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Botte E, Cui Y, Magliaro C, Tenje M, Koren K, Rinaldo A, Stocker R, Behrendt L, Ahluwalia A. Size-related variability of oxygen consumption rates in individual human hepatic cells. LAB ON A CHIP 2024; 24:4128-4137. [PMID: 39069914 PMCID: PMC11334764 DOI: 10.1039/d4lc00204k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
Accurate descriptions of the variability in single-cell oxygen consumption and its size-dependency are key to establishing more robust tissue models. By combining microfabricated devices with multiparameter identification algorithms, we demonstrate that single human hepatocytes exhibit an oxygen level-dependent consumption rate and that their maximal oxygen consumption rate is significantly lower than that of typical hepatic cell cultures. Moreover, we found that clusters of two or more cells competing for a limited oxygen supply reduced their maximal consumption rate, highlighting their ability to adapt to local resource availability and the presence of nearby cells. We used our approach to characterize the covariance of size and oxygen consumption rate within a cell population, showing that size matters, since oxygen metabolism covaries lognormally with cell size. Our study paves the way for linking the metabolic activity of single human hepatocytes to their tissue- or organ-level metabolism and describing its size-related variability through scaling laws.
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Affiliation(s)
- Ermes Botte
- Research Centre "E. Piaggio", University of Pisa, Pisa, Italy.
- Department of Information Engineering, University of Pisa, Pisa, Italy
| | - Yuan Cui
- Department of Organismal Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
- Department of Materials Science and Engineering, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Chiara Magliaro
- Research Centre "E. Piaggio", University of Pisa, Pisa, Italy.
- Department of Information Engineering, University of Pisa, Pisa, Italy
| | - Maria Tenje
- Department of Materials Science and Engineering, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Klaus Koren
- Aarhus University Centre for Water Technology, Department of Biology, Aahrus University, 8000 Aarhus, Denmark
| | - Andrea Rinaldo
- Laboratory of Ecohydrology ECHO/IIE/ENAC, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Civil, Environmental and Architectural Engineering, University of Padova, Padova, Italy
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Lars Behrendt
- Department of Organismal Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Arti Ahluwalia
- Research Centre "E. Piaggio", University of Pisa, Pisa, Italy.
- Department of Information Engineering, University of Pisa, Pisa, Italy
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Wang J, Zeng C, Feng Y. Meta-analysis reveals responses of coccolithophores and diatoms to warming. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106275. [PMID: 37992480 DOI: 10.1016/j.marenvres.2023.106275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 11/02/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023]
Abstract
A meta-analysis was conducted to explore the effects of warming on the physiological processes of coccolithophores and diatoms by synthesizing a large number of published literatures. A total of 154 studies consisting 301 experiments were synthesized in this study. Under a projected temperature increase of 3-5 °C by IPCC AR6 at the end of this century, our results suggest that the growth and photosynthetic rate of coccolithophores were significantly enhanced by the rising temperature, while the calcification of coccolithophores was only slightly promoted. Warming also had significantly positive effects on the growth but not photosynthesis of diatoms. In comparison, the effect size of warming on the growth rate of coccolithophores was larger than that of diatoms. However, there was no significant effect of warming on either the ratio of particulate inorganic carbon to particulate organic carbon (PIC:POC) of coccolithophores or the ratio of biogenic silica to carbon (BSi:C) of diatoms. Furthermore, the results reveal latitudinal and size-specific patterns of the effect sizes of warming. For diatoms, the effects of warming on growth were more prominent in high latitudes, specifically for the Southern Hemisphere species. In addition, the effect size of warming on the small-sized diatoms was larger than that of the large-sized diatoms. For coccolithophores, the growth of the Southern Hemisphere temperate strains was significantly promoted by warming. Overall, the results based on the meta-analysis indicate that the projected warming of the end of this century will be more favor to the growth of coccolithophores than that of diatoms, thus potentially affect the competitive advantages of coccolithophores over diatoms; while the mid-to high latitude species/strains of both coccolithophores and diatoms will benefit more than their counterparts in the lower latitudes. Therefore, this study offers novel insights into predicting both the inter- and intra-group competitive advantages of diatoms and coccolithophores under the future warming climate change scenario.
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Affiliation(s)
- Jiawei Wang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Frontiers Science Center of Polar Research, Shanghai, 200030, China
| | - Cong Zeng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yuanyuan Feng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Frontiers Science Center of Polar Research, Shanghai, 200030, China.
