1
|
Ma X, Fernández FM. Advances in mass spectrometry imaging for spatial cancer metabolomics. MASS SPECTROMETRY REVIEWS 2024; 43:235-268. [PMID: 36065601 PMCID: PMC9986357 DOI: 10.1002/mas.21804] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 05/09/2023]
Abstract
Mass spectrometry (MS) has become a central technique in cancer research. The ability to analyze various types of biomolecules in complex biological matrices makes it well suited for understanding biochemical alterations associated with disease progression. Different biological samples, including serum, urine, saliva, and tissues have been successfully analyzed using mass spectrometry. In particular, spatial metabolomics using MS imaging (MSI) allows the direct visualization of metabolite distributions in tissues, thus enabling in-depth understanding of cancer-associated biochemical changes within specific structures. In recent years, MSI studies have been increasingly used to uncover metabolic reprogramming associated with cancer development, enabling the discovery of key biomarkers with potential for cancer diagnostics. In this review, we aim to cover the basic principles of MSI experiments for the nonspecialists, including fundamentals, the sample preparation process, the evolution of the mass spectrometry techniques used, and data analysis strategies. We also review MSI advances associated with cancer research in the last 5 years, including spatial lipidomics and glycomics, the adoption of three-dimensional and multimodal imaging MSI approaches, and the implementation of artificial intelligence/machine learning in MSI-based cancer studies. The adoption of MSI in clinical research and for single-cell metabolomics is also discussed. Spatially resolved studies on other small molecule metabolites such as amino acids, polyamines, and nucleotides/nucleosides will not be discussed in the context.
Collapse
Affiliation(s)
- Xin Ma
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
2
|
Li DW, Tan JZ, Li ZF, Ou LJ. Membrane lipid remodeling and autophagy to cope with phosphorus deficiency in the dinoflagellate Prorocentrum shikokuense. CHEMOSPHERE 2024; 349:140844. [PMID: 38042419 DOI: 10.1016/j.chemosphere.2023.140844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
Dinoflagellates, which are responsible for more than 80% of harmful algal blooms in coastal waters, are competitive in low-phosphate environments. However, the specific acclimated phosphorus strategies to adapt to phosphorus deficiency in dinoflagellates, particularly through intracellular phosphorus metabolism, remain largely unknown. Comprehensive physiological, biochemical, and transcriptomic analyses were conducted to investigate intracellular phosphorus modulation in a model dinoflagellate, Prorocentrum shikokuense, with a specific focus on membrane lipid remodeling and autophagy in response to phosphorus deficiency. Under phosphorus deficiency, P. shikokuense exhibited a preference to spare phospholipids with nonphospholipids. The major phospholipid classes of phosphatidylcholine and phosphatidylethanolamine decreased in content, whereas the betaine lipid class of diacylglyceryl carboxyhydroxymethylcholine increased in content. Furthermore, under phosphorus deficiency, P. shikokuense induced autophagy as a mechanism to conserve and recycle cellular phosphorus resources. The present study highlights the effective modulation of intracellular phosphorus in P. shikokuense through membrane phospholipid remodeling and autophagy and contributes to a comprehensive understanding of the acclimation strategies to low-phosphorus conditions in dinoflagellates.
