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Kiørboe T. Organismal trade-offs and the pace of planktonic life. Biol Rev Camb Philos Soc 2024. [PMID: 38855937 DOI: 10.1111/brv.13108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024]
Abstract
No one is perfect, and organisms that perform well in some habitat or with respect to some tasks, do so at the cost of performance in others: there are inescapable trade-offs. Organismal trade-offs govern the structure and function of ecosystems and attempts to demonstrate and quantify trade-offs have therefore been an important goal for ecologists. In addition, trade-offs are a key component in trait-based ecosystem models. Here, I synthesise evidence of trade-offs in plankton organisms, from bacteria to zooplankton, and show how a slow-fast gradient in life histories emerges. I focus on trade-offs related to the main components of an organism's Darwinian fitness, that is resource acquisition, survival, and propagation. All consumers need to balance the need to eat without being eaten, and diurnal vertical migration, where zooplankton hide at depth during the day to avoid visual predators but at the cost of missed feeding opportunities in the productive surface layer, is probably the best documented result of this trade-off. However, there are many other more subtle but equally important behaviours that similarly are the result of an optimisation of these trade-offs. Most plankton groups have also developed more explicit defence mechanisms, such as toxin production or evasive behaviours that are harnessed in the presence of their predators; the costs of these have often proved difficult to quantify or even demonstrate, partly because they only materialise under natural conditions. Finally, all multicellular organisms must allocate time and resources among growth, reproduction, and maintenance (e.g. protein turnover and DNA repair), and mate finding may compromise both survival and feeding. The combined effects of all these trade-offs is the emergence of a slow-fast gradient in the pace-of-life, likely the most fundamental principle for the organisation of organismal life histories. This crystallisation of trade-offs may offer a path to further simplification of trait-based models of marine ecosystems.
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Affiliation(s)
- Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, 2800 Kgs, Kemitorvet, Kgs. Lyngby, Denmark
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2
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Zhang S, Zheng T, Zhou M, Niu B, Li Y. Exposure to the mixotrophic dinoflagellate Lepidodinium sp. and its cues increase toxin production of Pseudo-nitzschia multiseries. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169812. [PMID: 38181942 DOI: 10.1016/j.scitotenv.2023.169812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
The present study examined the defense responses of toxigenic Pseudo-nitzschia species (P. multiseries) to a mixotrophic dinoflagellate, Lepidodinium sp., and its associated cues. We evaluated their responses to different predation risks, including direct physical contact and indirect interactions facilitated by cues from Lepidodinium sp. during active feeding on heterospecific prey (Rhodonomas salina), limited feeding on conspecific prey (P. multiseries) and non-feeding (autotrophic growth in f/2 medium) states. This study is the first investigation of these trophic interactions. Our results demonstrated a significant increase in cellular domoic acid (cDA) in P. multiseries when exposed to Lepidodinium sp. and its associated cues, which was 1.38 to 2.42 times higher than the non-induced group. Notably, this increase was observed regardless of Lepidodinium sp. feeding on this toxic diatom and nutritional modes. However, the most significant increase occurred when they directly interacted. These findings suggest that P. multiseries evaluates predation risk and increases cDA production as a defensive strategy against potential grazing threats. No morphological changes were observed in P. multiseries in response to Lepidodinium sp. or its cues. P. multiseries cultured in flasks of Group L+P-P showed a decrease in growth, but Group L-P and Group L+R-P did not exhibit any decrease. These results suggest a lack of consistent trade-offs between the defense response and growth, thus an increase in cDA production may be a sustainable and efficient defense strategy for P. multiseries. Furthermore, our findings indicate that P. multiseries had no significant impact on the fitness (cell size, growth and/or grazing) of Lepidodinium sp. and R. salina, which suggests no evident toxic or allelopathic impacts on these two phytoplankton species. This study enhances our understanding of the trophic interactions between toxic diatoms and mixotrophic dinoflagellates and helps elucidate the dynamics of Harmful Algal Blooms, toxin transmission, and their impact on ecosystem health.
