1
|
Angulo-Cánovas E, Bartual A, López-Igual R, Luque I, Radzinski NP, Shilova I, Anjur-Dietrich M, García-Jurado G, Úbeda B, González-Reyes JA, Díez J, Chisholm SW, García-Fernández JM, del Carmen Muñoz-Marín M. Direct interaction between marine cyanobacteria mediated by nanotubes. SCIENCE ADVANCES 2024; 10:eadj1539. [PMID: 38781331 PMCID: PMC11114229 DOI: 10.1126/sciadv.adj1539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Microbial associations and interactions drive and regulate nutrient fluxes in the ocean. However, physical contact between cells of marine cyanobacteria has not been studied thus far. Here, we show a mechanism of direct interaction between the marine cyanobacteria Prochlorococcus and Synechococcus, the intercellular membrane nanotubes. We present evidence of inter- and intra-genus exchange of cytoplasmic material between neighboring and distant cells of cyanobacteria mediated by nanotubes. We visualized and measured these structures in xenic and axenic cultures and in natural samples. We show that nanotubes are produced between living cells, suggesting that this is a relevant system of exchange material in vivo. The discovery of nanotubes acting as exchange bridges in the most abundant photosynthetic organisms in the ocean may have important implications for their interactions with other organisms and their population dynamics.
Collapse
Affiliation(s)
- Elisa Angulo-Cánovas
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - Ana Bartual
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Rocío López-Igual
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Nikolai P. Radzinski
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Maya Anjur-Dietrich
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gema García-Jurado
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Bárbara Úbeda
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - José Antonio González-Reyes
- Departamento de Biología Celular, Fisiología e Inmunología, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - María del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| |
Collapse
|
2
|
Cai L, Li H, Deng J, Zhou R, Zeng Q. Biological interactions with Prochlorococcus: implications for the marine carbon cycle. Trends Microbiol 2024; 32:280-291. [PMID: 37722980 DOI: 10.1016/j.tim.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023]
Abstract
The unicellular picocyanobacterium Prochlorococcus is the most abundant photoautotroph and contributes substantially to global CO2 fixation. In the vast euphotic zones of the open ocean, Prochlorococcus converts CO2 into organic compounds and supports diverse organisms, forming an intricate network of interactions that regulate the magnitude of carbon cycling and storage in the ocean. An understanding of the biological interactions with Prochlorococcus is critical for accurately estimating the contributions of Prochlorococcus and interacting organisms to the marine carbon cycle. This review synthesizes the primary production contributed by Prochlorococcus in the global ocean. We outline recent progress on the interactions of Prochlorococcus with heterotrophic bacteria, phages, and grazers that multifacetedly determine Prochlorococcus carbon production and fate. We discuss that climate change might affect the biological interactions with Prochlorococcus and thus the marine carbon cycle.
Collapse
Affiliation(s)
- Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China
| | - Junwei Deng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ruiqian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China; Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong, China.
| |
Collapse
|
3
|
Thompson AW, Nyerges G, Brevick K, Sutherland KR. Ubiquitous filter feeders shape open ocean microbial community structure and function. PNAS NEXUS 2024; 3:pgae091. [PMID: 38505693 PMCID: PMC10949910 DOI: 10.1093/pnasnexus/pgae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/13/2024] [Indexed: 03/21/2024]
Abstract
The mechanism of mortality plays a large role in how microorganisms in the open ocean contribute to global energy and nutrient cycling. Salps are ubiquitous pelagic tunicates that are a well-known mortality source for large phototrophic microorganisms in coastal and high-latitude systems, but their impact on the immense populations of smaller prokaryotes in the tropical and subtropical open ocean gyres is not well quantified. We used robustly quantitative techniques to measure salp clearance and enrichment of specific microbial functional groups in the North Pacific Subtropical Gyre, one of the largest ecosystems on Earth. We discovered that salps are a previously unknown predator of the globally abundant nitrogen fixer Crocosphaera; thus, salps restrain new nitrogen delivery to the marine ecosystem. We show that the ocean's two numerically dominant cells, Prochlorococcus and SAR11, are not consumed by salps, which offers a new explanation for the dominance of small cells in open ocean systems. We also identified a double bonus for Prochlorococcus, wherein it not only escapes salp predation but the salps also remove one of its major mixotrophic predators, the prymnesiophyte Chrysochromulina. When we modeled the interaction between salp mesh and particles, we found that cell size alone could not account for these prey selection patterns. Instead, the results suggest that alternative mechanisms, such as surface property, shape, nutritional quality, or even prey behavior, determine which microbial cells are consumed by salps. Together, these results identify salps as a major factor in shaping the structure, function, and ecology of open ocean microbial communities.
Collapse
Affiliation(s)
- Anne W Thompson
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Györgyi Nyerges
- Department of Biology, Pacific University, Forest Grove, OR 97116, USA
| | - Kylee Brevick
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
| | - Kelly R Sutherland
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR 97403, USA
| |
Collapse
|
4
|
Prathapan P. Characterisation of the fig-fig wasp holobiont. Biosystems 2024; 237:105162. [PMID: 38395103 DOI: 10.1016/j.biosystems.2024.105162] [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: 11/13/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
Plants and animals have long been considered distinct kingdoms, yet here a 'plant-animal' is described. An extraordinary symbiosis in which neither organism can reproduce without the other, the fig tree (Ficus) provides the habitat for its exclusive pollinator: the fig wasp (Agaonidae). Characterising the 'fig-fig wasp holobiont' acknowledges, for the first time, 'plant-animal symbiogenesis'.
Collapse
Affiliation(s)
- Praveen Prathapan
- New Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| |
Collapse
|
5
|
Weinberger VP, Zalaquett N, Abades S. How greedy is too greedy? A network toy model for evaluating the sustainability of biased evolutionary dynamics. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220260. [PMID: 37952630 PMCID: PMC10645075 DOI: 10.1098/rstb.2022.0260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/12/2023] [Indexed: 11/14/2023] Open
Abstract
Modern humanity has changed the biosphere at a global scale, threatening its own sustainability. It is claimed that through technology humans maximize the extraction of energy from the natural system towards their own benefit, with rates of appropriation that surpass the time-scales for systemic adaptation. This time-decoupled coevolutionary dynamic is at the core of human societal unsustainability. Here, we developed in silico experiments of an open energy-based flowing network toy model of natural systems and study the effects that greedy evolutionary strategies, resembling human societal demands, have upon the performance and scarcity tolerance of the system. We aim to determine the flexibility that those biased evolutionary dynamics have for matching or surpassing natural evolution outcomes. We studied four different indexes of system's growth and development (total system throughflow (TST), average mutual information, ascendency and entropy difference) and compare their scarcity tolerance and performance outcomes with respect to four different greedy scenarios. The results showed that greedy strategies rarely surpassed the tolerance and performance achieved by natural systemic evolution. The nature of the greedy scenarios developed were closely related to increases in TST and therefore, we emphasized this comparison. Here, the maximum percentage of greedy networks capable of surpassing natural dynamics was around one-third (approx. [Formula: see text]). However, results suggest the existence of a space parameter where local increases of energy flow can outperform the outcomes of natural systemic evolution, but no evident network property seems to characterize those greedy networks. A mild inverse relationship was found between the number of links that greedy nodes have towards the output and their capacity to outpass the control evolution. As many of the human societal effect upon biospheric processes have dissipative byproducts, knowing that such dynamics might diminish the systems tolerance and performance suggest care in their (ab)use. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'.
