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Jeon Y, Li L, Bhatia M, Ryu H, Santo Domingo JW, Brown J, Goetz J, Seo Y. Impact of harmful algal bloom severity on bacterial communities in a full-scale biological filtration system for drinking water treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:171301. [PMID: 38423320 DOI: 10.1016/j.scitotenv.2024.171301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/15/2023] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
The occurrence of harmful algal blooms (HABs) in freshwater environments has been expanded worldwide with growing frequency and severity. HABs can pose a threat to public water supplies, raising concerns about safety of treated water. Many studies have provided valuable information about the impacts of HABs and management strategies on the early-stage treatment processes (e.g., pre-oxidation and coagulation/flocculation) in conventional drinking water treatment plants (DWTPs). However, the potential effect of HAB-impacted water in the granular media filtration has not been well studied. Biologically-active filters (BAFs), which are used in drinking water treatment and rely largely on bacterial community interactions, have not been examined during HABs in full-scale DWTPs. In this study, we assessed the bacterial community structure of BAFs, functional profiles, assembly processes, and bio-interactions in the community during both severe and mild HABs. Our findings indicate that bacterial diversity in BAFs significantly decreases during severe HABs due to the predominance of bloom-associated bacteria (e.g., Spingopyxis, Porphyrobacter, and Sphingomonas). The excitation-emission matrix combined with parallel factor analysis (EEM-PARAFAC) confirmed that filter influent affected by the severe HAB contained a higher portion of protein-like substances than filter influent samples during a mild bloom. In addition, BAF community functions showed increases in metabolisms associated with intracellular algal organic matter (AOM), such as lipids and amino acids, during severe HABs. Further ecological process and network analyses revealed that severe HAB, accompanied by the abundance of bloom-associated taxa and increased nutrient availability, led to not only strong stochastic processes in the assembly process, but also a bacterial community with lower complexity in BAFs. Overall, this study provides deeper insights into BAF bacterial community structure, function, and assembly in response to HABs.
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Affiliation(s)
- Youchul Jeon
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH 43606, United States of America
| | - Lei Li
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH 43606, United States of America
| | - Mudit Bhatia
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH 43606, United States of America
| | - Hodon Ryu
- Water Infrastructure Division, Center for Environmental Solutions and Emergency Response, U.S. Environmental Protection Agency, Cincinnati, OH 45268, United States of America
| | - Jorge W Santo Domingo
- Water Infrastructure Division, Center for Environmental Solutions and Emergency Response, U.S. Environmental Protection Agency, Cincinnati, OH 45268, United States of America
| | - Jess Brown
- Carollo Engineers' Research and Development Practice, Costa Mesa, CA 92626, United States of America
| | - Jake Goetz
- City of Toledo Colins Park Water Treatment, Toledo, OH 43605, United States of America
| | - Youngwoo Seo
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH 43606, United States of America; Department of Chemical and Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH 43606, United States of America.
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2
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Sumner DY. Oxygenation of Earth's atmosphere induced metabolic and ecologic transformations recorded in the Lomagundi-Jatuli carbon isotopic excursion. Appl Environ Microbiol 2024:e0009324. [PMID: 38819147 DOI: 10.1128/aem.00093-24] [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: 01/16/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024] Open
Abstract
The oxygenation of Earth's atmosphere represents the quintessential transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution; molecular clock models indicate the diversification and ecological expansion of respiratory metabolisms in the several hundred million years following atmospheric oxygenation. Across this same interval, the geological record preserves 13C enrichment in some carbonate rocks, called the Lomagundi-Jatuli excursion (LJE). By combining data from geologic and genomic records, a self-consistent metabolic evolution model emerges for the LJE. First, fermentation and methanogenesis were major processes remineralizing organic carbon before atmospheric oxygenation. Once an ozone layer formed, shallow water and exposed environments were shielded from UVB/C radiation, allowing the expansion of cyanobacterial primary productivity. High primary productivity and methanogenesis led to preferential removal of 12C into organic carbon and CH4. Extreme and variable 13C enrichments in carbonates were caused by 13C-depleted CH4 loss to the atmosphere. Through time, aerobic respiration diversified and became ecologically widespread, as did other new metabolisms. Respiration displaced fermentation and methanogenesis as the dominant organic matter remineralization processes. As CH4 loss slowed, dissolved inorganic carbon in shallow environments was no longer highly 13C enriched. Thus, the loss of extreme 13C enrichments in carbonates marks the establishment of a new microbial mat ecosystem structure, one dominated by respiratory processes distributed along steep redox gradients. These gradients allowed the exchange of metabolic by-products among metabolically diverse organisms, providing novel metabolic opportunities. Thus, the microbially induced oxygenation of Earth's atmosphere led to the transformation of microbial ecosystems, an archetypal example of planetary microbiology.IMPORTANCEThe oxygenation of Earth's atmosphere represents the most extensive known chemical transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution by providing oxidants independent of the sites of photosynthesis. Thus, the evolutionary changes during this interval and their effects on planetary-scale biogeochemical cycles are fundamental to our understanding of the interdependencies among genomes, organisms, ecosystems, elemental cycles, and Earth's surface chemistry through time.
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Affiliation(s)
- Dawn Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California, USA
- Microbiology Graduate Group, University of California, Davis, Davis, California, USA
- Feminist Research Institute, University of California, Davis, Davis, California, USA
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3
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Lyons TW, Tino CJ, Fournier GP, Anderson RE, Leavitt WD, Konhauser KO, Stüeken EE. Co-evolution of early Earth environments and microbial life. Nat Rev Microbiol 2024:10.1038/s41579-024-01044-y. [PMID: 38811839 DOI: 10.1038/s41579-024-01044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/31/2024]
Abstract
Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.
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Affiliation(s)
- Timothy W Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA.
| | - Christopher J Tino
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rika E Anderson
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- Biology Department, Carleton College, Northfield, MN, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eva E Stüeken
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, UK
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4
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Liu MY, Liu XY, Guo YY, Ma JY, Duan JL, Zhang M, Han Y, Sun XD, Sun YC, Wang Y, Yuan XZ, Feng LJ. Nitrogen Forms Regulate the Response of Microcystis aeruginosa to Nanoplastics at Environmentally Relevant Nitrogen Concentrations. ACS NANO 2024; 18:11828-11836. [PMID: 38659192 DOI: 10.1021/acsnano.4c00739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
As essential primary producers, cyanobacteria play a major role in global carbon and nitrogen cycles. Though the influence of nanoplastics on the carbon metabolism of cyanobacteria is well-studied, little is known about how nanoplastics affect their nitrogen metabolism, especially under environmentally relevant nitrogen concentrations. Here, we show that nitrogen forms regulated growth inhibition, nitrogen consumption, and the synthesis and release of microcystin (MC) in Microcystis aeruginosa exposed to 10 μg/mL amino-modified polystyrene nanoplastics (PS-NH2) with a particle size of 50 nm under environmentally relevant nitrogen concentrations of nitrate, ammonium, and urea. We demonstrate that PS-NH2 inhibit M. aeruginosa differently in nitrate, urea, and ammonium, with inhibition rates of 51.87, 39.70, and 36.69%, respectively. It is caused through the differences in impairing cell membrane integrity, disrupting redox homeostasis, and varying nitrogen transport pathways under different nitrogen forms. M. aeruginosa respond to exposure of PS-NH2 by utilizing additional nitrogen to boost the production of amino acids, thereby enhancing the synthesis of MC, extracellular polymeric substances, and membrane phospholipids. Our results found that the threat of nanoplastics on primary producers can be regulated by the nitrogen forms in freshwater ecosystems, contributing to a better understanding of nanoplastic risks under environmentally relevant conditions.
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Affiliation(s)
- Mei-Yan Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Xiao-Yu Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Yu-Yu Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Jing-Ya Ma
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Jian-Lu Duan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Mou Zhang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Yi Han
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Xiao-Dong Sun
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Yu-Chen Sun
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Yue Wang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Xian-Zheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
- Sino-French Research Institute for Ecology and Environment (ISFREE), Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Li-Juan Feng
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
- College of Geography and Environment, Shandong Normal University, Jinan, Shandong 250014, P. R. China
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5
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Ślesak I, Ślesak H. From cyanobacteria and cyanophages to chloroplasts: the fate of the genomes of oxyphototrophs and the genes encoding photosystem II proteins. THE NEW PHYTOLOGIST 2024; 242:1055-1067. [PMID: 38439684 DOI: 10.1111/nph.19633] [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: 11/14/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024]
Abstract
Chloroplasts are the result of endosymbiosis of cyanobacterial organisms with proto-eukaryotes. The psbA, psbD and psbO genes are present in all oxyphototrophs and encode the D1/D2 proteins of photosystem II (PSII) and PsbO, respectively. PsbO is a peripheral protein that stabilizes the O2-evolving complex in PSII. Of these genes, psbA and psbD remained in the chloroplastic genome, while psbO was transferred to the nucleus. The genomes of selected cyanobacteria, chloroplasts and cyanophages carrying psbA and psbD, respectively, were analysed. The highest density of genes and coding sequences (CDSs) was estimated for the genomes of cyanophages, cyanobacteria and chloroplasts. The synonymous mutation rate (rS) of psbA and psbD in chloroplasts remained almost unchanged and is lower than that of psbO. The results indicate that the decreasing genome size in chloroplasts is more similar to the genome reduction observed in contemporary endosymbiotic organisms than in streamlined genomes of free-living cyanobacteria. The rS of atpA, which encodes the α-subunit of ATP synthase in chloroplasts, suggests that psbA and psbD, and to a lesser extent psbO, are ancient and conservative and arose early in the evolution of oxygenic photosynthesis. The role of cyanophages in the evolution of oxyphototrophs and chloroplastic genomes is discussed.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Halina Ślesak
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
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6
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García-Oneto TM, Moyano-Bellido C, Domínguez-Martín MA. Structure and function of the light-protective orange carotenoid protein families. Curr Res Struct Biol 2024; 7:100141. [PMID: 38736459 PMCID: PMC11087925 DOI: 10.1016/j.crstbi.2024.100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 05/14/2024] Open
Abstract
Orange carotenoid proteins (OCPs) are unique photoreceptors that are critical for cyanobacterial photoprotection. Upon exposure to blue-green light, OCPs are activated from a stable orange form, OCPO, to an active red form, OCPR, which binds to phycobilisomes (PBSs) and performs photoprotective non-photochemical quenching (NPQ). OCPs can be divided into three main families: the most abundant and best studied OCP1, and two others, OCP2 and OCP3, which have different activation and quenching properties and are yet underexplored. Crystal structures have been acquired for the three OCP clades, providing a glimpse into the conformational underpinnings of their light-absorption and energy dissipation attributes. Recently, the structure of the PBS-OCPR complex has been obtained allowing for an unprecedented insight into the photoprotective action of OCPs. Here, we review the latest findings in the field that have substantially improved our understanding of how cyanobacteria protect themselves from the toxic consequences of excess light absorption. Furthermore, current research is applying the structure of OCPs to bio-inspired optogenetic tools, to function as carotenoid delivery devices, as well as engineering the NPQ mechanism of cyanobacteria to enhance their photosynthetic biomass production.
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Affiliation(s)
| | | | - M. Agustina Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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7
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Grosjean N, Yee EF, Kumaran D, Chopra K, Abernathy M, Biswas S, Byrnes J, Kreitler DF, Cheng JF, Ghosh A, Almo SC, Iwai M, Niyogi KK, Pakrasi HB, Sarangi R, van Dam H, Yang L, Blaby IK, Blaby-Haas CE. A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nat Commun 2024; 15:3167. [PMID: 38609367 PMCID: PMC11014987 DOI: 10.1038/s41467-024-47486-z] [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: 05/02/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.
