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Garcia NS, Du M, Guindani M, McIlvin MR, Moran DM, Saito MA, Martiny AC. Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change. THE ISME JOURNAL 2024; 18:wrae046. [PMID: 38513256 PMCID: PMC11020310 DOI: 10.1093/ismejo/wrae046] [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: 10/06/2023] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]
Abstract
Recent studies have demonstrated regional differences in marine ecosystem C:N:P with implications for carbon and nutrient cycles. Due to strong co-variance, temperature and nutrient stress explain variability in C:N:P equally well. A reductionistic approach can link changes in individual environmental drivers with changes in biochemical traits and cell C:N:P. Thus, we quantified effects of temperature and nutrient stress on Synechococcus chemistry using laboratory chemostats, chemical analyses, and data-independent acquisition mass spectrometry proteomics. Nutrient supply accounted for most C:N:Pcell variability and induced tradeoffs between nutrient acquisition and ribosomal proteins. High temperature prompted heat-shock, whereas thermal effects via the "translation-compensation hypothesis" were only seen under P-stress. A Nonparametric Bayesian Local Clustering algorithm suggested that changes in lipopolysaccharides, peptidoglycans, and C-rich compatible solutes may also contribute to C:N:P regulation. Physiological responses match field-based trends in ecosystem stoichiometry and suggest a hierarchical environmental regulation of current and future ocean C:N:P.
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Affiliation(s)
- Nathan S Garcia
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, United States
| | - Mingyu Du
- Department of Statistics, University of California, Irvine, Irvine, CA 92697, United States
| | - Michele Guindani
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Matthew R McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Dawn M Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Adam C Martiny
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, United States
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
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2
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Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [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: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
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Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
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3
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Wang Y, Ferrinho S, Connaris H, Goss RJM. The Impact of Viral Infection on the Chemistries of the Earth's Most Abundant Photosynthesizes: Metabolically Talented Aquatic Cyanobacteria. Biomolecules 2023; 13:1218. [PMID: 37627283 PMCID: PMC10452541 DOI: 10.3390/biom13081218] [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: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Cyanobacteria are the most abundant photosynthesizers on earth, and as such, they play a central role in marine metabolite generation, ocean nutrient cycling, and the control of planetary oxygen generation. Cyanobacteriophage infection exerts control on all of these critical processes of the planet, with the phage-ported homologs of genes linked to photosynthesis, catabolism, and secondary metabolism (marine metabolite generation). Here, we analyze the 153 fully sequenced cyanophages from the National Center for Biotechnology Information (NCBI) database and the 45 auxiliary metabolic genes (AMGs) that they deliver into their hosts. Most of these AMGs are homologs of those found within cyanobacteria and play a key role in cyanobacterial metabolism-encoding proteins involved in photosynthesis, central carbon metabolism, phosphate metabolism, methylation, and cellular regulation. A greater understanding of cyanobacteriophage infection will pave the way to a better understanding of carbon fixation and nutrient cycling, as well as provide new tools for synthetic biology and alternative approaches for the use of cyanobacteria in biotechnology and sustainable manufacturing.
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Affiliation(s)
- Yunpeng Wang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Scarlet Ferrinho
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Helen Connaris
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
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Géron A, Werner J, Wattiez R, Matallana-Surget S. Towards the discovery of novel molecular clocks in Prokaryotes. Crit Rev Microbiol 2023:1-13. [PMID: 37330701 DOI: 10.1080/1040841x.2023.2220789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/17/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
Diel cycle is of enormous biological importance as it imposes daily oscillation in environmental conditions, which temporally structures most ecosystems. Organisms developed biological time-keeping mechanisms - circadian clocks - that provide a significant fitness advantage over competitors by optimising the synchronisation of their biological activities. While circadian clocks are ubiquitous in Eukaryotes, they are so far only characterised in Cyanobacteria within Prokaryotes. However, growing evidence suggests that circadian clocks are widespread in the bacterial and archaeal domains. As Prokaryotes are at the heart of crucial environmental processes and are essential to human health, unravelling their time-keeping systems provides numerous applications in medical research, environmental sciences, and biotechnology. In this review, we elaborate on how novel circadian clocks in Prokaryotes offer research and development perspectives. We compare and contrast the different circadian systems in Cyanobacteria and discuss about their evolution and taxonomic distribution. We necessarily provide an updated phylogenetic analysis of bacterial and archaeal species that harbour homologs of the main cyanobacterial clock components. Finally, we elaborate on new potential clock-controlled microorganisms that represent opportunities of ecological and industrial relevance in prokaryotic groups such as anoxygenic photosynthetic bacteria, methanogenic archaea, methanotrophs or sulphate-reducing bacteria.
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Affiliation(s)
- Augustin Géron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), University of Tübingen, Tübingen, Germany
| | - Ruddy Wattiez
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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5
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Masuda T, Bečková M, Turóczy Z, Pilný J, Sobotka R, Trinugroho JP, Nixon PJ, Prášil O, Komenda J. Accumulation of Cyanobacterial Photosystem II Containing the 'Rogue' D1 Subunit Is Controlled by FtsH Protease and Synthesis of the Standard D1 Protein. PLANT & CELL PHYSIOLOGY 2023; 64:660-673. [PMID: 36976618 DOI: 10.1093/pcp/pcad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 06/16/2023]
Abstract
Unicellular diazotrophic cyanobacteria contribute significantly to the photosynthetic productivity of the ocean and the fixation of molecular nitrogen, with photosynthesis occurring during the day and nitrogen fixation during the night. In species like Crocosphaera watsonii WH8501, the decline in photosynthetic activity in the night is accompanied by the disassembly of oxygen-evolving photosystem II (PSII) complexes. Moreover, in the second half of the night phase, a small amount of rogue D1 (rD1), which is related to the standard form of the D1 subunit found in oxygen-evolving PSII, but of unknown function, accumulates but is quickly degraded at the start of the light phase. We show here that the removal of rD1 is independent of the rD1 transcript level, thylakoid redox state and trans-thylakoid pH but requires light and active protein synthesis. We also found that the maximal level of rD1 positively correlates with the maximal level of chlorophyll (Chl) biosynthesis precursors and enzymes, which suggests a possible role for rogue PSII (rPSII) in the activation of Chl biosynthesis just before or upon the onset of light, when new photosystems are synthesized. By studying strains of Synechocystis PCC 6803 expressing Crocosphaera rD1, we found that the accumulation of rD1 is controlled by the light-dependent synthesis of the standard D1 protein, which triggers the fast FtsH2-dependent degradation of rD1. Affinity purification of FLAG-tagged rD1 unequivocally demonstrated the incorporation of rD1 into a non-oxygen-evolving PSII complex, which we term rPSII. The complex lacks the extrinsic proteins stabilizing the oxygen-evolving Mn4CaO5 cluster but contains the Psb27 and Psb28-1 assembly factors.
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Affiliation(s)
- Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Martina Bečková
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Zoltán Turóczy
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Jan Pilný
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Roman Sobotka
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice 370 05, Czech Republic
| | - Joko P Trinugroho
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Peter J Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Josef Komenda
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice 370 05, Czech Republic
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Alonso-Sáez L, Palacio AS, Cabello AM, Robaina-Estévez S, González JM, Garczarek L, López-Urrutia Á. Transcriptional Mechanisms of Thermal Acclimation in Prochlorococcus. mBio 2023:e0342522. [PMID: 37052490 DOI: 10.1128/mbio.03425-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30°C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17°C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones. IMPORTANCE Prochlorococcus is a major marine primary producer with a global impact on atmospheric CO2 fixation. This cyanobacterium is widely distributed across the temperate ocean, but virtually absent at latitudes above 40° for yet unknown reasons. Temperature has been suggested as a major limiting factor, but the exact mechanisms behind Prochlorococcus thermal growth restriction remain unexplored. This study brings us closer to understanding how Prochlorococcus functions under challenging temperature conditions, by focusing on its transcriptional response after long-term acclimation from its optimum to its thermal thresholds. Our results show that the drop in Prochlorococcus growth rate under cold conditions was paralleled by a transcriptional suppression of the photosynthetic machinery during daytime and a loss in the organism's regulatory capacity to maintain circadian expression patterns. Notably, warm temperature induced a marked shrinkage of the organism's cellular transcript inventory, which may also induce regulatory imbalances in the future functioning of this cyanobacterium.
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Affiliation(s)
- Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Antonio S Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ana M Cabello
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, IEO-CSIC, Gijón, Asturias, Spain
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7
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Larkin AA, Hagstrom GI, Brock ML, Garcia NS, Martiny AC. Basin-scale biogeography of Prochlorococcus and SAR11 ecotype replication. THE ISME JOURNAL 2023; 17:185-194. [PMID: 36273241 PMCID: PMC9589681 DOI: 10.1038/s41396-022-01332-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022]
Abstract
Establishing links between microbial diversity and environmental processes requires resolving the high degree of functional variation among closely related lineages or ecotypes. Here, we implement and validate an improved metagenomic approach that estimates the spatial biogeography and environmental regulation of ecotype-specific replication patterns (RObs) across ocean regions. A total of 719 metagenomes were analyzed from meridional Bio-GO-SHIP sections in the Atlantic and Indian Ocean. Accounting for sequencing bias and anchoring replication estimates in genome structure were critical for identifying physiologically relevant biological signals. For example, ecotypes within the dominant marine cyanobacteria Prochlorococcus exhibited distinct diel cycles in RObs that peaked between 19:00-22:00. Additionally, both Prochlorococcus ecotypes and ecotypes within the highly abundant heterotroph Pelagibacter (SAR11) demonstrated systematic biogeographies in RObs that differed from spatial patterns in relative abundance. Finally, RObs was significantly regulated by nutrient stress and temperature, and explained by differences in the genomic potential for nutrient transport, energy production, cell wall structure, and replication. Our results suggest that our new approach to estimating replication is reflective of gross population growth. Moreover, this work reveals that the interaction between adaptation and environmental change drives systematic variability in replication patterns across ocean basins that is ecotype-specific, adding an activity-based dimension to our understanding of microbial niche space.
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Affiliation(s)
- Alyse A Larkin
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - George I Hagstrom
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Melissa L Brock
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Nathan S Garcia
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Adam C Martiny
- Department of Earth System Science, University of California, Irvine, CA, USA.