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Rocca JD, Yammine A, Simonin M, Gibert JP. Protist Predation Influences the Temperature Response of Bacterial Communities. Front Microbiol 2022; 13:847964. [PMID: 35464948 PMCID: PMC9022080 DOI: 10.3389/fmicb.2022.847964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/08/2022] [Indexed: 01/04/2023] Open
Abstract
Temperature strongly influences microbial community structure and function, in turn contributing to global carbon cycling that can fuel further warming. Recent studies suggest that biotic interactions among microbes may play an important role in determining the temperature responses of these communities. However, how predation regulates these microbiomes under future climates is still poorly understood. Here, we assess whether predation by a key global bacterial consumer-protists-influences the temperature response of the community structure and function of a freshwater microbiome. To do so, we exposed microbial communities to two cosmopolitan protist species-Tetrahymena thermophila and Colpidium sp.-at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to community shifts, these responses changed over time and in the presence of protists. Protists influenced microbial biomass and respiration rate through direct and indirect effects on bacterial community structure, and predator presence actually reduced microbial respiration at elevated temperature. Indicator species analyses showed that these predator effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities but also demonstrates that the presence of a large predator can mediate these responses to warming.
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Affiliation(s)
- Jennifer D. Rocca
- Department of Biology, Duke University, Durham, NC, United States
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Andrea Yammine
- Department of Biology, Duke University, Durham, NC, United States
| | - Marie Simonin
- Department of Biology, Duke University, Durham, NC, United States
- University of Angers, Institut Agro, Institut National de la Recherche Agronomique, L’Institut de Recherche en Horticulture et Semences, Structure Fédérative de Recherche Qualité et Santé du Végétal, Angers, France
| | - Jean P. Gibert
- Department of Biology, Duke University, Durham, NC, United States
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Serre-Fredj L, Chasselin L, Jolly O, Jacqueline F, Claquin P. Colimitation assessment of phytoplankton growth using a resource use efficiency approach in the Bay of Seine (French-English Channel). JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 306:114487. [PMID: 35065361 DOI: 10.1016/j.jenvman.2022.114487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 01/09/2022] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Eutrophication and dystrophy are two of the main problems affecting coastal ecosystems. In the Bay of Seine, phosphorus (P) inputs from the Seine estuary have been largely reduced in the last decade, in contrast to nitrogen (N), which leads to high N/P ratio inputs. To study the effect of dystrophy, an enrichment bioassay using water sampled from the Bay of Seine was repeated 19 times over a period of 18 months with six different enrichments. After a few days, chlorophyll a (chl a), alkaline phosphatase activity (APA), transparent exopolymeric particles (TEPs), cytometric size structure, and maximum quantum yield of photosystem II were measured. The data provide strong evidence for an N & P colimitation system in the vast majority of the incubations, as only the N + P and N + P + Si enrichments supported phytoplankton growth, and Si only appeared to play a secondary role in our incubations. A N/P ratio of 16 equal to the Redfield ratio was identified as the optimum for balanced growth, as chl a was the highest and TEP and APA production was the lowest at this ratio. To fit the requirements of the colimited system, a new resource use efficiency (RUENP) calculation was developed to account for N and P colimitation instead of only one nutrient, as is usually the case. This calculation allows better representation of RUE in dystrophic conditions, as found in many highly anthropized ecosystems. The relationships between RUENP and the size structure of the phytoplankton community were explored, and a significant positive correlation between RUENP and larger cells (>2 μm) and a negative correlation with smaller cells (<2 μm) were noted, showing a better use of nutrients by larger cells. This study highlights an increase of RUENP with the phytoplankton cell size in a colimited system.