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Affiliation(s)
- Shuwen Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China
| | - Tingting Zheng
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China
| | - Muyao Zhou
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China
| | - Biaobiao Niu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China
| | - Yang Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China.
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3
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Kiørboe T. Predation in a Microbial World: Mechanisms and Trade-Offs of Flagellate Foraging. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:361-381. [PMID: 37368955 DOI: 10.1146/annurev-marine-020123-102001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Heterotrophic nanoflagellates are the main consumers of bacteria and picophytoplankton in the ocean and thus play a key role in ocean biogeochemistry. They are found in all major branches of the eukaryotic tree of life but are united by all being equipped with one or a few flagella that they use to generate a feeding current. These microbial predators are faced with the challenges that viscosity at this small scale impedes predator-prey contact and that their foraging activity disturbs the ambient water and thus attracts their own flow-sensing predators. Here, I describe some of the diverse adaptations of the flagellum to produce sufficient force to overcome viscosity and of the flagellar arrangement to minimize fluid disturbances, and thus of the various solutions to optimize the foraging-predation risk trade-off. I demonstrate how insights into this trade-off can be used to develop robust trait-based models of microbial food webs.
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Affiliation(s)
- Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kongens Lyngby, Denmark;
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Jansson JK. Soil viruses: Understudied agents of soil ecology. Environ Microbiol 2023; 25:143-146. [PMID: 36271323 PMCID: PMC10100255 DOI: 10.1111/1462-2920.16258] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/21/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Janet K Jansson
- Department of Biosciences, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
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Lineage-Specific Growth Curves Document Large Differences in Response of Individual Groups of Marine Bacteria to the Top-Down and Bottom-Up Controls. mSystems 2021; 6:e0093421. [PMID: 34581594 PMCID: PMC8547455 DOI: 10.1128/msystems.00934-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Marine bacterioplankton represent a diverse assembly of species differing largely in their abundance, physiology, metabolic activity, and role in microbial food webs. To analyze their sensitivity to bottom-up and top-down controls, we performed a manipulation experiment where grazers were removed, with or without the addition of phosphate. Using amplicon-reads normalization by internal standard (ARNIS), we reconstructed growth curves for almost 300 individual phylotypes. Grazer removal caused a rapid growth of most bacterial groups, which grew at rates of 0.6 to 3.5 day−1, with the highest rates (>4 day−1) recorded among Rhodobacteraceae, Oceanospirillales, Alteromonadaceae, and Arcobacteraceae. Based on their growth response, the phylotypes were divided into three basic groups. Most of the phylotypes responded positively to both grazer removal as well as phosphate addition. The second group (containing, e.g., Rhodobacterales and Rhizobiales) responded to the grazer removal but not to the phosphate addition. Finally, some clades, such as SAR11 and Flavobacteriaceae, responded only to phosphate amendment but not to grazer removal. Our results show large differences in bacterial responses to experimental manipulations at the phylotype level and document different life strategies of marine bacterioplankton. In addition, growth curves of 130 phylogroups of aerobic anoxygenic phototrophs were reconstructed based on changes of the functional pufM gene. The use of functional genes together with rRNA genes may significantly expand the scientific potential of the ARNIS technique. IMPORTANCE Growth is one of the main manifestations of life. It is assumed generally that bacterial growth is constrained mostly by nutrient availability (bottom-up control) and grazing (top-down control). Since marine bacteria represent a very diverse assembly of species with different metabolic properties, their growth characteristics also largely differ accordingly. Currently, the growth of marine microorganisms is typically evaluated using microscopy in combination with fluorescence in situ hybridization (FISH). However, these laborious techniques are limited in their throughput and taxonomical resolution. Therefore, we combined a classical manipulation experiment with next-generation sequencing to resolve the growth dynamics of almost 300 bacterial phylogroups in the coastal Adriatic Sea. The analysis documented that most of the phylogroups responded positively to both grazer removal and phosphate addition. We observed significant differences in growth kinetics among closely related species, which could not be distinguished by the classical FISH technique.