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
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8
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Muñoz-Marín MDC, Duhamel S, Björkman KM, Magasin JD, Díez J, Karl DM, García-Fernández JM. Differential Timing for Glucose Assimilation in Prochlorococcus and Coexistent Microbial Populations in the North Pacific Subtropical Gyre. Microbiol Spectr 2022; 10:e0246622. [PMID: 36098532 PMCID: PMC9602893 DOI: 10.1128/spectrum.02466-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 01/04/2023] Open
Abstract
The marine cyanobacterium Prochlorococcus can utilize glucose as a source of carbon. However, the relative importance of inorganic and organic carbon assimilation and the timing of glucose assimilation are still poorly understood in these numerically dominant cyanobacteria. Here, we investigated whole microbial community and group-specific primary production and glucose assimilation using incubations with radioisotopes combined with flow cytometry cell sorting. We also studied changes in the microbial community structure in response to glucose enrichments and analyzed the transcription of Prochlorocccus genes involved in carbon metabolism and photosynthesis. Our results showed a diel variation for glucose assimilation in Prochlorococcus, with maximum assimilation at midday and minimum at midnight (~2-fold change), which was different from that of the total microbial community. This suggests that the timing in glucose assimilation in Prochlorococcus is coupled to photosynthetic light reactions producing energy, it being more convenient for Prochlorococcus to show maximum glucose uptake precisely when the rest of microbial populations have their minimum glucose uptake. Many transcriptional responses to glucose enrichment occurred after 12- and 24-h periods, but community composition did not change. High-light Prochlorococcus strains were the most impacted by glucose addition, with transcript-level increases observed for genes in pathways for glucose metabolism, such as the pentose phosphate pathway, the Entner-Doudoroff pathway, glycolysis, respiration, and glucose transport. While Prochlorococcus C assimilation from glucose represented less than 0.1% of the bacterium's photosynthetic C fixation, increased assimilation during the day and glcH gene upregulation upon glucose enrichment indicate an important role of mixotrophic C assimilation by natural populations of Prochlorococcus. IMPORTANCE Several studies have demonstrated that Prochlorococcus, the most abundant photosynthetic organism on Earth, can assimilate organic molecules, such as amino acids, amino sugars, ATP, phosphonates, and dimethylsulfoniopropionate. This autotroph can also assimilate small amounts of glucose, supporting the hypothesis that Prochlorococcus is mixotrophic. Our results show, for the first time, a diel variability in glucose assimilation by natural populations of Prochlorococcus with maximum assimilation during midday. Based on our previous results, this indicates that Prochlorococcus could maximize glucose uptake by using ATP made during the light reactions of photosynthesis. Furthermore, Prochlorococcus showed a different timing of glucose assimilation from the total population, which may offer considerable fitness advantages over competitors "temporal niches." Finally, we observed transcriptional changes in some of the genes involved in carbon metabolism, suggesting that Prochlorococcus can use both pathways previously proposed in cyanobacteria to metabolize glucose.
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Affiliation(s)
- María del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Solange Duhamel
- Lamont-Doherty Earth Observatory of Columbia University, Division of Biology and Paleo Environment, Palisades, New York, USA
| | - Karin M. Björkman
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii at Manoa, C-MORE Hale, Honolulu, Hawaii, USA
| | - Jonathan D. Magasin
- Ocean Sciences Department, University of California, Santa Cruz, California, USA
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - David M. Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii at Manoa, C-MORE Hale, Honolulu, Hawaii, USA
| | - José M. García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
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Antosiak A, Šulčius S, Malec P, Tokodi N, Łobodzińska A, Dziga D. Cyanophage infections reduce photosynthetic activity and expression of CO 2 fixation genes in the freshwater bloom-forming cyanobacterium Aphanizomenon flos-aquae. HARMFUL ALGAE 2022; 116:102215. [PMID: 35710200 DOI: 10.1016/j.hal.2022.102215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria play a significant role in ecosystem functioning as photosynthetic and CO2 fixing microorganisms. Whether and to what extent cyanophages alter these carbon and energy cycles in their cyanobacterial hosts is still poorly understood. In this study, we investigated changes in photosynthetic activity (PSII), expression of genes associated with the light phase of photosynthesis (psbA, petA, ndhK) and carbon metabolism (rbcL, zwf) as well as intracellular ATP and NADHP concentrations in freshwater bloom-forming filamentous cyanobacterium Aphanizomenon flos-aquae infected by cyanophage vB_AphaS-CL131. We found that PSII activity and expression level of rbcL genes, indicating potential for CO2 fixation, had decreased in response to cyanophage adsorption and DNA injection. During the period of viral DNA replication and assembly, PSII performance and gene expression remained at this decreased level and did not change significantly, indicating lack of transcriptional shutdown by the cyanophage. Combined, these observations suggest that although there is little to no interference between cyanophage DNA replication, host transcription and cellular metabolism, A. flos-aquae underwent a physiological state-shift toward lower efficiency of carbon and energy cycling. This further suggest potential cascading effect for co-occurring non-infected members of the microbial community.
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Affiliation(s)
- Adam Antosiak
- Laboratory of Metabolomics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland.
| | - Sigitas Šulčius
- Laboratory of Algology and Microbial Ecology, Nature Research Centre, Akademijos str. 2, 08412 Vilnius, Lithuania.
| | - Przemysław Malec
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland.
| | - Nada Tokodi
- Laboratory of Metabolomics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland; Department of Biology and Ecology, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia.
| | - Antonia Łobodzińska
- Laboratory of Metabolomics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland.
| | - Dariusz Dziga
- Laboratory of Metabolomics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland.
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10
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Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B, Pandey R. Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome. Microbiol Spectr 2022; 10:e0231121. [PMID: 35579429 PMCID: PMC9241827 DOI: 10.1128/spectrum.02311-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/17/2022] [Indexed: 12/13/2022] Open
Abstract
The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.
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Affiliation(s)
- Priti Devi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Uzma Shamim
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aanchal Yadav
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Akshay Kanakan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kriti Khare
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Janani Srinivasa Vasudevan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Shweta Sahni
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Pallavi Mishra
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Akansha Tyagi
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sujeet Jha
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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11
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Rijo-Ferreira F, Takahashi JS. Circadian rhythms in infectious diseases and symbiosis. Semin Cell Dev Biol 2022; 126:37-44. [PMID: 34625370 PMCID: PMC9183220 DOI: 10.1016/j.semcdb.2021.09.004] [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: 05/20/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 10/20/2022]
Abstract
Timing is everything. Many organisms across the tree of life have evolved timekeeping mechanisms that regulate numerous of their cellular functions to optimize timing by anticipating changes in the environment. The specific environmental changes that are sensed depends on the organism. For animals, plants, and free-living microbes, environmental cues include light/dark cycles, daily temperature fluctuations, among others. In contrast, for a microbe that is never free-living, its rhythmic environment is its host's rhythmic biology. Here, we describe recent research on the interactions between hosts and microbes, from the perspective both of symbiosis as well as infections. In addition to describing the biology of the microbes, we focus specifically on how circadian clocks modulate these host-microbe interactions.
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Affiliation(s)
- Filipa Rijo-Ferreira
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States.
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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12
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Heller P. Diel gene expression improves software prediction of cyanobacterial operons. PeerJ 2022; 10:e13259. [PMID: 35433132 PMCID: PMC9009326 DOI: 10.7717/peerj.13259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/22/2022] [Indexed: 01/13/2023] Open
Abstract
Cyanobacteria are important participants in global biogeochemical process, but their metabolic processes and genomic functions are incompletely understood. In particular, operon structure, which can provide valuable metabolic and genomic insight, is difficult to determine experimentally, and algorithmic operon predictions probably underestimate actual operon extent. A software method is presented for enhancing current operon predictions by incorporating information from whole-genome time-series expression studies, using a Machine Learning classifier. Results are presented for the marine cyanobacterium Crocosphaera watsonii. A total of 15 operon enhancements are proposed. The source code is publicly available.
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13
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Prochlorococcus Exudate Stimulates Heterotrophic Bacterial Competition with Rival Phytoplankton for Available Nitrogen. mBio 2022; 13:e0257121. [PMID: 35012332 PMCID: PMC8749424 DOI: 10.1128/mbio.02571-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine cyanobacterium Prochlorococcus numerically dominates the phytoplankton community of the nutrient-limited open ocean, establishing itself as the most abundant photosynthetic organism on Earth. This ecological success has been attributed to lower cell quotas for limiting nutrients, superior resource acquisition, and other advantages associated with cell size reduction and genome streamlining. In this study, we tested the prediction that Prochlorococcus outcompetes its rivals for scarce nutrients and that this advantage leads to its numerical success in nutrient-limited waters. Strains of Prochlorococcus and its sister genus Synechococcus grew well in both mono- and cocultures when nutrients were replete. However, in nitrogen-limited medium, Prochlorococcus outgrew Synechococcus but only when heterotrophic bacteria were also present. In the nitrogen-limited medium, the heterotroph Alteromonas macleodii outcompeted Synechococcus for nitrogen but only if stimulated by the exudate released by Prochlorococcus or if a proxy organic carbon source was provided. Genetic analysis of Alteromonas suggested that it outcompetes Synechococcus for nitrate and/or nitrite, during which cocultured Prochlorococcus grows on ammonia or other available nitrogen species. We propose that Prochlorococcus can stimulate antagonism between heterotrophic bacteria and potential phytoplankton competitors through a metabolic cross-feeding interaction, and this stimulation could contribute to the numerical success of Prochlorococcus in nutrient-limited regions of the ocean. IMPORTANCE In nutrient-poor habitats, competition for limited resources is thought to select for organisms with an enhanced ability to scavenge nutrients and utilize them efficiently. Such adaptations characterize the cyanobacterium Prochlorococcus, the most abundant photosynthetic organism in the nutrient-limited open ocean. In this study, the competitive superiority of Prochlorococcus over a rival cyanobacterium, Synechococcus, was captured in laboratory culture. Critically, this outcome was achieved only when key aspects of the open ocean were simulated: a limited supply of nitrogen and the presence of heterotrophic bacteria. The results indicate that Prochlorococcus promotes its numerical dominance over Synechococcus by energizing the heterotroph's ability to outcompete Synechococcus for available nitrogen. This study demonstrates how interactions between trophic groups can influence interactions within trophic groups and how these interactions likely contribute to the success of the most abundant photosynthetic microorganism.
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14
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Mattern JP, Glauninger K, Britten GL, Casey JR, Hyun S, Wu Z, Armbrust EV, Harchaoui Z, Ribalet F. A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series. PLoS Comput Biol 2022; 18:e1009733. [PMID: 35030163 PMCID: PMC8794270 DOI: 10.1371/journal.pcbi.1009733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/27/2022] [Accepted: 12/08/2021] [Indexed: 11/19/2022] Open
Abstract
The rates of cell growth, division, and carbon loss of microbial populations are key parameters for understanding how organisms interact with their environment and how they contribute to the carbon cycle. However, the invasive nature of current analytical methods has hindered efforts to reliably quantify these parameters. In recent years, size-structured matrix population models (MPMs) have gained popularity for estimating division rates of microbial populations by mechanistically describing changes in microbial cell size distributions over time. Motivated by the mechanistic structure of these models, we employ a Bayesian approach to extend size-structured MPMs to capture additional biological processes describing the dynamics of a marine phytoplankton population over the day-night cycle. Our Bayesian framework is able to take prior scientific knowledge into account and generate biologically interpretable results. Using data from an exponentially growing laboratory culture of the cyanobacterium Prochlorococcus, we isolate respiratory and exudative carbon losses as critical parameters for the modeling of their population dynamics. The results suggest that this modeling framework can provide deeper insights into microbial population dynamics provided by size distribution time-series data.
