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Lennon JT, Abramoff RZ, Allison SD, Burckhardt RM, DeAngelis KM, Dunne JP, Frey SD, Friedlingstein P, Hawkes CV, Hungate BA, Khurana S, Kivlin SN, Levine NM, Manzoni S, Martiny AC, Martiny JBH, Nguyen NK, Rawat M, Talmy D, Todd-Brown K, Vogt M, Wieder WR, Zakem EJ. Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction. mBio 2024; 15:e0045524. [PMID: 38526088 PMCID: PMC11078004 DOI: 10.1128/mbio.00455-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a "top 10" list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.
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Affiliation(s)
- J. T. Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - R. Z. Abramoff
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Ronin Institute, Montclair, New Jersey, USA
| | - S. D. Allison
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
- Department of Earth System Science, University of California Irvine, Irvine, California, USA
| | | | - K. M. DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - J. P. Dunne
- NOAA/OAR Geophysical Fluid Dynamics Laboratory, Princeton, New Jersey, USA
| | - S. D. Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - P. Friedlingstein
- College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - C. V. Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - B. A. Hungate
- Department of Biological Sciences, Center for Ecosystem Science, Northern Arizona University, Flagstaff, Arizona, USA
| | - S. Khurana
- Department of Physical Geography, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - S. N. Kivlin
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - N. M. Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - S. Manzoni
- Department of Physical Geography, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - A. C. Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - J. B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - N. K. Nguyen
- American Society for Microbiology, Washington, DC, USA
| | - M. Rawat
- National Science Foundation, Washington, DC, USA
| | - D. Talmy
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - K. Todd-Brown
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - M. Vogt
- Institute for Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - W. R. Wieder
- National Center for Atmospheric Research, Boulder, Colorado, USA
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
| | - E. J. Zakem
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
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2
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Yang Q, Li D, Chen W, Zhu L, Zou X, Hu L, Yuan Y, He S, Shi F. Dynamics of Bacterioplankton Communities during Wet and Dry Seasons in the Danjiangkou Reservoir in Hubei, China. Life (Basel) 2023; 13:life13051206. [PMID: 37240851 DOI: 10.3390/life13051206] [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: 04/03/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Water quality is directly linked to drinking water safety for millions of people receiving the water. The Danjiangkou Reservoir is the main water source for the Middle Route of the South-to-North Water Diversion Project (MR-SNWDP), located in the vicinity of Henan and Hubei provinces in China. Aquatic microorganisms are key indicators of biologically assessing and monitoring the water quality of the reservoir as they are sensitive to environmental and water quality changes. This study aimed to investigate the spatiotemporal variations in bacterioplankton communities during wet (April) and dry (October) seasons at eight monitoring points in Hanku reservoir and five monitoring points in Danku reservoir. Each time point had three replicates, labeled as wet season Hanku (WH), wet season Danku (WD), dry season Hanku (DH), and dry season Danku (DD) of Danjiangkou Reservoir in 2021. High-throughput sequencing (Illumina PE250) of the 16S rRNA gene was performed, and alpha (ACE and Shannon) and beta (PCoA and NDMS) diversity indices were analyzed. The results showed that the dry season (DH and DD) had more diverse bacterioplankton communities compared to the wet season (WH and WD). Proteobacteria, Actinobacteria, and Firmicutes were the most abundant phyla, and Acinetobacter, Exiguobacterium, and Planomicrobium were abundant in the wet season, while polynucleobacter was abundant in the dry season. The functional prediction of metabolic pathways revealed six major functions including carbohydrate metabolism, membrane transport, amino acid metabolism, signal transduction, and energy metabolism. Redundancy analysis showed that environmental parameters greatly affected bacterioplankton diversity during the dry season compared to the wet season. The findings suggest that seasonality has a significant impact on bacterioplankton communities, and the dry season has more diverse communities influenced by environmental parameters. Further, the relatively high abundance of certain bacteria such as Acinetobacter deteriorated the water quality during the wet season compared to the dry season. Our findings have significant implications for water resource management in China, and other countries facing similar challenges. However, further investigations are required to elucidate the role of environmental parameters in influencing bacterioplankton diversity in order to devise potential strategies for improving water quality management in the reservoir.