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Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria. mBio 2021; 12:e0087321. [PMID: 34060332 PMCID: PMC8262939 DOI: 10.1128/mbio.00873-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The mechanisms driving cyanobacterial harmful algal blooms (HABs) like those caused by Microcystis aeruginosa remain elusive, but improved defense against viral predation has been implicated for success in eutrophic environments. Our genus-level analyses of 139,023 genomes revealed that HAB-forming cyanobacteria carry vastly more restriction modification systems per genome (RMPG) than nearly all other prokaryotic genera, suggesting that viral defense is a cornerstone of their ecological success. In contrast, picocyanobacteria that numerically dominate nutrient-poor systems have the fewest RMPG within the phylum Cyanobacteria. We used classic resource competition models to explore the hypothesis that nutrient enrichments drive ecological selection for high RMPG due to increased host-phage contact rate. These classic models, agnostic to the mechanism of defense, explain how nutrient loading can select for increased RMPG but, importantly, fail to explain the extreme accumulation of these defense systems. However, extreme accumulation of RMPG can be achieved in a novel “memory” model that accounts for a unique activity of restriction modification systems: the accidental methylation of viral DNA by the methyltransferase. The methylated virus “remembers” the RM defenses of its former host and can evade these defenses if they are present in the next host. This viral memory leads to continual RM system devaluation; RMs accumulate extensively because the benefit of each addition is diminished. Our modeling leads to the hypothesis that nutrient loading and virion methylation drive the extreme accumulation of RMPG in HAB-forming cyanobacteria. Finally, our models suggest that hosts with different RMPG values can coexist when hosts have unique sets of RM systems.
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Temperate infection in a virus-host system previously known for virulent dynamics. Nat Commun 2020; 11:4626. [PMID: 32934228 PMCID: PMC7493887 DOI: 10.1038/s41467-020-18078-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
The blooming cosmopolitan coccolithophore Emiliania huxleyi and its viruses (EhVs) are a model for density-dependent virulent dynamics. EhVs commonly exhibit rapid viral reproduction and drive host death in high-density laboratory cultures and mesocosms that simulate blooms. Here we show that this system exhibits physiology-dependent temperate dynamics at environmentally relevant E. huxleyi host densities rather than virulent dynamics, with viruses switching from a long-term non-lethal temperate phase in healthy hosts to a lethal lytic stage as host cells become physiologically stressed. Using this system as a model for temperate infection dynamics, we present a template to diagnose temperate infection in other virus-host systems by integrating experimental, theoretical, and environmental approaches. Finding temperate dynamics in such an established virulent host-virus model system indicates that temperateness may be more pervasive than previously considered, and that the role of viruses in bloom formation and decline may be governed by host physiology rather than by host-virus densities.
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Thingstad TF, Våge S. Host-virus-predator coexistence in a grey-box model with dynamic optimization of host fitness. THE ISME JOURNAL 2019; 13:3102-3111. [PMID: 31527663 PMCID: PMC6864060 DOI: 10.1038/s41396-019-0496-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 08/01/2019] [Accepted: 08/15/2019] [Indexed: 11/09/2022]
Abstract
Lytic viruses are believed to affect both flow patterns and host diversity in microbial food webs. Models resolving host and virus communities into subgroups can represent both aspects. However, when flow pattern is the prime interest, such models may seem unnecessary complex. This has led to proposals of black-box models using only total community sizes as state variables. This simplification creates a coexistence problem, however, since predator and virus communities then compete for the same, shared, prey = host community. Mathematically, this problem can be solved by introducing feedbacks allowing community-level properties to adapt. The different mathematical alternatives for such feedback represent different ecological assumptions and thus different hypotheses for how the balance between predators and viruses is controlled in nature. We here explore a model where the feedback works through an increase in host community resistance in response to high virus abundances, thereby reducing virus production. We use a dynamic "strategy" index S to describe the balance between defensive and competitive abilities in the host community, and assume the rate of change in S to be proportional to the local slope of the per capita fitness gradient for the host. We explore how such a "grey-box" model can allow stable coexistence of viruses and predators, and how equilibrium food web structure, virus-to-host ratio, and partitioning of host production varies; both as functions of host community traits, and as functions of external bottom-up and top-down drivers.