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Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Estella F Yee
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, USA
| | - Macon Abernathy
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sandeep Biswas
- Department of Biology, Washington University, St. Louis, MO, USA
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masakazu Iwai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | | | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hubertus van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Ian K Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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8
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Ray M, Manu S, Rastogi G, Umapathy G. Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution. J Mol Evol 2024; 92:121-137. [PMID: 38489069 DOI: 10.1007/s00239-024-10159-y] [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: 10/14/2023] [Accepted: 01/24/2024] [Indexed: 03/17/2024]
Abstract
Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied. This knowledge gap is partially attributed to the challenges associated with culturing cyanobacteria in controlled laboratory conditions and the limited understanding of their specific growth requirements. This can be circumvented partially by the culture-independent methods which can shed light on the genomic potential of cyanobacterial species and answer more profound questions about the evolution of other key biogeochemical functions. In this study, we assembled 83 cyanobacterial genomes from metagenomic data generated from environmental DNA extracted from a brackish water lagoon (Chilika Lake, India). We taxonomically classified these metagenome-assembled genomes (MAGs) and found that about 92.77% of them are novel genomes at the species level. We then annotated these cyanobacterial MAGs for all the encoded functions using KEGG Orthology. Interestingly, we found two previously unreported functions in Cyanobacteria, namely, DNRA (Dissimilatory Nitrate Reduction to Ammonium) and DMSP (Dimethylsulfoniopropionate) synthesis in multiple MAGs using nirBD and dsyB genes as markers. We validated their presence in several publicly available cyanobacterial isolate genomes. Further, we identified incongruities between the evolutionary patterns of species and the marker genes and elucidated the underlying reasons for these discrepancies. This study expands our overall comprehension of the contribution of cyanobacteria to the biogeochemical cycling in coastal brackish ecosystems.
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Affiliation(s)
- Manisha Ray
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.
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9
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Muñoz-Marín MDC, López-Lozano A, Moreno-Cabezuelo JÁ, Díez J, García-Fernández JM. Mixotrophy in cyanobacteria. Curr Opin Microbiol 2024; 78:102432. [PMID: 38325247 DOI: 10.1016/j.mib.2024.102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Cyanobacteria evolved the oxygenic photosynthesis to generate organic matter from CO2 and sunlight, and they were responsible for the production of oxygen in the Earth's atmosphere. This made them a model for photosynthetic organisms, since they are easier to study than higher plants. Early studies suggested that only a minority among cyanobacteria might assimilate organic compounds, being considered mostly autotrophic for decades. However, compelling evidence from marine and freshwater cyanobacteria, including toxic strains, in the laboratory and in the field, has been obtained in the last decades: by using physiological and omics approaches, mixotrophy has been found to be a more widespread feature than initially believed. Furthermore, dominant clades of marine cyanobacteria can take up organic compounds, and mixotrophy is critical for their survival in deep waters with very low light. Hence, mixotrophy seems to be an essential trait in the metabolism of most cyanobacteria, which can be exploited for biotechnological purposes.
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Affiliation(s)
- María Del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain
| | - José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain.
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain.
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10
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Baunach M, Guljamow A, Miguel-Gordo M, Dittmann E. Harnessing the potential: advances in cyanobacterial natural product research and biotechnology. Nat Prod Rep 2024; 41:347-369. [PMID: 38088806 DOI: 10.1039/d3np00045a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Covering: 2000 to 2023Cyanobacteria produce a variety of bioactive natural products that can pose a threat to humans and animals as environmental toxins, but also have potential for or inspire pharmaceutical use. As oxygenic phototrophs, cyanobacteria furthermore hold great promise for sustainable biotechnology. Yet, the necessary tools for exploiting their biotechnological potential have so far been established only for a few model strains of cyanobacteria, while large untapped biosynthetic resources are hidden in slow-growing cyanobacterial genera that are difficult to access by genetic techniques. In recent years, several approaches have been developed to circumvent the bottlenecks in cyanobacterial natural product research. Here, we summarize current progress that has been made in unlocking or characterizing cryptic metabolic pathways using integrated omics techniques, orphan gene cluster activation, use of genetic approaches in original producers, heterologous expression and chemo-enzymatic techniques. We are mainly highlighting genomic mining concepts and strategies towards high-titer production of cyanobacterial natural products from the last 10 years and discuss the need for further research developments in this field.
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Affiliation(s)
- Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
- University of Bonn, Institute of Pharmaceutical Biology, Nußallee 6, 53115 Bonn, Germany
| | - Arthur Guljamow
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - María Miguel-Gordo
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
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11
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Shu HY, Zhao L, Jia Y, Liu FF, Chen J, Chang CM, Jin T, Yang J, Shu WS. CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5024-5034. [PMID: 38454313 PMCID: PMC10956431 DOI: 10.1021/acs.est.3c11096] [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: 12/30/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024]
Abstract
Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson's R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1-100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques.
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Affiliation(s)
- Hao-Yue Shu
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
- School
of Food and Drug, Shenzhen Polytechnic, Shenzhen 518081, PR China
| | - Liang Zhao
- Institute
of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity
and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology
for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510006, PR China
| | - Yanyan Jia
- School
of Ecology, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Fei-Fei Liu
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
| | - Jiang Chen
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
| | - Chih-Min Chang
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
| | - Tao Jin
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
- One
Health Biotechnology (Suzhou) Co., Ltd., Suzhou 215009, PR China
| | - Jian Yang
- School
of Food and Drug, Shenzhen Polytechnic, Shenzhen 518081, PR China
| | - Wen-Sheng Shu
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
- Institute
of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity
and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology
for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510006, PR China
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12
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Lee C, Han SI, Na H, Kim Z, Ahn JW, Oh B, Kim HS. Comprehensive understanding of the mutant 'giant' Arthrospira platensis developed via ultraviolet mutagenesis. FRONTIERS IN PLANT SCIENCE 2024; 15:1369976. [PMID: 38567133 PMCID: PMC10985164 DOI: 10.3389/fpls.2024.1369976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
Introduction Cyanobacteria are typically of a size that can be observed under a microscope. Here, we present cyanobacteria of a size that can be observed with the naked eye. Arthrospira platensis NCB002 strain showed differentiated morphological characteristics compared to previously reported Arthrospira spp. Methods Arthrospira platensis NCB002 was obtained by the UV irradiation of Arthrospira sp. NCB001, which was isolated from freshwater and owned by NCell Co., Ltd. A. platensis NIES-39 was obtained from the National Institute for Environmental Studies (Tsukuba, Japan). We used various analytical techniques to determine its overall characteristics. Results and discussion The draft genome of strain NCB002 consists of five contigs comprising 6,864,973 bp with a G+C content of 44.3 mol%. The strain NCB002 had an average length of 11.69 ± 1.35 mm and a maximum of 15.15 mm, which is 23.4-50.5 times longer than the length (0.3-0.5 mm) of previously known Arthrospira spp., allowing it to be harvested using a thin sieve. Transcriptome analysis revealed that these morphological differences resulted from changes in cell wall formation mechanisms and increased cell division. Our results show that NCB002 has outstanding industrial value and provides a comprehensive understanding of it.
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Affiliation(s)
- Changsu Lee
- Bio Division, NCell. Co., Ltd., Seoul, Republic of Korea
| | - Sang-Il Han
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Ho Na
- Bio Division, NCell. Co., Ltd., Seoul, Republic of Korea
| | - Zun Kim
- Bio Division, NCell. Co., Ltd., Seoul, Republic of Korea
| | - Joon Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Byeolnim Oh
- Department of Electronic Engineering, Kwangwoon University, Seoul, Republic of Korea
| | - Hyun Soo Kim
- Department of Electronic Engineering, Kwangwoon University, Seoul, Republic of Korea
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13
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Arévalo S, Pérez Rico D, Abarca D, Dijkhuizen LW, Sarasa-Buisan C, Lindblad P, Flores E, Nierzwicki-Bauer S, Schluepmann H. Genome Engineering by RNA-Guided Transposition for Anabaena sp. PCC 7120. ACS Synth Biol 2024; 13:901-912. [PMID: 38445989 PMCID: PMC10949235 DOI: 10.1021/acssynbio.3c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/30/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In genome engineering, the integration of incoming DNA has been dependent on enzymes produced by dividing cells, which has been a bottleneck toward increasing DNA insertion frequencies and accuracy. Recently, RNA-guided transposition with CRISPR-associated transposase (CAST) was reported as highly effective and specific in Escherichia coli. Here, we developed Golden Gate vectors to test CAST in filamentous cyanobacteria and to show that it is effective in Anabaena sp. strain PCC 7120. The comparatively large plasmids containing CAST and the engineered transposon were successfully transferred into Anabaena via conjugation using either suicide or replicative plasmids. Single guide (sg) RNA encoding the leading but not the reverse complement strand of the target were effective with the protospacer-associated motif (PAM) sequence included in the sgRNA. In four out of six cases analyzed over two distinct target loci, the insertion site was exactly 63 bases after the PAM. CAST on a replicating plasmid was toxic, which could be used to cure the plasmid. In all six cases analyzed, only the transposon cargo defined by the sequence ranging from left and right elements was inserted at the target loci; therefore, RNA-guided transposition resulted from cut and paste. No endogenous transposons were remobilized by exposure to CAST enzymes. This work is foundational for genome editing by RNA-guided transposition in filamentous cyanobacteria, whether in culture or in complex communities.
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Affiliation(s)
- Sergio Arévalo
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Daniel Pérez Rico
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dolores Abarca
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Laura W. Dijkhuizen
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cristina Sarasa-Buisan
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Peter Lindblad
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
| | - Enrique Flores
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Sandra Nierzwicki-Bauer
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Henriette Schluepmann
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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14
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Liao X, Wang Y, Malghani S, Zhu X, Cai W, Qin Z, Wang F. Methane and nitrous oxide emissions and related microbial communities from mangrove stems on Qi'ao Island, Pearl River Estuary in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170062. [PMID: 38220023 DOI: 10.1016/j.scitotenv.2024.170062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Mangrove forests, crucial carbon-rich ecosystems, are increasingly vulnerable to soil carbon loss and greenhouse gas (GHG) emissions due to human disturbance. However, the contribution of mangrove trees to GHG emissions remains poorly understood. This study monitored CO2, CH4, and N2O fluxes from the stems of two mangrove species, native Kandelia obovata (KO) and exotic Sonneratia apetala (SA), at three heights (0.7 m, 1.2 m, and 1.7 m) during the dry winter period on Qi'ao Island, Pearl River Estuary, China. Heartwood samples were analyzed to identify potential functional groups related to gas fluxes. Our study found that tree stems acted as both sinks and sources for N2O (ranging from -9.49 to 28.35 μg m-2 h-1 for KO and from -6.73 to 28.95 μg m-2 h-1 for SA) and CH4. SA exhibited significantly higher stem CH4 flux (from -26.67 to 97.33 μg m-2 h-1) compared to KO (from -44.13 to 88.0 μg m-2 h-1) (P < 0.05). When upscaled to the community level, both species were net emitters of CH4, contributing approximately 4.68 % (KO) and 0.51 % (SA) to total CH4 emissions. The decrease in stem CH4 flux with increasing height, indicates a soil source. Microbial analysis in the heartwood using the KEGG database indicated aceticlastic methanogenesis as the dominant CH4 pathway. The presence of methanogens, methanotrophs, denitrifiers, and nitrifiers suggests microbial involvement in CH4 and N2O production and consumption. Remarkably, the dominance of Cyanobacteria in the heartwood microbiome (with the relative abundance of 97.5 ± 0.6 % for KO and 99.1 ± 0.2 % for SA) implies roles in carbon and nitrogen fixation for mangroves coping with nitrogen limitation in coastal wetlands, and possibly in CH4 production. Although the present study has limitations in sampling duration and area, it highlights the significant role of tree stems in GHG emissions which is crucial for a holistic evaluation of the global carbon sequestration capability of mangrove ecosystems. Future research should broaden spatial and temporal scales to enhance the accuracy of upscaling tree stem gas fluxes to the mangrove ecosystem level.