Collapse
Affiliation(s)
- Da-Wei Li
- College of Life Science and Technology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, Guangzhou, China
| | - Jin-Zhou Tan
- College of Life Science and Technology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, Guangzhou, China
| | - Zhuo-Fan Li
- College of Life Science and Technology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, Guangzhou, China
| | - Lin-Jian Ou
- College of Life Science and Technology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
| |
Collapse
|
3
|
Ehrenfels B, Baumann KBL, Niederdorfer R, Mbonde AS, Kimirei IA, Kuhn T, Magyar PM, Odermatt D, Schubert CJ, Bürgmann H, Lehmann MF, Wehrli B, Callbeck CM. Hydrodynamic regimes modulate nitrogen fixation and the mode of diazotrophy in Lake Tanganyika. Nat Commun 2023; 14:6591. [PMID: 37852975 PMCID: PMC10584864 DOI: 10.1038/s41467-023-42391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
The factors that govern the geographical distribution of nitrogen fixation are fundamental to providing accurate nitrogen budgets in aquatic environments. Model-based insights have demonstrated that regional hydrodynamics strongly impact nitrogen fixation. However, the mechanisms establishing this physical-biological coupling have yet to be constrained in field surveys. Here, we examine the distribution of nitrogen fixation in Lake Tanganyika - a model system with well-defined hydrodynamic regimes. We report that nitrogen fixation is five times higher under stratified than under upwelling conditions. Under stratified conditions, the limited resupply of inorganic nitrogen to surface waters, combined with greater light penetration, promotes the activity of bloom-forming photoautotrophic diazotrophs. In contrast, upwelling conditions support predominantly heterotrophic diazotrophs, which are uniquely suited to chemotactic foraging in a more dynamic nutrient landscape. We suggest that these hydrodynamic regimes (stratification versus mixing) play an important role in governing both the rates and the mode of nitrogen fixation.
Collapse
Affiliation(s)
- Benedikt Ehrenfels
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
- ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zurich, Switzerland
| | - Kathrin B L Baumann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
- ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zurich, Switzerland
| | - Robert Niederdorfer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
| | | | - Ismael A Kimirei
- TAFIRI, Tanzania Fisheries Research Institute, Kigoma, Tanzania
- TAFIRI, Tanzania Fisheries Research Institute, Dar es Salaam, Tanzania
| | - Thomas Kuhn
- University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Paul M Magyar
- University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Daniel Odermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
| | - Carsten J Schubert
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
- ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zurich, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
| | - Moritz F Lehmann
- University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Bernhard Wehrli
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland
- ETH Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zurich, Switzerland
| | - Cameron M Callbeck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department Surface Waters - Research and Management, Kastanienbaum, Switzerland.
- University of Basel, Department of Environmental Sciences, Basel, Switzerland.
| |
Collapse
|
4
|
Li W, Shao C, Li C, Zhou H, Yu L, Yang J, Wan H, He Y. Metabolomics: A useful tool for ischemic stroke research. J Pharm Anal 2023; 13:968-983. [PMID: 37842657 PMCID: PMC10568109 DOI: 10.1016/j.jpha.2023.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/14/2023] [Accepted: 05/29/2023] [Indexed: 10/17/2023] Open
Abstract
Ischemic stroke (IS) is a multifactorial and heterogeneous disease. Despite years of studies, effective strategies for the diagnosis, management and treatment of stroke are still lacking in clinical practice. Metabolomics is a growing field in systems biology. It is starting to show promise in the identification of biomarkers and in the use of pharmacometabolomics to help patients with certain disorders choose their course of treatment. The development of metabolomics has enabled further and more biological applications. Particularly, metabolomics is increasingly being used to diagnose diseases, discover new drug targets, elucidate mechanisms, and monitor therapeutic outcomes and its potential effect on precision medicine. In this review, we reviewed some recent advances in the study of metabolomics as well as how metabolomics might be used to identify novel biomarkers and understand the mechanisms of IS. Then, the use of metabolomics approaches to investigate the molecular processes and active ingredients of Chinese herbal formulations with anti-IS capabilities is summarized. We finally summarized recent developments in single cell metabolomics for exploring the metabolic profiles of single cells. Although the field is relatively young, the development of single cell metabolomics promises to provide a powerful tool for unraveling the pathogenesis of IS.