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Affiliation(s)
| | - Selina Våge
- Department of Biological Sciences, University of Bergen, 5020, Bergen, Norway
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9
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Budaev S, Jørgensen C, Mangel M, Eliassen S, Giske J. Decision-Making From the Animal Perspective: Bridging Ecology and Subjective Cognition. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00164] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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10
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Cadier M, Andersen KH, Visser AW, Kiørboe T. Competition–defense tradeoff increases the diversity of microbial plankton communities and dampens trophic cascades. OIKOS 2019. [DOI: 10.1111/oik.06101] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Mathilde Cadier
- Centre for Ocean Life, DTU Aqua, Technical Univ. of Denmark 2800 Kgs. Lyngby Denmark
| | - Ken H. Andersen
- Centre for Ocean Life, DTU Aqua, Technical Univ. of Denmark 2800 Kgs. Lyngby Denmark
| | - Andre W. Visser
- Centre for Ocean Life, DTU Aqua, Technical Univ. of Denmark 2800 Kgs. Lyngby Denmark
| | - Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical Univ. of Denmark 2800 Kgs. Lyngby Denmark
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Kurm V, van der Putten WH, Hol WHG. Cultivation-success of rare soil bacteria is not influenced by incubation time and growth medium. PLoS One 2019; 14:e0210073. [PMID: 30629606 PMCID: PMC6328151 DOI: 10.1371/journal.pone.0210073] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 12/17/2018] [Indexed: 11/27/2022] Open
Abstract
Rare bacterial species have recently attracted interest due to their many potential beneficial functions. However, only little is known about their cultivability. In this study we test the hypotheses that the use of flow cell-sorting for cultivation results in a high proportion of rare soil bacterial isolates relative to bacterial taxa that are abundant in soil. Moreover, we investigate whether different oligotrophic cultivation media and a prolonged incubation time increase the number of cultivated rare species. In a cultivation study we used flow cell sorting to select for small cells and to separate single cells, and grew bacteria on different oligotrophic media with prolonged incubation times. The abundance of the isolates in the field was assessed by comparing them to a 454-sequencing dataset from the same soil. Consequentially, all bacterial isolates were classified as either rare (<0.01% relative abundance) or abundant (>0.01% relative abundance) in the field soil. We found more bacterial taxa among the isolates that were abundant in soil than would be expected by the proportion of abundant species in the field. Neither incubation time nor growth medium had an influence on the recovery of rare species. However, we did find differences in time until visible growth on the plate between different phylogenetic classes of the isolates. These results indicate that rare cultivable species are active and not more likely to be dormant than abundant species, as has been suggested as a reason for their rarity. Moreover, future studies should be aware of the influence incubation time might have on the phylogenetic composition of the isolate collection.