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Affiliation(s)
- Xiaolin Liao
- College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Ying Wang
- School of Atmospheric Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, Guangdong, China
| | - Saadatullah Malghani
- College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Xudong Zhu
- Key Laboratory of the Coastal and Wetland Ecosystems (Ministry of Education), College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China; Fujian Key Laboratory of Severe Weather, Fuzhou 350008, Fujian, China
| | - Wenqi Cai
- School of Atmospheric Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, Guangdong, China
| | - Zhangcai Qin
- School of Atmospheric Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, Guangdong, China; Key Laboratory of Tropical Atmosphere-Ocean System, Ministry of Education, Zhuhai 519082, China
| | - Fan Wang
- School of Atmospheric Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, Guangdong, China; Key Laboratory of Tropical Atmosphere-Ocean System, Ministry of Education, Zhuhai 519082, China; School of Ecology, Sun Yat-sen University, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, Guangdong, China.
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15
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Yu B, Chao DY, Zhao Y. How plants sense and respond to osmotic stress. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:394-423. [PMID: 38329193 DOI: 10.1111/jipb.13622] [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: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
Drought is one of the most serious abiotic stresses to land plants. Plants sense and respond to drought stress to survive under water deficiency. Scientists have studied how plants sense drought stress, or osmotic stress caused by drought, ever since Charles Darwin, and gradually obtained clues about osmotic stress sensing and signaling in plants. Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level, including changes in turgor, cell wall stiffness and integrity, membrane tension, and cell fluid volume, and plants may sense some of these stimuli and trigger downstream responses. In this review, we emphasized water potential and movements in organisms, compared putative signal inputs in cell wall-containing and cell wall-free organisms, prospected how plants sense changes in turgor, membrane tension, and cell fluid volume under osmotic stress according to advances in plants, animals, yeasts, and bacteria, summarized multilevel biochemical and physiological signal outputs, such as plasma membrane nanodomain formation, membrane water permeability, root hydrotropism, root halotropism, Casparian strip and suberin lamellae, and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors. We also discussed the core scientific questions, provided perspective about the future directions in this field, and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.
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Affiliation(s)
- Bo Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 200032, China
- Key Laboratory of Plant Carbon Capture, The Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, The Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 200032, China
- Key Laboratory of Plant Carbon Capture, The Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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16
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Mehta N, Bradbury H, Benzerara K. Calcium isotope fractionation by intracellular amorphous calcium carbonate (ACC) forming cyanobacteria. GEOBIOLOGY 2024; 22:e12596. [PMID: 38591761 DOI: 10.1111/gbi.12596] [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: 10/30/2023] [Revised: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
The formation of intracellular amorphous calcium carbonate (ACC) by various cyanobacteria is a widespread biomineralization process, yet its mechanism and importance in past and modern environments remain to be fully comprehended. This study explores whether calcium (Ca) isotope fractionation, linked to ACC-forming cyanobacteria, can serve as a reliable tracer for detecting these microorganisms in modern and ancient settings. Accordingly, we measured stable Ca isotope fractionation during Ca uptake by the intracellular ACC-forming cyanobacterium Cyanothece sp. PCC 7425. Our results show that Cyanothece sp. PCC 7425 cells are enriched in lighter Ca isotopes relative to the solution. This finding is consistent with the kinetic isotope effects observed in the Ca isotope fractionation during biogenic carbonate formation by marine calcifying organisms. The Ca isotope composition of Cyanothece sp. PCC 7425 was accurately modeled using a Rayleigh fractionation model, resulting in a Ca isotope fractionation factor (Δ44Ca) equal to -0.72 ± 0.05‰. Numerical modeling suggests that Ca uptake by these cyanobacteria is primarily unidirectional, with minimal back reaction observed over the duration of the experiment. Finally, we compared our Δ44Ca values with those of other biotic and abiotic carbonates, revealing similarities with organisms that form biogenic calcite. These similarities raise questions about the effectiveness of using the Ca isotope fractionation factor as a univocal tracer of ACC-forming cyanobacteria in the environment. We propose that the use of Δ44Ca in combination with other proposed tracers of ACC-forming cyanobacteria such as Ba and Sr isotope fractionation factors and/or elevated Ba/Ca and Sr/Ca ratios may provide a more reliable approach.
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Affiliation(s)
- Neha Mehta
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique Des Matériaux et de Cosmochimie (IMPMC), Paris, France
- Department of Geosciences, Environment and Society, Université Libre de Bruxelles, Brussels, Belgium
| | - Harold Bradbury
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique Des Matériaux et de Cosmochimie (IMPMC), Paris, France
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17
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Fernandes KA, Fadul JC, Fiore MF, Pinto E. A systematic review on guanitoxin: General characteristics and ecological risks. CHEMOSPHERE 2024; 352:141277. [PMID: 38307340 DOI: 10.1016/j.chemosphere.2024.141277] [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: 05/30/2023] [Revised: 11/17/2023] [Accepted: 01/20/2024] [Indexed: 02/04/2024]
Abstract
Guanitoxin (GNT) is a potent cyanotoxin, with a relatively low number of publications (n = 51) compared to other cyanotoxins. Among the published studies, 35 % were on the effect of the toxin in animals, mainly in rodents and in vitro testing, followed by studies that identified species of cyanobacteria that produce GNT in aquatic systems and consequently accidental poisoning in wild and domestic animals (27 %). Studies that developed or tested methods for identifying the molecule, based on colorimetric and analytical techniques, represented 14 %, while 8 % were on GNT biosynthesis. Review articles and chemical isolation (6 %) and on the stability of the molecule (4 %) were the topics with the lowest number of publications. The results show the occurrence of GNT was identified mainly in eutrophic environments with a higher incidence in the American continent. Chemical characteristics of the molecule, such as short half-life in the environment, instability in solutions with alkaline pH values, temperature >23 °C, added to the lack of an analytical standard, are factors that make it difficult to identify and quantify it. However, GNT monitoring can be performed using LC-MS-MRM methods or genes specific to the newly discovered molecule.
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Affiliation(s)
- Kelly Afonsina Fernandes
- Center for Nuclear Energy in Agriculture, University of São Paulo. Piracicaba, São Paulo, Brazil.
| | - Jéssica Chaves Fadul
- Center for Nuclear Energy in Agriculture, University of São Paulo. Piracicaba, São Paulo, Brazil
| | - Marli Fátima Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo. Piracicaba, São Paulo, Brazil
| | - Ernani Pinto
- Center for Nuclear Energy in Agriculture, University of São Paulo. Piracicaba, São Paulo, Brazil
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18
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Demoulin CF, Sforna MC, Lara YJ, Cornet Y, Somogyi A, Medjoubi K, Grolimund D, Sanchez DF, Tachoueres RT, Addad A, Fadel A, Compère P, Javaux EJ. Polysphaeroides filiformis, a proterozoic cyanobacterial microfossil and implications for cyanobacteria evolution. iScience 2024; 27:108865. [PMID: 38313056 PMCID: PMC10837632 DOI: 10.1016/j.isci.2024.108865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/29/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Deciphering the fossil record of cyanobacteria is crucial to understand their role in the chemical and biological evolution of the early Earth. They profoundly modified the redox conditions of early ecosystems more than 2.4 Ga ago, the age of the Great Oxidation Event (GOE), and provided the ancestor of the chloroplast by endosymbiosis, leading the diversification of photosynthetic eukaryotes. Here, we analyze the morphology, ultrastructure, chemical composition, and metals distribution of Polysphaeroides filiformis from the 1040-1006 Ma Mbuji-Mayi Supergroup (DR Congo). We evidence trilaminar and bilayered ultrastructures for the sheath and the cell wall, respectively, and the preservation of Ni-tetrapyrrole moieties derived from chlorophyll in intracellular inclusions. This approach allows an unambiguous interpretation of P. filiformis as a branched and multiseriate photosynthetic cyanobacterium belonging to the family of Stigonemataceae. It also provides a possible minimum age for the emergence of multiseriate true branching nitrogen-fixing and probably heterocytous cyanobacteria.
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Affiliation(s)
- Catherine F Demoulin
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | - Marie Catherine Sforna
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
- Centre de Biophysique Moléculaire, (UPR CNRS 4301), 45071 Orléans, France
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | - Yohan Cornet
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | | | | | - Daniel Grolimund
- Paul Scherrer Institut, Swiss Light Source, 5232 Villigen PSI, Switzerland
| | | | | | - Ahmed Addad
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, 59650 Villeneuve d'Ascq, France
| | - Alexandre Fadel
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, 59650 Villeneuve d'Ascq, France
| | - Philippe Compère
- Functional and Evolutive Morphology, UR FOCUS, and Center for Applied Research and Education in Microscopy (CAREM-ULiege), University of Liège, 4000 Liège, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
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19
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Pi HW, Chiang YR, Li WH. Mapping Geological Events and Nitrogen Fixation Evolution Onto the Timetree of the Evolution of Nitrogen-Fixation Genes. Mol Biol Evol 2024; 41:msae023. [PMID: 38319744 PMCID: PMC10881105 DOI: 10.1093/molbev/msae023] [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: 10/09/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 02/08/2024] Open
Abstract
Nitrogen is essential for all organisms, but biological nitrogen fixation (BNF) occurs only in a small fraction of prokaryotes. Previous studies divided nitrogenase-gene-carrying prokaryotes into Groups I to IV and provided evidence that BNF first evolved in bacteria. This study constructed a timetree of the evolution of nitrogen-fixation genes and estimated that archaea evolved BNF much later than bacteria and that nitrogen-fixing cyanobacteria evolved later than 1,900 MYA, considerably younger than the previous estimate of 2,200 MYA. Moreover, Groups III and II/I diverged ∼2,280 MYA, after the Kenorland supercontinent breakup (∼2,500-2,100 MYA) and the Great Oxidation Event (∼2,400-2,100 MYA); Groups III and Vnf/Anf diverged ∼2,086 MYA, after the Yarrabubba impact (∼2,229 MYA); and Groups II and I diverged ∼1,920 MYA, after the Vredefort impact (∼2,023 MYA). In summary, this study provided a timescale of BNF events and discussed the possible effects of geological events on BNF evolution.