Collapse
Affiliation(s)
- Wentao Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chongyu Shao
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chang Li
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Huifen Zhou
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Li Yu
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiehong Yang
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Haitong Wan
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yu He
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| |
Collapse
|
5
|
Xiao M, Burford MA, Prentice MJ, Galvanese EF, Chuang A, Hamilton DP. Phosphorus storage and utilization strategies of two bloom-forming freshwater cyanobacteria. Proc Biol Sci 2023; 290:20231204. [PMID: 37464756 DOI: 10.1098/rspb.2023.1204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023] Open
Abstract
The inter-relationships between cellular phosphorus (P) storage, dissolved inorganic P (DIP) uptake affinity, alkaline phosphatase activity (APA) and dissolved inorganic nitrogen (DIN) concentrations were studied in two ubiquitous diazotrophic freshwater cyanobacteria, Raphidiopsis raciborskii (six strains) and Chrysosporum ovalisporum (two strains). DIP uptake kinetics were measured using rates of incorporation of the radio-isotope, 33P and APA as a proxy for DOP-ester utilization. The study showed that DIP uptake of individual strains followed Michaelis-Menten kinetics (modified in our study to incorporate cellular P quotas), but differed with DIN and P availability, and between growth stages. High-affinity DIP uptake and APA were activated below a P quota threshold of approximately 0.01 µg P µg-1 C across the species and strains. C. ovalisporum had significantly higher APA and P quotas (per unit C and cell) but lower uptake affinity than R. raciborskii. Demand for DIP by C. ovalisporum increased when N fixation occurred, but typically not for R. raciborskii. Our results indicate that cyanobacterial species and strains differ in their strategies to P limiting conditions, and highlight the interplay between N and P. Physiological adaptations like APA and diazotrophy of cyanobacteria adapting to low DIP and/or DIN conditions may occur simultaneously and drive species dominance in oligotrophic environments.
Collapse
Affiliation(s)
- Man Xiao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Michele A Burford
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Matthew J Prentice
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
- Environmental Research Institute, The University of Waikato, Hamilton 3240, New Zealand
| | - Elena F Galvanese
- Laboratório de Análise e Síntese em Biodiversidade, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR 81531-980, Brazil
- Programa de Pós-graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba PR 80060-140, Brazil
| | - Ann Chuang
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - David P Hamilton
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| |
Collapse
|
6
|
Seidel L, Broman E, Nilsson E, Ståhle M, Ketzer M, Pérez-Martínez C, Turner S, Hylander S, Pinhassi J, Forsman A, Dopson M. Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities. THE ISME JOURNAL 2023; 17:855-869. [PMID: 36977742 DOI: 10.1038/s41396-023-01395-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023]
Abstract
Besides long-term average temperature increases, climate change is projected to result in a higher frequency of marine heatwaves. Coastal zones are some of the most productive and vulnerable ecosystems, with many stretches already under anthropogenic pressure. Microorganisms in coastal areas are central to marine energy and nutrient cycling and therefore, it is important to understand how climate change will alter these ecosystems. Using a long-term heated bay (warmed for 50 years) in comparison with an unaffected adjacent control bay and an experimental short-term thermal (9 days at 6-35 °C) incubation experiment, this study provides new insights into how coastal benthic water and surface sediment bacterial communities respond to temperature change. Benthic bacterial communities in the two bays reacted differently to temperature increases with productivity in the heated bay having a broader thermal tolerance compared with that in the control bay. Furthermore, the transcriptional analysis showed that the heated bay benthic bacteria had higher transcript numbers related to energy metabolism and stress compared to the control bay, while short-term elevated temperatures in the control bay incubation experiment induced a transcript response resembling that observed in the heated bay field conditions. In contrast, a reciprocal response was not observed for the heated bay community RNA transcripts exposed to lower temperatures indicating a potential tipping point in community response may have been reached. In summary, long-term warming modulates the performance, productivity, and resilience of bacterial communities in response to warming.