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Affiliation(s)
- Viola Kurm
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- * E-mail:
| | - Wim H. van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - W. H. Gera Hol
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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12
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Silva L, Calleja ML, Huete-Stauffer TM, Ivetic S, Ansari MI, Viegas M, Morán XAG. Low Abundances but High Growth Rates of Coastal Heterotrophic Bacteria in the Red Sea. Front Microbiol 2019; 9:3244. [PMID: 30666244 PMCID: PMC6330340 DOI: 10.3389/fmicb.2018.03244] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/13/2018] [Indexed: 11/29/2022] Open
Abstract
Characterized by some of the highest naturally occurring sea surface temperatures, the Red Sea remains unexplored regarding the dynamics of heterotrophic prokaryotes. Over 16 months, we used flow cytometry to characterize the abundance and growth of four physiological groups of heterotrophic bacteria: membrane-intact (Live), high and low nucleic acid content (HNA and LNA) and actively respiring (CTC+) cells in shallow coastal waters. Chlorophyll a, dissolved organic matter (DOC and DON) concentrations, and their fluorescent properties were also measured as proxies of bottom-up control. We performed short-term incubations (6 days) with the whole microbial community (Community treatment), and with the bacterial community only after removing predators by filtration (Filtered treatment). Initial bacterial abundances ranged from 1.46 to 4.80 × 105 cells mL-1. Total specific growth rates in the Filtered treatment ranged from 0.76 to 2.02 d-1. Live and HNA cells displayed similar seasonal patterns, with higher values during late summer and fall (2.13 and 2.33 d-1, respectively) and lower in late spring (1.02 and 1.01 d-1, respectively). LNA cells were outgrown by the other physiological groups (0.33-1.08 d-1) while CTC+ cells (0.28-1.85 d-1) showed weaker seasonality. The Filtered treatment yielded higher bacterial abundances than the Community treatment in all but 2 of the incubations, and carrying capacities peaked in November 2016 (1.04 × 106 cells mL-1), with minimum values (3.61 × 105 cells mL-1) observed in May 2017. The high temperatures experienced from May through October 2016 (33.4 ± 0.4°C) did not constrain the growth of heterotrophic bacteria. Indeed, bacterial growth efficiencies were positively correlated with environmental temperature, reflecting the presence of more labile compounds (high DON concentrations resulting in lower C:N ratios) in summer. The overall high specific growth rates and the consistently higher carrying capacities in the Filtered treatment suggest that strong top-down control by protistan grazers was the likely cause for the low heterotrophic bacteria abundances.
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Affiliation(s)
- Luis Silva
- Division of Biological and Environmental Sciences and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | | | | | | | | | - Xosé Anxelu G. Morán
- Division of Biological and Environmental Sciences and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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13
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Chakraborty S, Pančić M, Andersen KH, Kiørboe T. The cost of toxin production in phytoplankton: the case of PST producing dinoflagellates. THE ISME JOURNAL 2019; 13:64-75. [PMID: 30108304 PMCID: PMC6298997 DOI: 10.1038/s41396-018-0250-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/29/2018] [Accepted: 07/19/2018] [Indexed: 01/23/2023]
Abstract
Many species of phytoplankton produce toxins that may provide protection from grazing. In that case one would expect toxin production to be costly; else all species would evolve toxicity. However, experiments have consistently failed to show any costs. Here, we show that costs of toxin production are environment dependent but can be high. We develop a fitness optimization model to estimate rate, costs, and benefits of toxin production, using PST (paralytic shellfish toxin) producing dinoflagellates as an example. Costs include energy and material (nitrogen) costs estimated from well-established biochemistry of PSTs, and benefits are estimated from relationship between toxin content and grazing mortality. The model reproduces all known features of PST production: inducibility in the presence of grazer cues, low toxicity of nitrogen-starved cells, but high toxicity of P-limited and light-limited cells. The model predicts negligible reduction in cell division rate in nitrogen replete cells, consistent with observations, but >20% reduction when nitrogen is limiting and abundance of grazers high. Such situation is characteristic of coastal and oceanic waters during summer when blooms of toxic algae typically develop. The investment in defense is warranted, since the net growth rate is always higher in defended than in undefended cells.
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Affiliation(s)
- Subhendu Chakraborty
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kemitorvet, Kgs.2800, Lyngby, Denmark.