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Affiliation(s)
- Qing Yang
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Dewang Li
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Wei Chen
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Liming Zhu
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Xi Zou
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Lian Hu
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Yujie Yuan
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Shan He
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Fang Shi
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
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3
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He Z, Ma Z, Yang D, Chen Q, He Z, Hu J, Deng F, Zhang Q, He J, Ye L, Chen H, He L, Huang X, Luo W, Yang S, Gu X, Zhang M, Yan T. Circular RNA expression profiles and CircSnd1-miR-135b/c-foxl2 axis analysis in gonadal differentiation of protogynous hermaphroditic ricefield eel Monopterus albus. BMC Genomics 2022; 23:552. [PMID: 35922747 PMCID: PMC9347082 DOI: 10.1186/s12864-022-08783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The expression and biological functions of circular RNAs (circRNAs) in reproductive organs have been extensively reported. However, it is still unclear whether circRNAs are involved in sex change. To this end, RNA sequencing (RNA-seq) was performed in gonads at 5 sexual stages (ovary, early intersexual stage gonad, middle intersexual stage gonad, late intersexual stage gonad, and testis) of ricefield eel, and the expression profiles and potential functions of circRNAs were studied. RESULTS Seven hundred twenty-one circRNAs were identified, and the expression levels of 10 circRNAs were verified by quantitative real-time PCR (qRT-PCR) and found to be in accordance with the RNA-seq data, suggesting that the RNA-seq data were reliable. Then, the sequence length, category, sequence composition and the relationship between the parent genes of the circRNAs were explored. A total of 147 circRNAs were differentially expressed in the sex change process, and GO and KEGG analyses revealed that some differentially expressed (such as novel_circ_0000659, novel_circ_0004005 and novel_circ_0005865) circRNAs were closely involved in sex change. Furthermore, expression pattern analysis demonstrated that both circSnd1 and foxl2 were downregulated in the process of sex change, which was contrary to mal-miR-135b. Finally, dual-luciferase reporter assay and RNA immunoprecipitation showed that circSnd1 and foxl2 can combine with mal-miR-135b and mal-miR-135c. These data revealed that circSnd1 regulates foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. CONCLUSION Our results are the first to demonstrate that circRNAs have potential effects on sex change in ricefield eel; and circSnd1 could regulate foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. These data will be useful for enhancing our understanding of sequential hermaphroditism and sex change in ricefield eel or other teleosts.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhijun Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhide He
- Luzhou City Department of Agricultural and Rural Affairs, Luzhou, 646000, Sichuan, China
| | - Jiaxiang Hu
- Sichuan Water Conservancy Vocational College, Chengdu, 611231, Sichuan, China
| | - Faqiang Deng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qian Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiayang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lijuan Ye
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hongjun Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Liang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shiyong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaobin Gu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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4
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Plankton under Pressure: How Water Conditions Alter the Phytoplankton–Zooplankton Link in Coastal Lagoons. WATER 2022. [DOI: 10.3390/w14060974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Transitional waters (TWs), such as coastal lagoons, are bodies of surface water at the transition between saline and freshwater domains. These environments play a vital role in guaranteeing ecosystem services, including provision of food, protection against meteorological events, as anthropogenic carbon sinks, and in filtering of pollutants. Due to the escalating overpopulation characterising coastlines worldwide, transitional systems are over-exploited, degraded, and reduced in their macroscopic features. However, information on the impact of anthropogenic pressures on planktonic organisms in these systems is still scanty and fragmented. Herein, we summarise the literature, with a special focus on coastal lagoons undergoing anthropogenic pressure. Specifically, we report on the implications of human impacts on the ecological state of plankton, i.e., a fundamental ecological component of aquatic ecosystems. Literature information indicates that human forces may alter ecosystem structures and functions in coastal lagoons, as in other TWs such as estuaries, hampering the phytoplankton–zooplankton link, i.e., the main trophic process occurring in those communities, and which sustains aquatic productivity. Changes in the dominance and lifestyle of key planktonic players, plus the invasion of ‘alien’ species, and consequent regime shifts, are among the most common outcomes of human disturbance.