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Affiliation(s)
- Hong-Wei Pi
- Biodiversity Research Center, Academia Sinica, Taipei 115201, Taiwan
- Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei 115201, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei 115201, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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20
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Zhang H, Tan Y, Zhou Y, Liu J, Xia X. Light-dark fluctuated metabolic features of diazotrophic and non-diazotrophic cyanobacteria and their coexisting bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 910:168702. [PMID: 37992836 DOI: 10.1016/j.scitotenv.2023.168702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Cyanobacteria, the most abundant photosynthetic organisms in oceans, are tightly associated with diverse microbiota. However, the relationships between heterotrophic bacteria and cyanobacteria, particularly the diazotrophic group, are not fully understood. Here, we compared diel gene expressions of N2 fixing cyanobacteria Crocosphaera watsonii WH0003 and non-diazotrophic Synechococcus sp. RS9902 and their associated bacteria using metatranscriptomics approach. WH0003 showed significant up-regulation of O2 restriction and oxidative phosphorylation related genes at nighttime due to large carbon and energy investments for active N2 fixation. In contrast, RS9902 had higher expression for those genes at daytime. The two cyanobacteria hosted distinct bacterial communities with clear separate substrate utilization niches to reduce competition. Light-dark partitioning of nutrient acquisition among the dominant bacterial groups likely contributed to the dynamic balance for community coexistence. Moreover, particle-attached (PA) bacteria in RS9902 largely expressed glycoside hydrolases to hydrolyze complex carbohydrate compounds, while free-living (FL) bacteria priorly assimilated soluble, diffusible molecules. Spatial partitioning of nutrient acquisition between PA and FL bacteria implied that location initially influenced metabolic features of host associated bacteria. Our results advance knowledge on light-dark regulated metabolic activities of diazotrophic and non-diazotrophic cyanobacteria, and provide new insights into the coexisting strategies of different bacterial groups.
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Affiliation(s)
- Hao Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Youping Zhou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiaxing Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China..
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China..
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Zhang Q, Fu B, Chen Q, Lu J, Zhu Z, Yan C, Guan F, Wang P, Fu L, Yu P. Biosynthesis of the phycocyanin β-subunit in Escherichia coli BL21 and its antioxidant activity and application in the preservation of fresh-cut apples. Int J Biol Macromol 2024; 258:128951. [PMID: 38143054 DOI: 10.1016/j.ijbiomac.2023.128951] [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: 06/14/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
In this study, the biosynthesis of phycocyanin β-subunit (CpcB) in Escherichia coli BL21 was investigated, and its antioxidant activity and application in anti-browning of fresh-cut apples was explored. Four genes (cpcB, cpeS, hox1 and pcyA) involved in the biosynthesis of CpcB were cloned and transformed into E. coli BL21 by constructing recombinant plasmid pETDuet-5. The positive transformant was screened by ampicillin resistance. The analysis of SDS-PAGE and zinc fluorescence spectrum showed that CpcB was successfully expressed in E. coli BL21 with a molecular weight of 21 kDa. The purified CpcB had a maximum absorption peak at 615 nm, and its maximum florescence emission wavelength was 640 nm. It exhibited a stronger ability to scavenge four free radicals than Vc. The color change in fresh-cut apples was obviously delayed by the CpcB treatment. These results suggest that CpcB may be used as a potential anti-browning agent for food preservation.
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Affiliation(s)
- Qili Zhang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China
| | - Bing Fu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China; College of Forestry Science and Technology, Lishui Vocational and Technical College, 357 Zhongshan Street North, Lishui, Zhejiang Province 323000, People's Republic of China
| | - Qingwei Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China
| | - Jiajie Lu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China
| | - Zhiwen Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China
| | - Chuyang Yan
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China
| | - Fuyao Guan
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China
| | - Peize Wang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China
| | - Linglin Fu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China
| | - Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province 310035, People's Republic of China.
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22
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Garuglieri E, Marasco R, Odobel C, Chandra V, Teillet T, Areias C, Sánchez-Román M, Vahrenkamp V, Daffonchio D. Searching for microbial contribution to micritization of shallow marine sediments. Environ Microbiol 2024; 26:e16573. [PMID: 38217094 DOI: 10.1111/1462-2920.16573] [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: 07/25/2023] [Accepted: 12/21/2023] [Indexed: 01/15/2024]
Abstract
Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.
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Affiliation(s)
- Elisa Garuglieri
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ramona Marasco
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Charlene Odobel
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Viswasanthi Chandra
- Ali I. Al-Naimi Petroleum Engineering Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Thomas Teillet
- Ali I. Al-Naimi Petroleum Engineering Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Camila Areias
- Department of Earth Sciences, Faculty of Science, Vrije Universiteit, Amsterdam, the Netherlands
| | - Mónica Sánchez-Román
- Department of Earth Sciences, Faculty of Science, Vrije Universiteit, Amsterdam, the Netherlands
| | - Volker Vahrenkamp
- Ali I. Al-Naimi Petroleum Engineering Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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23
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Bianchini G, Sánchez‐Baracaldo P. TreeViewer: Flexible, modular software to visualise and manipulate phylogenetic trees. Ecol Evol 2024; 14:e10873. [PMID: 38314311 PMCID: PMC10834882 DOI: 10.1002/ece3.10873] [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: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024] Open
Abstract
Phylogenetic trees illustrate evolutionary relationships between taxa or genes. Tree figures are crucial when presenting results and data, and by creating clear and effective plots, researchers can describe many kinds of evolutionary patterns. However, producing tree plots can be a time-consuming task, especially as multiple different programs are often needed to adjust and illustrate all data associated with a tree. We present TreeViewer, a new software to draw phylogenetic trees. TreeViewer is flexible, modular, and user-friendly. Plots are produced as the result of a user-defined pipeline, which can be finely customised and easily applied to different trees. Every feature of the program is documented and easily accessible, either in the online manual or within the program's interface. We show how TreeViewer can be used to produce publication-ready figures, saving time by not requiring additional graphical post-processing tools. TreeViewer is freely available for Windows, macOS, and Linux operating systems and distributed under an AGPLv3 licence from https://treeviewer.org. It has a graphical user interface (GUI), as well as a command-line interface, which is useful to work with very large trees and for automated pipelines. A detailed user manual with examples and tutorials is also available. TreeViewer is mainly aimed at users wishing to produce highly customised, publication-quality tree figures using a single GUI software tool. Compared to other GUI tools, TreeViewer offers a richer feature set and a finer degree of customisation. Compared to command-line-based tools and software libraries, TreeViewer's graphical interface is more accessible. The flexibility of TreeViewer's approach to phylogenetic tree plotting enables the program to produce a wide variety of publication-ready figures. Users are encouraged to create their own custom modules to expand the functionalities of the program. This sets the scene for an ever-expanding and ever-adapting software framework that can easily adjust to respond to new challenges.
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24
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Algeo TJ, Shen J. Theory and classification of mass extinction causation. Natl Sci Rev 2024; 11:nwad237. [PMID: 38116094 PMCID: PMC10727847 DOI: 10.1093/nsr/nwad237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 12/21/2023] Open
Abstract
Theory regarding the causation of mass extinctions is in need of systematization, which is the focus of this contribution. Every mass extinction has both an ultimate cause, i.e. the trigger that leads to various climato-environmental changes, and one or more proximate cause(s), i.e. the specific climato-environmental changes that result in elevated biotic mortality. With regard to ultimate causes, strong cases can be made that bolide (i.e. meteor) impacts, large igneous province (LIP) eruptions and bioevolutionary events have each triggered one or more of the Phanerozoic Big Five mass extinctions, and that tectono-oceanic changes have triggered some second-order extinction events. Apart from bolide impacts, other astronomical triggers (e.g. solar flares, gamma bursts and supernova explosions) remain entirely in the realm of speculation. With regard to proximate mechanisms, most extinctions are related to either carbon-release or carbon-burial processes, the former being associated with climatic warming, ocean acidification, reduced marine productivity and lower carbonate δ13C values, and the latter with climatic cooling, increased marine productivity and higher carbonate δ13C values. Environmental parameters such as marine redox conditions and terrestrial weathering intensity do not show consistent relationships with carbon-cycle changes. In this context, mass extinction causation can be usefully classified using a matrix of ultimate and proximate factors. Among the Big Five mass extinctions, the end-Cretaceous biocrisis is an example of a bolide-triggered carbon-release event, the end-Permian and end-Triassic biocrises are examples of LIP-triggered carbon-release events, and the Late Ordovician and Late Devonian biocrises are examples of bioevolution-triggered carbon-burial events. Whereas the bolide-impact and LIP-eruption mechanisms appear to invariably cause carbon release, bioevolutionary triggers can result in variable carbon-cycle changes, e.g. carbon burial during the Late Ordovician and Late Devonian events, carbon release associated with modern anthropogenic climate warming, and little to no carbon-cycle impact due to certain types of ecosystem change (e.g. the advent of the first predators around the end-Ediacaran; the appearance of Paleolithic human hunters in Australasia and the Americas). Broadly speaking, studies of mass extinction causation have suffered from insufficiently critical thinking-an impartial survey of the extant evidence shows that (i) hypotheses of a common ultimate cause (e.g. bolide impacts or LIP eruptions) for all Big Five mass extinctions are suspect given manifest differences in patterns of environmental and biotic change among them; (ii) the Late Ordovician and Late Devonian events were associated with carbon burial and long-term climatic cooling, i.e. changes that are inconsistent with a bolide-impact or LIP-eruption mechanism; and (iii) claims of periodicity in Phanerozoic mass extinctions depended critically on the now-disproven idea that they shared a common extrinsic trigger (i.e. bolide impacts).
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Affiliation(s)
- Thomas J Algeo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences—Wuhan, Wuhan430074, China
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences—Wuhan, Wuhan430074, China
- Department of Geosciences, University of Cincinnati, Cincinnati, OH45221, USA
| | - Jun Shen
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences—Wuhan, Wuhan430074, China
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25
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Demoulin CF, Lara YJ, Lambion A, Javaux EJ. Oldest thylakoids in fossil cells directly evidence oxygenic photosynthesis. Nature 2024; 625:529-534. [PMID: 38172638 DOI: 10.1038/s41586-023-06896-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/23/2023] [Indexed: 01/05/2024]
Abstract
Today oxygenic photosynthesis is unique to cyanobacteria and their plastid relatives within eukaryotes. Although its origin before the Great Oxidation Event is still debated1-4, the accumulation of O2 profoundly modified the redox chemistry of the Earth and the evolution of the biosphere, including complex life. Understanding the diversification of cyanobacteria is thus crucial to grasping the coevolution of our planet and life, but their early fossil record remains ambiguous5. Extant cyanobacteria include the thylakoid-less Gloeobacter-like group and the remainder of cyanobacteria that acquired thylakoid membranes6,7. The timing of this divergence is indirectly estimated at between 2.7 and 2.0 billion years ago (Ga) based on molecular clocks and phylogenies8-11 and inferred from the earliest undisputed fossil record of Eoentophysalis belcherensis, a 2.018-1.854 Ga pleurocapsalean cyanobacterium preserved in silicified stromatolites12,13. Here we report the oldest direct evidence of thylakoid membranes in a parallel-to-contorted arrangement within the enigmatic cylindrical microfossils Navifusa majensis from the McDermott Formation, Tawallah Group, Australia (1.78-1.73 Ga), and in a parietal arrangement in specimens from the Grassy Bay Formation, Shaler Supergroup, Canada (1.01-0.9 Ga). This discovery extends their fossil record by at least 1.2 Ga and provides a minimum age for the divergence of thylakoid-bearing cyanobacteria at roughly 1.75 Ga. It allows the unambiguous identification of early oxygenic photosynthesizers and a new redox proxy for probing early Earth ecosystems, highlighting the importance of examining the ultrastructure of fossil cells to decipher their palaeobiology and early evolution.
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Affiliation(s)
- Catherine F Demoulin
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium.
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Alexandre Lambion
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium.
