Guan
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chengzong Hou
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yi Zhong
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhihao Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Xu
- 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 National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Díez J, López-Lozano A, Domínguez-Martín MA, Gómez-Baena G, Muñoz-Marín MC, Melero-Rubio Y, García-Fernández JM. Regulatory and metabolic adaptations in the nitrogen assimilation of marine picocyanobacteria. FEMS Microbiol Rev 2023; 47:6794272. [PMID: 36323406 DOI: 10.1093/femsre/fuac043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Prochlorococcus and Synechococcus are the two most abundant photosynthetic organisms on Earth, with a strong influence on the biogeochemical carbon and nitrogen cycles. Early reports demonstrated the streamlining of regulatory mechanisms in nitrogen metabolism and the removal of genes not strictly essential. The availability of a large series of genomes, and the utilization of latest generation molecular techniques have allowed elucidating the main mechanisms developed by marine picocyanobacteria to adapt to the environments where they thrive, with a particular interest in the strains inhabiting oligotrophic oceans. Given that nitrogen is often limited in those environments, a series of studies have explored the strategies utilized by Prochlorococcus and Synechococcus to exploit the low concentrations of nitrogen-containing molecules available in large areas of the oceans. These strategies include the reduction in the GC and the cellular protein contents; the utilization of truncated proteins; a reduced average amount of N in the proteome; the development of metabolic mechanisms to perceive and utilize nanomolar nitrate concentrations; and the reduced responsiveness of key molecular regulatory systems such as NtcA to 2-oxoglutarate. These findings are in sharp contrast with the large body of knowledge obtained in freshwater cyanobacteria. We will outline the main discoveries, stressing their relevance to the ecological success of these important microorganisms.
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Affiliation(s)
- J Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - A López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - G Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M C Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - Y Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - J M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
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42
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Li C, Wang R, Wang J, Liu L, Li H, Zheng H, Ni J. A Highly Compatible Phototrophic Community for Carbon-Negative Biosynthesis. Angew Chem Int Ed Engl 2023; 62:e202215013. [PMID: 36378012 DOI: 10.1002/anie.202215013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
CO2 sequestration engineering is promising for carbon-negative biosynthesis, and artificial communities can solve more complex problems than monocultures. However, obtaining an ideal photosynthetic community is still a great challenge. Herein, we describe the development of a highly compatible photosynthetic community (HCPC) by integrating a sucrose-producing CO2 sequestration module and a super-coupled module. The cyanobacteria CO2 sequestration module was obtained using stepwise metabolic engineering and then coupled with the efficient sucrose utilization module Vibrio natriegens. Integrated omics analysis indicated that enhanced photosynthetic electron transport and extracellular vesicles promote intercellular communication. Additionally, the HCPC was used to channel CO2 into valuable chemicals, enabling the overall release of -22.27 to -606.59 kgCO2 e kg-1 in the end products. This novel light-driven community could facilitate circular economic implementation in the future.
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Affiliation(s)
- Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ruoyu Wang
- School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
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43
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Holland SI, Vázquez-Campos X, Ertan H, Edwards RJ, Manefield MJ, Lee M. Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ' Candidatus Formimonas warabiya' strain DCMF. Front Microbiol 2022; 13:1035247. [PMID: 36569084 PMCID: PMC9768040 DOI: 10.3389/fmicb.2022.1035247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood-Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, 'Candidatus Formimonas warabiya' strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.