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5
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Annunziata R, Mele BH, Marotta P, Volpe M, Entrambasaguas L, Mager S, Stec K, d’Alcalà MR, Sanges R, Finazzi G, Iudicone D, Montresor M, Ferrante MI. Trade-off between sex and growth in diatoms: Molecular mechanisms and demographic implications. SCIENCE ADVANCES 2022; 8:eabj9466. [PMID: 35044817 PMCID: PMC8769554 DOI: 10.1126/sciadv.abj9466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Diatoms are fast-growing and winning competitors in aquatic environments, possibly due to optimized growth performance. However, their life cycles are complex, heteromorphic, and not fully understood. Here, we report on the fine control of cell growth and physiology during the sexual phase of the marine diatom Pseudo-nitzschia multistriata. We found that mating, under nutrient replete conditions, induces a prolonged growth arrest in parental cells. Transcriptomic analyses revealed down-regulation of genes related to major metabolic functions from the early phases of mating. Single-cell photophysiology also pinpointed an inhibition of photosynthesis and storage lipids accumulated in the arrested population, especially in gametes and zygotes. Numerical simulations revealed that growth arrest affects the balance between parental cells and their siblings, possibly favoring the new generation. Thus, in addition to resources availability, life cycle traits contribute to shaping the species ecological niches and must be considered to describe and understand the structure of plankton communities.
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Affiliation(s)
- Rossella Annunziata
- Stazione Zoologica Anton Dohrn, Napoli, Italy
- Corresponding author. (R.A.); (M.I.F.)
| | | | | | | | | | | | | | | | - Remo Sanges
- International School for Advanced Studies (SISSA), Via Bonomea 265, Trieste 34136, Italy
| | - Giovanni Finazzi
- Université Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique, Energies Alternatives (CEA), Institut National Recherche Agriculture, Alimentation, Environnement (INRAE), Interdisciplinary Research Institute of Grenoble, IRIG-Laboratoire de Physiologie Cellulaire et Végétale, Grenoble, France
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6
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Hörstmann C, Buttigieg PL, John U, Raes EJ, Wolf-Gladrow D, Bracher A, Waite AM. Microbial diversity through an oceanographic lens: refining the concept of ocean provinces through trophic-level analysis and productivity-specific length scales. Environ Microbiol 2021; 24:404-419. [PMID: 34766422 DOI: 10.1111/1462-2920.15832] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023]
Abstract
In the marine realm, microorganisms are responsible for the bulk of primary production, thereby sustaining marine life across all trophic levels. Longhurst provinces have distinct microbial fingerprints; however, little is known about how microbial diversity and primary productivity change at finer spatial scales. Here, we sampled the Atlantic Ocean from south to north (~50°S-50°N), every ~0.5° latitude. We conducted measurements of primary productivity, chlorophyll-a and relative abundance of 16S and 18S rRNA genes, alongside analyses of the physicochemical and hydrographic environment. We analysed the diversity of autotrophs, mixotrophs and heterotrophs, and noted distinct patterns among these guilds across provinces with high and low chlorophyll-a conditions. Eukaryotic autotrophs and prokaryotic heterotrophs showed a shared inter-province diversity pattern, distinct from the diversity pattern shared by mixotrophs, cyanobacteria and eukaryotic heterotrophs. Additionally, we calculated samplewise productivity-specific length scales, the potential horizontal displacement of microbial communities by surface currents to an intrinsic biological rate (here, specific primary productivity). This scale provides key context for our trophically disaggregated diversity analysis that we could relate to underlying oceanographic features. We integrate this element to provide more nuanced insights into the mosaic-like nature of microbial provincialism, linking diversity patterns to oceanographic transport through primary production.