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Affiliation(s)
- Léon Serre-Fredj
- Normandie Université, Université de Caen Normandie, Esplanade de la Paix, 14032, Caen, France; Laboratoire Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA, UMR CNRS 8067), Muséum National d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, IRD 207, Université des Antilles. Centre de Recherches en Environnement Côtier (CREC) - Station Marine, BP49, 54, Rue du Docteur Charcot, 14530, Luc-sur-Mer, France
| | - Léo Chasselin
- Normandie Université, Université de Caen Normandie, Esplanade de la Paix, 14032, Caen, France; Centre de Recherches en Environnement Côtier (CREC) - Station Marine de l'Université de Caen Normandie, BP49, 54, Rue du Docteur Charcot - 14530Ifremer LER/N, Avenue du Général de Gaulle, 14520, Port-en-Bessin, France
| | - Orianne Jolly
- Normandie Université, Université de Caen Normandie, Esplanade de la Paix, 14032, Caen, France; Centre de Recherches en Environnement Côtier (CREC) - Station Marine de l'Université de Caen Normandie, BP49, 54, Rue du Docteur Charcot - 14530Ifremer LER/N, Avenue du Général de Gaulle, 14520, Port-en-Bessin, France
| | - Franck Jacqueline
- Ifremer LER/N, Avenue du Général de Gaulle, 14520, Port-en-Bessin, France
| | - Pascal Claquin
- Normandie Université, Université de Caen Normandie, Esplanade de la Paix, 14032, Caen, France; Laboratoire Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA, UMR CNRS 8067), Muséum National d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, IRD 207, Université des Antilles. Centre de Recherches en Environnement Côtier (CREC) - Station Marine, BP49, 54, Rue du Docteur Charcot, 14530, Luc-sur-Mer, France.
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Hillebrand H, Acevedo‐Trejos E, Moorthi SD, Ryabov A, Striebel M, Thomas PK, Schneider M. Cell size as driver and sentinel of phytoplankton community structure and functioning. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Helmut Hillebrand
- Institute for Chemistry and Biology of Marine Environments [ICBM] Plankton Ecology Lab Carl‐von‐Ossietzky University Oldenburg Wilhelmshaven Germany
- Helmholtz‐Institute for Functional Marine Biodiversity at the University of Oldenburg [HIFMB] Oldenburg Germany
- Alfred Wegener Institute Helmholtz‐Centre for Polar and Marine Research [AWI] Bremerhaven Germany
| | - Esteban Acevedo‐Trejos
- Earth Surface Process Modelling Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam Germany
| | - Stefanie D. Moorthi
- Institute for Chemistry and Biology of Marine Environments [ICBM] Plankton Ecology Lab Carl‐von‐Ossietzky University Oldenburg Wilhelmshaven Germany
| | - Alexey Ryabov
- Institute for Chemistry and Biology of Marine Environments [ICBM] Mathematical Modelling Carl‐von‐Ossietzky University Oldenburg Oldenburg Germany
- Institute of Forest Growth and Computer Science Technische Universität Dresden Tharandt Germany
| | - Maren Striebel
- Institute for Chemistry and Biology of Marine Environments [ICBM] Plankton Ecology Lab Carl‐von‐Ossietzky University Oldenburg Wilhelmshaven Germany
| | - Patrick K. Thomas
- Institute for Chemistry and Biology of Marine Environments [ICBM] Plankton Ecology Lab Carl‐von‐Ossietzky University Oldenburg Wilhelmshaven Germany
| | - Marie‐Luise Schneider
- Institute for Chemistry and Biology of Marine Environments [ICBM] Plankton Ecology Lab Carl‐von‐Ossietzky University Oldenburg Wilhelmshaven Germany
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Scaling of joint mass and metabolism fluctuations in in silico cell-laden spheroids. Proc Natl Acad Sci U S A 2021; 118:2025211118. [PMID: 34526399 PMCID: PMC8463845 DOI: 10.1073/pnas.2025211118] [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] [Accepted: 08/05/2021] [Indexed: 11/24/2022] Open
Abstract
Allometric scaling has many applications, from the prediction of pharmacokinetics in animals and humans to the probing of ecosystem dynamics. Most studies have neglected to account for variations and fluctuations, although they are intrinsic features of all biological systems. To understand how metabolic scaling emerges in the presence of variations, we developed computer-generated models of cell-laden spheroids to define the experimental size range of cell cultures with quantifiable similitudes in terms of fluctuations and metabolic scaling with living organisms. We show that the estimates of scaling exponents may change with increasing variability in both mass and metabolic rate. The computational pipeline described underpins the sound design of statistically meaningful cell-based models, with impacts in both biomedical science and ecology. Variations and fluctuations are characteristic features of biological systems and are also manifested in cell cultures. Here, we describe a computational pipeline for identifying the range of three-dimensional (3D) cell-aggregate sizes in which nonisometric scaling emerges in the presence of joint mass and metabolic rate fluctuations. The 3D cell-laden spheroids with size and single-cell metabolic rates described by probability density functions were randomly generated in silico. The distributions of the resulting metabolic rates of the spheroids were computed by modeling oxygen diffusion and reaction. Then, a method for estimating scaling exponents of correlated variables through statistically significant data collapse of joint probability distributions was developed. The method was used to identify a physiologically relevant range of spheroid sizes, where both nonisometric scaling and a minimum oxygen concentration (0.04 mol⋅m−3) is maintained. The in silico pipeline described enables the prediction of the number of experiments needed for an acceptable collapse and, thus, a consistent estimate of scaling parameters. Using the pipeline, we also show that scaling exponents may be significantly different in the presence of joint mass and metabolic-rate variations typically found in cells. Our study highlights the importance of incorporating fluctuations and variability in size and metabolic rates when estimating scaling exponents. It also suggests the need for taking into account their covariations for better understanding and interpreting experimental observations both in vitro and in vivo and brings insights for the design of more predictive and physiologically relevant in vitro models.