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Affiliation(s)
- Sophie I. Holland
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Haluk Ertan
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael J. Manefield
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
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44
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Thangaraj S, Liu H, Kim IN, Sun J. Acclimation traits determine the macromolecular basis of harmful dinoflagellate Alexandrium minutum in response to changing climate conditions. HARMFUL ALGAE 2022; 118:102313. [PMID: 36195427 DOI: 10.1016/j.hal.2022.102313] [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: 03/09/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Ocean warming and acidification are expected to have profound impacts on the marine ecosystem, although the dinoflagellate Alexandrium minutum is reported to be acclimated to such conditions. However, it is unknown on the transition time scale how this species physiologically adjusts their element accumulation and associated resource allocation for this process. We designed a set of experiments to examine how different culture generations (1st, 5th, and 10th) change their cell physiology, cellular quotas and macromolecular cellular contents related to functional processes in A. minutum grown with future (pCO2, 1000 ppm; 25°C) and present (pCO2, 400 ppm; 21°C) ocean conditions. The differing cell sizes and storage capacity at different generations confirmed that compared to ancestors (1st generation), acclimation cells (10th generation) gained increases in quota carbon (QC; 55%; [p < 0.05]) and quota phosphate (QP; 23% [ p < 0.05]). This variation in C:P and N:P influences was transition-specific and largely determined by phosphate-based molecules. It was observed that A. minutum was initially dependent on P molecules, which help cells act as alternative lipids for quick acclimation until N molecules resume carbon-based lipids for their long-term acclimation. Our study demonstrated that rising temperature and pCO2 concentrations in ocean may increase A. minutum based on the comprehensive analysis of different physiological modifications, including its growth, element accumulation, transformation, and functional allocation.
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Affiliation(s)
- Satheeswaran Thangaraj
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China; Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Il-Nam Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Jun Sun
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.
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45
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Nair S, Zhang Z, Li H, Zhao H, Shen H, Kao SJ, Jiao N, Zhang Y. Inherent tendency of Synechococcus and heterotrophic bacteria for mutualism on long-term coexistence despite environmental interference. SCIENCE ADVANCES 2022; 8:eabf4792. [PMID: 36179022 PMCID: PMC9524826 DOI: 10.1126/sciadv.abf4792] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/17/2022] [Indexed: 06/12/2023]
Abstract
Mutualism between Synechococcus and heterotrophic bacteria has been found to support their prolonged survival in nutrient-depleted conditions. However, environmental interference on the fate of their mutualism is not understood. Here, we show that exogenous nutrients disrupt their established mutualism. Once the exogenous nutrients were exhausted, Synechococcus and heterotrophic bacteria gradually reestablished their metabolic mutualism during 450 days of culture, which revived unhealthy Synechococcus cells. Using metagenomics, metatranscriptomics, and the 15N tracer method, we reveal that the associated bacterial nitrogen fixation triggered the reestablishment of the mutualism and revival of Synechococcus health. During this process, bacterial community structure and functions underwent tremendous adjustments to achieve the driving effect, and a cogeneration of nitrogen, phosphorus, iron, and vitamin by the heterotrophic bacteria sustained Synechococcus's prolonged healthy growth. Our findings suggest that Synechococcus and heterotrophic bacteria may have an inherent tendency toward mutualism despite environmental interference. This may exhibit their coevolutionary adaptations in nutrient-deficient environments.
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Affiliation(s)
- Shailesh Nair
- 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
| | - Zenghu Zhang
- 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
| | - Hongmei Li
- 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
| | - Hanshuang Zhao
- 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
| | - Hui Shen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou 570228, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou 570228, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
| | - Yongyu Zhang
- 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
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46
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Ghotbi M, Kelting O, Blümel M, Tasdemir D. Gut and Gill-Associated Microbiota of the Flatfish European Plaice ( Pleuronectes platessa): Diversity, Metabolome and Bioactivity against Human and Aquaculture Pathogens. Mar Drugs 2022; 20:md20090573. [PMID: 36135762 PMCID: PMC9500656 DOI: 10.3390/md20090573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Similar to other marine holobionts, fish are colonized by complex microbial communities that promote their health and growth. Fish-associated microbiota is emerging as a promising source of bioactive metabolites. Pleuronectes platessa (European plaice, plaice), a flatfish with commercial importance, is common in the Baltic Sea. Here we used a culture-dependent survey followed by molecular identification to identify microbiota associated with the gills and the gastrointestinal tract (GIT) of P. platessa, then profiled their antimicrobial activity and metabolome. Altogether, 66 strains (59 bacteria and 7 fungi) were isolated, with Proteobacteria being the most abundant phylum. Gill-associated microbiota accounted for higher number of isolates and was dominated by the Proteobacteria (family Moraxellaceae) and Actinobacteria (family Nocardiaceae), whereas Gram-negative bacterial families Vibrionaceae and Shewanellaceae represented the largest group associated with the GIT. The EtOAc extracts of the solid and liquid media cultures of 21 bacteria and 2 fungi representing the diversity of cultivable plaice-associated microbiota was profiled for their antimicrobial activity against three fish pathogens, human bacterial pathogen panel (ESKAPE) and two human fungal pathogens. More than half of all tested microorganisms, particularly those originating from the GIT epithelium, exhibited antagonistic effect against fish pathogens (Lactococcus garvieae, Vibrio ichthyoenteri) and/or human pathogens (Enterococcus faecium, methicillin-resistant Staphylococcus aureus). Proteobacteria represented the most active isolates. Notably, the solid media extracts displayed higher activity against fish pathogens, while liquid culture extracts were more active against human pathogens. Untargeted metabolomics approach using feature-based molecular networking showed the high chemical diversity of the liquid extracts that contained undescribed clusters. This study highlights plaice-associated microbiota as a potential source of antimicrobials for the control of human and the aquaculture-associated infections. This is the first study reporting diversity, bioactivity and chemical profile of culture-dependent microbiota of plaice.