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Affiliation(s)
- Jann Paul Mattern
- Ocean Sciences Department, UC Santa Cruz, Santa Cruz, California, United States of America
| | - Kristof Glauninger
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
| | - Gregory L. Britten
- Program in Atmospheres, Oceans, and Climate, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - John R. Casey
- Program in Atmospheres, Oceans, and Climate, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Oceanography, University of Hawai‘i at Manoa, Honolulu, Hawaii, United States of America
| | - Sangwon Hyun
- Department of Data Sciences and Operations, University of Southern California, Los Angeles, California, United States of America
| | - Zhen Wu
- Program in Atmospheres, Oceans, and Climate, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - E. Virginia Armbrust
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - Zaid Harchaoui
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
| | - François Ribalet
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
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15
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Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O 2 Cyanobacterial Mat Community. mSystems 2021; 6:e0104221. [PMID: 34874776 PMCID: PMC8651085 DOI: 10.1128/msystems.01042-21] [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] [Indexed: 11/20/2022] Open
Abstract
Cyanobacterial mats profoundly influenced Earth’s biological and geochemical evolution and still play important ecological roles in the modern world. However, the biogeochemical functioning of cyanobacterial mats under persistent low-O2 conditions, which dominated their evolutionary history, is not well understood. To investigate how different metabolic and biogeochemical functions are partitioned among community members, we conducted metagenomics and metatranscriptomics on cyanobacterial mats in the low-O2, sulfidic Middle Island sinkhole (MIS) in Lake Huron. Metagenomic assembly and binning yielded 144 draft metagenome assembled genomes, including 61 of medium quality or better, and the dominant cyanobacteria and numerous Proteobacteria involved in sulfur cycling. Strains of a Phormidium autumnale-like cyanobacterium dominated the metagenome and metatranscriptome. Transcripts for the photosynthetic reaction core genes psaA and psbA were abundant in both day and night. Multiple types of psbA genes were expressed from each cyanobacterium, and the dominant psbA transcripts were from an atypical microaerobic type of D1 protein from Phormidium. Further, cyanobacterial transcripts for photosystem I genes were more abundant than those for photosystem II, and two types of Phormidium sulfide quinone reductase were recovered, consistent with anoxygenic photosynthesis via photosystem I in the presence of sulfide. Transcripts indicate active sulfur oxidation and reduction within the cyanobacterial mat, predominately by Gammaproteobacteria and Deltaproteobacteria, respectively. Overall, these genomic and transcriptomic results link specific microbial groups to metabolic processes that underpin primary production and biogeochemical cycling in a low-O2 cyanobacterial mat and suggest mechanisms for tightly coupled cycling of oxygen and sulfur compounds in the mat ecosystem. IMPORTANCE Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyanobacterial mats were critical agents of Earth’s biological and chemical evolution through geological time, little is known about how they function under the low-oxygen conditions that characterized most of their natural history. Here, we performed sequencing of the DNA and RNA of modern cyanobacterial mat communities under low-oxygen and sulfur-rich conditions from the Middle Island sinkhole in Lake Huron. The results reveal the organisms and metabolic pathways that are responsible for both oxygen-producing and non-oxygen-producing photosynthesis as well as interconversions of sulfur that likely shape how much O2 is produced in such ecosystems. These findings indicate tight metabolic reactions between community members that help to explain the limited the amount of O2 produced in cyanobacterial mat ecosystems.
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16
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Coe A, Biller SJ, Thomas E, Boulias K, Bliem C, Arellano A, Dooley K, Rasmussen AN, LeGault K, O'Keefe TJ, Stover S, Greer EL, Chisholm SW. Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation. LIMNOLOGY AND OCEANOGRAPHY 2021; 66:3300-3312. [PMID: 34690365 PMCID: PMC8518828 DOI: 10.1002/lno.11880] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/22/2021] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
The picocyanobacteria Prochlorococcus and Synechococcus are found throughout the ocean's euphotic zone, where the daily light:dark cycle drives their physiology. Periodic deep mixing events can, however, move cells below this region, depriving them of light for extended periods of time. Here, we demonstrate that members of these genera can adapt to tolerate repeated periods of light energy deprivation. Strains kept in the dark for 3 d and then returned to the light initially required 18-26 d to resume growth, but after multiple rounds of dark exposure they began to regrow after only 1-2 d. This dark-tolerant phenotype was stable and heritable; some cultures retained the trait for over 132 generations even when grown in a standard 13:11 light:dark cycle. We found no genetic differences between the dark-tolerant and parental strains of Prochlorococcus NATL2A, indicating that an epigenetic change is likely responsible for the adaptation. To begin to explore this possibility, we asked whether DNA methylation-one potential mechanism mediating epigenetic inheritance in bacteria-occurs in Prochlorococcus. LC-MS/MS analysis showed that while DNA methylations, including 6 mA and 5 mC, are found in some other Prochlorococcus strains, there were no methylations detected in either the parental or dark-tolerant NATL2A strains. These findings suggest that Prochlorococcus utilizes a yet-to-be-determined epigenetic mechanism to adapt to the stress of extended light energy deprivation, and highlights phenotypic heterogeneity as an additional dimension of Prochlorococcus diversity.
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Affiliation(s)
- Allison Coe
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Steven J. Biller
- Department of Biological SciencesWellesley CollegeWellesleyMassachusettsUSA
| | - Elaina Thomas
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Konstantinos Boulias
- Division of Newborn MedicineBoston Children's HospitalBostonMassachusettsUSA
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
| | - Christina Bliem
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Aldo Arellano
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Keven Dooley
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Anna N. Rasmussen
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Kristen LeGault
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Tyler J. O'Keefe
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Sarah Stover
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Eric L. Greer
- Division of Newborn MedicineBoston Children's HospitalBostonMassachusettsUSA
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
| | - Sallie W. Chisholm
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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17
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Jacobson TB, Callaghan MM, Amador-Noguez D. Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 2021; 75:515-539. [PMID: 34348026 DOI: 10.1146/annurev-micro-060621-043448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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18
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Bilcke G, Osuna-Cruz CM, Santana Silva M, Poulsen N, D'hondt S, Bulankova P, Vyverman W, De Veylder L, Vandepoele K. Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:315-336. [PMID: 33901335 DOI: 10.1111/tpj.15291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Coastal regions contribute an estimated 20% of annual gross primary production in the oceans, despite occupying only 0.03% of their surface area. Diatoms frequently dominate coastal sediments, where they experience large variations in light regime resulting from the interplay of diurnal and tidal cycles. Here, we report on an extensive diurnal transcript profiling experiment of the motile benthic diatom Seminavis robusta. Nearly 90% (23 328) of expressed protein-coding genes and 66.9% (1124) of expressed long intergenic non-coding RNAs showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24 h. Phylostratigraphic analysis found that rhythmic genes are enriched in highly conserved genes, while diatom-specific genes are predominantly associated with midnight expression. Integration of genetic and physiological cell cycle markers with silica depletion data revealed potential new silica cell wall-associated gene families specific to diatoms. Additionally, we observed 1752 genes with a remarkable semidiurnal (12-h) periodicity, while the expansion of putative circadian transcription factors may reflect adaptations to cope with highly unpredictable external conditions. Taken together, our results provide new insights into the adaptations of diatoms to the benthic environment and serve as a valuable resource for the study of diurnal regulation in photosynthetic eukaryotes.
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Affiliation(s)
- Gust Bilcke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, Ghent, 9000, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, 9000, Belgium
| | - Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
| | - Marta Santana Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Nicole Poulsen
- B CUBE Center for Molecular Bioengineering, Technical University of Dresden, Tatzberg 41, Dresden, 01307, Germany
| | - Sofie D'hondt
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, Ghent, 9000, Belgium
| | - Petra Bulankova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Wim Vyverman
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, Ghent, 9000, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
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19
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Ofaim S, Sulheim S, Almaas E, Sher D, Segrè D. Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus. Front Genet 2021; 12:586293. [PMID: 33633777 PMCID: PMC7900632 DOI: 10.3389/fgene.2021.586293] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 01/14/2021] [Indexed: 12/02/2022] Open
Abstract
Microbial life in the oceans impacts the entire marine ecosystem, global biogeochemistry and climate. The marine cyanobacterium Prochlorococcus, an abundant component of this ecosystem, releases a significant fraction of the carbon fixed through photosynthesis, but the amount, timing and molecular composition of released carbon are still poorly understood. These depend on several factors, including nutrient availability, light intensity and glycogen storage. Here we combine multiple computational approaches to provide insight into carbon storage and exudation in Prochlorococcus. First, with the aid of a new algorithm for recursive filling of metabolic gaps (ReFill), and through substantial manual curation, we extended an existing genome-scale metabolic model of Prochlorococcus MED4. In this revised model (iSO595), we decoupled glycogen biosynthesis/degradation from growth, thus enabling dynamic allocation of carbon storage. In contrast to standard implementations of flux balance modeling, we made use of forced influx of carbon and light into the cell, to recapitulate overflow metabolism due to the decoupling of photosynthesis and carbon fixation from growth during nutrient limitation. By using random sampling in the ensuing flux space, we found that storage of glycogen or exudation of organic acids are favored when the growth is nitrogen limited, while exudation of amino acids becomes more likely when phosphate is the limiting resource. We next used COMETS to simulate day-night cycles and found that the model displays dynamic glycogen allocation and exudation of organic acids. The switch from photosynthesis and glycogen storage to glycogen depletion is associated with a redistribution of fluxes from the Entner–Doudoroff to the Pentose Phosphate pathway. Finally, we show that specific gene knockouts in iSO595 exhibit dynamic anomalies compatible with experimental observations, further demonstrating the value of this model as a tool to probe the metabolic dynamic of Prochlorococcus.
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Affiliation(s)
- Shany Ofaim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Snorre Sulheim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Daniel Sher
- Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Daniel Segrè
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biomedical Engineering, Boston University, Boston, MA, United States.,Department of Physics, Boston University, Boston, MA, United States.,Department of Biology, Boston University, Boston, MA, United States
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20
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Mairet F, Bayen T. The promise of dawn: Microalgae photoacclimation as an optimal control problem of resource allocation. J Theor Biol 2021; 515:110597. [PMID: 33476606 DOI: 10.1016/j.jtbi.2021.110597] [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: 09/07/2020] [Revised: 12/11/2020] [Accepted: 01/14/2021] [Indexed: 11/19/2022]
Abstract
Photosynthetic microorganisms are known to adjust their photosynthetic capacity according to light intensity. This so-called photoacclimation process is thought to maximize growth at equilibrium, but its dynamics under varying conditions remains less understood. To tackle this problem, microalgae growth and photoacclimation are represented by a (coarse-grained) resource allocation model. Using optimal control theory (the Pontryagin maximum principle) and numerical simulations, we determine the optimal strategy of resource allocation to maximize microalgal growth rate over a time horizon. We show that, after a transient, the optimal trajectory approaches the optimal steady state, a behavior known as the turnpike property. Then, a bi-level optimization problem is solved numerically to estimate model parameters from experimental data. The fitted trajectory represents well a Dunaliella tertiolecta culture facing a light down-shift. Finally, we study photoacclimation dynamics under day/night cycle. In the optimal trajectory, the synthesis of the photosynthetic apparatus surprisingly starts a few hours before dawn. This anticipatory behavior has actually been observed both in the laboratory and in the field. This shows the algal predictive capacity and the interest of our method which predicts this phenomenon.