Collapse
Affiliation(s)
- V. P. Weinberger
- Center for Resilience, Adaptation and Mitigation (CReAM), Universidad Mayor, Temuco, 4801043, Chile
| | - N. Zalaquett
- PLR Physics Ludique Research, Santiago, 9761013, Chile
| | - S. Abades
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, 8580745, Chile
| |
Collapse
|
6
|
Fuchsman CA, Hays MD. Increased cyanophage infection at the bottom of the euphotic zone, especially in the fall. Environ Microbiol 2023; 25:3349-3363. [PMID: 37861083 DOI: 10.1111/1462-2920.16525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023]
Abstract
Picocyanobacteria contribute greatly to offshore primary production with cells extending through the deep euphotic zone. Literature indicates high viral infection of cyanobacteria in ocean transition zones. We postulate that the bottom of the euphotic zone is a transition zone, where communities transition from phototrophic to aphotic processes. We use single-copy core genes to examine cyanophage to cyanobacteria ratios in cellular metagenomes in the subtropical North Atlantic and Pacific. Cyanophage to cyanobacteria terL/rpoB ratios generally increase to >10 in the deep euphotic zone. As light levels decrease in the fall, Prochlorococcus in the deep euphotic zone experience reduced light levels. We find clear differences between spring (Geotraces GA02) and fall (GA03) in the North Atlantic, with terL/rpoB ratios increasing to >40 in the fall. When examining 23 months of the North Pacific Hawaii Ocean Timeseries, the depth of elevated cyanophage to cyanobacteria ratios in cellular metagenomes negatively correlated with surface photosynthetic radiation (PAR), particularly with the change in PAR, which reflected the season. In fall, all picocyanobacteria ecotypes were found at depths enriched with viruses, while in summer, only low light ecotypes were affected. Thus, we find high cyanophage infection both in the deep euphotic zone and during seasonal transitions.
Collapse
Affiliation(s)
- Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Matthew D Hays
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| |
Collapse
|
7
|
Kujawinski EB, Braakman R, Longnecker K, Becker JW, Chisholm SW, Dooley K, Kido Soule MC, Swarr GJ, Halloran K. Metabolite diversity among representatives of divergent Prochlorococcus ecotypes. mSystems 2023; 8:e0126122. [PMID: 37815355 PMCID: PMC10654061 DOI: 10.1128/msystems.01261-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/31/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE Approximately half of the annual carbon fixation on Earth occurs in the surface ocean through the photosynthetic activities of phytoplankton such as the ubiquitous picocyanobacterium Prochlorococcus. Ecologically distinct subpopulations (or ecotypes) of Prochlorococcus are central conduits of organic substrates into the ocean microbiome, thus playing important roles in surface ocean production. We measured the chemical profile of three cultured ecotype strains, observing striking differences among them that have implications for the likely chemical impact of Prochlorococcus subpopulations on their surroundings in the wild. Subpopulations differ in abundance along gradients of temperature, light, and nutrient concentrations, suggesting that these chemical differences could affect carbon cycling in different ocean strata and should be considered in models of Prochlorococcus physiology and marine carbon dynamics.
Collapse
Affiliation(s)
- Elizabeth B. Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Rogier Braakman
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Krista Longnecker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Jamie W. Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Science Department, Alvernia University, Reading, Pennsylvania, USA
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Keven Dooley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Melissa C. Kido Soule
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Gretchen J. Swarr
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Kathryn Halloran
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Sciences and Engineering, Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| |
Collapse
|
8
|
D'Angelo T, Goordial J, Lindsay MR, McGonigle J, Booker A, Moser D, Stepanauskus R, Orcutt BN. Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota. THE ISME JOURNAL 2023; 17:891-902. [PMID: 37012337 DOI: 10.1038/s41396-023-01397-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.
Collapse
Affiliation(s)
- Timothy D'Angelo
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Jacqueline Goordial
- University of Guelph, School of Environmental Sciences, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Melody R Lindsay
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Julia McGonigle
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
- Basepaws Pet Genetics, 1820 W. Carson Street, Suite 202-351, Torrance, CA, 90501, USA
| | - Anne Booker
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Duane Moser
- Desert Research Institute, 755 East Flamingo Road, Las Vegas, NV, 89119, USA
| | - Ramunas Stepanauskus
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA.
| |
Collapse
|
9
|
Santos-Merino M, Yun L, Ducat DC. Cyanobacteria as cell factories for the photosynthetic production of sucrose. Front Microbiol 2023; 14:1126032. [PMID: 36865782 PMCID: PMC9971976 DOI: 10.3389/fmicb.2023.1126032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Biofuels and other biologically manufactured sustainable goods are growing in popularity and demand. Carbohydrate feedstocks required for industrial fermentation processes have traditionally been supplied by plant biomass, but the large quantities required to produce replacement commodity products may prevent the long-term feasibility of this approach without alternative strategies to produce sugar feedstocks. Cyanobacteria are under consideration as potential candidates for sustainable production of carbohydrate feedstocks, with potentially lower land and water requirements relative to plants. Several cyanobacterial strains have been genetically engineered to export significant quantities of sugars, especially sucrose. Sucrose is not only naturally synthesized and accumulated by cyanobacteria as a compatible solute to tolerate high salt environments, but also an easily fermentable disaccharide used by many heterotrophic bacteria as a carbon source. In this review, we provide a comprehensive summary of the current knowledge of the endogenous cyanobacterial sucrose synthesis and degradation pathways. We also summarize genetic modifications that have been found to increase sucrose production and secretion. Finally, we consider the current state of synthetic microbial consortia that rely on sugar-secreting cyanobacterial strains, which are co-cultivated alongside heterotrophic microbes able to directly convert the sugars into higher-value compounds (e.g., polyhydroxybutyrates, 3-hydroxypropionic acid, or dyes) in a single-pot reaction. We summarize recent advances reported in such cyanobacteria/heterotroph co-cultivation strategies and provide a perspective on future developments that are likely required to realize their bioindustrial potential.
Collapse
Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Lisa Yun
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| |
Collapse
|
10
|
Díez J, López-Lozano A, Domínguez-Martín MA, Gómez-Baena G, Muñoz-Marín MC, Melero-Rubio Y, García-Fernández JM. Regulatory and metabolic adaptations in the nitrogen assimilation of marine picocyanobacteria. FEMS Microbiol Rev 2023; 47:6794272. [PMID: 36323406 DOI: 10.1093/femsre/fuac043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Prochlorococcus and Synechococcus are the two most abundant photosynthetic organisms on Earth, with a strong influence on the biogeochemical carbon and nitrogen cycles. Early reports demonstrated the streamlining of regulatory mechanisms in nitrogen metabolism and the removal of genes not strictly essential. The availability of a large series of genomes, and the utilization of latest generation molecular techniques have allowed elucidating the main mechanisms developed by marine picocyanobacteria to adapt to the environments where they thrive, with a particular interest in the strains inhabiting oligotrophic oceans. Given that nitrogen is often limited in those environments, a series of studies have explored the strategies utilized by Prochlorococcus and Synechococcus to exploit the low concentrations of nitrogen-containing molecules available in large areas of the oceans. These strategies include the reduction in the GC and the cellular protein contents; the utilization of truncated proteins; a reduced average amount of N in the proteome; the development of metabolic mechanisms to perceive and utilize nanomolar nitrate concentrations; and the reduced responsiveness of key molecular regulatory systems such as NtcA to 2-oxoglutarate. These findings are in sharp contrast with the large body of knowledge obtained in freshwater cyanobacteria. We will outline the main discoveries, stressing their relevance to the ecological success of these important microorganisms.
Collapse
Affiliation(s)
- J Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - A López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - G Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M C Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - Y Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - J M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| |
Collapse
|
11
|
Barreto Filho MM, Lu Z, Walker M, Morris JJ. Community context and pCO 2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria. ISME COMMUNICATIONS 2022; 2:113. [PMID: 37938752 PMCID: PMC9723591 DOI: 10.1038/s43705-022-00197-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 09/20/2023]
Abstract
Many microbial photoautotrophs depend on heterotrophic bacteria for accomplishing essential functions. Environmental changes, however, could alter or eliminate such interactions. We investigated the effects of changing pCO2 on gene transcription in co-cultures of 3 strains of picocyanobacteria (Synechococcus strains CC9311 and WH8102 and Prochlorococcus strain MIT9312) paired with the 'helper' bacterium Alteromonas macleodii EZ55. Co-culture with cyanobacteria resulted in a much higher number of up- and down-regulated genes in EZ55 than pCO2 by itself. Pathway analysis revealed significantly different transcription of genes involved in carbohydrate metabolism, stress response, and chemotaxis, with different patterns of up- or down-regulation in co-culture with different cyanobacterial strains. Gene transcription patterns of organic and inorganic nutrient transporter and catabolism genes in EZ55 suggested resources available in the culture media were altered under elevated (800 ppm) pCO2 conditions. Altogether, changing transcription patterns were consistent with the possibility that the composition of cyanobacterial excretions changed under the two pCO2 regimes, causing extensive ecophysiological changes in both members of the co-cultures. Additionally, significant downregulation of oxidative stress genes in MIT9312/EZ55 cocultures at 800 ppm pCO2 were consistent with a link between the predicted reduced availability of photorespiratory byproducts (i.e., glycolate/2PG) under this condition and observed reductions in internal oxidative stress loads for EZ55, providing a possible explanation for the previously observed lack of "help" provided by EZ55 to MIT9312 under elevated pCO2. If similar broad alterations in microbial ecophysiology occur in the ocean as atmospheric pCO2 increases, they could lead to substantially altered ecosystem functioning and community composition.