| | - Marina Pančić
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kemitorvet, Kgs.2800, Lyngby, Denmark
| | - Ken H Andersen
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kemitorvet, Kgs.2800, Lyngby, Denmark
| | - Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kemitorvet, Kgs.2800, Lyngby, Denmark
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14
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Dou C, Xiong J, Gu Y, Yin K, Wang J, Hu Y, Zhou D, Fu X, Qi S, Zhu X, Yao S, Xu H, Nie C, Liang Z, Yang S, Wei Y, Cheng W. Structural and functional insights into the regulation of the lysis-lysogeny decision in viral communities. Nat Microbiol 2018; 3:1285-1294. [PMID: 30323253 DOI: 10.1038/s41564-018-0259-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/31/2018] [Indexed: 02/05/2023]
Abstract
Communication is vital for all organisms including microorganisms, which is clearly demonstrated by the bacterial quorum-sensing system. However, the molecular mechanisms underlying communication among viruses (phages) via the quorum-sensing-like 'arbitrium' system remain unclear. Viral or host densities are known to be related to an increased prevalence of lysogeny; however, how the switch from the lytic to the lysogenic pathway occurs is unknown. Thus, we sought to reveal mechanisms of communication among viruses and determine the lysogenic dynamics involved. Structural and functional analyses of the phage-derived SAIRGA and GMPRGA peptides and their corresponding receptors, phAimR and spAimR, indicated that SAIRGA directs the lysis-lysogeny decision of phi3T by modulating conformational changes in phAimR, whereas GMPRGA regulates the lysis-lysogeny pathway by stabilizing spAimR in the dimeric state. Although temperate viruses are thought to share a similar lytic-lysogenic cycle switch model, our study suggests the existence of alternative strain-specific mechanisms that regulate the lysis-lysogeny decision. Collectively, these findings provide insights into the molecular mechanisms underlying communication among viruses, offering theoretical applications for the treatment of infectious viral diseases.
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Affiliation(s)
- Chao Dou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Jie Xiong
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yijun Gu
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Shanghai, China
| | - Kun Yin
- Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Disease, Jining, China
| | - Jinjing Wang
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yuehong Hu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Dan Zhou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Xianghui Fu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shiqian Qi
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Xiaofeng Zhu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shaohua Yao
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Heng Xu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Chunlai Nie
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Zongan Liang
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shengyong Yang
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yuquan Wei
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.
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15
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Koffel T, Daufresne T, Massol F, Klausmeier CA. Plant Strategies along Resource Gradients. Am Nat 2018; 192:360-378. [DOI: 10.1086/698600] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Pančić M, Kiørboe T. Phytoplankton defence mechanisms: traits and trade-offs. Biol Rev Camb Philos Soc 2018; 93:1269-1303. [DOI: 10.1111/brv.12395] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Marina Pančić
- Centre for Ocean Life; Technical University of Denmark, DTU Aqua, Kemitorvet B201; Kongens Lyngby DK-2800 Denmark
| | - Thomas Kiørboe
- Centre for Ocean Life; Technical University of Denmark, DTU Aqua, Kemitorvet B201; Kongens Lyngby DK-2800 Denmark
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Sheldon spectrum and the plankton paradox: two sides of the same coin—a trait-based plankton size-spectrum model. J Math Biol 2017; 76:67-96. [PMID: 28547211 PMCID: PMC5754429 DOI: 10.1007/s00285-017-1132-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 04/18/2017] [Indexed: 01/25/2023]
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Abstract
SAR11 is a group of small, carbon-oxidizing bacteria that reach a global estimated population size of 2.4×1028 cells-approximately 25% of all plankton. They are found throughout the oceans but reach their largest numbers in stratified, oligotrophic gyres, which are an expanding habitat in the warming oceans. SAR11 likely had a Precambrian origin and, over geological time, evolved into the niche of harvesting labile, low-molecular-weight dissolved organic matter (DOM). SAR11 cells are minimal in size and complexity, a phenomenon known as streamlining that is thought to benefit them by lowering the material costs of replication and maximizing transport functions that are essential to competition at ultralow nutrient concentrations. One of the surprises in SAR11 metabolism is their ability to both oxidize and produce a variety of volatile organic compounds that can diffuse into the atmosphere. SAR11 cells divide slowly and lack many forms of regulation commonly used by bacterial cells to adjust to changing environmental conditions. As a result of genome reduction, they require an unusual range of nutrients, which leads to complex biochemical interactions with other plankton. The study of SAR11 is providing insight into the biogeochemistry of labile DOM and is affecting microbiology beyond marine science by providing a model for understanding the evolution and function of streamlined cells.