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Affiliation(s)
- Francis Mairet
- Ifremer, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311 Nantes, France.
| | - Térence Bayen
- Avignon Université, Laboratoire de Mathématiques d'Avignon (EA 2151), F-84018, France.
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21
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Tschoeke D, Salazar VW, Vidal L, Campeão M, Swings J, Thompson F, Thompson C. Unlocking the Genomic Taxonomy of the Prochlorococcus Collective. MICROBIAL ECOLOGY 2020; 80:546-558. [PMID: 32468160 DOI: 10.1007/s00248-020-01526-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.
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Affiliation(s)
- Diogo Tschoeke
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Vinicius W Salazar
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Livia Vidal
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Mariana Campeão
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Jean Swings
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
- Laboratory of Microbiology, Ghent University, Gent, Belgium
| | - Fabiano Thompson
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Cristiane Thompson
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil.
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22
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Predetermined clockwork microbial worlds: Current understanding of aquatic microbial diel response from model systems to complex environments. ADVANCES IN APPLIED MICROBIOLOGY 2020; 113:163-191. [PMID: 32948266 DOI: 10.1016/bs.aambs.2020.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In the photic zone of aquatic ecosystems, microorganisms with different metabolisms and their viruses form complex interactions and food webs. Within these interactions, phototrophic microorganisms such as eukaryotic microalgae and cyanobacteria interact directly with sunlight, and thereby generate circadian rhythms. Diel cycling originally generated in microbial phototrophs is directly transmitted toward heterotrophic microorganisms utilizing the photosynthetic products as they are excreted or exuded. Such diel cycling seems to be indirectly propagated toward heterotrophs as a result of complex biotic interactions. For example, cell death of phototrophic microorganisms induced by viral lysis and protistan grazing provides additional resources of dissolved organic matter to the microbial community, and so generates diel cycling in other heterotrophs with different nutrient dependencies. Likewise, differences in the diel transmitting pathway via complex interactions among heterotrophs, and between heterotrophs and their viruses, may also generate higher variation and time lag diel rhythms in different heterotrophic taxa. Thus, sunlight and photosynthesis not only contribute energy and carbon supply, but also directly or indirectly control diel cycling of the microbial community through complex interactions in the photic zone of aquatic ecosystems.
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23
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Palacio AS, Cabello AM, García FC, Labban A, Morán XAG, Garczarek L, Alonso-Sáez L, López-Urrutia Á. Changes in Population Age-Structure Obscure the Temperature-Size Rule in Marine Cyanobacteria. Front Microbiol 2020; 11:2059. [PMID: 32983043 PMCID: PMC7485217 DOI: 10.3389/fmicb.2020.02059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 08/05/2020] [Indexed: 11/13/2022] Open
Abstract
The temperature-size Rule (TSR) states that there is a negative relationship between ambient temperature and body size. This rule has been independently evaluated for different phases of the life cycle in multicellular eukaryotes, but mostly for the average population in unicellular organisms. We acclimated two model marine cyanobacterial strains (Prochlorococcus marinus MIT9301 and Synechococcus sp. RS9907) to a gradient of temperatures and measured the changes in population age-structure and cell size along their division cycle. Both strains displayed temperature-dependent diel changes in cell size, and as a result, the relationship between temperature and average cell size varied along the day. We computed the mean cell size of new-born cells in order to test the prediction of the TSR on a single-growth stage. Our work reconciles previous inconsistent results when testing the TSR on unicellular organisms, and shows that when a single-growth stage is considered the predicted negative response to temperature is revealed.
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Affiliation(s)
- Antonio S. Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ana María Cabello
- Spanish Institute of Oceanography (IEO), Oceanographic Center of Malaga, Málaga, Spain
| | - Francisca C. García
- Environment and Sustainability Institute, University of Exeter, Exeter, United Kingdom
| | - Abbrar Labban
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
| | - Xosé Anxelu G. Morán
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
- Spanish Institute of Oceanography (IEO), Oceanographic Center of Gijón/Xixón, Gijón, Spain
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Roscoff, France
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ángel López-Urrutia
- Spanish Institute of Oceanography (IEO), Oceanographic Center of Gijón/Xixón, Gijón, Spain
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24
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Prochlorococcus Cells Rely on Microbial Interactions Rather than on Chlorotic Resting Stages To Survive Long-Term Nutrient Starvation. mBio 2020; 11:mBio.01846-20. [PMID: 32788385 PMCID: PMC7439483 DOI: 10.1128/mbio.01846-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The ability of microorganisms to withstand long periods of nutrient starvation is key to their survival and success under highly fluctuating conditions that are common in nature. Therefore, one would expect this trait to be prevalent among organisms in the nutrient-poor open ocean. Here, we show that this is not the case for Prochlorococcus, a globally abundant and ecologically important marine cyanobacterium. Instead, Prochlorococcus relies on co-occurring heterotrophic bacteria to survive extended phases of nutrient and light starvation. Our results highlight the power of microbial interactions to drive major biogeochemical cycles in the ocean and elsewhere with consequences at the global scale. Many microorganisms produce resting cells with very low metabolic activity that allow them to survive phases of prolonged nutrient or energy stress. In cyanobacteria and some eukaryotic phytoplankton, the production of resting stages is accompanied by a loss of photosynthetic pigments, a process termed chlorosis. Here, we show that a chlorosis-like process occurs under multiple stress conditions in axenic laboratory cultures of Prochlorococcus, the dominant phytoplankton linage in large regions of the oligotrophic ocean and a global key player in ocean biogeochemical cycles. In Prochlorococcus strain MIT9313, chlorotic cells show reduced metabolic activity, measured as C and N uptake by Nanoscale secondary ion mass spectrometry (NanoSIMS). However, unlike many other cyanobacteria, chlorotic Prochlorococcus cells are not viable and do not regrow under axenic conditions when transferred to new media. Nevertheless, cocultures with a heterotrophic bacterium, Alteromonas macleodii HOT1A3, allowed Prochlorococcus to survive nutrient starvation for months. We propose that reliance on co-occurring heterotrophic bacteria, rather than the ability to survive extended starvation as resting cells, underlies the ecological success of Prochlorococcus.
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25
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Guyet U, Nguyen NA, Doré H, Haguait J, Pittera J, Conan M, Ratin M, Corre E, Le Corguillé G, Brillet-Guéguen L, Hoebeke M, Six C, Steglich C, Siegel A, Eveillard D, Partensky F, Garczarek L. Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803. Front Microbiol 2020; 11:1707. [PMID: 32793165 PMCID: PMC7393227 DOI: 10.3389/fmicb.2020.01707] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022] Open
Abstract
Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.
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Affiliation(s)
- Ulysse Guyet
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Ngoc A Nguyen
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Hugo Doré
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Julie Haguait
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Justine Pittera
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Maël Conan
- DYLISS (INRIA-IRISA)-INRIA, CNRS UMR 6074, Université de Rennes 1, Rennes, France
| | - Morgane Ratin
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Erwan Corre
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Gildas Le Corguillé
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Loraine Brillet-Guéguen
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France.,CNRS, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Mark Hoebeke
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Christophe Six
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | | | - Anne Siegel
- DYLISS (INRIA-IRISA)-INRIA, CNRS UMR 6074, Université de Rennes 1, Rennes, France
| | - Damien Eveillard
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Frédéric Partensky
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Laurence Garczarek
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
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26
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Kawamoto N, Ito H, Tokuda IT, Iwasaki H. Damped circadian oscillation in the absence of KaiA in Synechococcus. Nat Commun 2020; 11:2242. [PMID: 32382052 PMCID: PMC7205874 DOI: 10.1038/s41467-020-16087-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 04/09/2020] [Indexed: 01/05/2023] Open
Abstract
Proteins KaiA, KaiB and KaiC constitute a biochemical circadian oscillator in the cyanobacterium Synechococcus elongatus. It has been reported kaiA inactivation completely abolishes circadian oscillations. However, we show here that kaiBC promoter activity exhibits a damped, low-amplitude oscillation with a period of approximately 24 h in kaiA-inactivated strains. The damped rhythm resonates with external cycles with a period of 24–26 h, indicating that its natural frequency is similar to that of the circadian clock. Double-mutation experiments reveal that kaiC, kaiB, and sasA (encoding a KaiC-binding histidine kinase) are all required for the damped oscillation. Further analysis suggests that the kaiA-less damped transcriptional rhythm requires KaiB-KaiC complex formation and the transcription-translation feedback loop, but not the KaiC phosphorylation cycle. Our results provide insights into mechanisms that could potentially underlie the diurnal/circadian behaviors observed in other bacterial species that possess kaiB and kaiC homologues but lack a kaiA homologue. Proteins KaiA, KaiB and KaiC constitute a biochemical circadian oscillator in Synechococcus cyanobacteria. Here, Kawamoto et al. show that kaiBC promoter activity exhibits a damped, low-amplitude circadian oscillation in the absence of KaiA, which could explain the circadian rhythms observed in other bacteria that lack a kaiA homologue.
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Affiliation(s)
- Naohiro Kawamoto
- Department of Electrical Engineering and Biological Science, Waseda University, Tokyo, 162-0056, Japan
| | - Hiroshi Ito
- Faculty of Design, Kyushu University, Fukuoka, 815-8540, Japan
| | - Isao T Tokuda
- Graduate School of Science and Engineering, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Hideo Iwasaki
- Department of Electrical Engineering and Biological Science, Waseda University, Tokyo, 162-0056, Japan.