Collapse
Affiliation(s)
| | - Zhiying Lu
- University of Alabama at Birmingham Department of Biology, 1300 University Blvd CH464, Birmingham, AL, 35294, USA
| | - Melissa Walker
- University of Alabama at Birmingham Department of Biology, 1300 University Blvd CH464, Birmingham, AL, 35294, USA
| | - J Jeffrey Morris
- University of Alabama at Birmingham Department of Biology, 1300 University Blvd CH464, Birmingham, AL, 35294, USA.
| |
Collapse
|
12
|
Rajpurohit H, Eiteman MA. Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals. Microorganisms 2022; 10:2226. [PMID: 36363817 PMCID: PMC9695796 DOI: 10.3390/microorganisms10112226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 08/24/2023] Open
Abstract
Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals.
Collapse
Affiliation(s)
| | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Gibbs T, Zhang Y, Miller ZR, O’Dwyer JP. Stability criteria for the consumption and exchange of essential resources. PLoS Comput Biol 2022; 18:e1010521. [PMID: 36074781 PMCID: PMC9488833 DOI: 10.1371/journal.pcbi.1010521] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 09/20/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
Models of consumer effects on a shared resource environment have helped clarify how the interplay of consumer traits and resource supply impact stable coexistence. Recent models generalize this picture to include the exchange of resources alongside resource competition. These models exemplify the fact that although consumers shape the resource environment, the outcome of consumer interactions is context-dependent: such models can have either stable or unstable equilibria, depending on the resource supply. However, these recent models focus on a simplified version of microbial metabolism where the depletion of resources always leads to consumer growth. Here, we model an arbitrarily large system of consumers governed by Liebig’s law, where species require and deplete multiple resources, but each consumer’s growth rate is only limited by a single one of these resources. Resources that are taken up but not incorporated into new biomass are leaked back into the environment, possibly transformed by intracellular reactions, thereby tying the mismatch between depletion and growth to cross-feeding. For this set of dynamics, we show that feasible equilibria can be either stable or unstable, again depending on the resource environment. We identify special consumption and production networks which protect the community from instability when resources are scarce. Using simulations, we demonstrate that the qualitative stability patterns derived analytically apply to a broader class of network structures and resource inflow profiles, including cases where multiple species coexist on only one externally supplied resource. Our stability criteria bear some resemblance to classic stability results for pairwise interactions, but also demonstrate how environmental context can shape coexistence patterns when resource limitation and exchange are modeled directly.
Collapse
Affiliation(s)
- Theo Gibbs
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
| | - Yifan Zhang
- Department of Plant Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Zachary R. Miller
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - James P. O’Dwyer
- Department of Plant Biology, University of Illinois, Urbana, Illinois, United States of America
| |
Collapse
|
15
|
Comstock J, Nelson CE, James A, Wear E, Baetge N, Remple K, Juknavorian A, Carlson CA. Bacterioplankton communities reveal horizontal and vertical influence of an Island Mass Effect. Environ Microbiol 2022; 24:4193-4208. [PMID: 35691616 PMCID: PMC9796716 DOI: 10.1111/1462-2920.16092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 01/07/2023]
Abstract
Coral reefs are highly productive ecosystems with distinct biogeochemistry and biology nestled within unproductive oligotrophic gyres. Coral reef islands have often been associated with a nearshore enhancement in phytoplankton, a phenomenon known as the Island Mass Effect (IME). Despite being documented more than 60 years ago, much remains unknown about the extent and drivers of IMEs. Here we utilized 16S rRNA gene metabarcoding as a biological tracer to elucidate horizontal and vertical influence of an IME around the islands of Mo'orea and Tahiti, French Polynesia. We show that those nearshore oceanic stations with elevated chlorophyll a included bacterioplankton found in high abundance in the reef environment, suggesting advection of reef water is the source of altered nearshore biogeochemistry. We also observed communities in the nearshore deep chlorophyll maximum (DCM) with enhanced abundances of upper euphotic bacterioplankton that correlated with intrusions of low-density, O2 rich water, suggesting island influence extends into the DCM.
Collapse
Affiliation(s)
- Jacqueline Comstock
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Craig E. Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College ProgramUniversity of Hawai'i at MānoaHonoluluHIUSA
| | - Anna James
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Emma Wear
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Nicholas Baetge
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Kristina Remple
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College ProgramUniversity of Hawai'i at MānoaHonoluluHIUSA
| | | | - Craig A. Carlson
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| |
Collapse
|
16
|
Gonzalez-Nayeck AC, Mohr W, Tang T, Sattin S, Parenteau MN, Jahnke LL, Pearson A. Absence of canonical trophic levels in a microbial mat. GEOBIOLOGY 2022; 20:726-740. [PMID: 35831948 DOI: 10.1111/gbi.12511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
In modern ecosystems, the carbon stable isotope (δ13 C) ratios of consumers generally conform to the principle "you are what you eat, +1‰." However, this metric may not apply to microbial mat systems where diverse communities, using a variety of carbon substrates via multiple assimilation pathways, live in close physical association and phagocytosis is minimal or absent. To interpret the δ13 C record of the Proterozoic and early Paleozoic, when mat-based productivity likely was widespread, it is necessary to understand how a microbially driven producer-consumer structure affects the δ13 C compositions of biomass and preservable lipids. Protein Stable Isotope Fingerprinting (P-SIF) is a recently developed method that allows measurement of the δ13 C values of whole proteins, separated from environmental samples and identified taxonomically via proteomics. Here, we use P-SIF to determine the trophic relationships in a microbial mat sample from Chocolate Pots Hot Springs, Yellowstone National Park (YNP), USA. In this mat, proteins from heterotrophic bacteria are indistinguishable from cyanobacterial proteins, indicating that "you are what you eat, +1‰" is not applicable. To explain this finding, we hypothesize that sugar production and consumption dominate the net ecosystem metabolism, yielding a community in which producers and consumers share primary photosynthate as a common resource. This idea was validated by confirming that glucose moieties in exopolysaccharide were equal in δ13 C composition to both cyanobacterial and heterotrophic proteins, and by confirming that highly 13 C-depleted fatty acids (FAs) of Cyanobacteria dominate the lipid pool, consistent with flux-balance expectations for systems that overproduce primary photosynthate. Overall, the results confirm that the δ13 C composition of microbial biomass and lipids is tied to specific metabolites, rather than to autotrophy versus heterotrophy or to individual trophic levels. Therefore, we suggest that aerobic microbial heterotrophy is simply a case of "you are what you eat."