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Affiliation(s)
- Cora Hörstmann
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany.,Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, Germany
| | | | - Uwe John
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Eric J Raes
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Dieter Wolf-Gladrow
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany
| | - Astrid Bracher
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany.,Institute of Environmental Physics, University of Bremen, Bremen, Germany
| | - Anya M Waite
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada
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Faure E, Ayata SD, Bittner L. Towards omics-based predictions of planktonic functional composition from environmental data. Nat Commun 2021; 12:4361. [PMID: 34272373 PMCID: PMC8285379 DOI: 10.1038/s41467-021-24547-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Marine microbes play a crucial role in climate regulation, biogeochemical cycles, and trophic networks. Unprecedented amounts of data on planktonic communities were recently collected, sparking a need for innovative data-driven methodologies to quantify and predict their ecosystemic functions. We reanalyze 885 marine metagenome-assembled genomes through a network-based approach and detect 233,756 protein functional clusters, from which 15% are functionally unannotated. We investigate all clusters' distributions across the global ocean through machine learning, identifying biogeographical provinces as the best predictors of protein functional clusters' abundance. The abundances of 14,585 clusters are predictable from the environmental context, including 1347 functionally unannotated clusters. We analyze the biogeography of these 14,585 clusters, identifying the Mediterranean Sea as an outlier in terms of protein functional clusters composition. Applicable to any set of sequences, our approach constitutes a step towards quantitative predictions of functional composition from the environmental context.
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Affiliation(s)
- Emile Faure
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Institut Universitaire de France, Paris, France
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8
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Fanelli E, Aguzzi J, Marini S, del Rio J, Nogueras M, Canese S, Stefanni S, Danovaro R, Conversano F. Towards Naples Ecological REsearch for Augmented Observatories (NEREA): The NEREA-Fix Module, a Stand-Alone Platform for Long-Term Deep-Sea Ecosystem Monitoring. SENSORS 2020; 20:s20102911. [PMID: 32455611 PMCID: PMC7285156 DOI: 10.3390/s20102911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 12/11/2022]
Abstract
Deep-sea ecological monitoring is increasingly recognized as indispensable for the comprehension of the largest biome on Earth, but at the same time it is subjected to growing human impacts for the exploitation of biotic and abiotic resources. Here, we present the Naples Ecological REsearch (NEREA) stand-alone observatory concept (NEREA-fix), an integrated observatory with a modular, adaptive structure, characterized by a multiparametric video-platform to be deployed in the Dohrn canyon (Gulf of Naples, Tyrrhenian Sea) at ca. 650 m depth. The observatory integrates a seabed platform with optoacoustic and oceanographic/geochemical sensors connected to a surface transmission buoy, plus a mooring line (also equipped with depth-staged environmental sensors). This reinforced high-frequency and long-lasting ecological monitoring will integrate the historical data conducted over 40 years for the Long-Term Ecological Research (LTER) at the station “Mare Chiara”, and ongoing vessel-assisted plankton (and future environmental DNA-eDNA) sampling. NEREA aims at expanding the observational capacity in a key area of the Mediterranean Sea, representing a first step towards the establishment of a bentho-pelagic network to enforce an end-to-end transdisciplinary approach for the monitoring of marine ecosystems across a wide range of animal sizes (from bacteria to megafauna).
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Affiliation(s)
- Emanuela Fanelli
- Department of Life and Environmental Science, Polytechnic University of Marche, 60131 Ancona, Italy;
- Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; (J.A.); (S.M.); (S.C.); (S.S.); (F.C.)