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27
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Shilova IN, Magasin JD, Mills MM, Robidart JC, Turk-Kubo KA, Zehr JP. Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system. PLoS One 2020; 15:e0231771. [PMID: 32310982 PMCID: PMC7170224 DOI: 10.1371/journal.pone.0231771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/31/2020] [Indexed: 11/18/2022] Open
Abstract
Marine phytoplankton are responsible for approximately half of photosynthesis on Earth. However, their ability to drive ocean productivity depends on critical nutrients, especially bioavailable nitrogen (N) which is scarce over vast areas of the ocean. Phytoplankton differ in their preferences for N substrates as well as uptake efficiencies and minimal N requirements relative to other critical nutrients, including iron (Fe) and phosphorus. In this study, we used the MicroTOOLs high-resolution environmental microarray to examine transcriptomic responses of phytoplankton communities in the California Current System (CCS) transition zone to added urea, ammonium, nitrate, and also Fe in the late summer when N depletion is common. Transcript level changes of photosynthetic, carbon fixation, and nutrient stress genes indicated relief of N limitation in many strains of Prochlorococcus, Synechococcus, and eukaryotic phytoplankton. The transcriptomic responses helped explain shifts in physiological and growth responses observed later. All three phytoplankton groups had increased transcript levels of photosynthesis and/or carbon fixation genes in response to all N substrates. However, only Prochlorococcus had decreased transcript levels of N stress genes and grew substantially, specifically after urea and ammonium additions, suggesting that Prochlorococcus outcompeted other community members in these treatments. Diatom transcript levels of carbon fixation genes increased in response to Fe but not to Fe with N which might have favored phytoplankton that were co-limited by N and Fe. Moreover, transcription patterns of closely related strains indicated variability in N utilization, including nitrate utilization by some high-light adapted Prochlorococcus. Finally, up-regulation of urea transporter genes by both Prochlorococcus and Synechococcus in response to filtered deep water suggested a regulatory mechanism other than classic control via the global N regulator NtcA. This study indicated that co-existing phytoplankton strains experience distinct nutrient stresses in the transition zone of the CCS, an understudied region where oligotrophic and coastal communities naturally mix.
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Affiliation(s)
- Irina N. Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (INS); (JPZ)
| | - Jonathan D. Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Matthew M. Mills
- Department of Earth System Science, Stanford University, Stanford, California, United States of America
| | - Julie C. Robidart
- Ocean Technology and Engineering, National Oceanography Centre, Southampton, England, United Kingdom
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (INS); (JPZ)
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28
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Linking Light-Dependent Life History Traits with Population Dynamics for Prochlorococcus and Cyanophage. mSystems 2020; 5:5/2/e00586-19. [PMID: 32234774 PMCID: PMC7112961 DOI: 10.1128/msystems.00586-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prochlorococcus cyanobacteria grow in diurnal rhythms driven by diel cycles. Their ecology depends on light, nutrients, and top-down mortality processes, including lysis by viruses. Cyanophage, viruses that infect cyanobacteria, are also impacted by light. For example, the extracellular viability and intracellular infection kinetics of some cyanophage vary between light and dark conditions. Nonetheless, it remains unclear whether light-dependent viral life history traits scale up to influence population-level dynamics. Here, we examined the impact of diel forcing on both cellular- and population-scale dynamics in multiple Prochlorococcus-phage systems. To do so, we developed a light-driven population model, including both cellular growth and viral infection dynamics. We then tested the model against measurements of experimental infection dynamics with diel forcing to examine the extent to which population level changes in both viral and host abundances could be explained by light-dependent life history traits. Model-data integration reveals that light-dependent adsorption can improve fits to population dynamics for some virus-host pairs. However, light-dependent variation alone does not fully explain realized host and virus population dynamics. Instead, we show evidence consistent with lysis saturation at relatively high virus-to-cell ratios. Altogether, our study represents a quantitative approach to integrate mechanistic models to reconcile Prochlorococcus-virus dynamics spanning cellular-to-population scales.IMPORTANCE The cyanobacterium Prochlorococcus is an essential member of global ocean ecosystems. Light rhythms drive Prochlorococcus photosynthesis, ecology, and interactions with potentially lethal viruses. At present, the impact of light on Prochlorococcus-virus interactions is not well understood. Here, we analyzed Prochlorococcus and virus population dynamics with a light-driven population model and compared our results with experimental data. Our approach revealed that light profoundly drives both cellular- and population-level dynamics for some host-virus systems. However, we also found that additional mechanisms, including lysis saturation, are required to explain observed host-virus dynamics at the population scale. This study provides the basis for future work to understand the intertwined fates of Prochlorococcus and associated viruses in the surface ocean.
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29
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Alonso-Sáez L, Morán XAG, González JM. Transcriptional Patterns of Biogeochemically Relevant Marker Genes by Temperate Marine Bacteria. Front Microbiol 2020; 11:465. [PMID: 32265888 PMCID: PMC7098952 DOI: 10.3389/fmicb.2020.00465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
Environmental microbial gene expression patterns remain largely unexplored, particularly at interannual time scales. We analyzed the variability in the expression of marker genes involved in ecologically relevant biogeochemical processes at a temperate Atlantic site over two consecutive years. Most of nifH transcripts, involved in nitrogen (N) fixation, were affiliated with the symbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa, suggesting a key role as N providers in this system. The expression of nifH and amoA (i.e., marker for ammonia oxidation) showed consistent maxima in summer and autumn, respectively, suggesting a temporal succession of these important N cycling processes. The patterns of expression of genes related to the oxidation of carbon monoxide (coxL) and reduced sulfur (soxB) were different from that of amoA, indicating alternate timings for these energy conservation strategies. We detected expression of alkaline phosphatases, induced under phosphorus limitation, in agreement with the reported co-limitation by this nutrient at the study site. In contrast, low-affinity phosphate membrane transporters (pit) typically expressed under phosphorus luxury conditions, were mainly detected in post-bloom conditions. Rhodobacteraceae dominated the expression of soxB, coxL and ureases, while Pelagibacteraceae dominated the expression of proteorhodopsins. Bacteroidetes and Gammaproteobacteria were major contributors to the uptake of inorganic nutrients (pit and amt transporters). Yet, in autumn, Thauma- and Euryarchaeota unexpectedly contributed importantly to the uptake of ammonia and phosphate, respectively. We provide new hints on the active players and potential dynamics of ecologically relevant functions in situ, highlighting the potential of metatranscriptomics to provide significant input to future omics-driven marine ecosystem assessment.
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Affiliation(s)
- Laura Alonso-Sáez
- Marine Research Division, AZTI, Sukarrieta, Spain.,Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía (IEO), Gijón/Xixón, Spain
| | - Xosé Anxelu G Morán
- Biological and Environmental Sciences and Engineering Division, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
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30
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Lambrecht SJ, Steglich C, Hess WR. A minimum set of regulators to thrive in the ocean. FEMS Microbiol Rev 2020; 44:232-252. [DOI: 10.1093/femsre/fuaa005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT
Marine cyanobacteria of the genus Prochlorococcus thrive in high cell numbers throughout the euphotic zones of the world's subtropical and tropical oligotrophic oceans, making them some of the most ecologically relevant photosynthetic microorganisms on Earth. The ecological success of these free-living phototrophs suggests that they are equipped with a regulatory system competent to address many different stress situations. However, Prochlorococcus genomes are compact and streamlined, with the majority encoding only five different sigma factors, five to six two-component systems and eight types of other transcriptional regulators. Here, we summarize the existing information about the functions of these protein regulators, about transcriptomic responses to defined stress conditions, and discuss the current knowledge about riboswitches, RNA-based regulation and the roles of certain metabolites as co-regulators. We focus on the best-studied isolate, Prochlorococcus MED4, but extend to other strains and ecotypes when appropriate, and we include some information gained from metagenomic and metatranscriptomic analyses.
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Affiliation(s)
- S Joke Lambrecht
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
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31
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Circadian clock helps cyanobacteria manage energy in coastal and high latitude ocean. ISME JOURNAL 2019; 14:560-568. [PMID: 31685937 DOI: 10.1038/s41396-019-0547-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 10/09/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
Abstract
The circadian clock coordinates cellular functions over the diel cycle in many organisms. The molecular mechanisms of the cyanobacterial clock are well characterized, but its ecological role remains a mystery. We present an agent-based model of Synechococcus (harboring a self-sustained, bona fide circadian clock) that explicitly represents genes (e.g., kaiABC), transcripts, proteins, and metabolites. The model is calibrated to data from laboratory experiments with wild type and no-clock mutant strains, and it successfully reproduces the main observed patterns of glycogen metabolism. Comparison of wild type and no-clock mutant strains suggests a main benefit of the clock is due to energy management. For example, it inhibits glycogen synthesis early in the day when it is not needed and energy is better used for making the photosynthesis apparatus. To explore the ecological role of the clock, we integrate the model into a dynamic, three-dimensional global circulation model that includes light variability due to seasonal and diel incident radiation and vertical extinction. Model output is compared with field data, including in situ gene transcript levels. We simulate cyanobaceria with and without a circadian clock, which allows us to quantify the fitness benefit of the clock. Interestingly, the benefit is weakest in the low latitude open ocean, where Prochlorococcus (lacking a self-sustained clock) dominates. However, our attempt to experimentally validate this testable prediction failed. Our study provides insights into the role of the clock and an example for how models can be used to integrate across multiple levels of biological organization.
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Vislova A, Sosa OA, Eppley JM, Romano AE, DeLong EF. Diel Oscillation of Microbial Gene Transcripts Declines With Depth in Oligotrophic Ocean Waters. Front Microbiol 2019; 10:2191. [PMID: 31608031 PMCID: PMC6769238 DOI: 10.3389/fmicb.2019.02191] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/06/2019] [Indexed: 11/13/2022] Open
Abstract
Diel oscillations in primary and secondary production, growth, metabolic activity, and gene expression commonly occur in marine microbial communities in ocean surface waters. Diel periodicity of gene transcription has been demonstrated in photoautotrophic and heterotrophic microbes in both coastal and open ocean environments. To better define the spatiotemporal distribution and patterns of these daily oscillations, we investigated how diel periodicity in gene transcripts changed with depth from the surface waters to the upper mesopelagic. We postulated that diel oscillation of transcript abundances would diminish at greater depths across the collective microbial community due to decreasing light availability. The results showed that the number and total proportion of gene transcripts and taxa exhibiting diel periodicity were greatest in the shallow sunlit mixed layer, diminished rapidly with increasing depth to the base of the euphotic zone, and could not be detected in the mesopelagic. The results confirmed an overall decrease in microbial diel transcript oscillation with depth through the euphotic zone and suggested a relationship between abundance of diel oscillating transcripts and the daily integrated light exposure experienced by planktonic microbes in the water column. Local dissolved macronutrient concentration also appeared to influence the diel transcriptional patterns of specific microbial genes. The diminishing diel transcript oscillations found at increasing depths suggest that diel patterns of other microbial processes and interactions may likewise be attenuated at depth.
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Affiliation(s)
- Alice Vislova
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States
| | - Oscar A Sosa
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States
| | - Anna E Romano
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States
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Form III RubisCO-mediated transaldolase variant of the Calvin cycle in a chemolithoautotrophic bacterium. Proc Natl Acad Sci U S A 2019; 116:18638-18646. [PMID: 31451656 DOI: 10.1073/pnas.1904225116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Calvin-Benson-Bassham (CBB) cycle assimilates CO2 for the primary production of organic matter in all plants and algae, as well as in some autotrophic bacteria. The key enzyme of the CBB cycle, ribulose-bisphosphate carboxylase/oxygenase (RubisCO), is a main determinant of de novo organic matter production on Earth. Of the three carboxylating forms of RubisCO, forms I and II participate in autotrophy, and form III so far has been associated only with nucleotide and nucleoside metabolism. Here, we report that form III RubisCO functions in the CBB cycle in the thermophilic chemolithoautotrophic bacterium Thermodesulfobium acidiphilum, a phylum-level lineage representative. We further show that autotrophic CO2 fixation in T. acidiphilum is accomplished via the transaldolase variant of the CBB cycle, which has not been previously demonstrated experimentally and has been considered unlikely to occur. Thus, this work reveals a distinct form of the key pathway of CO2 fixation.