Collapse
Affiliation(s)
- Ana C Gonzalez-Nayeck
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Wiebke Mohr
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Tiantian Tang
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- State Key Laboratory of Marine Environmental Science (Xiamen University), Xiamen, Fujian, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Sarah Sattin
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | | | - Linda L Jahnke
- NASA Ames Research Center, Moffett Field, California, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
17
|
Vujovic F, Hunter N, Farahani RM. Cellular self-organization: An overdrive in Cambrian diversity? Bioessays 2022; 44:e2200033. [PMID: 35900058 DOI: 10.1002/bies.202200033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 11/10/2022]
Abstract
During the early Cambrian period metazoan life forms diverged at an accelerated rate to occupy multiple ecological niches on earth. A variety of explanations have been proposed to address this major evolutionary phenomenon termed the "Cambrian explosion." While most hypotheses address environmental, developmental, and ecological factors that facilitated evolutionary innovations, the biological basis for accelerated emergence of species diversity in the Cambrian period remains largely conjectural. Herein, we posit that morphogenesis by self-organization enables the uncoupling of genomic mutational landscape from phenotypic diversification. Evidence is provided for a two-tiered interpretation of genomic changes in metazoan animals wherein mutations not only impact upon function of individual cells, but also alter the self-organization outcome during developmental morphogenesis. We provide evidence that the morphological impacts of mutations on self-organization could remain repressed if associated with an unmet negative energetic cost. We posit that accelerated morphological diversification in transition to the Cambrian period has occurred by emergence of dormant (i.e., reserved) morphological novelties whose molecular underpinnings were seeded in the Precambrian period.
Collapse
Affiliation(s)
- Filip Vujovic
- IDR/Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Ramin M Farahani
- IDR/Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
18
|
Zachar I, Boza G. The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.798045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the community under higher-level selection. In certain cases, cooperation can lead to a transition in individuality, when freely reproducing, unrelated entities (genes, microbes, etc.) irreversibly integrate to form a new evolutionary unit. The textbook example is endosymbiosis, prevalent among eukaryotes but virtually lacking among prokaryotes. Concerning the ubiquity of syntrophic microbial communities, it is intriguing why evolution has not lead to more transitions in individuality in the microbial domain. We set out to distinguish syntrophy-specific aspects of major transitions, to investigate why a transition in individuality within a syntrophic pair or community is so rare. We review the field of metabolic communities to identify potential evolutionary trajectories that may lead to a transition. Community properties, like joint metabolic capacity, functional profile, guild composition, assembly and interaction patterns are important concepts that may not only persist stably but according to thought-provoking theories, may provide the heritable information at a higher level of selection. We explore these ideas, relating to concepts of multilevel selection and of informational replication, to assess their relevance in the debate whether microbial communities may inherit community-level information or not.
Collapse
|
19
|
Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braakman R, Brown CT, Covert MW, Doney SC, Dyhrman ST, Edison AS, Eren AM, Levine NM, Li L, Ross AC, Saito MA, Santoro AE, Segrè D, Shade A, Sullivan MB, Vardi A. Microbial metabolites in the marine carbon cycle. Nat Microbiol 2022; 7:508-523. [PMID: 35365785 DOI: 10.1038/s41564-022-01090-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/23/2022] [Indexed: 01/08/2023]
Abstract
One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.
Collapse
Affiliation(s)
- Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Shady A Amin
- Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nicholas R Bates
- Bermuda Institute of Ocean Sciences, St George's, Bermuda.,School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rogier Braakman
- Departments of Earth, Atmospheric and Planetary Sciences, and Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Titus Brown
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Scott C Doney
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Science, Columbia University, Palisades, NY, USA
| | - Arthur S Edison
- Departments of Biochemistry and Genetics, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Helmholtz-Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Naomi M Levine
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Mak A Saito
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Daniel Segrè
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
20
|
Munné-Bosch S. Spatiotemporal limitations in plant biology research. TRENDS IN PLANT SCIENCE 2022; 27:346-354. [PMID: 34750071 DOI: 10.1016/j.tplants.2021.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 09/15/2021] [Accepted: 10/15/2021] [Indexed: 05/12/2023]
Abstract
The way we currently capture biological processes in space and time often limits our understanding of plant development and stress responses, leading to an incomplete picture of plant life. Choosing the correct time frame for the study of every biological process, from seed germination to senescence or in plant stress responses, is essential, despite methodological limitations. A greater effort is needed in current plant biology studies to incorporate spatiotemporal approaches so that scientific knowledge meets the possibilities technological advances currently provide. From molecular, biochemical, and cellular approaches to (eco)physiological and population studies scaled up to the ecosystem level, there is an urgent need to link space and time using integrative and scalable data.
Collapse
Affiliation(s)
- Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain; Institute of Research in Biodiversity (IRBio), University of Barcelona, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain; Institute of Nutrition and Food Safety (INSA), University of Barcelona, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
| |
Collapse
|
21
|
Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom. THE ISME JOURNAL 2022; 16:569-579. [PMID: 34482372 PMCID: PMC8776772 DOI: 10.1038/s41396-021-01084-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/13/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023]
Abstract
Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a proteomic proxy for regulatory cost, which showed that SAR11 had the lowest regulatory cost of any taxa we observed at our summertime Southern Ocean study site. Haptophytes had lower regulatory cost than diatoms, which may underpin haptophyte-to-diatom bloom progression in the Ross Sea. We were able to make these proteomic trait inferences by assessing various sources of bias in metaproteomics, providing practical recommendations for researchers in the field. We have quantified several proteomic traits (ribosomal and photosynthetic proteomic proportions, regulatory cost) in eukaryotic and bacterial taxa, which can then be incorporated into trait-based models of microbial communities that reflect resource allocation strategies.
Collapse
|
22
|
Casey JR, Boiteau RM, Engqvist MKM, Finkel ZV, Li G, Liefer J, Müller CL, Muñoz N, Follows MJ. Basin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiology. SCIENCE ADVANCES 2022; 8:eabl4930. [PMID: 35061539 PMCID: PMC8782455 DOI: 10.1126/sciadv.abl4930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Extensive microdiversity within Prochlorococcus, the most abundant marine cyanobacterium, occurs at scales from a single droplet of seawater to ocean basins. To interpret the structuring role of variations in genetic potential, as well as metabolic and physiological acclimation, we developed a mechanistic constraint-based modeling framework that incorporates the full suite of genes, proteins, metabolic reactions, pigments, and biochemical compositions of 69 sequenced isolates spanning the Prochlorococcus pangenome. Optimizing each strain to the local, observed physical and chemical environment along an Atlantic Ocean transect, we predicted variations in strain-specific patterns of growth rate, metabolic configuration, and physiological state, defining subtle niche subspaces directly attributable to differences in their encoded metabolic potential. Predicted growth rates covaried with observed ecotype abundances, affirming their significance as a measure of fitness and inferring a nonlinear density dependence of mortality. Our study demonstrates the potential to interpret global-scale ecosystem organization in terms of cellular-scale processes.
Collapse
Affiliation(s)
- John R. Casey
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Ocean and Earth Science and Technology, University of Hawai‘i at Ma¯noa, Honolulu, HI, USA
| | - Rene M. Boiteau
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Martin K. M. Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Zoe V. Finkel
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Gang Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Justin Liefer
- Department of Biology, Mount Allison University, Sackville, NB, Canada
| | | | - Nathalie Muñoz
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratories, Richland, WA, USA
| | - Michael J. Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
23
|
Tucker SJ, Freel KC, Monaghan EA, Sullivan CES, Ramfelt O, Rii YM, Rappé MS. Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean. PeerJ 2021; 9:e12274. [PMID: 34760357 PMCID: PMC8572523 DOI: 10.7717/peerj.12274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/19/2021] [Indexed: 01/04/2023] Open
Abstract
Surveys of microbial communities across transitions coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāneʻohe Bay on the island of Oʻahu, Hawaiʻi, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria (order Pelagibacterales) over a 2-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and exact amplicon sequence variants (ASVs) were evaluated. Seven of eight SAR11 subclades detected in this study showed distinct subclade distributions across the coastal to offshore environments. The SAR11 community was dominated by seven (of 106 total) SAR11 ASVs that made up an average of 77% of total SAR11. These seven ASVs spanned five different SAR11 subclades (Ia, Ib, IIa, IV, and Va), and were recovered from all samples collected from either the coastal environment, the offshore, or both. SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts, with the highest diversity within the little-studied subclade IIa. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.