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26
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Gupta A, Pandey P, Gupta R, Tiwari S, Singh SP. Responding to light signals: a comprehensive update on photomorphogenesis in cyanobacteria. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1915-1930. [PMID: 38222287 PMCID: PMC10784256 DOI: 10.1007/s12298-023-01386-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 01/16/2024]
Abstract
Cyanobacteria are ancestors of chloroplast and perform oxygen-evolving photosynthesis similar to higher plants and algae. However, an obligatory requirement of photons for their growth results in the exposure of cyanobacteria to varying light conditions. Therefore, the light environment could act as a signal to drive the developmental processes, in addition to photosynthesis, in cyanobacteria. These Gram-negative prokaryotes exhibit characteristic light-dependent developmental processes that maximize their fitness and resource utilization. The development occurring in response to radiance (photomorphogenesis) involves fine-tuning cellular physiology, morphology and metabolism. The best-studied example of cyanobacterial photomorphogenesis is chromatic acclimation (CA), which allows a selected number of cyanobacteria to tailor their light-harvesting antenna called phycobilisome (PBS). The tailoring of PBS under existing wavelengths and abundance of light gives an advantage to cyanobacteria over another photoautotroph. In this work, we will provide a comprehensive update on light-sensing, molecular signaling and signal cascades found in cyanobacteria. We also include recent developments made in other aspects of CA, such as mechanistic insights into changes in the size and shape of cells, filaments and carboxysomes.
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Affiliation(s)
- Anjali Gupta
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Priyul Pandey
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Rinkesh Gupta
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Sapna Tiwari
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Shailendra Pratap Singh
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
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27
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Wu S, Zheng H, Wang Y, Wang L, Chen W. Cyanobacterial bioreporter of nitrate bioavailability in aquatic ecosystems. WATER RESEARCH 2023; 247:120749. [PMID: 37918203 DOI: 10.1016/j.watres.2023.120749] [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: 03/27/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
The water eutrophication, resulting from the discharge of industrial and agricultural wastewater, leads to ecological degradation. However, to date, how to assess and manage the risks of water pollution, especially nitrogen pollution, remains a particularly noteworthy issue. Nitrate, the most important nitrogen compound, has become a bottleneck restricting total nitrogen management. The development of bioreporters monitoring nitrate pollution contributes to the estimation of water quality, especially the availability of nutrients. In this study, we obtained 9 bioreporters from 40 cyanobacterial derivatives which were constructed based on different hosts, copy numbers, and sensing elements and evaluated the performance of bioreporters. The results showed that single-celled Synechocystis was more sensitive to nitrate than filamentous Anabaena, that the reporter gene luxABCDE responded faster than sfgfp in most bioreporters, and that relatively medium-copy plasmid improved the performance of sensing elements. Nine bioreporters performed well in bioavailable nitrate detection, of which AD-AS-X and AR-NI-X, activated by nitrate repletion, had the shortest response time (2 h) and the widest response range (20-800 μM), respectively. Moreover, SR-GLN-SG, activated by nitrate deficiency, exhibited the best linear response (R2 = 0.998). After parameter optimization, exponential growth phase bioreporters, culture temperature of 30 °C, sample volume of 200 μL were determined as optimal monitoring conditions. We found that common water contaminants (copper, cadmium, and phosphorus) had no impact on the performance of bioreporters, indicating the stability of bioreporters. Six out of 9 bioreporters, especially the SR-NB-X, were highly effective in detecting the bioavailable nitrate in wastewater sample. This study provides valuable references for developing more cyanobacterial bioreporters and their practical application in nitrate detection.
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Affiliation(s)
- Shanyu Wu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hongyan Zheng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuwei Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Li Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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28
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Jiang HB, Hutchins DA, Ma W, Zhang RF, Wells M, Jiao N, Wang Y, Chai F. Natural ocean iron fertilization and climate variability over geological periods. GLOBAL CHANGE BIOLOGY 2023; 29:6856-6866. [PMID: 37855153 DOI: 10.1111/gcb.16990] [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: 07/18/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023]
Abstract
Marine primary producers are largely dependent on and shape the Earth's climate, although their relationship with climate varies over space and time. The growth of phytoplankton and associated marine primary productivity in most of the modern global ocean is limited by the supply of nutrients, including the micronutrient iron. The addition of iron via episodic and frequent events drives the biological carbon pump and promotes the sequestration of atmospheric carbon dioxide (CO2 ) into the ocean. However, the dependence between iron and marine primary producers adaptively changes over different geological periods due to the variation in global climate and environment. In this review, we examined the role and importance of iron in modulating marine primary production during some specific geological periods, that is, the Great Oxidation Event (GOE) during the Huronian glaciation, the Snowball Earth Event during the Cryogenian, the glacial-interglacial cycles during the Pleistocene, and the period from the last glacial maximum to the late Holocene. Only the change trend of iron bioavailability and climate in the glacial-interglacial cycles is consistent with the Iron Hypothesis. During the GOE and the Snowball Earth periods, although the bioavailability of iron in the ocean and the climate changed dramatically, the changing trend of many factors contradicted the Iron Hypothesis. By detangling the relationship among marine primary productivity, iron availability and oceanic environments in different geological periods, this review can offer some new insights for evaluating the impact of ocean iron fertilization on removing CO2 from the atmosphere and regulating the climate.
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Affiliation(s)
- Hai-Bo Jiang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Wentao Ma
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
| | - Rui-Feng Zhang
- School of Oceanography, Shanghai Jiaotong University, Shanghai, Shanghai, China
| | - Mark Wells
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- School of Marine Sciences, University of Maine, Orono, Maine, USA
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yuntao Wang
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
| | - Fei Chai
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian, China
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29
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Olivan-Muro I, Sarasa-Buisan C, Guio J, Arenas J, Sevilla E, Fillat MF. Unbalancing Zur (FurB)-mediated homeostasis in Anabaena sp. PCC7120: Consequences on metal trafficking, heterocyst development and biofilm formation. Environ Microbiol 2023; 25:2142-2162. [PMID: 37315963 DOI: 10.1111/1462-2920.16434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]
Abstract
Zinc is required for the activity of many enzymes and plays an essential role in gene regulation and redox homeostasis. In Anabaena (Nostoc) sp. PCC7120, the genes involved in zinc uptake and transport are controlled by the metalloregulator Zur (FurB). Comparative transcriptomics of a zur mutant (Δzur) with the parent strain unveiled unexpected links between zinc homeostasis and other metabolic pathways. A notable increase in the transcription of numerous desiccation tolerance-related genes, including genes involved in the synthesis of trehalose and the transference of saccharide moieties, among many others, was detected. Biofilm formation analysis under static conditions revealed a reduced capacity of Δzur filaments to form biofilms compared to the parent strain, and such capacity was enhanced when Zur was overexpressed. Furthermore, microscopy analysis revealed that zur expression is required for the correct formation of the envelope polysaccharide layer in the heterocyst, as Δzur cells showed reduced staining with alcian blue compared to Anabaena sp. PCC7120. We suggest that Zur is an important regulator of the enzymes involved in the synthesis and transport of the envelope polysaccharide layer, influencing heterocyst development and biofilm formation, both relevant processes for cell division and interaction with substrates in its ecological niche.
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Affiliation(s)
- Irene Olivan-Muro
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences and Institute of Bioinformatics and Physical of Complex Systems, University of Zaragoza, Zaragoza, Spain
| | - Cristina Sarasa-Buisan
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences and Institute of Bioinformatics and Physical of Complex Systems, University of Zaragoza, Zaragoza, Spain
| | - Jorge Guio
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences and Institute of Bioinformatics and Physical of Complex Systems, University of Zaragoza, Zaragoza, Spain
| | - Jesús Arenas
- Department of Animal Pathology, Unit of Microbiology and Immunology, Faculty of Veterinary, University of Zaragoza, Zaragoza, Spain
| | - Emma Sevilla
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences and Institute of Bioinformatics and Physical of Complex Systems, University of Zaragoza, Zaragoza, Spain
| | - Maria F Fillat
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences and Institute of Bioinformatics and Physical of Complex Systems, University of Zaragoza, Zaragoza, Spain
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30
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Metcalf JS, Banack SA, Wyatt PB, Nunn PB, Cox PA. A Direct Analysis of β- N-methylamino-l-alanine Enantiomers and Isomers and Its Application to Cyanobacteria and Marine Mollusks. Toxins (Basel) 2023; 15:639. [PMID: 37999501 PMCID: PMC10674937 DOI: 10.3390/toxins15110639] [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: 08/17/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 11/25/2023] Open
Abstract
Of the wide variety of toxic compounds produced by cyanobacteria, the neurotoxic amino acid β-N-methylamino-l-alanine (BMAA) has attracted attention as a result of its association with chronic human neurodegenerative diseases such as ALS and Alzheimer's. Consequently, specific detection methods are required to assess the presence of BMAA and its isomers in environmental and clinical materials, including cyanobacteria and mollusks. Although the separation of isomers such as β-amino-N-methylalanine (BAMA), N-(2-aminoethyl)glycine (AEG) and 2,4-diaminobutyric acid (DAB) from BMAA has been demonstrated during routine analysis, a further compounding factor is the potential presence of enantiomers for some of these isomers. Current analytical methods for BMAA mostly do not discriminate between enantiomers, and the chiral configuration of BMAA in cyanobacteria is still largely unexplored. To understand the potential for the occurrence of D-BMAA in cyanobacteria, a chiral UPLC-MS/MS method was developed to separate BMAA enantiomers and isomers and to determine the enantiomeric configuration of endogenous free BMAA in a marine Lyngbya mat and two mussel reference materials. After extraction, purification and derivatization with N-(4-nitrophenoxycarbonyl)-l-phenylalanine 2-methoxyethyl ester ((S)-NIFE), both L- and D-BMAA were identified as free amino acids in cyanobacterial materials, whereas only L-BMAA was identified in mussel tissues. The finding of D-BMAA in biological environmental materials raises questions concerning the source and role of BMAA enantiomers in neurological disease.
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Affiliation(s)
- James S. Metcalf
- Brain Chemistry Labs, Box 3464, Jackson, WY 83001, USA; (S.A.B.); (P.A.C.)
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Sandra Anne Banack
- Brain Chemistry Labs, Box 3464, Jackson, WY 83001, USA; (S.A.B.); (P.A.C.)
| | - Peter B. Wyatt
- The School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (P.B.W.); (P.B.N.)
| | - Peter B. Nunn
- The School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (P.B.W.); (P.B.N.)
| | - Paul A. Cox
- Brain Chemistry Labs, Box 3464, Jackson, WY 83001, USA; (S.A.B.); (P.A.C.)
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31
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Li L, Huang D, Hu Y, Rudling NM, Canniffe DP, Wang F, Wang Y. Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle. Nat Commun 2023; 14:6450. [PMID: 37833297 PMCID: PMC10576062 DOI: 10.1038/s41467-023-42193-7] [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: 02/24/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Photosynthesis is a fundamental biogeochemical process, thought to be restricted to a few bacterial and eukaryotic phyla. However, understanding the origin and evolution of phototrophic organisms can be impeded and biased by the difficulties of cultivation. Here, we analyzed metagenomic datasets and found potential photosynthetic abilities encoded in the genomes of uncultivated bacteria within the phylum Myxococcota. A putative photosynthesis gene cluster encoding a type-II reaction center appears in at least six Myxococcota families from three classes, suggesting vertical inheritance of these genes from an early common ancestor, with multiple independent losses in other lineages. Analysis of metatranscriptomic datasets indicate that the putative myxococcotal photosynthesis genes are actively expressed in various natural environments. Furthermore, heterologous expression of myxococcotal pigment biosynthesis genes in a purple bacterium supports that the genes can drive photosynthetic processes. Given that predatory abilities are thought to be widespread across Myxococcota, our results suggest the intriguing possibility of a chimeric lifestyle (combining predatory and photosynthetic abilities) in members of this phylum.