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Braakman R. Evolution of cellular metabolism and the rise of a globally productive biosphere. Free Radic Biol Med 2019; 140:172-187. [PMID: 31082508 DOI: 10.1016/j.freeradbiomed.2019.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/28/2019] [Accepted: 05/02/2019] [Indexed: 01/14/2023]
Abstract
Metabolic processes in cells and chemical processes in the environment are fundamentally intertwined and have evolved in concert for most of Earth's existence. Here I argue that intrinsic properties of cellular metabolism imposed central constraints on the historical trajectories of biopsheric productivity and atmospheric oxygenation. Photosynthesis depends on iron, but iron is highly insoluble under the aerobic conditions produced by oxygenic photosynthesis. These counteracting constraints led to two major stages of Earth oxygenation. After a cyanobacteria-driven biospheric expansion near the Archean-Proterozoic boundary, productivity remained largely restricted to continental boundaries and shallow aquatic environments where weathering inputs made iron more accessible. The anoxic deep open ocean was rich in free iron during the Proterozoic, but this iron was largely inaccessible, partly because an otherwise nutrient-poor ocean was limiting to photosynthesis, but also because a photosynthetic expansion would have quenched its own iron supply. Near the Proterozoic-Phanerozoic boundary, bioenergetics innovations allowed eukaryotic photosynthesis to overcome these interconnected negative feedbacks and begin expanding into the deep open oceans and onto the continents, where nutrients are inherently harder to come by. Key insights into what drove the ecological rise of eukaryotic photosynthesis emerge from analyses of marine Synechococcus and Prochlorococcus, abundant marine picocyanobacteria whose ancestors colonized the oceans in the Neoproterozoic. The reconstructed evolution of this group reveals a sequence of innovations that ultimately produced a form of photosynthesis in Prochlorococcus that is more like that of green plant cells than other cyanobacteria. Innovations increased the energy flux of cells, thereby enhancing their ability to acquire sparse nutrients, and as by-product also increased the production of organic carbon waste. Some of these organic waste products had the ability to chelate iron and make it bioavailable, thereby indirectly pushing the oceans through a transition from an anoxic state rich in free iron to an oxygenated state with organic carbon-bound iron. Resulting conditions (and parallel processes on the continents) in turn led to a series of positive feedbacks that increased the availability of other nutrients, thereby promoting the rise of a globally productive biosphere. In addition to the occurrence of major biospheric expansions, the several hundred million-year periods around the Archean-Proterozoic and Proterozoic-Phanerozoic boundaries share a number of other parallels. Both epochs have also been linked to major carbon cycle perturbations and global glaciations, as well as changes in the nature of plate tectonics and increases in continental exposure and weathering. This suggests the dynamics of life and Earth are intimately intertwined across many levels and that general principles governed transitions in these coupled dynamics at both times in Earth history.
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Affiliation(s)
- Rogier Braakman
- Department of Civil & Environmental Engineering, Massachusetts Institute of Technology, USA; Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, USA.
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Pereira N, Shilova IN, Zehr JP. Use of the high-affinity phosphate transporter gene, pstS, as an indicator for phosphorus stress in the marine diazotroph Crocosphaera watsonii (Chroococcales, Cyanobacteria). JOURNAL OF PHYCOLOGY 2019; 55:752-761. [PMID: 30929262 DOI: 10.1111/jpy.12863] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
The marine diazotroph Crocosphaera watsonii provides fixed carbon (C) and nitrogen (N) to open-ocean regimes, where nutrient deficiency controls productivity. The growth of Crocosphaera can be limited by low phosphorus (P) concentrations in these oligotrophic environments. Biomarkers such as the high-affinity ABC transporter phosphate-binding gene, pstS, are commonly used to monitor when such organisms are under P stress; however, transcriptional regulation of these markers is often complex and not well-understood. In this study, we interrogated changes in pstS transcript levels in C. watsonii cells under P starvation, and in response to added dissolved inorganic phosphorus (DIP), dissolved organic phosphorus (DOP), and changing light levels. We observed elevated relative pstS transcript levels in C. watsonii WH8501 at DIP concentrations below 60 and above 20 nmol · L-1 . Transcript levels were suppressed by both inorganic and bioavailable organic phosphorus; however, the P stress response was more sensitive to DIP than DOP sources. Increasing light intensity resulted in increased relative pstS transcript abundances independently of low external P, and seemed to exacerbate the physiological effects of P stress. The variable response to different P compounds and rapid and transient influence of high light on pstS transcript abundances suggests that pstS is an indicator of internal P status in Crocosphaera.
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Affiliation(s)
- Nicole Pereira
- Ocean Sciences Department, University of California, 1156 High Street, Santa Cruz, California, 95064, USA
- Second Genome, 341 Allerton Avenue, South San Francisco, California, 94080, USA
| | - Irina N Shilova
- Ocean Sciences Department, University of California, 1156 High Street, Santa Cruz, California, 95064, USA
- Second Genome, 341 Allerton Avenue, South San Francisco, California, 94080, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, 1156 High Street, Santa Cruz, California, 95064, USA
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Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME JOURNAL 2019; 13:2817-2833. [PMID: 31320727 PMCID: PMC6794264 DOI: 10.1038/s41396-019-0472-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 06/11/2019] [Accepted: 06/15/2019] [Indexed: 01/06/2023]
Abstract
Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.
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Werner A, Broeckling CD, Prasad A, Peebles CAM. A comprehensive time-course metabolite profiling of the model cyanobacterium Synechocystis sp. PCC 6803 under diurnal light:dark cycles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:379-388. [PMID: 30889309 DOI: 10.1111/tpj.14320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 05/07/2023]
Abstract
Cyanobacteria are a model photoautotroph and a chassis for the sustainable production of fuels and chemicals. Knowledge of photoautotrophic metabolism in the natural environment of day/night cycles is lacking, yet has implications for improved yield from plants, algae and cyanobacteria. Here, a thorough approach to characterizing diverse metabolites-including carbohydrates, lipids, amino acids, pigments, cofactors, nucleic acids and polysaccharides-in the model cyanobacterium Synechocystis sp. PCC 6803 (S. 6803) under sinusoidal diurnal light:dark cycles was developed and applied. A custom photobioreactor and multi-platform mass spectrometry workflow enabled metabolite profiling every 30-120 min across a 24-h diurnal sinusoidal LD ('sinLD') cycle peaking at 1600 μmol photons m-2 sec-1 . We report widespread oscillations across the sinLD cycle with 90%, 94% and 40% of the identified polar/semi-polar, non-polar and polymeric metabolites displaying statistically significant oscillations, respectively. Microbial growth displayed distinct lag, biomass accumulation and cell division phases of growth. During the lag phase, amino acids and nucleic acids accumulated to high levels per cell followed by decreased levels during the biomass accumulation phase, presumably due to protein and DNA synthesis. Insoluble carbohydrates displayed sharp oscillations per cell at the day-to-night transition. Potential bottlenecks in central carbon metabolism are highlighted. Together, this report provides a comprehensive view of photosynthetic metabolite behavior with high temporal resolution, offering insight into the impact of growth synchronization to light cycles via circadian rhythms. Incorporation into computational modeling and metabolic engineering efforts promises to improve industrially relevant strain design.
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Affiliation(s)
- Allison Werner
- Cell and Molecular Biology Program, Colorado State University, 1005 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, 2021 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Ashok Prasad
- Cell and Molecular Biology Program, Colorado State University, 1005 Campus Delivery, Fort Collins, CO, 80523, USA
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Christie A M Peebles
- Cell and Molecular Biology Program, Colorado State University, 1005 Campus Delivery, Fort Collins, CO, 80523, USA
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO, 80523, USA
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Abstract
To adapt to the daily light–dark cycle, diurnal rhythms are used by the photosynthetic cyanobacteria Prochlorococcus and Synechococcus, which are the most abundant photosynthetic organisms on earth. Field studies revealed that cyanobacterial virus (cyanophage) populations in the oceans showed transcriptional rhythms. To explore the underlying mechanism, we used cyanophage laboratory cultures to find that some showed adsorption rhythms and all showed transcriptional rhythms. We discovered that the cyanophage transcriptional rhythm is partially caused by the photosynthetic activity of host cells, explaining transcriptional rhythms of field cyanophage populations. Our study shows that cultured viruses have diurnal infection rhythms which are critical for understanding how light–dark cycles shape the interaction of cyanophages and their hosts in the oceans. As an adaptation to the daily light–dark (diel) cycle, cyanobacteria exhibit diurnal rhythms of gene expression and cell cycle. The light–dark cycle also affects the life cycle of viruses (cyanophages) that infect the unicellular picocyanobacteria Prochlorococcus and Synechococcus, which are the major primary producers in the oceans. For example, the adsorption of some cyanophages to the host cells depends on light, and the burst sizes of cyanophages are positively correlated to the length of light exposure during infection. Recent metatranscriptomic studies revealed transcriptional rhythms of field cyanophage populations. However, the underlying mechanism remains to be determined, as cyanophage laboratory cultures have not been shown to exhibit diurnal transcriptional rhythms. Here, we studied variation in infection patterns and gene expression of Prochlorococcus phages in laboratory culture conditions as a function of light. We found three distinct diel-dependent life history traits in dark conditions (diel traits): no adsorption (cyanophage P-HM2), adsorption but no replication (cyanophage P-SSM2), and replication (cyanophage P-SSP7). Under light–dark cycles, each cyanophage exhibited rhythmic transcript abundance, and cyanophages P-HM2 and P-SSM2 also exhibited rhythmic adsorption patterns. Finally, we show evidence to link the diurnal transcriptional rhythm of cyanophages to the photosynthetic activity of the host, thus providing a mechanistic explanation for the field observations of cyanophage transcriptional rhythms. Our study identifies that cultured viruses can exhibit diurnal rhythms during infection, which might impact cyanophage population-level dynamics in the oceans.
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Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nat Commun 2019; 10:1169. [PMID: 30862830 PMCID: PMC6414667 DOI: 10.1038/s41467-019-09106-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/21/2019] [Indexed: 12/11/2022] Open
Abstract
Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent study of viruses. Many studies assemble new viral genomes and study viral diversity using marker genes from free viruses. Here we use cellular metatranscriptomics to study active community-wide viral infections. Recruitment to viral contigs allows tracking infection dynamics over time and space. Our assemblies represent viral populations, but appear biased towards low diversity viral taxa. Tracking relatives of published T4-like cyanophages and pelagiphages reveals high genomic continuity. We determine potential hosts by matching dynamics of infection with abundance of particular microbial taxa. Finally, we quantify the relative contribution of cyanobacteria and viruses to photosystem-II psbA (reaction center) expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression is of viral origin, highlighting the contribution of viruses to photosynthesis and oxygen production. Here, Sieradzki et al. use metatranscriptomics to study active community-wide viral infections at three coastal California sites throughout a year, identify potential viral hosts, and show that viruses can contribute a substantial amount to photosystem-II psbA expression.