Collapse
Affiliation(s)
- Sarah J Tucker
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Kelle C Freel
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
| | - Elizabeth A Monaghan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Clarisse E S Sullivan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Oscar Ramfelt
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Yoshimi M Rii
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,He'eia National Estuarine Research Reserve, Kāne'ohe, Hawai'i, United States
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
| |
Collapse
|
24
|
Closed microbial communities self-organize to persistently cycle carbon. Proc Natl Acad Sci U S A 2021; 118:2013564118. [PMID: 34740965 PMCID: PMC8609437 DOI: 10.1073/pnas.2013564118] [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] [Accepted: 09/24/2021] [Indexed: 12/16/2022] Open
Abstract
Life on Earth depends on ecologically driven nutrient cycles to regenerate resources. Understanding how nutrient cycles emerge from a complex web of ecological processes is a central challenge in ecology. However, we lack model ecosystems that can be replicated, manipulated, and quantified in the laboratory, making it challenging to determine how changes in composition and the environment impact cycling. Enabled by a new high-precision method to quantify carbon cycling, we show that materially closed microbial ecosystems (CES) provided with only light self-organize to robustly cycle carbon. Studying replicate CES that support a carbon cycle reveals variable community composition but a conserved set of metabolic capabilities. Our study helps establish CES as model biospheres for studying how ecosystems persistently cycle nutrients. Cycles of nutrients (N, P, etc.) and resources (C) are a defining emergent feature of ecosystems. Cycling plays a critical role in determining ecosystem structure at all scales, from microbial communities to the entire biosphere. Stable cycles are essential for ecosystem persistence because they allow resources and nutrients to be regenerated. Therefore, a central problem in ecology is understanding how ecosystems are organized to sustain robust cycles. Addressing this problem quantitatively has proved challenging because of the difficulties associated with manipulating ecosystem structure while measuring cycling. We address this problem using closed microbial ecosystems (CES), hermetically sealed microbial consortia provided with only light. We develop a technique for quantifying carbon cycling in hermetically sealed microbial communities and show that CES composed of an alga and diverse bacterial consortia self-organize to robustly cycle carbon for months. Comparing replicates of diverse CES, we find that carbon cycling does not depend strongly on the taxonomy of the bacteria present. Moreover, despite strong taxonomic differences, self-organized CES exhibit a conserved set of metabolic capabilities. Therefore, an emergent carbon cycle enforces metabolic but not taxonomic constraints on ecosystem organization. Our study helps establish closed microbial communities as model ecosystems to study emergent function and persistence in replicate systems while controlling community composition and the environment.
Collapse
|
25
|
Bajić D, Rebolleda-Gómez M, Muñoz MM, Sánchez Á. The Macroevolutionary Consequences of Niche Construction in Microbial Metabolism. Front Microbiol 2021; 12:718082. [PMID: 34671327 PMCID: PMC8522508 DOI: 10.3389/fmicb.2021.718082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/20/2021] [Indexed: 12/01/2022] Open
Abstract
Microorganisms display a stunning metabolic diversity. Understanding the origin of this diversity requires understanding how macroevolutionary processes such as innovation and diversification play out in the microbial world. Metabolic networks, which govern microbial resource use, can evolve through different mechanisms, e.g., horizontal gene transfer or de novo evolution of enzymes and pathways. This process is governed by a combination of environmental factors, selective pressures, and the constraints imposed by the genetic architecture of metabolic networks. In addition, many independent results hint that the process of niche construction, by which organisms actively modify their own and each other’s niches and selective pressures, could play a major role in microbial innovation and diversification. Yet, the general principles by which niche construction shapes microbial macroevolutionary patterns remain largely unexplored. Here, we discuss several new hypotheses and directions, and suggest metabolic modeling methods that could allow us to explore large-scale empirical genotype-phenotype-(G-P)-environment spaces in order to study the macroevolutionary effects of niche construction. We hope that this short piece will further stimulate a systematic and quantitative characterization of macroevolutionary patterns and processes in microbial metabolism.
Collapse
Affiliation(s)
- Djordje Bajić
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.,Microbial Sciences Institute, Yale University, West Haven, CT, United States
| | - María Rebolleda-Gómez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.,Microbial Sciences Institute, Yale University, West Haven, CT, United States.,Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.,Microbial Sciences Institute, Yale University, West Haven, CT, United States
| |
Collapse
|
26
|
|
27
|
Szeinbaum N, Toporek Y, Reinhard CT, Glass JB. Microbial helpers allow cyanobacteria to thrive in ferruginous waters. GEOBIOLOGY 2021; 19:510-520. [PMID: 33871172 PMCID: PMC8349797 DOI: 10.1111/gbi.12443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/15/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
The Great Oxidation Event (GOE) was a rapid accumulation of oxygen in the atmosphere as a result of the photosynthetic activity of cyanobacteria. This accumulation reflected the pervasiveness of O2 on the planet's surface, indicating that cyanobacteria had become ecologically successful in Archean oceans. Micromolar concentrations of Fe2+ in Archean oceans would have reacted with hydrogen peroxide, a byproduct of oxygenic photosynthesis, to produce hydroxyl radicals, which cause cellular damage. Yet, cyanobacteria colonized Archean oceans extensively enough to oxygenate the atmosphere, which likely required protection mechanisms against the negative impacts of hydroxyl radical production in Fe2+ -rich seas. We identify several factors that could have acted to protect early cyanobacteria from the impacts of hydroxyl radical production and hypothesize that microbial cooperation may have played an important role in protecting cyanobacteria from Fe2+ toxicity before the GOE. We found that several strains of facultative anaerobic heterotrophic bacteria (Shewanella) with ROS defence mechanisms increase the fitness of cyanobacteria (Synechococcus) in ferruginous waters. Shewanella species with manganese transporters provided the most protection. Our results suggest that a tightly regulated response to prevent Fe2+ toxicity could have been important for the colonization of ancient ferruginous oceans, particularly in the presence of high manganese concentrations and may expand the upper bound for tolerable Fe2+ concentrations for cyanobacteria.
Collapse
Affiliation(s)
- Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Yael Toporek
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | | | - Jennifer B. Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA
| |
Collapse
|
28
|
Moyer D, Pacheco AR, Bernstein DB, Segrè D. Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure. J Mol Evol 2021; 89:472-483. [PMID: 34230992 PMCID: PMC8318951 DOI: 10.1007/s00239-021-10018-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/12/2021] [Indexed: 11/15/2022]
Abstract
Uncovering the general principles that govern the structure of metabolic networks is key to understanding the emergence and evolution of living systems. Artificial chemistries can help illuminate this problem by enabling the exploration of chemical reaction universes that are constrained by general mathematical rules. Here, we focus on artificial chemistries in which strings of characters represent simplified molecules, and string concatenation and splitting represent possible chemical reactions. We developed a novel Python package, ARtificial CHemistry NEtwork Toolbox (ARCHNET), to study string chemistries using tools from the field of stoichiometric constraint-based modeling. In addition to exploring the topological characteristics of different string chemistry networks, we developed a network-pruning algorithm that can generate minimal metabolic networks capable of producing a specified set of biomass precursors from a given assortment of environmental nutrients. We found that the composition of these minimal metabolic networks was influenced more strongly by the metabolites in the biomass reaction than the identities of the environmental nutrients. This finding has important implications for the reconstruction of organismal metabolic networks and could help us better understand the rise and evolution of biochemical organization. More generally, our work provides a bridge between artificial chemistries and stoichiometric modeling, which can help address a broad range of open questions, from the spontaneous emergence of an organized metabolism to the structure of microbial communities.
Collapse
Affiliation(s)
- Devlin Moyer
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Alan R Pacheco
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
- Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - David B Bernstein
- Biological Design Center, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA.
- Department of Biology, Boston University, Boston, MA, 02215, USA.
- Biological Design Center, Boston University, Boston, MA, 02215, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
- Department of Physics, Boston University, Boston, MA, 02215, USA.
| |
Collapse
|
29
|
Cyanobacteria and biogeochemical cycles through Earth history. Trends Microbiol 2021; 30:143-157. [PMID: 34229911 DOI: 10.1016/j.tim.2021.05.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022]
Abstract
Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis, transforming the biology and chemistry of our planet. Genomic and evolutionary studies have revolutionized our understanding of early oxygenic phototrophs, complementing and dramatically extending inferences from the geologic record. Molecular clock estimates point to a Paleoarchean origin (3.6-3.2 billion years ago, bya) of the core proteins of Photosystem II (PSII) involved in oxygenic photosynthesis and a Mesoarchean origin (3.2-2.8 bya) for the last common ancestor of modern cyanobacteria. Nonetheless, most extant cyanobacteria diversified after the Great Oxidation Event (GOE), an environmental watershed ca. 2.45 bya made possible by oxygenic photosynthesis. Throughout their evolutionary history, cyanobacteria have played a key role in the global carbon cycle.