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Affiliation(s)
- Liuyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Danyue Huang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yaoxun Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Nicola M Rudling
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Daniel P Canniffe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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de Lima Pinheiro MM, Temponi Santos BL, Vieira Dantas Filho J, Perez Pedroti V, Cavali J, Brito dos Santos R, Oliveira Carreira Nishiyama AC, Guedes EAC, de Vargas Schons S. First monitoring of cyanobacteria and cyanotoxins in freshwater from fish farms in Rondônia state, Brazil. Heliyon 2023; 9:e18518. [PMID: 37520970 PMCID: PMC10374934 DOI: 10.1016/j.heliyon.2023.e18518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023] Open
Abstract
The main aimed of this study was to evaluate the physicochemical parameters, abundance and density of cyanobacteria, determine their blooms and the ecotoxicological risk of their cyanotoxins in fish ponds water. This study was conducted out in 20 fish farms in Rondônia state (Brazilian Amazon), samplings were carried out in the rainy and dry seasons. The experiment was developed in a completely randomized factorial design 20 × 3 x 3 (20 fish farms, 3 ponds and 3 replications). Regarding the composition of qualitative samples, horizontal and vertical hauls were carried out on the water surface, quantitative samples was obtained using a plankton net (50 μm mesh opening). Meanwhile, with the use of a multiparametric probe, physicochemical analyzes in fish ponds water were carried out. Furthermore, the cyanobacteria found were classified taxonomically and its blooms were recorded. Finally, blood was collected from 60 Colossoma macropomum. Concerning the higher averages in the rainy season 6.13 mg L⁻1 of dissolved oxygen, 40.02 cm of transparency, 0.35 NO31⁻ of nitrate, 0.15 NO21⁻ of nitrite, 44.55 mg L⁻1 CaCO3 of alkalinity and 50.10 mg L⁻1 CaCO3 of hardness, while higher averages of pH, phosphate and phosphorus were found in the dry season. A total of 15 families and 29 species of cyanobacteria were identified in the different seasons. The families that showed the highest densities (rainy and dry seasons) were Microcystaceae (356 and 760 cells mL⁻1), Leptolyngbyaceae (126 and 287 cells mL⁻1) and Microcoleaceae (111 and 405 cells mL⁻1). The species that showed the highest densities were Microcystis aeruginosa (356 and 697 cells mL⁻1), Planktolyngbya limnetica (98 and 257 cells mL⁻1) and Planktothrix sp. (111 and 239 cells mL⁻1). There were significant Pearson's correlations (r > 0.85; p < 0.05) between family abundances and cyanotoxin volume between physicochemical water variables and seasonality. A total of 20 cyanobacteria blooms were recorded, all of which in the dry season showed an ecotoxicological risk. Concerning the assessment mutagenicity in fish blood cells, a total of 78 abnormalities per slide were observed. In the dry season, the expected volume of cyanotoxins in the ponds from fish farms F1 and F4 were above the quantification limit (>QL). Abundance and density of cyanobacteria and their blooms and cyanotoxins can be used as bioindicators of eutrophication and/or water quality and ecotoxicological risk in fish ponds.
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Affiliation(s)
| | | | | | - Vinícius Perez Pedroti
- Programa de Pós-Graduação Em Ciências Ambientais, Universidade Federal de Rondônia, Rolim de Moura, RO, Brazil
| | - Jucilene Cavali
- Programa de Pós-Graduação Em Sanidade e Produção Animal Sustentável Na Amazônia Ocidental, Universidade Federal Do Acre, Rio Branco, AC, Brazil
| | | | | | - Elica Amara Cecilia Guedes
- Centro de Ciências Agrárias e Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Sandro de Vargas Schons
- Programa de Pós-Graduação Em Ciências Ambientais, Universidade Federal de Rondônia, Rolim de Moura, RO, Brazil
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Zheng W, Zhou A, Sahoo SK, Nolan MR, Ostrander CM, Sun R, Anbar AD, Xiao S, Chen J. Recurrent photic zone euxinia limited ocean oxygenation and animal evolution during the Ediacaran. Nat Commun 2023; 14:3920. [PMID: 37400445 DOI: 10.1038/s41467-023-39427-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/12/2023] [Indexed: 07/05/2023] Open
Abstract
The Ediacaran Period (~635-539 Ma) is marked by the emergence and diversification of complex metazoans linked to ocean redox changes, but the processes and mechanism of the redox evolution in the Ediacaran ocean are intensely debated. Here we use mercury isotope compositions from multiple black shale sections of the Doushantuo Formation in South China to reconstruct Ediacaran oceanic redox conditions. Mercury isotopes show compelling evidence for recurrent and spatially dynamic photic zone euxinia (PZE) on the continental margin of South China during time intervals coincident with previously identified ocean oxygenation events. We suggest that PZE was driven by increased availability of sulfate and nutrients from a transiently oxygenated ocean, but PZE may have also initiated negative feedbacks that inhibited oxygen production by promoting anoxygenic photosynthesis and limiting the habitable space for eukaryotes, hence abating the long-term rise of oxygen and restricting the Ediacaran expansion of macroscopic oxygen-demanding animals.
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Affiliation(s)
- Wang Zheng
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Anwen Zhou
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
- Department of Earth, Ocean and Atmospheric Science and National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32306, USA
| | | | - Morrison R Nolan
- Department of Geosciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Chadlin M Ostrander
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Ruoyu Sun
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Ariel D Anbar
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jiubin Chen
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China.
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Yang N, Li Z, Wu Z, Liu X, Zhang Y, Sun T, Wang X, Zhao Y, Tong Y. Differential effects of nitrate and ammonium on the growth of algae and microcystin production by nitrogen-fixing Nostoc sp. and non-nitrogen-fixing Microcystis aeruginosa. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:136-150. [PMID: 37452539 PMCID: wst_2023_205 DOI: 10.2166/wst.2023.205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Cyanotoxins produced by cyanobacteria are a significant threat to human health. However, their responses to nitrogen (N) supplies could differ between N-fixing and non-N-fixing species, which has been poorly understood. This study aimed to compare the responses of the non-N-fixing Microcystis aeruginosa and N-fixing Nostoc sp. to varying concentrations of nitrate and ammonium. This comparison had been conducted by analyzing chlorophyll-a contents, maximum quantum efficiencies of photosystem II, microcystin production, and related gene expressions. Our findings revealed that nitrate substantially stimulated the growth of both M. aeruginosa and Nostoc sp. with biomass increase by 366.2 ± 56.5 and 93.0 ± 14.0%, respectively, at 16 mg-N/L. In contrast, high ammonium concentrations suppressed their growth. Furthermore, the intracellular concentration of microcystins produced by M. aeruginosa was higher under high nitrate. Extracellular microcystins showed an opposite trend to increases in nitrate and ammonium. Ammonium increases the production and releases microcystin from Nostoc sp. N metabolism genes showed a similar trend with toxin formation genes, which were up-regulated under the high N treatments. This study provides valuable insights into the impacts of N supplies on growths of N- and non-N-fixing cyanobacteria, as well as microcystin production, which helps to develop effective strategies for managing cyanobacterial blooms.
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Affiliation(s)
- Ning Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China E-mail:
| | - Zipeng Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Zhengyu Wu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Xianhua Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Yiyan Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Tao Sun
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, China; Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
| | - Xuejun Wang
- College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Yindong Tong
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; School of Ecology and Environment, Tibet University, Lhasa 850000, China
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35
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Shevela D, Kern JF, Govindjee G, Messinger J. Solar energy conversion by photosystem II: principles and structures. PHOTOSYNTHESIS RESEARCH 2023; 156:279-307. [PMID: 36826741 PMCID: PMC10203033 DOI: 10.1007/s11120-022-00991-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/01/2022] [Indexed: 05/23/2023]
Abstract
Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.
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Affiliation(s)
- Dmitry Shevela
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187, Umeå, Sweden.
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Govindjee Govindjee
- Department of Plant Biology, Department of Biochemistry and Center of Biophysics & Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Johannes Messinger
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187, Umeå, Sweden.
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, 75120, Uppsala, Sweden.
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36
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Cassier-Chauvat C, Marceau F, Farci S, Ouchane S, Chauvat F. The Glutathione System: A Journey from Cyanobacteria to Higher Eukaryotes. Antioxidants (Basel) 2023; 12:1199. [PMID: 37371929 DOI: 10.3390/antiox12061199] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
From bacteria to plants and humans, the glutathione system plays a pleiotropic role in cell defense against metabolic, oxidative and metal stresses. Glutathione (GSH), the γ-L-glutamyl-L-cysteinyl-glycine nucleophile tri-peptide, is the central player of this system that acts in redox homeostasis, detoxification and iron metabolism in most living organisms. GSH directly scavenges diverse reactive oxygen species (ROS), such as singlet oxygen, superoxide anion, hydrogen peroxide, hydroxyl radical, nitric oxide and carbon radicals. It also serves as a cofactor for various enzymes, such as glutaredoxins (Grxs), glutathione peroxidases (Gpxs), glutathione reductase (GR) and glutathione-S-transferases (GSTs), which play crucial roles in cell detoxication. This review summarizes what is known concerning the GSH-system (GSH, GSH-derived metabolites and GSH-dependent enzymes) in selected model organisms (Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana and human), emphasizing cyanobacteria for the following reasons. Cyanobacteria are environmentally crucial and biotechnologically important organisms that are regarded as having evolved photosynthesis and the GSH system to protect themselves against the ROS produced by their active photoautotrophic metabolism. Furthermore, cyanobacteria synthesize the GSH-derived metabolites, ergothioneine and phytochelatin, that play crucial roles in cell detoxication in humans and plants, respectively. Cyanobacteria also synthesize the thiol-less GSH homologs ophthalmate and norophthalmate that serve as biomarkers of various diseases in humans. Hence, cyanobacteria are well-suited to thoroughly analyze the role/specificity/redundancy of the players of the GSH-system using a genetic approach (deletion/overproduction) that is hardly feasible with other model organisms (E. coli and S. cerevisiae do not synthesize ergothioneine, while plants and humans acquire it from their soil and their diet, respectively).