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Carbon Fate and Flux in Prochlorococcus under Nitrogen Limitation. mSystems 2019; 4:mSystems00254-18. [PMID: 30834330 PMCID: PMC6392094 DOI: 10.1128/msystems.00254-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/28/2019] [Indexed: 11/20/2022] Open
Abstract
Primary production by Prochlorococcus, the smallest known free-living photosynthetic organism in terms of both physical and genomic size, is thought to have a significant role in global carbon cycles. Despite its small size and low growth rate, Prochlorococcus numerically dominates the phytoplankton community in the nutrient-poor oligotrophic ocean, the largest biome of the Earth's surface. How nutrient limitation, and nitrogen limitation in particular, affects the fate and flux of carbon fixed by Prochlorococcus is currently unknown. To address this gap in knowledge, we compared the bulk rates of photosynthesis and organic carbon release, the concentrations of intracellular metabolites, and the rates of assimilated carbon into the metabolite pools between replete and N-limited chemostat cultures. Total photosynthesis of our N-limited cultures was less than half of those observed in replete cultures, and nitrogen limitation also appears to cause a larger proportion of total fixed carbon to be released to the environment. Our data suggest this occurs in concert with the maintenance of large slow-moving pools of metabolites, including nitrogen-rich molecules such as glutamate. Additionally, we report field data suggesting metabolisms of Prochlorococcus are comparable to results we observe in our laboratory studies. Accounting for these observations, potential metabolic mechanisms utilized by Prochlorococcus are discussed as we build upon our understanding of nutrient-limited photosynthesis and carbon metabolism. IMPORTANCE Photosynthetic microbes are the predominant sources of organic carbon in the sunlit regions of the ocean. During photosynthesis, nitrogen and carbon metabolism are coordinated to synthesize nitrogen-containing organics such as amino acids and nucleic acids. In large regions of the ocean, nitrogen is thought to limit the growth of phytoplankton. The impact of nitrogen limitation on the synthesis of organic carbon is not well understood, especially for the most abundant photosynthetic organism in the nitrogen-limited regions of the ocean, Prochlorococcus. This study compares the carbon metabolism of nitrogen-replete and nitrogen-limited Prochlorococcus spp. to determine how nitrogen availability influences inorganic carbon assimilation into an organic form. Metabolomics and physiological data revealed that cells under nitrogen limitation have reduced metabolic flux and total carbon fixation rates while maintaining elevated metabolite pool levels and releasing a larger proportion of total fixed carbon to the environment.
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Uncertainties in the Geostationary Ocean Color Imager (GOCI) Remote Sensing Reflectance for Assessing Diurnal Variability of Biogeochemical Processes. REMOTE SENSING 2019. [DOI: 10.3390/rs11030295] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Short-term (sub-diurnal) biological and biogeochemical processes cannot be fully captured by the current suite of polar-orbiting satellite ocean color sensors, as their temporal resolution is limited to potentially one clear image per day. Geostationary sensors, such as the Geostationary Ocean Color Imager (GOCI) from the Republic of Korea, allow the study of these short-term processes because their orbit permit the collection of multiple images throughout each day for any area within the sensor’s field of regard. Assessing the capability to detect sub-diurnal changes in in-water properties caused by physical and biogeochemical processes characteristic of open ocean and coastal ocean ecosystems, however, requires an understanding of the uncertainties introduced by the instrument and/or geophysical retrieval algorithms. This work presents a study of the uncertainties during the daytime period for an ocean region with characteristically low-productivity with the assumption that only small and undetectable changes occur in the in-water properties due to biogeochemical processes during the daytime period. The complete GOCI mission data were processed using NASA’s SeaDAS/l2gen package. The assumption of homogeneity of the study region was tested using three-day sequences and diurnal statistics. This assumption was found to hold based on the minimal diurnal and day-to-day variability in GOCI data products. Relative differences with respect to the midday value were calculated for each hourly observation of the day in order to investigate what time of the day the variability is greater. Also, the influence of the solar zenith angle in the retrieval of remote sensing reflectances and derived products was examined. Finally, we determined that the uncertainties in water-leaving “remote-sensing” reflectance (Rrs) for the 412, 443, 490, 555, 660 and 680 nm bands on GOCI are 8.05 × 10−4, 5.49 × 10−4, 4.48 × 10−4, 2.51 × 10−4, 8.83 × 10−5, and 1.36 × 10−4 sr−1, respectively, and 1.09 × 10−2 mg m−3 for the chlorophyll-a concentration (Chl-a), 2.09 × 10−3 m−1 for the absorption coefficient of chromophoric dissolved organic matter at 412 nm (ag (412)), and 3.7 mg m−3 for particulate organic carbon (POC). These Rrs values can be considered the threshold values for detectable changes of the in-water properties due to biological, physical or biogeochemical processes from GOCI.
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The Transcriptional Cycle Is Suited to Daytime N 2 Fixation in the Unicellular Cyanobacterium " Candidatus Atelocyanobacterium thalassa" (UCYN-A). mBio 2019; 10:mBio.02495-18. [PMID: 30602582 PMCID: PMC6315102 DOI: 10.1128/mbio.02495-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The symbiotic N2-fixing cyanobacterium UCYN-A, which is closely related to Braarudosphaera bigelowii, and its eukaryotic algal host have been shown to be globally distributed and important in open-ocean N2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O2) or the O2 evolved through photosynthesis. This study showed that symbiosis between the N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N2 fixation, which is likely more energetically efficient than fixing N2 at night, as found in other unicellular marine cyanobacteria. Symbiosis between a marine alga and a N2-fixing cyanobacterium (Cyanobacterium UCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related to Braarudosphaera bigelowii. N2-fixing cyanobacteria use different strategies to avoid inhibition of N2 fixation by the oxygen evolved in photosynthesis. Most unicellular cyanobacteria temporally separate the two incompatible activities by fixing N2 only at night, but, surprisingly, UCYN-A appears to fix N2 during the day. The goal of this study was to determine how the unicellular UCYN-A strain coordinates N2 fixation and general metabolism compared to other marine cyanobacteria. We found that UCYN-A has distinct daily cycles of many genes despite the fact that it lacks two of the three circadian clock genes found in most cyanobacteria. We also found that the transcription patterns in UCYN-A are more similar to those in marine cyanobacteria that are capable of aerobic N2 fixation in the light, such as Trichodesmium and heterocyst-forming cyanobacteria, than to those in Crocosphaera or Cyanothece species, which are more closely related to unicellular marine cyanobacteria evolutionarily. Our findings suggest that the symbiotic interaction has resulted in a shift of transcriptional regulation to coordinate UCYN-A metabolism with that of the phototrophic eukaryotic host, thus allowing efficient coupling of N2 fixation (by the cyanobacterium) to the energy obtained from photosynthesis (by the eukaryotic unicellular alga) in the light.
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Partensky F, Mella-Flores D, Six C, Garczarek L, Czjzek M, Marie D, Kotabová E, Felcmanová K, Prášil O. Comparison of photosynthetic performances of marine picocyanobacteria with different configurations of the oxygen-evolving complex. PHOTOSYNTHESIS RESEARCH 2018; 138:57-71. [PMID: 29938315 DOI: 10.1007/s11120-018-0539-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
The extrinsic PsbU and PsbV proteins are known to play a critical role in stabilizing the Mn4CaO5 cluster of the PSII oxygen-evolving complex (OEC). However, most isolates of the marine cyanobacterium Prochlorococcus naturally miss these proteins, even though they have kept the main OEC protein, PsbO. A structural homology model of the PSII of such a natural deletion mutant strain (P. marinus MED4) did not reveal any obvious compensation mechanism for this lack. To assess the physiological consequences of this unusual OEC, we compared oxygen evolution between Prochlorococcus strains missing psbU and psbV (PCC 9511 and SS120) and two marine strains possessing these genes (Prochlorococcus sp. MIT9313 and Synechococcus sp. WH7803). While the low light-adapted strain SS120 exhibited the lowest maximal O2 evolution rates (Pmax per divinyl-chlorophyll a, per cell or per photosystem II) of all four strains, the high light-adapted strain PCC 9511 displayed even higher PChlmax and PPSIImax at high irradiance than Synechococcus sp. WH7803. Furthermore, thermoluminescence glow curves did not show any alteration in the B-band shape or peak position that could be related to the lack of these extrinsic proteins. This suggests an efficient functional adaptation of the OEC in these natural deletion mutants, in which PsbO alone is seemingly sufficient to ensure proper oxygen evolution. Our study also showed that Prochlorococcus strains exhibit negative net O2 evolution rates at the low irradiances encountered in minimum oxygen zones, possibly explaining the very low O2 concentrations measured in these environments, where Prochlorococcus is the dominant oxyphototroph.
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Affiliation(s)
- Frédéric Partensky
- Sorbonne Université, Station Biologique, CS 90074, 29688, Roscoff cedex, France.
- CNRS UMR 7144, Station Biologique, CS 90074, 29680, Roscoff, France.
| | - Daniella Mella-Flores
- Sorbonne Université, Station Biologique, CS 90074, 29688, Roscoff cedex, France
- CNRS UMR 7144, Station Biologique, CS 90074, 29680, Roscoff, France
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES-UC), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christophe Six
- Sorbonne Université, Station Biologique, CS 90074, 29688, Roscoff cedex, France
- CNRS UMR 7144, Station Biologique, CS 90074, 29680, Roscoff, France
| | - Laurence Garczarek
- Sorbonne Université, Station Biologique, CS 90074, 29688, Roscoff cedex, France
- CNRS UMR 7144, Station Biologique, CS 90074, 29680, Roscoff, France
| | - Mirjam Czjzek
- Sorbonne Université, Station Biologique, CS 90074, 29688, Roscoff cedex, France
- CNRS UMR 8227, Marine Glycobiology Group, Station Biologique, CS 90074, 29680, Roscoff, France
| | - Dominique Marie
- Sorbonne Université, Station Biologique, CS 90074, 29688, Roscoff cedex, France
- CNRS UMR 7144, Station Biologique, CS 90074, 29680, Roscoff, France
| | - Eva Kotabová
- Laboratory of Photosynthesis, Institute of Microbiology, MBU AVČR, Opatovický mlýn, 37981, Třeboň, Czech Republic
| | - Kristina Felcmanová
- Laboratory of Photosynthesis, Institute of Microbiology, MBU AVČR, Opatovický mlýn, 37981, Třeboň, Czech Republic
- Faculty of Sciences, University of South Bohemia, Branišovská, 37005, České Budějovice, Czech Republic
| | - Ondřej Prášil
- Laboratory of Photosynthesis, Institute of Microbiology, MBU AVČR, Opatovický mlýn, 37981, Třeboň, Czech Republic
- Faculty of Sciences, University of South Bohemia, Branišovská, 37005, České Budějovice, Czech Republic
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Robidart JC, Magasin JD, Shilova IN, Turk-Kubo KA, Wilson ST, Karl DM, Scholin CA, Zehr JP. Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre. ISME JOURNAL 2018; 13:374-387. [PMID: 30254320 DOI: 10.1038/s41396-018-0280-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Accepted: 08/26/2018] [Indexed: 11/09/2022]
Abstract
Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity in the surface ocean is constrained by nutrients which are supplied, in part, by mixing with deeper water. Little is known about the time scales, frequency, or impact of mixing on microbial communities. We combined in situ sampling using the Environmental Sample Processor and a small-scale mixing experiment with lower euphotic zone water to determine how individual populations respond to mixing. Transcriptional responses were measured using the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) microarray, which targets all three domains of life and viruses. The experiment showed that mixing substantially affects photosynthetic taxa as expected, but surprisingly also showed that populations respond differently to unfiltered deep water which contains particles (organisms and detritus) compared to filtered deep water that only contains nutrients and viruses, pointing to the impact of biological interactions associated with these events. Comparison between experimental and in situ population transcription patterns indicated that manipulated populations can serve as analogs for natural populations, and that natural populations may be frequently or continuously responding to nutrients from deeper waters. Finally, this study also shows that the microarray approach, which is complementary to metatranscriptomic sequencing, is useful for determining the physiological status of in situ microbial communities.