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Small phytoplankton contribute greatly to CO 2-fixation after the diatom bloom in the Southern Ocean. ISME JOURNAL 2021; 15:2509-2522. [PMID: 33712701 PMCID: PMC8397732 DOI: 10.1038/s41396-021-00915-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 01/04/2023]
Abstract
Phytoplankton is composed of a broad-sized spectrum of phylogenetically diverse microorganisms. Assessing CO2-fixation intra- and inter-group variability is crucial in understanding how the carbon pump functions, as each group of phytoplankton may be characterized by diverse efficiencies in carbon fixation and export to the deep ocean. We measured the CO2-fixation of different groups of phytoplankton at the single-cell level around the naturally iron-fertilized Kerguelen plateau (Southern Ocean), known for intense diatoms blooms suspected to enhance CO2 sequestration. After the bloom, small cells (<20 µm) composed of phylogenetically distant taxa (prymnesiophytes, prasinophytes, and small diatoms) were growing faster (0.37 ± 0.13 and 0.22 ± 0.09 division d-1 on- and off-plateau, respectively) than larger diatoms (0.11 ± 0.14 and 0.09 ± 0.11 division d-1 on- and off-plateau, respectively), which showed heterogeneous growth and a large proportion of inactive cells (19 ± 13%). As a result, small phytoplankton contributed to a large proportion of the CO2 fixation (41-70%). The analysis of pigment vertical distribution indicated that grazing may be an important pathway of small phytoplankton export. Overall, this study highlights the need to further explore the role of small cells in CO2-fixation and export in the Southern Ocean.
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Pacciani-Mori L, Giometto A, Suweis S, Maritan A. Dynamic metabolic adaptation can promote species coexistence in competitive microbial communities. PLoS Comput Biol 2020; 16:e1007896. [PMID: 32379752 PMCID: PMC7244184 DOI: 10.1371/journal.pcbi.1007896] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/22/2020] [Accepted: 04/21/2020] [Indexed: 01/19/2023] Open
Abstract
Microbes are capable of physiologically adapting to diverse environmental conditions by differentially varying the rates at which they uptake different nutrients. In particular, microbes can switch hierarchically between different energy sources, consuming first those that ensure the highest growth rate. Experimentally, this can result in biphasic growth curves called "diauxic shifts" that typically arise when microbes are grown in media containing several nutrients. Despite these observations are well known in microbiology and molecular biology, the mathematical models generally used to describe the population dynamics of microbial communities do not account for dynamic metabolic adaptation, thus implicitly assuming that microbes cannot switch dynamically from one resource to another. Here, we introduce dynamic metabolic adaptation in the framework of consumer-resource models, which are commonly used to describe competitive microbial communities, allowing each species to temporally change its preferred energy source to maximize its own relative fitness. We show that dynamic metabolic adaptation enables the community to self-organize, allowing several species to coexist even in the presence of few resources, and to respond optimally to a time-dependent environment, thus showing that dynamic metabolic adaptation could be an important mechanism for maintaining high levels of diversity even in environments with few energy sources. We show that introducing dynamic metabolic strategies in consumer-resource models is necessary for reproducing experimental growth curves of the baker's yeast Saccharomyces cerevisiae growing in the presence of two carbon sources. Even though diauxic shifts emerge naturally from the model when two resources are qualitatively very different, the model predicts that the existence of such shifts is not a prerequisite for species coexistence in competitive communities.
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Affiliation(s)
- Leonardo Pacciani-Mori
- Department of Physics and Astronomy “Galileo Galilei”, University of Padua, Padua, Italy
| | - Andrea Giometto
- Department of Physics and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Samir Suweis
- Department of Physics and Astronomy “Galileo Galilei”, University of Padua, Padua, Italy
| | - Amos Maritan
- Department of Physics and Astronomy “Galileo Galilei”, University of Padua, Padua, Italy
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