Collapse
Affiliation(s)
- Laura Seidel
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Emelie Nilsson
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Magnus Ståhle
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Marcelo Ketzer
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Clara Pérez-Martínez
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Stephanie Turner
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Samuel Hylander
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| |
Collapse
|
7
|
Zhao Y, Wang Z, Chen M, Huang X, Luo Z. Effects of nitrogen to phosphorus ratios on algal growth and arsenate metabolism by Microcystis aeruginosa with dissolved organic phosphorus and nitrate as nutrients. ALGAL RES 2023. [DOI: 10.1016/j.algal.2022.102922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
8
|
Karlson B, Arneborg L, Johansson J, Linders J, Liu Y, Olofsson M. A suggested climate service for cyanobacteria blooms in the Baltic Sea - Comparing three monitoring methods. HARMFUL ALGAE 2022; 118:102291. [PMID: 36195413 PMCID: PMC9559175 DOI: 10.1016/j.hal.2022.102291] [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: 12/31/2021] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 05/06/2023]
Abstract
Dense blooms of filamentous cyanobacteria are recurrent phenomena in the Baltic Sea, with occasional negative effects on the surrounding ecosystem, as well as on tourism, human health, aquaculture, and fisheries. Establishing a climate service is therefore suggested; including multi-method observations of cyanobacteria biomass, biodiversity, and biogeography, in correspondence to biotic and abiotic factors. Three different approaches were compared for determination of spatial and temporal variability and trends of the blooms; 1) microscopy-based long-term data, 2) satellite remote sensing, and 3) phycocyanin fluorescence mounted on a merchant vessel. Firstly, microscopy-based data on cyanobacteria biomass from the period 2000-2020 showed that the toxin producing genus Nodularia and non-toxic Aphanizomenon both had summer means of 15 µg C L-1, while Dolichospermum was less dominant with a mean of 8 µg C L-1. Some years also the Kattegat was affected by cyanobacteria blooms, likely transported here by ocean currents. Secondly, the satellite remote sensing time series for the period 2002-2020 indicated that near surface blooms were most frequent in the Northern Baltic Proper and that near surface blooms have increased in the Bothnian Sea, starting later in the season than in the Baltic Proper. The largest extents (i.e., total area covered) were observed in 2005, 2008, and 2018. Thirdly, phycocyanin fluorescence from a flow through sensor mounted on a merchant vessel was used as a proxy for cyanobacteria biomass and correlated to cyanobacteria biomass estimated by microscopy. However, the satellite remote sensing data on surface accumulations showed little resemblance to the data on cyanobacteria biomass based on water sampling and microscopy, interpreted as an effect of methods. Sensors on satellites mainly detect surface accumulations of cyanobacteria while the microscopy data was based on samples 0-10 m, thereby comprising a larger community. Data from satellite remote sensing of cyanobacteria was correlated to the phycocyanin fluorescence indicating that similar bio-optical properties are observed. Finally, results from a downscaled ocean climate model (NEMONordic) were used to produce future scenarios for temperature and salinity, which directly affects cyanobacteria blooms in the Baltic Sea, supposedly by increasing in abundance and change in species composition. Short-term forecasts can be used together with observations for early warning of cyanobacteria blooms, and we suggest an internationally coordinated cyanobacteria observation and warning system for the Baltic Sea area.
Collapse
Affiliation(s)
- Bengt Karlson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden.