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Affiliation(s)
- Marjan Ghotbi
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Ole Kelting
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
- Correspondence: ; Tel.: +49-431-600-4430
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47
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Domínguez-Martín MA, López-Lozano A, Melero-Rubio Y, Gómez-Baena G, Jiménez-Estrada JA, Kukil K, Diez J, García-Fernández JM. Marine Synechococcus sp. Strain WH7803 Shows Specific Adaptative Responses to Assimilate Nanomolar Concentrations of Nitrate. Microbiol Spectr 2022; 10:e0018722. [PMID: 35852322 PMCID: PMC9430850 DOI: 10.1128/spectrum.00187-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022] Open
Abstract
Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrient availability and temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to micromolar ammonium or nitrogen starvation. We found that Synechococcus has a specific response to a nanomolar nitrate concentration that differs from the response shown under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentrations of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural environment. IMPORTANCE Marine Synechococcus are a very abundant group of photosynthetic organisms on our planet. Previous studies have shown blooms of these organisms when nanomolar concentrations of nitrate become available. We have assessed the effect of nanomolar nitrate concentrations by studying the transcriptome and proteome of Synechococcus sp. WH7803, together with some physiological parameters. We found evidence that Synechococcus sp. strain WH7803 does sense and react to nanomolar concentrations of nitrate, suggesting the occurrence of specific adaptive mechanisms to allow their utilization. Thus, very low concentrations of nitrate in the ocean seem to be a significant nitrogen source for marine picocyanobacteria.
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Grants
- Ministerio de Ciencia e Innovacion, Government of Spain (cofunded by the FEDER program, European Union)
- Consejeria de Conocimiento, Investigacion y Universidad, Junta de Andalucia (Spain), cofunded by the FEDER program (European Union)
- Universidad de Cordoba (Spain), Programa Propio de Investigacion
- Junta de Andalucia (Spain), Programa Operativo de Empleo Juvenil, cofunded by the FEDER programme (European Union)
- Consejería de Transformación Económica, Industria, Conocimiento y Universidades, Junta de Andalucia (Spain), cofunded by the FEDER program (European Union)
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Affiliation(s)
- María Agustina Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Yesica Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Juan Andrés Jiménez-Estrada
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Kateryna Kukil
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Jesús Diez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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48
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Koch M, Noonan AJC, Qiu Y, Dofher K, Kieft B, Mottahedeh S, Shastri M, Hallam SJ. The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential. Front Bioeng Biotechnol 2022; 10:932695. [PMID: 36046667 PMCID: PMC9420970 DOI: 10.3389/fbioe.2022.932695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp. PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis (Spirulina). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].