- Correspondence:
| | - Jacopo Aguzzi
- Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; (J.A.); (S.M.); (S.C.); (S.S.); (F.C.)
- Instituto de Ciencias del Mar, CSIC, 08003 Barcelona, Spain
| | - Simone Marini
- Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; (J.A.); (S.M.); (S.C.); (S.S.); (F.C.)
- Institute of Marine Sciences, CNR, 19032 La Spezia, Italy
| | - Joaquin del Rio
- SARTI Research Group, Electronics Department, Universitat Politècnica de Catalunya, 08800 Vilanova i la Gertru, Spain; (J.d.R.); (M.N.)
| | - Marc Nogueras
- SARTI Research Group, Electronics Department, Universitat Politècnica de Catalunya, 08800 Vilanova i la Gertru, Spain; (J.d.R.); (M.N.)
| | - Simonepietro Canese
- Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; (J.A.); (S.M.); (S.C.); (S.S.); (F.C.)
| | - Sergio Stefanni
- Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; (J.A.); (S.M.); (S.C.); (S.S.); (F.C.)
| | - Roberto Danovaro
- Department of Life and Environmental Science, Polytechnic University of Marche, 60131 Ancona, Italy;
- Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; (J.A.); (S.M.); (S.C.); (S.S.); (F.C.)
| | - Fabio Conversano
- Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; (J.A.); (S.M.); (S.C.); (S.S.); (F.C.)
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9
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D'Alelio D, Rampone S, Cusano LM, Morfino V, Russo L, Sanseverino N, Cloern JE, Lomas MW. Machine learning identifies a strong association between warming and reduced primary productivity in an oligotrophic ocean gyre. Sci Rep 2020; 10:3287. [PMID: 32098970 PMCID: PMC7042350 DOI: 10.1038/s41598-020-59989-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
Phytoplankton play key roles in the oceans by regulating global biogeochemical cycles and production in marine food webs. Global warming is thought to affect phytoplankton production both directly, by impacting their photosynthetic metabolism, and indirectly by modifying the physical environment in which they grow. In this respect, the Bermuda Atlantic Time-series Study (BATS) in the Sargasso Sea (North Atlantic gyre) provides a unique opportunity to explore effects of warming on phytoplankton production across the vast oligotrophic ocean regions because it is one of the few multidecadal records of measured net primary productivity (NPP). We analysed the time series of phytoplankton primary productivity at BATS site using machine learning techniques (ML) to show that increased water temperature over a 27-year period (1990–2016), and the consequent weakening of vertical mixing in the upper ocean, induced a negative feedback on phytoplankton productivity by reducing the availability of essential resources, nitrogen and light. The unbalanced availability of these resources with warming, coupled with ecological changes at the community level, is expected to intensify the oligotrophic state of open-ocean regions that are far from land-based nutrient sources.
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Affiliation(s)
- Domenico D'Alelio
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121, Naples, Italy.
| | - Salvatore Rampone
- Università degli Studi del Sannio, Via Delle Puglie 76, I-82100, Benevento, Italy
| | - Luigi Maria Cusano
- Università degli Studi del Sannio, Via Delle Puglie 76, I-82100, Benevento, Italy
| | - Valerio Morfino
- Università degli Studi del Sannio, Via Delle Puglie 76, I-82100, Benevento, Italy
| | - Luca Russo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121, Naples, Italy
| | - Nadia Sanseverino
- Università degli Studi del Sannio, Via Delle Puglie 76, I-82100, Benevento, Italy
| | - James E Cloern
- United States Geological Survey (emeritus), Menlo Park, CA, USA
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
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10
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Hellweger FL. Combining Molecular Observations and Microbial Ecosystem Modeling: A Practical Guide. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:267-289. [PMID: 31226029 DOI: 10.1146/annurev-marine-010419-010829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Advances in technologies for molecular observation are leading to novel types of data, including gene, transcript, protein, and metabolite levels, which are fundamentally different from the types traditionally compared with microbial ecosystem models, such as biomass (e.g., chlorophyll a) and nutrient concentrations. A grand challenge is to use these data to improve predictive models and use models to explain observed patterns. This article presents a framework that aligns observations and models along the dimension of abstraction or biological organization-from raw sequences to ecosystem patterns for observations, and from sequence simulators to ecological theory for models. It then reviews 16 studies that compared model results with molecular observations. Molecular data can and are being combined with microbial ecosystem models, but to keep up with and take advantage of the full scope of observations, models need to become more mechanistically detailed and complex, which is a technical and cultural challenge for the ecological modeling community.