| | - Lars Arneborg
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Johannes Johansson
- Oceanographic Services, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Johanna Linders
- Oceanographic Services, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Ye Liu
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Malin Olofsson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
9
|
Reinl KL, Harris TD, Elfferich I, Coker A, Zhan Q, De Senerpont Domis LN, Morales-Williams AM, Bhattacharya R, Grossart HP, North RL, Sweetman JN. The role of organic nutrients in structuring freshwater phytoplankton communities in a rapidly changing world. WATER RESEARCH 2022; 219:118573. [PMID: 35643062 DOI: 10.1016/j.watres.2022.118573] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/27/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Carbon, nitrogen, and phosphorus are critical macroelements in freshwater systems. Historically, researchers and managers have focused on inorganic forms, based on the premise that the organic pool was not available for direct uptake by phytoplankton. We now know that phytoplankton can tap the organic nutrient pool through a number of mechanisms including direct uptake, enzymatic hydrolysis, mixotrophy, and through symbiotic relationships with microbial communities. In this review, we explore these mechanisms considering current and projected future anthropogenically-driven changes to freshwater systems. In particular, we focus on how naturally- and anthropogenically- derived organic nutrients can influence phytoplankton community structure. We also synthesize knowledge gaps regarding phytoplankton physiology and the potential challenges of nutrient management in an organically dynamic and anthropogenically modified world. Our review provides a basis for exploring these topics and suggests several avenues for future work on the relation between organic nutrients and eutrophication and their ecological implications in freshwater systems.
Collapse
Affiliation(s)
- Kaitlin L Reinl
- Lake Superior National Estuarine Research Reserve, University of Wisconsin-Madison Division of Extension, 14 Marina Drive, Superior, Wisconsin 54880, US; University of Wisconsin-Madison, Center for Limnology, 608 N. Park St., Madison, WI, US; University of Minnesota-Duluth, Large Lakes Observatory, 2205 E. 5th St., Duluth, MN, US.
| | - Ted D Harris
- Kansas Biological Survey and Center for Ecological Research, 2101 Constant Ave., Lawrence, KS, US
| | - Inge Elfferich
- Cardiff University, Earth and Environmental Sciences, Main Building, Park Place CF10 3AT, Cardiff, UK
| | - Ayooluwateso Coker
- University of Minnesota-Duluth, Large Lakes Observatory, 2205 E. 5th St., Duluth, MN, US
| | - Qing Zhan
- Netherlands Institute of Ecology, Dept. of Aquatic Ecology, Droevendaalsesteeg 10, Wageningen, NL
| | | | - Ana M Morales-Williams
- University of Vermont, Rubenstein School of Environment and Natural Resources, 81 Carrigan Drive, Burlington, VT, US
| | - Ruchi Bhattacharya
- University of Waterloo, Department of Earth and Environmental Sciences, 200 University Ave., N2L 1V6, Waterloo, ON, CA
| | - Hans-Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Dept. Plankton and Microbial Ecology, Zur alten Fischerhuette 2, D-16775 Stechlin, DE; Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam
| | - Rebecca L North
- University of Missouri-Columbia, School of Natural Resources, 303L Anheuser Busch Natural Resource Building, Columbia, MO, US
| | - Jon N Sweetman
- Pennsylvania State University, Ecological Science and Management, 457 Agriculture Sciences and Industries Building, State College, PA, US
| |
Collapse
|
10
|
Xiao M, Burford MA, Wood SA, Aubriot L, Ibelings BW, Prentice MJ, Galvanese EF, Harris TD, Hamilton DP. Schindler's legacy: from eutrophic lakes to the phosphorus utilization strategies of cyanobacteria. FEMS Microbiol Rev 2022; 46:6617595. [PMID: 35749580 PMCID: PMC9629505 DOI: 10.1093/femsre/fuac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/01/2022] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
David Schindler and his colleagues pioneered studies in the 1970s on the role of phosphorus in stimulating cyanobacterial blooms in North American lakes. Our understanding of the nuances of phosphorus utilization by cyanobacteria has evolved since that time. We review the phosphorus utilization strategies used by cyanobacteria, such as use of organic forms, alternation between passive and active uptake, and luxury storage. While many aspects of physiological responses to phosphorus of cyanobacteria have been measured, our understanding of the critical processes that drive species diversity, adaptation and competition remains limited. We identify persistent critical knowledge gaps, particularly on the adaptation of cyanobacteria to low nutrient concentrations. We propose that traditional discipline-specific studies be adapted and expanded to encompass innovative new methodologies and take advantage of interdisciplinary opportunities among physiologists, molecular biologists, and modellers, to advance our understanding and prediction of toxic cyanobacteria, and ultimately to mitigate the occurrence of blooms.