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Affiliation(s)
- Corinne Cassier-Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91190 Gif-sur-Yvette, France
| | - Fanny Marceau
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91190 Gif-sur-Yvette, France
| | - Sandrine Farci
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91190 Gif-sur-Yvette, France
| | - Soufian Ouchane
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91190 Gif-sur-Yvette, France
| | - Franck Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91190 Gif-sur-Yvette, France
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Sun C, Chang X, MacIsaac HJ, Wen J, Zhao L, Dai Z, Li J. Phytosphingosine inhibits cell proliferation by damaging DNA in human cell lines. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 256:114840. [PMID: 37001191 DOI: 10.1016/j.ecoenv.2023.114840] [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: 01/28/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Harmful cyanobacterial blooms have caused numerous biosecurity incidents owing to the production of hazardous secondary metabolites such as microcystin. Additionally, cyanobacteria also release many other components that have not been explored. We identified compounds of a toxic mixture exudated from a dominant, blooming species, Microcystis aeruginosa, and found that phytosphingosine (PHS) was one of the bioactive components. Since PHS exhibited toxicity and is deemed a hazardous substance by the European Chemicals Agency, we hypothesized that PHS is a potentially toxic compound in M. aeruginosa exudates. However, the mechanisms of PHS ecotoxicity remain unclear. We assessed the cytotoxicity of PHS using an in vitro cell model in eight human cell lines and observed that the nasopharyngeal carcinoma cell line CNE2 was the most sensitive. We exposed CNE2 cells to 0-25 µmol/L PHS for 24 hr to explore its toxicity and mechanism. PHS exposure resulted in abnormal nuclear morphology, micronuclei, and DNA damage. Moreover, PHS significantly inhibited cell proliferation and arrested cell cycle at S phase. The results of Western blot suggested that PHS increased the expression of DNA damage-related proteins (ATM, p-P53 and P21) and decreased the expression of S phase-related proteins (CDK2, CyclinA2 and CyclinE1), indicating the toxicological mechanism of PHS on CNE2 cells. These data provide evidence that PHS has genetic toxicity and inhibits cell proliferation by damaging DNA. Our study provides evidence that PHS inhibits cell proliferation by damaging DNA. While additional work is required, we propose that PHS been considered as a potentially toxic component in MaE in addition to other well-characterized secondary compounds.
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Affiliation(s)
- Chunxiao Sun
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China; Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Xuexiu Chang
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada; College of Agronomy and Life Sciences, Kunming University, Kunming 650214, China
| | - Hugh J MacIsaac
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China; College of Agronomy and Life Sciences, Kunming University, Kunming 650214, China
| | - Jiayao Wen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Lixing Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Zhi Dai
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Jiaojiao Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
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Aguiló-Nicolau P, Galmés J, Fais G, Capó-Bauçà S, Cao G, Iñiguez C. Singular adaptations in the carbon assimilation mechanism of the polyextremophile cyanobacterium Chroococcidiopsis thermalis. PHOTOSYNTHESIS RESEARCH 2023; 156:231-245. [PMID: 36941458 PMCID: PMC10154277 DOI: 10.1007/s11120-023-01008-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/16/2023] [Indexed: 05/03/2023]
Abstract
Cyanobacteria largely contribute to the biogeochemical carbon cycle fixing ~ 25% of the inorganic carbon on Earth. However, the carbon acquisition and assimilation mechanisms in Cyanobacteria are still underexplored regardless of being of great importance for shedding light on the origins of autotropism on Earth and providing new bioengineering tools for crop yield improvement. Here, we fully characterized these mechanisms from the polyextremophile cyanobacterium Chroococcidiopsis thermalis KOMAREK 1964/111 in comparison with the model cyanobacterial strain, Synechococcus sp. PCC6301. In particular, we analyzed the Rubisco kinetics along with the in vivo photosynthetic CO2 assimilation in response to external dissolved inorganic carbon, the effect of CO2 concentrating mechanism (CCM) inhibitors on net photosynthesis and the anatomical particularities of their carboxysomes when grown under either ambient air (0.04% CO2) or 2.5% CO2-enriched air. Our results show that Rubisco from C. thermalis possess the highest specificity factor and carboxylation efficiency ever reported for Cyanobacteria, which were accompanied by a highly effective CCM, concentrating CO2 around Rubisco more than 140-times the external CO2 levels, when grown under ambient CO2 conditions. Our findings provide new insights into the Rubisco kinetics of Cyanobacteria, suggesting that improved Sc/o values can still be compatible with a fast-catalyzing enzyme. The combination of Rubisco kinetics and CCM effectiveness in C. thermalis relative to other cyanobacterial species might indicate that the co-evolution between Rubisco and CCMs in Cyanobacteria is not as constrained as in other phylogenetic groups.
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Affiliation(s)
- Pere Aguiló-Nicolau
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain.
| | - Giacomo Fais
- Interdepartmental Centre of Environmental Science and Engineering, University of Cagliari, Via San Giorgio 12, 09124, Cagliari, Italy
| | - Sebastià Capó-Bauçà
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
| | - Giacomo Cao
- Interdepartmental Centre of Environmental Science and Engineering, University of Cagliari, Via San Giorgio 12, 09124, Cagliari, Italy
- Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, Via Marengo 2, 09123, Cagliari, Italy
| | - Concepción Iñiguez
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
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Cai W, Yu K, Yang W, Mu R, Lian C, Xie L, Yan Y, Liao S, Wang F. Prokaryotic Community Structure, Abundances, and Potential Ecological Functions in a Mars Analog Salt Lake. ASTROBIOLOGY 2023; 23:550-562. [PMID: 37130293 DOI: 10.1089/ast.2022.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Barkol Lake, situated northeast of the Tianshan Mountains, Xinjiang, is a hypersaline lake with abundant sulfate and chloride minerals, which can be a potential analog for microbial saline paleolakes on Mars. The lake water, sediments, and surrounding soils of Barkol Lake were sampled for geochemical analysis and 16S rRNA gene sequencing to investigate the prokaryotic community structure, abundances, interactions, and ecological functions. Results show that (1) prokaryotic community structure differs significantly between biotopes (water, sediment, and soil), with the highest abundances of archaea occurring in water samples and highest prokaryotic diversities in soil samples; (2) archaeal communities are dominated by Halobacterota, Nanoarchaeota, Thermoplasmatota, and Crenarchaeota, while bacterial communities are mainly Proteobacteria, Bacteroidetes, Actinobacteria, Desulfobacterota, Chloroflexi, Gemmatimonadetes, Firmicutes, and Cyanobacteria; (3) the prokaryotic community network for soil is far more complicated and stable than those for water and sediment; (4) soil prokaryotic communities could be significantly affected by environmental factors such as salinity, pH, total sulfur, and Ca2+; (5) archaeal communities may play an important role in the nitrogen cycle, while bacterial communities may mainly participate in the sulfur cycle. This study extends the data set of prokaryotic communities for hypersaline environments, which will provide perspectives into identification of the counterparts and help to understand potential microbial interactions and biogeochemical cycles occurring on Mars.
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Affiliation(s)
- Wenqi Cai
- School of Atmospheric Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Key Laboratory of Tropical Atmosphere-Ocean System, Ministry of Education, Zhuhai, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Wanting Yang
- School of Atmospheric Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Rong Mu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Chunang Lian
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Luhua Xie
- Key Laboratory of Ocean and Marginal Sea Geology, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, China
| | - Yan Yan
- Key Laboratory of Ocean and Marginal Sea Geology, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, China
| | - Shibin Liao
- Xinjiang Research Center for Mineral Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Fan Wang
- School of Atmospheric Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Key Laboratory of Tropical Atmosphere-Ocean System, Ministry of Education, Zhuhai, China
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Zhang C, Zhang G, Jin J, Zheng H, Zhou Z, Zhang S. Selenite-Catalyzed Reaction between Benzoquinone and Acetylacetone Deciphered the Enhanced Inhibition on Microcystis aeruginosa Growth. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:6188-6195. [PMID: 37011377 DOI: 10.1021/acs.est.2c09682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The coexistence of selenite (Se(IV)) and acetylacetone (AA) generated a synergistic effect on the growth inhibition of a bloom-forming cyanobacterium, Microcystis aeruginosa. The mechanism behind this phenomenon is of great significance in the control of harmful algal blooms. To elucidate the role of Se(IV) in this effect, the reactions in ternary solutions composed of Se(IV), AA (or two other similar hydrogen donors), and quinones, especially benzoquinone (BQ), were investigated. The transformation kinetic results demonstrate that Se(IV) played a catalytic role in the reactions between AA (or ascorbic acid) and quinones. By comparison with five other oxyanions (sulfite, sulfate, nitrite, nitrate, and phosphate) and two AA derivatives, the formation of an AA-Se(IV) complexation intermediate was confirmed as a key step in the accelerated reactions between BQ and AA. To our knowledge, this is the first report on Se(IV) as a catalyst for quinone-involved reactions. Since both quinones and Se are essential in cells and there are many other chemicals of similar electron-donating properties to that of AA, the finding here shed light on the regulation of electron transport chains in a variety of processes, especially the redox balances that are tuned by quinones and glutathione.
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Affiliation(s)
- Chengyang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Guoyang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Jiyuan Jin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Hongcen Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Zhiwei Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Shujuan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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Lefler FW, Berthold DE, Laughinghouse HD. Cyanoseq: A database of cyanobacterial 16S rRNA gene sequences with curated taxonomy. JOURNAL OF PHYCOLOGY 2023. [PMID: 37026389 DOI: 10.1111/jpy.13335] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 05/23/2023]
Abstract
Cyanobacteria are photosynthetic bacteria that occupy various habitats across the globe, playing critical roles in many of Earth's biogeochemical cycles both in both aquatic and terrestrial systems. Despite their well-known significance, their taxonomy remains problematic and is the subject of much research. Taxonomic issues of Cyanobacteria have consequently led to inaccurate curation within known reference databases, ultimately leading to problematic taxonomic assignment during diversity studies. Recent advances in sequencing technologies have increased our ability to characterize and understand microbial communities, leading to the generation of thousands of sequences that require taxonomic assignment. We herein propose CyanoSeq (https://zenodo.org/record/7569105), a database of cyanobacterial 16S rRNA gene sequences with curated taxonomy. The taxonomy of CyanoSeq is based on the current state of cyanobacterial taxonomy, with ranks from the domain to genus level. Files are provided for use with common naive Bayes taxonomic classifiers, such as those included in DADA2 or the QIIME2 platform. Additionally, FASTA files are provided for creation of de novo phylogenetic trees with (near) full-length 16S rRNA gene sequences to determine the phylogenetic relationship of cyanobacterial strains and/or ASV/OTUs. The database currently consists of 5410 cyanobacterial 16S rRNA gene sequences along with 123 Chloroplast, Bacterial, and Vampirovibrionia (formally Melainabacteria) sequences.
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Affiliation(s)
- Forrest W Lefler
- Agronomy Department, Fort Lauderdale Research and Education Center, University of Florida - IFAS, Davie, Florida, USA
| | - David E Berthold
- Agronomy Department, Fort Lauderdale Research and Education Center, University of Florida - IFAS, Davie, Florida, USA
| | - H Dail Laughinghouse
- Agronomy Department, Fort Lauderdale Research and Education Center, University of Florida - IFAS, Davie, Florida, USA
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Goodchild-Michelman IM, Church GM, Schubert MG, Tang TC. Light and carbon: Synthetic biology toward new cyanobacteria-based living biomaterials. Mater Today Bio 2023; 19:100583. [PMID: 36846306 PMCID: PMC9945787 DOI: 10.1016/j.mtbio.2023.100583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023] Open
Abstract
Cyanobacteria are ideal candidates to use in developing carbon neutral and carbon negative technologies; they are efficient photosynthesizers and amenable to genetic manipulation. Over the past two decades, researchers have demonstrated that cyanobacteria can make sustainable, useful biomaterials, many of which are engineered living materials. However, we are only beginning to see such technologies applied at an industrial scale. In this review, we explore the ways in which synthetic biology tools enable the development of cyanobacteria-based biomaterials. First we give an overview of the ecological and biogeochemical importance of cyanobacteria and the work that has been done using cyanobacteria to create biomaterials so far. This is followed by a discussion of commonly used cyanobacteria strains and synthetic biology tools that exist to engineer cyanobacteria. Then, three case studies-bioconcrete, biocomposites, and biophotovoltaics-are explored as potential applications of synthetic biology in cyanobacteria-based materials. Finally, challenges and future directions of cyanobacterial biomaterials are discussed.