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Affiliation(s)
- J C Robidart
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,National Oceanography Centre, Southampton, UK
| | - J D Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - I N Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,Second Genome, South San Francisco, CA, USA
| | - K A Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - S T Wilson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - D M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - C A Scholin
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - J P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.
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45
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Monti M, Lubensky DK, Ten Wolde PR. Robustness of Clocks to Input Noise. PHYSICAL REVIEW LETTERS 2018; 121:078101. [PMID: 30169070 DOI: 10.1103/physrevlett.121.078101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 03/30/2018] [Indexed: 06/08/2023]
Abstract
To estimate the time, many organisms, ranging from cyanobacteria to animals, employ a circadian clock which is based on a limit-cycle oscillator that can tick autonomously with a nearly 24 h period. Yet, a limit-cycle oscillator is not essential for knowing the time, as exemplified by bacteria that possess an "hourglass": a system that when forced by an oscillatory light input exhibits robust oscillations from which the organism can infer the time, but that in the absence of driving relaxes to a stable fixed point. Here, using models of the Kai system of cyanobacteria, we compare a limit-cycle oscillator with two hourglass models, one that without driving relaxes exponentially and one that does so in an oscillatory fashion. In the limit of low input noise, all three systems are equally informative on time, yet in the regime of high input-noise the limit-cycle oscillator is far superior. The same behavior is found in the Stuart-Landau model, indicating that our result is universal.
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Affiliation(s)
- Michele Monti
- FOM Institute AMOLF, Science Park 104, 1098 XE Amsterdam, Netherlands
| | - David K Lubensky
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1040, USA
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Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness. mSystems 2018; 3:mSystems00040-18. [PMID: 29854954 PMCID: PMC5974335 DOI: 10.1128/msystems.00040-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
Microbes evolve within complex ecological communities where biotic interactions impact both individual cells and the environment as a whole. Here we examine how cellular regulation in the marine cyanobacterium Prochlorococcus is influenced by a heterotrophic bacterium, Alteromonas macleodii, under different light conditions. We monitored the transcriptome of Prochlorococcus, grown either alone or in coculture, across a diel light:dark cycle and under the stress of extended darkness-a condition that cells would experience when mixed below the ocean's euphotic zone. More Prochlorococcus transcripts exhibited 24-h periodic oscillations in coculture than in pure culture, both over the normal diel cycle and after the shift to extended darkness. This demonstrates that biotic interactions, and not just light, can affect timing mechanisms in Prochlorococcus, which lacks a self-sustaining circadian oscillator. The transcriptomes of replicate pure cultures of Prochlorococcus lost their synchrony within 5 h of extended darkness and reflected changes in stress responses and metabolic functions consistent with growth cessation. In contrast, when grown with Alteromonas, replicate Prochlorococcus transcriptomes tracked each other for at least 13 h in the dark and showed signs of continued biosynthetic and metabolic activity. The transcriptome patterns suggest that the heterotroph may be providing energy or essential biosynthetic substrates to Prochlorococcus in the form of organic compounds, sustaining this autotroph when it is deprived of solar energy. Our findings reveal conditions where mixotrophic metabolism may benefit marine cyanobacteria and highlight new impacts of community interactions on basic Prochlorococcus cellular processes. IMPORTANCEProchlorococcus is the most abundant photosynthetic organism on the planet. These cells play a central role in the physiology of surrounding heterotrophs by supplying them with fixed organic carbon. It is becoming increasingly clear, however, that interactions with heterotrophs can affect autotrophs as well. Here we show that such interactions have a marked impact on the response of Prochlorococcus to the stress of extended periods of darkness, as reflected in transcriptional dynamics. These data suggest that diel transcriptional rhythms within Prochlorococcus, which are generally considered to be strictly under the control of light quantity, quality, and timing, can also be influenced by biotic interactions. Together, these findings provide new insights into the importance of microbial interactions on Prochlorococcus physiology and reveal conditions where heterotroph-derived compounds may support autotrophs-contrary to the canonical autotroph-to-heterotroph trophic paradigm.
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Rachik S, Christaki U, Li LL, Genitsaris S, Breton E, Monchy S. Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel). PLoS One 2018; 13:e0196987. [PMID: 29746519 PMCID: PMC5944946 DOI: 10.1371/journal.pone.0196987] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/24/2018] [Indexed: 01/02/2023] Open
Abstract
The diversity of planktonic eukaryotic microbes was studied at a coastal station of the eastern English Channel (EEC) from March 2011 to July 2015 (77 samples) using high throughput sequencing (454-pyrosequencing and Illumina) of the V2-V3 hypervariable region of the 18S SSU rDNA gene. Similar estimations of OTU relative abundance and taxonomic distribution for the dominant higher taxonomic groups (contributing >1% of the total number of OTUs) were observed with the two methods (Kolmogorov-Smirnov p-value = 0.22). Eight super-groups were identified throughout all samples: Alveolata, Stramenopiles, Opisthokonta, Hacrobia, Archeaplastida, Apusozoa, Rhizaria, and Amoebozoa (ordered by decreasing OTU richness). To gain further insight into microbial activity in the EEC, ribosomal RNA was extracted for samples from 2013–2015 (30 samples). Analysis of 18S rDNA and rRNA sequences led to the detection of 696 and 700 OTUs, respectively. Cluster analysis based on OTUs’ abundance indicated three major seasonal groups that were associated to spring, winter/autumn, and summer conditions. The clusters inferred from rRNA data showed a clearer seasonal representation of the community succession than the one based on rDNA. The rRNA/rDNA ratio was used as a proxy for relative cell activity. When all OTUs were considered, the average rRNA:rDNA ratio showed a linear trend around the 1:1 line, suggesting a linear relation between OTU abundance (rDNA) and activity (rRNA). However, this ratio was highly variable over time when considering individual OTUs. Interestingly, the OTU affiliated with P. globosa displayed rRNA:rDNA ratio that allowed to delimit high vs low abundance and high vs low activity periods. It unveiled quite well the Phaeocystis bloom dynamic regarding cell proliferation and activity, and could even be used as early indicator of an upcoming bloom.
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Affiliation(s)
- Sara Rachik
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Urania Christaki
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Luen Luen Li
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Savvas Genitsaris
- International Hellenic University, School of Economics, Business Administration & Legal Studies, Thessaloniki, Greece
| | - Elsa Breton
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Sébastien Monchy
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
- * E-mail:
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Abstract
Marine plankton elemental stoichiometric ratios can deviate from the Redfield ratio (106C:16N:1P); here, we examine physiological and biogeochemical mechanisms that lead to the observed variation across lineages, regions, and seasons. Many models of ecological stoichiometry blend together acclimative and adaptive responses to environmental conditions. These two pathways can have unique molecular mechanisms and stoichiometric outcomes, and we attempt to disentangle the two processes. We find that interactions between environmental conditions and cellular growth are key to understanding stoichiometric regulation, but the growth rates of most marine plankton populations are poorly constrained. We propose that specific physiological mechanisms have a strong impact on plankton and community stoichiometry in nutrient-rich environments, whereas biogeochemical interactions are important for the stoichiometry of the oligotrophic gyres. Finally, we outline key areas with missing information that is needed to advance understanding of the present and future ecological stoichiometry of ocean plankton.
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Affiliation(s)
- Allison R Moreno
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697;
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697;
- Department of Earth System Science, University of California, Irvine, California 92697
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Louyakis AS, Gourlé H, Casaburi G, Bonjawo RME, Duscher AA, Foster JS. A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles. Environ Microbiol 2017; 20:842-861. [DOI: 10.1111/1462-2920.14029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Artemis S. Louyakis
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Hadrien Gourlé
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
- Department of Animal Breeding and Genetics; Global Bioinformatics Centre, Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Giorgio Casaburi
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Rachelle M. E. Bonjawo
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Alexandrea A. Duscher
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Jamie S. Foster
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
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50
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Abstract
All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks. Here we propose a role for KaiC family ATPases, known to be key components of the circadian clock in cyanobacteria, in archaeal signal transduction. The KaiC family is notably expanded in most archaeal genomes, and although most of these ATPases remain poorly characterized, members of the KaiC family have been shown to control archaellum assembly and have been found to be a stable component of the gas vesicle system in Halobacteria Computational analyses described here suggest that KaiC-like ATPases and their homologues with inactivated ATPase domains are involved in many other archaeal signal transduction pathways and comprise major hubs of complex regulatory networks. We predict numerous input and output domains that are linked to KaiC-like proteins, including putative homologues of eukaryotic DEATH domains that could function as adapters in archaeal signaling networks. We further address the relationships of the archaeal family of KaiC homologues to the bona fide KaiC of cyanobacteria and implications for the existence of a KaiC-based circadian clock apparatus in archaea.IMPORTANCE Little is currently known about signal transduction pathways in Archaea Recent studies indicate that KaiC-like ATPases, known as key components of the circadian clock apparatus in cyanobacteria, are involved in the regulation of archaellum assembly and, likely, type IV pili and the gas vesicle system in Archaea We performed comprehensive comparative genomic analyses of the KaiC family. A vast protein interaction network was revealed, with KaiC family proteins as hubs for numerous input and output components, many of which are shared with two-component signal transduction systems. Putative KaiC-based signal transduction systems are predicted to regulate the activities of membrane-associated complexes and individual proteins, such as signal recognition particle and membrane transporters, and also could be important for oxidative stress response regulation. KaiC-centered signal transduction networks are predicted to play major roles in archaeal physiology, and this work is expected to stimulate their experimental characterization.
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