Collapse
Affiliation(s)
- Man Xiao
- Corresponding author: Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, Jiangsu, China. E-mail:
| | - Michele A Burford
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, 7010, New Zealand
| | - Luis Aubriot
- Phytoplankton Physiology and Ecology Group, Sección Limnología, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias; Universidad de la República, Montevideo, 11400, Uruguay
| | - Bas W Ibelings
- Department F.-A. Forel for Aquatic and Environmental Sciences and Institute for Environmental Sciences, University of Geneva, Geneva, 1290, Switzerland
| | - Matthew J Prentice
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Elena F Galvanese
- Laboratório de Análise e Síntese em Biodiversidade, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba-PR, 81531-998, Brazil,Programa de Pós-graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba-PR, 80060-140, Brazil
| | - Ted D Harris
- Kansas Biological Survey and Center for Ecological Research, Lawrence, KS, 66047, United States
| | - David P Hamilton
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
| |
Collapse
|
11
|
Bernthal FR, Armstrong JD, Nislow KH, Metcalfe NB. Nutrient limitation in Atlantic salmon rivers and streams: Causes, consequences, and management strategies. AQUATIC CONSERVATION : MARINE AND FRESHWATER ECOSYSTEMS 2022; 32:1073-1091. [PMID: 35915662 PMCID: PMC9314074 DOI: 10.1002/aqc.3811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 02/17/2022] [Accepted: 03/06/2022] [Indexed: 06/16/2023]
Abstract
Freshwater catchments can experience nutrient deficits that result in reduced primary and secondary productivity. The most commonly limiting nutrients are nitrogen and phosphorus, either separately or together. This review considers the impact of increasing nutrient limitation in temperate basin stream and river systems, focusing on upland areas that currently or previously supported wild Atlantic salmon (Salmo salar) populations.Anthropogenic changes to land use and increases in river barriers have altered upland nutrient dynamics, with particular impacts on salmon and other migratory fish species which may be net importers of nutrients to upland streams. Declining salmon populations may further reduce nutrient sources, reducing ecosystem and fisheries productivity below desired levels.Experimental manipulations of nutrient levels have examined the impacts of this cultural oligotrophication. There is evidence that growth and biomass of juvenile salmon can be increased via appropriate additions of nutrients, offering potential as a conservation tool. However, further research is required to understand the long-term effects of these additions on salmon populations and stream ecosystems, and to assess the vulnerability of downstream habitats to eutrophication as a result.Although purposeful nutrient addition with the aim of enhancing and conserving salmonid populations may be justified in some cases, it should be undertaken in an adaptive management framework. In addition, nutrient addition should be linked to nutrient retention and processing, and integrated into large-scale habitat restoration and recovery efforts.Both the scientific and the management community should recognize that the ecological costs and benefits associated with adding nutrients to salmon streams may change in a non-stationary world.