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Affiliation(s)
- Ferdi L Hellweger
- Specialty Area of Water Quality Engineering (Wasserreinhaltung), Institute of Environmental Science and Engineering, Technical University of Berlin, 10623 Berlin, Germany;
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11
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Abstract
Photosynthesis evolved in the ocean more than 2 billion years ago and is now performed by a wide range of evolutionarily distinct organisms, including both prokaryotes and eukaryotes. Our appreciation of their abundance, distributions, and contributions to primary production in the ocean has been increasing since they were first discovered in the seventeenth century and has now been enhanced by data emerging from the Tara Oceans project, which performed a comprehensive worldwide sampling of plankton in the upper layers of the ocean between 2009 and 2013. Largely using recent data from Tara Oceans, here we review the geographic distributions of phytoplankton in the global ocean and their diversity, abundance, and standing stock biomass. We also discuss how omics-based information can be incorporated into studies of photosynthesis in the ocean and show the likely importance of mixotrophs and photosymbionts.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
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12
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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.
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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.
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13
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Illumina MiSeq sequencing and network analysis the distribution and co-occurrence of bacterioplankton in Danjiangkou Reservoir, China. Arch Microbiol 2020; 202:859-873. [PMID: 31894394 DOI: 10.1007/s00203-019-01798-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 11/26/2019] [Accepted: 12/15/2019] [Indexed: 10/25/2022]
Abstract
Network analysis has contributed to studies of the interactions of microorganisms and the identification of key populations. However, such analysis has rarely been conducted in the study of reservoir bacterioplankton communities. This study investigated the bacterioplankton community composition in the surface water of the Danjiangkou Reservoir using the Illumina MiSeq sequencing platform. We observed that the bacterioplankton community primarily consisted of 27 phyla and 336 genera, including Actinobacteria, Proteobacteria, and Bacteroidetes, demonstrating the richness of the community composition. Redundancy analysis of the bacterioplankton communities and environmental variables showed that the total nitrogen (TN), pH, chemical oxygen demand (COD), and permanganate index (CODMn) were important factors affecting the bacterioplankton distribution. Network analysis was performed using the relative abundances of bacterioplankton based on the phylogenetic molecular ecological network (pMEN) method. The connectivity of node i within modules (Zi), the connectivity of node i among modules (Pi), and the number of key bacteria were high at the Taizishan and Heijizui sites, which were associated with higher TN contents than at the other sites. Among the physicochemical properties of water, TN, ammonia nitrogen (NH4-N), pH, COD, and dissolved oxygen (DO) might have great influences on the functional units of the bacterial communities in bacterioplankton molecular networks. This study improves the understanding of the structure and function of bacterioplankton communities in the Danjiangkou Reservoir.