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Våge S, Thingstad TF. Fractal Hypothesis of the Pelagic Microbial Ecosystem-Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web? Front Microbiol 2015; 6:1357. [PMID: 26648929 PMCID: PMC4664636 DOI: 10.3389/fmicb.2015.01357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/16/2015] [Indexed: 11/13/2022] Open
Abstract
Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales.
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Affiliation(s)
- Selina Våge
- Marine Microbial Ecology Group, Department of Biology, University of Bergen and Hjort Centre for Marine Ecosystem Dynamics Bergen, Norway
| | - T Frede Thingstad
- Marine Microbial Ecology Group, Department of Biology, University of Bergen and Hjort Centre for Marine Ecosystem Dynamics Bergen, Norway
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Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary. ISME JOURNAL 2015; 10:823-32. [PMID: 26394004 DOI: 10.1038/ismej.2015.156] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/10/2015] [Accepted: 07/15/2015] [Indexed: 02/01/2023]
Abstract
Interpretation of 16S ribosomal RNA (rRNA) to 16S rRNA gene ratios (rRNA:rDNA) is based on a limited number of studies with rapidly growing copiotrophic bacteria. The most abundant bacteria in the ocean are oligotrophs, which probably grow more slowly than those bacteria whose rRNA:rDNA versus growth rate relationships are known. To examine whether rRNA:rDNA varies differently in oligotrophic marine bacteria than in copiotrophic bacteria, we used quantitative PCR and reverse transcriptase quantitative PCR to measure rRNA:rDNA in two marine copiotrophs and in two marine oligotrophs, including Candidatus Pelagibacter ubique HTCC1062, a coastal isolate of SAR11, the most abundant bacterial clade in the ocean. The rRNA:rDNA ratios for the two copiotrophs were similar to those expected on the basis of an analysis of previously studied copiotrophic bacteria, while the ratios for the two oligotrophs were substantially lower than predicted even given their slow growth rates. The rRNA:rDNA ratios determined along a transect in the Delaware estuary suggested that SAR11 bacteria grow at rates close to the growth rate in culture, while rates of the two copiotrophs were far below those observed in laboratory cultures. Our results have implications for interpreting rRNA:rDNA from natural communities, understanding growth strategies and comparing regulatory mechanisms in copiotrophs and oligotrophs.
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van Velzen E, Etienne RS. The importance of ecological costs for the evolution of plant defense against herbivory. J Theor Biol 2015; 372:89-99. [PMID: 25747775 DOI: 10.1016/j.jtbi.2015.02.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 02/11/2015] [Accepted: 02/24/2015] [Indexed: 11/17/2022]
Abstract
Plant defense against herbivory comes at a cost, which can be either direct (reducing resources available for growth and reproduction) or indirect (through reducing ecological performance, for example intraspecific competitiveness). While direct costs have been well studied in theoretical models, ecological costs have received almost no attention. In this study we compare models with a direct trade-off (reduced growth rate) to models with an ecological trade-off (reduced competitive ability), using a combination of adaptive dynamics and simulations. In addition, we study the dependence of the level of defense that can evolve on the type of defense (directly by reducing consumption, or indirectly by inducing herbivore mortality (toxicity)), and on the type of herbivore against which the plant is defending itself (generalists or specialists). We find three major results: First, for both direct and ecological costs, defense only evolves if the benefit to the plant is direct (through reducing consumption). Second, the type of cost has a major effect on the evolutionary dynamics: direct costs always lead to a single optimal strategy against herbivores, but ecological costs can lead to branching and the coexistence of non-defending and defending plants; however, coexistence is only possible when defending against generalist herbivores. Finally, we find that fast-growing plants invest less than slow-growing plants when defending against generalist herbivores, as predicted by the Resource Availability Hypothesis, but invest more than slow-growing plants when defending against specialists. Our results clearly show that assumptions about ecological interactions are crucial for understanding the evolution of defense against herbivores.
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Affiliation(s)
- Ellen van Velzen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC Groningen, The Netherlands.
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC Groningen, The Netherlands.
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