Collapse
Affiliation(s)
- Fionn R. Bernthal
- Institute of Biodiversity Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - John D. Armstrong
- Marine Scotland – ScienceFreshwater Fisheries LaboratoryFaskallyPitlochryUK
| | - Keith H. Nislow
- USDA Forest Service Northern Research StationAmherstMassachusettsUSA
| | - Neil B. Metcalfe
- Institute of Biodiversity Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| |
Collapse
|
12
|
Geerlings NMJ, Kienhuis MVM, Hidalgo-Martinez S, Hageman R, Vasquez-Cardenas D, Middelburg JJ, Meysman FJR, Polerecky L. Polyphosphate Dynamics in Cable Bacteria. Front Microbiol 2022; 13:883807. [PMID: 35663875 PMCID: PMC9159916 DOI: 10.3389/fmicb.2022.883807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/14/2022] Open
Abstract
Cable bacteria are multicellular sulfide oxidizing bacteria that display a unique metabolism based on long-distance electron transport. Cells in deeper sediment layers perform the sulfide oxidizing half-reaction whereas cells in the surface layers of the sediment perform the oxygen-reducing half-reaction. These half-reactions are coupled via electron transport through a conductive fiber network that runs along the shared cell envelope. Remarkably, only the sulfide oxidizing half-reaction is coupled to biosynthesis and growth whereas the oxygen reducing half-reaction serves to rapidly remove electrons from the conductive fiber network and is not coupled to energy generation and growth. Cells residing in the oxic zone are believed to (temporarily) rely on storage compounds of which polyphosphate (poly-P) is prominently present in cable bacteria. Here we investigate the role of poly-P in the metabolism of cable bacteria within the different redox environments. To this end, we combined nanoscale secondary ion mass spectrometry with dual-stable isotope probing (13C-DIC and 18O-H2O) to visualize the relationship between growth in the cytoplasm (13C-enrichment) and poly-P activity (18O-enrichment). We found that poly-P was synthesized in almost all cells, as indicated by 18O enrichment of poly-P granules. Hence, poly-P must have an important function in the metabolism of cable bacteria. Within the oxic zone of the sediment, where little growth is observed, 18O enrichment in poly-P granules was significantly lower than in the suboxic zone. Thus, both growth and poly-P metabolism appear to be correlated to the redox environment. However, the poly-P metabolism is not coupled to growth in cable bacteria, as many filaments from the suboxic zone showed poly-P activity but did not grow. We hypothesize that within the oxic zone, poly-P is used to protect the cells against oxidative stress and/or as a resource to support motility, while within the suboxic zone, poly-P is involved in the metabolic regulation before cells enter a non-growing stage.
Collapse
Affiliation(s)
- Nicole M. J. Geerlings
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nicole M. J. Geerlings,
| | | | - Silvia Hidalgo-Martinez
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Renee Hageman
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Diana Vasquez-Cardenas
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
| | | | - Filip J. R. Meysman
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- Lubos Polerecky,
| |
Collapse
|
13
|
Polerecky L, Eichner M, Masuda T, Zavřel T, Rabouille S, Campbell DA, Halsey K. Calculation and Interpretation of Substrate Assimilation Rates in Microbial Cells Based on Isotopic Composition Data Obtained by nanoSIMS. Front Microbiol 2021; 12:621634. [PMID: 34917040 PMCID: PMC8670600 DOI: 10.3389/fmicb.2021.621634] [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] [Received: 10/27/2020] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
Stable isotope probing (SIP) combined with nano-scale secondary ion mass spectrometry (nanoSIMS) is a powerful approach to quantify assimilation rates of elements such as C and N into individual microbial cells. Here, we use mathematical modeling to investigate how the derived rate estimates depend on the model used to describe substrate assimilation by a cell during a SIP incubation. We show that the most commonly used model, which is based on the simplifying assumptions of linearly increasing biomass of individual cells over time and no cell division, can yield underestimated assimilation rates when compared to rates derived from a model that accounts for cell division. This difference occurs because the isotopic labeling of a dividing cell increases more rapidly over time compared to a non-dividing cell and becomes more pronounced as the labeling increases above a threshold value that depends on the cell cycle stage of the measured cell. Based on the modeling results, we present formulae for estimating assimilation rates in cells and discuss their underlying assumptions, conditions of applicability, and implications for the interpretation of intercellular variability in assimilation rates derived from nanoSIMS data, including the impacts of storage inclusion metabolism. We offer the formulae as a Matlab script to facilitate rapid data evaluation by nanoSIMS users.