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Sordino P, D'Aniello S, Pelletier E, Wincker P, Nittoli V, Stemmann L, Mazzocchi MG, Lombard F, Iudicone D, Caputi L. Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability. Mol Ecol 2019; 29:292-307. [PMID: 31793138 DOI: 10.1111/mec.15321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/07/2023]
Abstract
The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated with responses of pelagic tunicates to environmental variability. Herein, we present the effect of food availability increase on tunicate community and gene expression at the Marquesas Islands (South-East Pacific Ocean). By using data from the Tara Oceans expedition, we show that changes in phytoplankton density and composition trigger the success of a dominant larvacean species (an undescribed appendicularian). Transcriptional signature to the autotroph bloom suggests key functions in specific physiological processes, i.e., energy metabolism, muscle contraction, membrane trafficking, and proteostasis. The relative abundance of reverse transcription-related Pfams was lower at bloom conditions, suggesting a link with adaptive genetic diversity in tunicates in natural ecosystems. Downstream of the bloom, pelagic tunicates were outcompeted by copepods. Our work represents the first metaomics study of the biological effects of phytoplankton bloom on a key zooplankton taxon.
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Affiliation(s)
| | | | - Eric Pelletier
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Patrick Wincker
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | | | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
| | | | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
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15
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Ribera d’Alcalà M. Similarities, differences and mechanisms of climate impact on terrestrial vs. marine ecosystems. NATURE CONSERVATION 2019. [DOI: 10.3897/natureconservation.34.30923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Comparisons between terrestrial and marine ecosystems are generally not in the main stream of scientific literature even though Webb (2012) listed several points for which the transfer of knowledge and concepts related to one or to the other system would benefit our understanding of both. Even sharing this view, the leading hypothesis behind this contribution is that the pelagic system, where the dominant biotic component by number and biomass is microscopic, has specific features which strongly differentiate it from the above-the-surface terrestrial systems. Due to this, climate change, i.e. changes in temperature, precipitation and most importantly in the dynamics of the two fluid media, atmosphere and ocean, act with different mechanisms which prevents proceeding with analogies in many cases. In addition, the non-linearity of most of the processes and responses to perturbations requires, in order to obtain reliable forecasts or hindcasts, a detailed analysis of the path followed by the system which is normally overlooked in the step-change simulations or projections.
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16
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Modelling the complexity of plankton communities exploiting omics potential: From present challenges to an integrative pipeline. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2018.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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17
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Faure E, Not F, Benoiston AS, Labadie K, Bittner L, Ayata SD. Mixotrophic protists display contrasted biogeographies in the global ocean. ISME JOURNAL 2019; 13:1072-1083. [PMID: 30643201 DOI: 10.1038/s41396-018-0340-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/13/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
Mixotrophy, or the ability to acquire carbon from both auto- and heterotrophy, is a widespread ecological trait in marine protists. Using a metabarcoding dataset of marine plankton from the global ocean, 318,054 mixotrophic metabarcodes represented by 89,951,866 sequences and belonging to 133 taxonomic lineages were identified and classified into four mixotrophic functional types: constitutive mixotrophs (CM), generalist non-constitutive mixotrophs (GNCM), endo-symbiotic specialist non-constitutive mixotrophs (eSNCM), and plastidic specialist non-constitutive mixotrophs (pSNCM). Mixotrophy appeared ubiquitous, and the distributions of the four mixotypes were analyzed to identify the abiotic factors shaping their biogeographies. Kleptoplastidic mixotrophs (GNCM and pSNCM) were detected in new zones compared to previous morphological studies. Constitutive and non-constitutive mixotrophs had similar ranges of distributions. Most lineages were evenly found in the samples, yet some of them displayed strongly contrasted distributions, both across and within mixotypes. Particularly divergent biogeographies were found within endo-symbiotic mixotrophs, depending on the ability to form colonies or the mode of symbiosis. We showed how metabarcoding can be used in a complementary way with previous morphological observations to study the biogeography of mixotrophic protists and to identify key drivers of their biogeography.