Collapse
|
30
|
Yamagishi JF, Saito N, Kaneko K. Adaptation of metabolite leakiness leads to symbiotic chemical exchange and to a resilient microbial ecosystem. PLoS Comput Biol 2021; 17:e1009143. [PMID: 34161322 PMCID: PMC8260005 DOI: 10.1371/journal.pcbi.1009143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/06/2021] [Accepted: 06/03/2021] [Indexed: 02/03/2023] Open
Abstract
Microbial communities display remarkable diversity, facilitated by the secretion of chemicals that can create new niches. However, it is unclear why cells often secrete even essential metabolites after evolution. Based on theoretical results indicating that cells can enhance their own growth rate by leaking even essential metabolites, we show that such "leaker" cells can establish an asymmetric form of mutualism with "consumer" cells that consume the leaked chemicals: the consumer cells benefit from the uptake of the secreted metabolites, while the leaker cells also benefit from such consumption, as it reduces the metabolite accumulation in the environment and thereby enables further secretion, resulting in frequency-dependent coexistence of multiple microbial species. As supported by extensive simulations, such symbiotic relationships generally evolve when each species has a complex reaction network and adapts its leakiness to optimize its own growth rate under crowded conditions and nutrient limitations. Accordingly, symbiotic ecosystems with diverse cell species that leak and exchange many metabolites with each other are shaped by cell-level adaptation of leakiness of metabolites. Moreover, the resultant ecosystems with entangled metabolite exchange are resilient against structural and environmental perturbations. Thus, we present a theory for the origin of resilient ecosystems with diverse microbes mediated by secretion and exchange of essential chemicals.
Collapse
Affiliation(s)
- Jumpei F. Yamagishi
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Nen Saito
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Kunihiko Kaneko
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, Japan
| |
Collapse
|
31
|
Raes EJ, Karsh K, Sow SLS, Ostrowski M, Brown MV, van de Kamp J, Franco-Santos RM, Bodrossy L, Waite AM. Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries. Nat Commun 2021; 12:2213. [PMID: 33850115 PMCID: PMC8044245 DOI: 10.1038/s41467-021-22409-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/09/2021] [Indexed: 02/01/2023] Open
Abstract
Global oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.
Collapse
Affiliation(s)
- Eric J Raes
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada.
| | | | - Swan L S Sow
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Den Burg, The Netherlands
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | | | - Rita M Franco-Santos
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | - Anya M Waite
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| |
Collapse
|
32
|
The cyanobacterium Prochlorococcus has divergent light-harvesting antennae and may have evolved in a low-oxygen ocean. Proc Natl Acad Sci U S A 2021; 118:2025638118. [PMID: 33707213 PMCID: PMC7980375 DOI: 10.1073/pnas.2025638118] [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] [Indexed: 01/01/2023] Open
Abstract
The marine unicellular cyanobacterium Prochlorococcus is the most abundant photosynthetic organism on Earth. Members of this genus are classically thought to be adapted to high-oxygen and nutrient-poor ocean conditions, with a principle divergence between high-light and low-light ecotypes. We show that the most basal Prochlorococcus lineages are adapted to the low-oxygen, low-light, and high-nutrient conditions found in the dimly illuminated waters of anoxic marine zones. The most basal lineages have retained phycobilisomes as light-harvesting antennae—a characteristic of most other cyanobacteria—whose loss was thought to define all Prochlorococcus. As oxygenic photosynthesis drove ocean oxidation in the ancient Earth, oxygen appears to have played as much a role as light and nutrients in driving Prochlorococcus evolution. Marine picocyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic organisms in the modern ocean, where they exert a profound influence on elemental cycling and energy flow. The use of transmembrane chlorophyll complexes instead of phycobilisomes as light-harvesting antennae is considered a defining attribute of Prochlorococcus. Its ecology and evolution are understood in terms of light, temperature, and nutrients. Here, we report single-cell genomic information on previously uncharacterized phylogenetic lineages of this genus from nutrient-rich anoxic waters of the eastern tropical North and South Pacific Ocean. The most basal lineages exhibit optical and genotypic properties of phycobilisome-containing cyanobacteria, indicating that the characteristic light-harvesting antenna of the group is not an ancestral attribute. Additionally, we found that all the indigenous lineages analyzed encode genes for pigment biosynthesis under oxygen-limited conditions, a trait shared with other freshwater and coastal marine cyanobacteria. Our findings thus suggest that Prochlorococcus diverged from other cyanobacteria under low-oxygen conditions before transitioning from phycobilisomes to transmembrane chlorophyll complexes and may have contributed to the oxidation of the ancient ocean.
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Aylward FO. The coevolutionary history of the microbial planet. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:12-14. [PMID: 32939975 DOI: 10.1111/1758-2229.12888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| |
Collapse
|
35
|
Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:85/1/e00135-20. [PMID: 33441489 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
Collapse
|
36
|
Kearney SM, Thomas E, Coe A, Chisholm SW. Microbial diversity of co-occurring heterotrophs in cultures of marine picocyanobacteria. ENVIRONMENTAL MICROBIOME 2021; 16:1. [PMID: 33902739 PMCID: PMC8067657 DOI: 10.1186/s40793-020-00370-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The cyanobacteria Prochlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; heterotrophs grow on organic carbon supplied by the photolithoautotrophs. For examining the selective pressures shaping autotroph/heterotroph interactions, we have made use of unialgal enrichment cultures of Prochlorococcus and Synechococcus maintained for hundreds to thousands of generations in the lab. We examine the diversity of heterotrophs in 74 enrichment cultures of these picocyanobacteria obtained from diverse areas of the global oceans. RESULTS Heterotroph community composition differed between clades and ecotypes of the autotrophic 'hosts' but there was significant overlap in heterotroph community composition across these cultures. Collectively, the cultures were comprised of many shared taxa, even at the genus level. Yet, observed differences in community composition were associated with time since isolation, location, depth, and methods of isolation. The majority of heterotrophs in the cultures are rare in the global ocean, but enrichment conditions favor the opportunistic outgrowth of these rare bacteria. However, we found a few examples, such as bacteria in the family Rhodobacteraceae, of heterotrophs that were ubiquitous and abundant in cultures and in the global oceans. We found their abundance in the wild is also positively correlated with that of picocyanobacteria. CONCLUSIONS Particular conditions surrounding isolation have a persistent effect on long-term culture composition, likely from bottlenecking and selection that happen during the early stages of enrichment for the picocyanobacteria. We highlight the potential for examining ecologically relevant relationships by identifying patterns of distribution of culture-enriched organisms in the global oceans.
Collapse
Affiliation(s)
- Sean M. Kearney
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, MA 02139 USA
| | - Elaina Thomas
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, MA 02139 USA
| | - Allison Coe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, MA 02139 USA
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, MA 02139 USA
| |
Collapse
|
37
|
Laurenceau R, Raho N, Forget M, Arellano AA, Chisholm SW. Frequency of mispackaging of Prochlorococcus DNA by cyanophage. THE ISME JOURNAL 2021; 15:129-140. [PMID: 32929209 PMCID: PMC7852597 DOI: 10.1038/s41396-020-00766-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/27/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023]
Abstract
Prochlorococcus cells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages-a podovirus, a siphovirus, and a myovirus-to mispackage host DNA in their capsids while infecting Prochlorococcus, the first step in phage-mediated horizontal gene transfer. We find the mispackaging frequencies are distinctly different among the three phages. Myoviruses mispackage host DNA at low and seemingly fixed frequencies, while podo- and siphoviruses vary in their mispackaging frequencies by orders of magnitude depending on growth light intensity. We link this difference to the concentration of intracellular reactive oxygen species and protein synthesis rates, both parameters increasing in response to higher light intensity. Based on our findings, we propose a model of mispackaging frequency determined by the imbalance between the production of capsids and the number of phage genome copies during infection: when protein synthesis rate increase to levels that the phage cannot regulate, they lead to an accumulation of empty capsids, in turn triggering more frequent host DNA mispackaging errors.