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Affiliation(s)
- Moritz Koch
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Avery J. C. Noonan
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
| | - Yilin Qiu
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Kalen Dofher
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Steven J. Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Steven J. Hallam,
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49
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Zadjelovic V, Erni-Cassola G, Obrador-Viel T, Lester D, Eley Y, Gibson MI, Dorador C, Golyshin PN, Black S, Wellington EMH, Christie-Oleza JA. A mechanistic understanding of polyethylene biodegradation by the marine bacterium Alcanivorax. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129278. [PMID: 35739790 DOI: 10.1016/j.jhazmat.2022.129278] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Polyethylene (PE) is one of the most recalcitrant carbon-based synthetic materials produced and, currently, the most ubiquitous plastic pollutant found in nature. Over time, combined abiotic and biotic processes are thought to eventually breakdown PE. Despite limited evidence of biological PE degradation and speculation that hydrocarbon-degrading bacteria found within the plastisphere is an indication of biodegradation, there is no clear mechanistic understanding of the process. Here, using high-throughput proteomics, we investigated the molecular processes that take place in the hydrocarbon-degrading marine bacterium Alcanivorax sp. 24 when grown in the presence of low density PE (LDPE). As well as efficiently utilising and assimilating the leachate of weathered LDPE, the bacterium was able to reduce the molecular weight distribution (Mw from 122 to 83 kg/mol) and overall mass of pristine LDPE films (0.9 % after 34 days of incubation). Most interestingly, Alcanivorax acquired the isotopic signature of the pristine plastic and induced an extensive array of metabolic pathways for aliphatic compound degradation. Presumably, the primary biodegradation of LDPE by Alcanivorax sp. 24 is possible via the production of extracellular reactive oxygen species as observed both by the material's surface oxidation and the measurement of superoxide in the culture with LDPE. Our findings confirm that hydrocarbon-biodegrading bacteria within the plastisphere may in fact have a role in degrading PE.
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Affiliation(s)
- Vinko Zadjelovic
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Gabriel Erni-Cassola
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Program Man-Society-Environment (MGU), University of Basel, 4051 Basel, Switzerland
| | - Theo Obrador-Viel
- Department of Biology, University of the Balearic Islands, Palma 07122, Spain
| | - Daniel Lester
- Polymer Characterisation Research Technology Platform, University of Warwick, Coventry CV4 7AL, UK
| | - Yvette Eley
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Chile; Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta Angamos 601, Antofagasta, Chile; Centre for Biotechnology & Bioengineering (CeBiB) Santiago, Chile
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Stuart Black
- Department of Geography and Environmental Science, University of Reading, UK
| | | | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Department of Biology, University of the Balearic Islands, Palma 07122, Spain.
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50
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Wang J, Li Y, Yang Z, Sun T, Yu X, Zhao Y, Tang X, Xiao H. Sex plays a role in the construction of epiphytic bacterial communities on the algal bodies and receptacles of Sargassum thunbergii. Front Microbiol 2022; 13:935222. [PMID: 35958132 PMCID: PMC9360977 DOI: 10.3389/fmicb.2022.935222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/01/2022] [Indexed: 11/21/2022] Open
Abstract
The community structures of epiphytic bacteria on the surface of macroalgae are closely related to their host algae, but there is a lack of research on the differences between the epiphytic bacterial communities of male and female algae and their reproductive tissues. In this study, high-throughput sequencing was used to compare epiphytic bacterial community structures on the intertidal macroalgae Sargassum thunbergii and their receptacles between male and female samples. The epiphytic bacteria on the male and female algal bodies and receptacles had similar community structures with a large number of shared bacteria, but the samples clearly clustered separately, and the abundances of dominant taxa, specific bacteria, and indicator species differed, indicating that epiphytic bacterial communities differed significantly between the male and female S. thunbergii and their receptacles. In addition, the abundance of many predicted functional genes was significantly different between epiphytic bacteria on male and female algal bodies and receptacles, especially metabolism-related genes, and the abundances of predicted functional genes of epiphytic bacteria were significantly higher on both types of male samples than on female samples. Our study confirmed that the sex of the host algae influenced the epiphytic bacterial community structures on algae and algal reproductive tissues, and this role was mainly related to the host metabolism. The results reveal the role of host plant sex in the formation of epiphytic bacterial communities. These findings are helpful for obtaining an in-depth understanding of the construction mechanism of algae-associated bacteria.
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Affiliation(s)
- Jing Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhibo Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tao Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinlong Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yayun Zhao
- 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 National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Xuexi Tang,
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Hui Xiao,
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