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Affiliation(s)
- Emile Faure
- Sorbonne Université, CNRS, Laboratoire d'océanographie de Villefranche, LOV, 06230, Villefranche-sur-Mer, France. .,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 50, 57 rue Cuvier, 75005, Paris, France.
| | - Fabrice Not
- Sorbonne Université, CNRS, UMR7144 Adaptation and Diversity in Marine Environment (AD2M) Laboratory, Ecology of Marine Plankton team, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Anne-Sophie Benoiston
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 50, 57 rue Cuvier, 75005, Paris, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Evry, France, 91057, Evry, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 50, 57 rue Cuvier, 75005, Paris, France
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'océanographie de Villefranche, LOV, 06230, Villefranche-sur-Mer, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 50, 57 rue Cuvier, 75005, Paris, France
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18
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Berliner AJ, Mochizuki T, Stedman KM. Astrovirology: Viruses at Large in the Universe. ASTROBIOLOGY 2018; 18:207-223. [PMID: 29319335 DOI: 10.1089/ast.2017.1649] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viruses are the most abundant biological entities on modern Earth. They are highly diverse both in structure and genomic sequence, play critical roles in evolution, strongly influence terran biogeochemistry, and are believed to have played important roles in the origin and evolution of life. However, there is yet very little focus on viruses in astrobiology. Viruses arguably have coexisted with cellular life-forms since the earliest stages of life, may have been directly involved therein, and have profoundly influenced cellular evolution. Viruses are the only entities on modern Earth to use either RNA or DNA in both single- and double-stranded forms for their genetic material and thus may provide a model for the putative RNA-protein world. With this review, we hope to inspire integration of virus research into astrobiology and also point out pressing unanswered questions in astrovirology, particularly regarding the detection of virus biosignatures and whether viruses could be spread extraterrestrially. We present basic virology principles, an inclusive definition of viruses, review current virology research pertinent to astrobiology, and propose ideas for future astrovirology research foci. Key Words: Astrobiology-Virology-Biosignatures-Origin of life-Roadmap. Astrobiology 18, 207-223.
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Affiliation(s)
| | | | - Kenneth M Stedman
- 3 Center for Life in Extreme Environments and Biology Department, Portland State University , Oregon, USA
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19
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Kreft JU, Plugge CM, Prats C, Leveau JHJ, Zhang W, Hellweger FL. From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality. Front Microbiol 2017; 8:2299. [PMID: 29230200 PMCID: PMC5711835 DOI: 10.3389/fmicb.2017.02299] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/07/2017] [Indexed: 01/04/2023] Open
Abstract
Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality) is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression), stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s) underlying it for the specific microbial system and question investigated is essential for selecting the optimal modeling strategy.
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Affiliation(s)
- Jan-Ulrich Kreft
- Centre for Computational Biology, Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Clara Prats
- Department of Physics, School of Agricultural Engineering of Barcelona, Universitat Politècnica de Catalunya-BarcelonaTech, Castelldefels, Spain
| | - Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ferdi L Hellweger
- Civil and Environmental Engineering Department, Marine and Environmental Sciences Department, Bioengineering Department, Northeastern University, Boston, MA, United States
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Abstract
Constraint-based metabolic modelling (CBMM) consists in the use of computational methods and tools to perform genome-scale simulations and predict metabolic features at the whole cellular level. This approach is rapidly expanding in microbiology, as it combines reliable predictive abilities with conceptually and technically simple frameworks. Among the possible outcomes of CBMM, the capability to i) guide a focused planning of metabolic engineering experiments and ii) provide a system-level understanding of (single or community-level) microbial metabolic circuits also represent primary aims in present-day marine microbiology. In this work we briefly introduce the theoretical formulation behind CBMM and then review the most recent and effective case studies of CBMM of marine microbes and communities. Also, the emerging challenges and possibilities in the use of such methodologies in the context of marine microbiology/biotechnology are discussed. As the potential applications of CBMM have a very broad range, the topics presented in this review span over a large plethora of fields such as ecology, biotechnology and evolution.
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Affiliation(s)
- Marco Fondi
- Dep. of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy.
| | - Renato Fani
- Dep. of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
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