Collapse
Affiliation(s)
- Raphaël Laurenceau
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Nicolas Raho
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mathieu Forget
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institut de Biologie de l'Ecole Normale Supérieure, Département de Biologie, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Aldo A Arellano
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
38
|
Characterization of Light-Enhanced Respiration in Cyanobacteria. Int J Mol Sci 2020; 22:ijms22010342. [PMID: 33396191 PMCID: PMC7796093 DOI: 10.3390/ijms22010342] [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] [Received: 11/06/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 01/12/2023] Open
Abstract
In eukaryotic algae, respiratory O2 uptake is enhanced after illumination, which is called light-enhanced respiration (LER). It is likely stimulated by an increase in respiratory substrates produced during photosynthetic CO2 assimilation and function in keeping the metabolic and redox homeostasis in the light in eukaryotic cells, based on the interactions among the cytosol, chloroplasts, and mitochondria. Here, we first characterize LER in photosynthetic prokaryote cyanobacteria, in which respiration and photosynthesis share their metabolisms and electron transport chains in one cell. From the physiological analysis, the cyanobacterium Synechocystis sp. PCC 6803 performs LER, similar to eukaryotic algae, which shows a capacity comparable to the net photosynthetic O2 evolution rate. Although the respiratory and photosynthetic electron transports share the interchain, LER was uncoupled from photosynthetic electron transport. Mutant analyses demonstrated that LER is motivated by the substrates directly provided by photosynthetic CO2 assimilation, but not by glycogen. Further, the light-dependent activation of LER was observed even with exogenously added glucose, implying a regulatory mechanism for LER in addition to the substrate amounts. Finally, we discuss the physiological significance of the large capacity of LER in cyanobacteria and eukaryotic algae compared to those in plants that normally show less LER.
Collapse
|
39
|
Co‐culture with
Synechococcus
facilitates growth of
Prochlorococcus
under ocean acidification conditions. Environ Microbiol 2020; 22:4876-4889. [DOI: 10.1111/1462-2920.15277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 12/01/2022]
|
40
|
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.
Collapse
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.
| |
Collapse
|
41
|
Kontopoulos D, Smith TP, Barraclough TG, Pawar S. Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate. PLoS Biol 2020; 18:e3000894. [PMID: 33064736 PMCID: PMC7592915 DOI: 10.1371/journal.pbio.3000894] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 10/28/2020] [Accepted: 09/14/2020] [Indexed: 12/23/2022] Open
Abstract
Developing a thorough understanding of how ectotherm physiology adapts to different thermal environments is of crucial importance, especially in the face of global climate change. A key aspect of an organism's thermal performance curve (TPC)-the relationship between fitness-related trait performance and temperature-is its thermal sensitivity, i.e., the rate at which trait values increase with temperature within its typically experienced thermal range. For a given trait, the distribution of thermal sensitivities across species, often quantified as "activation energy" values, is typically right-skewed. Currently, the mechanisms that generate this distribution are unclear, with considerable debate about the role of thermodynamic constraints versus adaptive evolution. Here, using a phylogenetic comparative approach, we study the evolution of the thermal sensitivity of population growth rate across phytoplankton (Cyanobacteria and eukaryotic microalgae) and prokaryotes (bacteria and archaea), 2 microbial groups that play a major role in the global carbon cycle. We find that thermal sensitivity across these groups is moderately phylogenetically heritable, and that its distribution is shaped by repeated evolutionary convergence throughout its parameter space. More precisely, we detect bursts of adaptive evolution in thermal sensitivity, increasing the amount of overlap among its distributions in different clades. We obtain qualitatively similar results from evolutionary analyses of the thermal sensitivities of 2 physiological rates underlying growth rate: net photosynthesis and respiration of plants. Furthermore, we find that these episodes of evolutionary convergence are consistent with 2 opposing forces: decrease in thermal sensitivity due to environmental fluctuations and increase due to adaptation to stable environments. Overall, our results indicate that adaptation can lead to large and relatively rapid shifts in thermal sensitivity, especially in microbes for which rapid evolution can occur at short timescales. Thus, more attention needs to be paid to elucidating the implications of rapid evolution in organismal thermal sensitivity for ecosystem functioning.
Collapse
Affiliation(s)
- Dimitrios—Georgios Kontopoulos
- Science and Solutions for a Changing Planet DTP, Imperial College London, London, United Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, United Kingdom
| | - Thomas P. Smith
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, United Kingdom
| | - Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, United Kingdom
- Department of Zoology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Samraat Pawar
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, United Kingdom
| |
Collapse
|
42
|
Lee MD. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 2020; 35:4162-4164. [PMID: 30865266 PMCID: PMC6792077 DOI: 10.1093/bioinformatics/btz188] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 11/12/2022] Open
Abstract
Summary Genome-level evolutionary inference (i.e. phylogenomics) is becoming an increasingly essential step in many biologists’ work. Accordingly, there are several tools available for the major steps in a phylogenomics workflow. But for the biologist whose main focus is not bioinformatics, much of the computational work required—such as accessing genomic data on large scales, integrating genomes from different file formats, performing required filtering, stitching different tools together etc.—can be prohibitive. Here I introduce GToTree, a command-line tool that can take any combination of fasta files, GenBank files and/or NCBI assembly accessions as input and outputs an alignment file, estimates of genome completeness and redundancy, and a phylogenomic tree based on a specified single-copy gene (SCG) set. Although GToTree can work with any custom hidden Markov Models (HMMs), also included are 13 newly generated SCG-set HMMs for different lineages and levels of resolution, built based on searches of ∼12 000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees. Availability and implementation GToTree is open-source and freely available for download from: github.com/AstrobioMike/GToTree. It is implemented primarily in bash with helper scripts written in python. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| |
Collapse
|
43
|
Minimal cobalt metabolism in the marine cyanobacterium Prochlorococcus. Proc Natl Acad Sci U S A 2020; 117:15740-15747. [PMID: 32576688 DOI: 10.1073/pnas.2001393117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite very low concentrations of cobalt in marine waters, cyanobacteria in the genus Prochlorococcus retain the genetic machinery for the synthesis and use of cobalt-bearing cofactors (cobalamins) in their genomes. We explore cobalt metabolism in a Prochlorococcus isolate from the equatorial Pacific Ocean (strain MIT9215) through a series of growth experiments under iron- and cobalt-limiting conditions. Metal uptake rates, quantitative proteomic measurements of cobalamin-dependent enzymes, and theoretical calculations all indicate that Prochlorococcus MIT9215 can sustain growth with less than 50 cobalt atoms per cell, ∼100-fold lower than minimum iron requirements for these cells (∼5,100 atoms per cell). Quantitative descriptions of Prochlorococcus cobalt limitation are used to interpret the cobalt distribution in the equatorial Pacific Ocean, where surface concentrations are among the lowest measured globally but Prochlorococcus biomass is high. A low minimum cobalt quota ensures that other nutrients, notably iron, will be exhausted before cobalt can be fully depleted, helping to explain the persistence of cobalt-dependent metabolism in marine cyanobacteria.
Collapse
|
44
|
Muñoz-Marín MC, Gómez-Baena G, López-Lozano A, Moreno-Cabezuelo JA, Díez J, García-Fernández JM. Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus. THE ISME JOURNAL 2020; 14:1065-1073. [PMID: 32034281 PMCID: PMC7174365 DOI: 10.1038/s41396-020-0603-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 12/23/2022]
Abstract
Marine picocyanobacteria of the Prochlorococcus and Synechococcus genera have been longtime considered as autotrophic organisms. However, compelling evidence published over the last 15 years shows that these organisms can use different organic compounds containing key elements to survive in oligotrophic oceans, such as N (amino acids, amino sugars), S (dimethylsulfoniopropionate, DMSP), or P (ATP). Furthermore, marine picocyanobacteria can also take up glucose and use it as a source of carbon and energy, despite the fact that this compound is devoid of limiting elements and can also be synthesized by using standard metabolic pathways. This review will outline the main findings suggesting mixotrophy in the marine picocyanobacteria Prochlorococcus and Synechococcus, and its ecological relevance for these important primary producers.