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Affiliation(s)
- Isabella M. Goodchild-Michelman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Tzu-Chieh Tang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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Gomes PH, Pereira SP, Tavares TCL, Garcia TM, Soares MO. Impacts of desalination discharges on phytoplankton and zooplankton: Perspectives on current knowledge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160671. [PMID: 36481138 DOI: 10.1016/j.scitotenv.2022.160671] [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: 07/27/2022] [Revised: 11/07/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Large-scale application of desalination technology can result in impacts to the marine biota, such as phytoplankton and zooplankton, basal components of marine trophic webs. In this context, our perspective aimed to summarize the impacts of effluent discharges from desalination plants on phytoplankton and zooplankton in order to identify the main gaps and challenges in this theme, propose solutions, and provide recommendations for future work. We identified two main approaches to assess the desalination impacts: laboratory experiments and field studies. Most of these studies were conducted in areas impacted by effluent discharges using the BACI (before, after, and control-impact) approach. They primarily aimed to set out the impacts of hypersaline brine on the surrounding environment and, to a lesser extent, the high-temperature effluents and contaminants from desalination plants. Moreover, phytoplankton was more sensitive to effluent discharges than zooplankton. The main changes observed were a decrease in primary productivity, a loss in diversity, and a change in the community structure of planktonic populations due to the dominance of saline-tolerant groups, which highlights the importance improving treatment or dilution of effluent discharges to minimize the impacts over whole neritic trophic webs, which depend on phytoplankton. From the impacts related to effluent discharges analyzed herein, RO technology was related to most cases of negative impact related to salinity modifications. However, coagulants were related to negative effects in all study cases. Future work should focus on escalate the impacts of such effluents on other trophic levels that could be directly or indirectly impacted as well as on how to improve the quality of effluent discharges. Also, we highlight the importance of further baseline and long-term monitoring studies to investigate desalination-induced changes and community resilience to these impacts, as well as studies to provide alternatives to the use of toxic chemicals in the pre-treatment phases.
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Affiliation(s)
- Pedro Henrique Gomes
- Instituto de Ciências do Mar (LABOMAR), Universidade Federal do Ceará (UFC), Abolição Avenue 3207, Fortaleza, Brazil.
| | - Silvano Porto Pereira
- Companhia de Água e Esgoto do Ceará (CAGECE), Fortaleza, Brazil; University of Alicante
| | - Tallita Cruz Lopes Tavares
- Instituto de Ciências do Mar (LABOMAR), Universidade Federal do Ceará (UFC), Abolição Avenue 3207, Fortaleza, Brazil
| | - Tatiane Martins Garcia
- Instituto de Ciências do Mar (LABOMAR), Universidade Federal do Ceará (UFC), Abolição Avenue 3207, Fortaleza, Brazil
| | - Marcelo O Soares
- Instituto de Ciências do Mar (LABOMAR), Universidade Federal do Ceará (UFC), Abolição Avenue 3207, Fortaleza, Brazil; Reef Systems Group, Leibniz Center for Tropical Marine Research (ZMT), Bremen, Germany
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Control of Cell Size by c-di-GMP Requires a Two-Component Signaling System in the Cyanobacterium Anabaena sp. Strain PCC 7120. Microbiol Spectr 2023; 11:e0422822. [PMID: 36625639 PMCID: PMC9927289 DOI: 10.1128/spectrum.04228-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Each bacterial species possesses a specific cell size and morphology, which constitute important and recognizable physical traits. How bacteria maintain their particular cell size and morphology remains an essential question in microbiology. Cyanobacteria are oxygen-evolving photosynthetic prokaryotes. Although monophyletic, these organisms are highly diverse in their cell morphology and cell size. How these physical traits of cyanobacteria are controlled is poorly understood. Here, we report the identification of a two-component signaling system, composed of a histidine kinase CdgK and a response regulator CdgS, involved in cell size regulation in the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Inactivation of cdgK or cdgS led to reduction of cell length and width with little effect on cell growth capacity. CdgS has a GGDEF domain responsible for the synthesis of the second messenger c-di-GMP. Based on genetic and biochemical studies, we proposed a signaling pathway initiated by CdgK, leading to the phosphorylation of CdgS, and thereby an enhanced enzymatic activity for c-di-GMP synthesis of the latter. The GGDEF domain of CdgS was essential in cell size control, and the reduction of cell size observed in various mutants could be rescued by the expression of a c-di-GMP synthetase from E. coli. These results provided evidence that a minimal threshold of c-di-GMP level was required for maintaining cell size in Anabaena. IMPORTANCE Cyanobacteria are considered the first organisms to produce oxygen on Earth, and their activities shaped the evolution of our ecosystems. Cell size is an important trait fixed early in evolution, with the diversification of micro- and macrocyanobacterial species during the Great Oxidation Event. However, the genetic basis underlying cell size control in cyanobacteria was not understood. Our studies demonstrated that the CdgK-CdgS signaling pathway participates in the control of cell size, and their absence did not affect cell growth. CdgK has multiple domains susceptible to signal input, which are necessary for cell size regulation. This observation suggests that cell size in Anabaena could respond to environmental signals. These studies paved the way for genetic dissection of cell size regulation in cyanobacteria.
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Rastogi RP, Shree A, Patel HM, Chaudhry S, Madamwar D. Characterization, UV-induction, antioxidant function and role in photo-protection of mycosporine-like amino acids (MAAs) in a unicellular cyanobacterium, Euhalothece sp.WR7. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Stüeken EE, Kirsimäe K, Lepland A, Prave AR. Hydrothermal Regeneration of Ammonium as a Basin-Scale Driver of Primary Productivity. ASTROBIOLOGY 2023; 23:195-212. [PMID: 36577019 DOI: 10.1089/ast.2021.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Hydrothermal vents are important targets in the search for life on other planets due to their potential to generate key catalytic surfaces and organic compounds for biogenesis. Less well studied, however, is the role of hydrothermal circulation in maintaining a biosphere beyond its origin. In this study, we explored this question with analyses of organic carbon, nitrogen abundances, and isotopic ratios from the Paleoproterozoic Zaonega Formation (2.0 Ga), NW Russia, which is composed of interbedded sedimentary and mafic igneous rocks. Previous studies have documented mobilization of hydrocarbons, likely associated with magmatic intrusions into unconsolidated sediments. The igneous bodies are extensively hydrothermally altered. Our data reveal strong nitrogen enrichments of up to 0.6 wt % in these altered igneous rocks, suggesting that the hydrothermal fluids carried ammonium concentrations in the millimolar range, which is consistent with some modern hydrothermal vents. Furthermore, large isotopic offsets of ∼10‰ between organic-bound and silicate-bound nitrogen are most parsimoniously explained by partial biological uptake of ammonium from the vent fluid. Our results, therefore, show that hydrothermal activity in ancient marine basins could provide a locally high flux of recycled nitrogen. Hydrothermal nutrient recycling may thus be an important mechanism for maintaining a large biosphere on anoxic worlds.
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Affiliation(s)
- Eva E Stüeken
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, United Kingdom
| | - Kalle Kirsimäe
- Department of Geology, University of Tartu, Tartu, Estonia
| | - Aivo Lepland
- Department of Geology, University of Tartu, Tartu, Estonia
- Geological Survey of Norway, Trondheim, Norway
- Institute of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Anthony R Prave
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, United Kingdom
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47
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Remick KA, Helmann JD. The elements of life: A biocentric tour of the periodic table. Adv Microb Physiol 2023; 82:1-127. [PMID: 36948652 PMCID: PMC10727122 DOI: 10.1016/bs.ampbs.2022.11.001] [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] [Indexed: 01/31/2023]
Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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48
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Reconciling discrepant minor sulfur isotope records of the Great Oxidation Event. Nat Commun 2023; 14:279. [PMID: 36650167 PMCID: PMC9845385 DOI: 10.1038/s41467-023-35820-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Understanding the timing and trajectory of atmospheric oxygenation remains fundamental to deciphering its causes and consequences. Given its origin in oxygen-free photochemistry, mass-independent sulfur isotope fractionation (S-MIF) is widely accepted as a geochemical fingerprint of an anoxic atmosphere. Nevertheless, S-MIF recycling through oxidative sulfide weathering-commonly termed the crustal memory effect (CME)-potentially decouples the multiple sulfur isotope (MSI) record from coeval atmospheric chemistry. Herein, however, after accounting for unrecognised temporal and spatial biases within the Archaean-early-Palaeoproterozoic MSI record, we demonstrate that the global expression of the CME is barely resolvable; thereby validating S-MIF as a tracer of contemporaneous atmospheric chemistry during Earth's incipient oxygenation. Next, utilising statistical approaches, supported by new MSI data, we show that the reconciliation of adjacent, yet seemingly discrepant, South African MSI records requires that the rare instances of post-2.3-billion-year-old S-MIF are stratigraphically restricted. Accepting others' primary photochemical interpretation, our approach demands that these implied atmospheric dynamics were ephemeral, operating on sub-hundred-thousand-year timescales. Importantly, these apparent atmospheric relapses were fundamentally different from older putative oxygenation episodes, implicating an intermediate, and potentially uniquely feedback-sensitive, Earth system state in the wake of the Great Oxidation Event.
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49
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Badger MR, Sharwood RE. Rubisco, the imperfect winner: it's all about the base. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:562-580. [PMID: 36412307 DOI: 10.1093/jxb/erac458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles' heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth's multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily have identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubisco's catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base that functions both as an activator and a proton abstractor to create the enediol as a key to understanding how Rubisco may optimize its kinetic properties. The ways in which Rubisco and its partners have overcome catalytic and activation imperfections and thrived in a world of high O2, low CO2, and variable climatic regimes is remarkable.
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Affiliation(s)
- Murray R Badger
- Research School of Biology, Building 134 Linnaeus Way, Canberra ACT, 2601, Australia
| | - Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Bourke St, Richmond, NSW, 2753, Australia
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50
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Moore KR, Daye M, Gong J, Williford K, Konhauser K, Bosak T. A review of microbial-environmental interactions recorded in Proterozoic carbonate-hosted chert. GEOBIOLOGY 2023; 21:3-27. [PMID: 36268586 PMCID: PMC10092529 DOI: 10.1111/gbi.12527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The record of life during the Proterozoic is preserved by several different lithologies, but two in particular are linked both spatially and temporally: chert and carbonate. These lithologies capture a snapshot of dominantly peritidal environments during the Proterozoic. Early diagenetic chert preserves some of the most exceptional Proterozoic biosignatures in the form of microbial body fossils and mat textures. This fossiliferous and kerogenous chert formed in shallow marine environments, where chert nodules, layers, and lenses are often surrounded by and encased within carbonate deposits that themselves often contain kerogen and evidence of former microbial mats. Here, we review the record of biosignatures preserved in peritidal Proterozoic chert and chert-hosting carbonate and discuss this record in the context of experimental and environmental studies that have begun to shed light on the roles that microbes and organic compounds may have played in the formation of these deposits. Insights gained from these studies suggest temporal trends in microbial-environmental interactions and place new constraints on past environmental conditions, such as the concentration of silica in Proterozoic seawater, interactions among organic compounds and cations in seawater, and the influence of microbial physiology and biochemistry on selective preservation by silicification.
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Affiliation(s)
- Kelsey R. Moore
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Mirna Daye
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Jian Gong
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | | | - Kurt Konhauser
- Department of Earth and Atmospheric SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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