Collapse
Affiliation(s)
- M C Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - G Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - A López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - J A Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - J Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - J M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain.
| |
Collapse
|
45
|
Laurenceau R, Bliem C, Osburne MS, Becker JW, Biller SJ, Cubillos-Ruiz A, Chisholm SW. Toward a genetic system in the marine cyanobacterium Prochlorococcus. Access Microbiol 2020; 2:acmi000107. [PMID: 33005871 PMCID: PMC7523629 DOI: 10.1099/acmi.0.000107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/30/2020] [Indexed: 11/26/2022] Open
Abstract
As the smallest and most abundant primary producer in the oceans, the cyanobacterium Prochlorococcus is of interest to diverse branches of science. For the past 30 years, research on this minimal phototroph has led to a growing understanding of biological organization across multiple scales, from the genome to the global ocean ecosystem. Progress in understanding drivers of its diversity and ecology, as well as molecular mechanisms underpinning its streamlined simplicity, has been hampered by the inability to manipulate these cells genetically. Multiple attempts have been made to develop an efficient genetic transformation method for Prochlorococcus over the years; all have been unsuccessful to date, despite some success with their close relative, Synechococcus. To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery into Prochlorococcus cells. We also report a novel protocol for obtaining axenic colonies and a new method for differentiating live and dead cells. The electroporation method can be used to optimize DNA delivery into any bacterium, making it a useful tool for advancing transformation systems in other genetically recalcitrant microorganisms.
Collapse
Affiliation(s)
- Raphaël Laurenceau
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christina Bliem
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marcia S Osburne
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Department of Molecular Biology and Microbiology Tufts University School of Medicine, Boston, MA, USA
| | - Jamie W Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Department of Biology, Haverford College, Haverford, PA, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Andres Cubillos-Ruiz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Present address: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
46
|
Abstract
Marine microbe growth is limited by iron over about half of the global ocean surface. Dissolved iron is quickly lost from the ocean, but its availability to marine microbes may be enhanced by binding with organic molecules which, in turn, are produced by microbes. We hypothesize this forms a reinforcing cycle between biological activity and iron cycling that locally matches the availability of iron and other nutrients, leading to global-scale resource colimitation between macronutrients and micronutrients, and maximizing biological productivity. Idealized models support this hypothesis, depending on the specific relationships between microbial sources and sinks of organic molecules. An evolutionary selection may have occurred which optimizes these characteristics, resulting in “just enough” iron in the ocean. Iron is the limiting factor for biological production over a large fraction of the surface ocean because free iron is rapidly scavenged or precipitated under aerobic conditions. Standing stocks of dissolved iron are maintained by association with organic molecules (ligands) produced by biological processes. We hypothesize a positive feedback between iron cycling, microbial activity, and ligand abundance: External iron input fuels microbial production, creating organic ligands that support more iron in seawater, leading to further macronutrient consumption until other microbial requirements such as macronutrients or light become limiting, and additional iron no longer increases productivity. This feedback emerges in numerical simulations of the coupled marine cycles of macronutrients and iron that resolve the dynamic microbial production and loss of iron-chelating ligands. The model solutions resemble modern nutrient distributions only over a finite range of prescribed ligand source/sink ratios where the model ocean is driven to global-scale colimitation by micronutrients and macronutrients and global production is maximized. We hypothesize that a global-scale selection for microbial ligand cycling may have occurred to maintain “just enough” iron in the ocean.
Collapse
|
47
|
Wheeler LC, Smith SD. Computational Modeling of Anthocyanin Pathway Evolution: Biases, Hotspots, and Trade-offs. Integr Comp Biol 2020; 59:585-598. [PMID: 31120530 DOI: 10.1093/icb/icz049] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The alteration of metabolic pathways is a common mechanism underlying the evolution of new phenotypes. Flower color is a striking example of the importance of metabolic evolution in a complex phenotype, wherein shifts in the activity of the underlying pathway lead to a wide range of pigments. Although experimental work has identified common classes of mutations responsible for transitions among colors, we lack a unifying model that relates pathway function and activity to the evolution of distinct pigment phenotypes. One challenge in creating such a model is the branching structure of pigment pathways, which may lead to evolutionary trade-offs due to competition for shared substrates. In order to predict the effects of shifts in enzyme function and activity on pigment production, we created a simple kinetic model of a major plant pigmentation pathway: the anthocyanin pathway. This model describes the production of the three classes of blue, purple, and red anthocyanin pigments, and accordingly, includes multiple branches and substrate competition. We first studied the general behavior of this model using a naïve set of parameters. We then stochastically evolved the pathway toward a defined optimum and analyzed the patterns of fixed mutations. This approach allowed us to quantify the probability density of trajectories through pathway state space and identify the types and number of changes. Finally, we examined whether our simulated results qualitatively align with experimental observations, i.e., the predominance of mutations which change color by altering the function of branching genes in the pathway. These analyses provide a theoretical framework that can be used to predict the consequences of new mutations in terms of both pigment phenotypes and pleiotropic effects.
Collapse
Affiliation(s)
- L C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80302, USA
| | - S D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80302, USA
| |
Collapse
|
48
|
Hennon GMM, Dyhrman ST. Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms. HARMFUL ALGAE 2020; 91:101587. [PMID: 32057337 DOI: 10.1016/j.hal.2019.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/10/2023]
Abstract
Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.
Collapse
Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks, AK, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.
| |
Collapse
|
49
|
Mende DR, Boeuf D, DeLong EF. Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre. Front Microbiol 2019; 10:2273. [PMID: 31632377 PMCID: PMC6779783 DOI: 10.3389/fmicb.2019.02273] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/18/2019] [Indexed: 01/23/2023] Open
Abstract
Marine microbial communities are responsible for many important ecosystem processes in the oceans. Their variability across time and depths is well recognized, but mostly at a coarse-grained taxonomic resolution. To gain a deeper perspective on ecological patterns of bacterioplankton diversity in the North Pacific Subtropical Gyre, we characterized bacterioplankton communities throughout the water column at a fine-grained taxonomic level with a focus on temporally persistent (core) populations. Considerable intra-clade microdiversity was evident in virtually every microbial clade examined. While some of the most abundant populations comprised only a small fraction of the intra-clade microdiversity, they formed a temporally persistent core within a more diverse array of less abundant ephemeral populations. The depth-stratified population structure within many phylogenetically disparate clades suggested that ecotypic variation was the rule among most planktonic bacterial and archaeal lineages. Our results suggested that the abundant, persistent core populations comprised the bulk of the biomass within any given clade. As such, we postulate that these core populations are largely responsible for microbially driven ecosystem processes, and so represent ideal targets for elucidating key microbial processes in the open-ocean water column.
Collapse
Affiliation(s)
- Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Dominique Boeuf
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
| |
Collapse
|
50
|
The efficiency paradox: How wasteful competitors forge thrifty ecosystems. Proc Natl Acad Sci U S A 2019; 116:17619-17623. [PMID: 31420512 DOI: 10.1073/pnas.1901785116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Organic waste, an inevitable byproduct of metabolism, increases in amount as metabolic rates (per capita power) of animals and plants rise. Most of it is recycled within aerobic ecosystems, but some is lost to the system and is sequestered in the crust for millions of years. Here, I identify and resolve a previously overlooked paradox concerning the long-term loss of organic matter. In this efficiency paradox, high-powered species are inefficient in that they release copious waste, but the ecosystems they inhabit lose almost no organic matter. Systems occupied by more efficient low-powered species suffer greater losses because of less efficient recycling. Over Phanerozoic time, ecosystems have become more productive and increasingly efficient at retaining and redistributing organic matter even as opportunistic and highly competitive producers and consumers gained power and became less efficient. These patterns and trends are driven by natural selection at the level of individuals and coherent groups, which favors winners that are more powerful, active, and wasteful. The activities of these competitors collectively create conditions that are increasingly conducive to more efficient recycling and retention of organic matter in the ecosystem.
Collapse
|