Collapse
Affiliation(s)
- Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Meri Eichner
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Takako Masuda
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Tomáš Zavřel
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Sophie Rabouille
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-mer, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-mer, France
| | | | - Kimberly Halsey
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
14
|
Kuster AC, Huser BJ, Thongdamrongtham S, Padungthon S, Junggoth R, Kuster AT. Drinking water treatment residual as a ballast to sink Microcystis cyanobacteria and inactivate phosphorus in tropical lake water. WATER RESEARCH 2021; 207:117792. [PMID: 34717209 DOI: 10.1016/j.watres.2021.117792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/14/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
The combination of a low dose of coagulant with a ballast that can inactive phosphorus (P) in lake sediment-a technique known as "flock and lock"-is one method for restoration of eutrophic lakes. The effectiveness of a drinking water treatment residual (DWTR) as a ballast in flock and lock was assessed using assays of eutrophic lake water from Thailand dominated by Microcystis aeruginosa cyanobacteria colonies by measuring changes in chlorophyll-a, pH, and zeta potential. P sorption isotherms were developed from long-term batch equilibrium experiments; desorption of nutrients and metals was assessed via leaching experiments; and morphological changes to cellular structure were assessed using scanning electron microscopy. Results showed that combining DWTR with a low dose of aluminum sulfate (0.6-4.0 mg Al/L) effectively sank 74-96% of Microcystis, with DWTR dose (50-400 mg/L), initial chlorophyll-a concentration (92-976 µg/L), pH (7.4-9.3), and alkalinity (99-108 ppm CaCO3) identified as factors significantly associated with sinking efficacy. P sorption capacity of the DWTR (7.12 mg/g) was significantly higher than a local soil (0.33 mg/g), enabling the DWTR to inactivate P in lake sediment. Desorption of Al, Fe, Ca and N from the DWTR was estimated to contribute to a marginal increase in concentrations of those compounds in the water column of a small shallow lake (1.2, 0.66, 53.4, and 0.07 µg/L, respectively) following a simulated application. Therefore, pre-treated DWTRs may be a viable alternative ballast in the flock and lock approach to lake restoration, supplementing or replacing modified local soils or lanthanum modified clays.
Collapse
Affiliation(s)
- Anthony C Kuster
- Faculty of Public Health, Khon Kaen University, Khon Kaen, Thailand
| | - Brian J Huser
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Surapol Padungthon
- Environmental Engineering Program, Faculty of Engineering, Khon Kaen University, Khon Kaen, Thailand
| | - Rittirong Junggoth
- Department of Environmental Health and Occupational Health and Safety, Faculty of Public Health, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Anootnara T Kuster
- Department of Environmental Health and Occupational Health and Safety, Faculty of Public Health, Khon Kaen University, Khon Kaen 40002, Thailand.
| |
Collapse
|
15
|
Taylor M, Lukowski JK, Anderton CR. Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:872-894. [PMID: 33656885 PMCID: PMC8033567 DOI: 10.1021/jasms.0c00439] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 05/02/2023]
Abstract
Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.
Collapse
Affiliation(s)
- Michael
J. Taylor
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jessica K. Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| |
Collapse
|
16
|
Liu R, Yang Z. Single cell metabolomics using mass spectrometry: Techniques and data analysis. Anal Chim Acta 2021; 1143:124-134. [PMID: 33384110 PMCID: PMC7775990 DOI: 10.1016/j.aca.2020.11.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023]
Abstract
Mass spectrometry (MS) based techniques are gaining popularity for metabolomics research due to their high sensitivity, wide detection range, and capability of molecular identification. Utilizing such powerful technique to explore the cellular metabolism at the single cell level not only appreciates the subtle cell-to-cell difference (i.e., cell heterogeneity), but also gains biological merits corresponding to individual cells or small cell subpopulations. In this review article, we first briefly summarize recent advances in single cell MS experimental techniques, and then emphasize on the single cell metabolomics data analysis approaches. Through implementation of statistical analysis and more advanced data analysis methods, single cell metabolomics is expected to find more potential applications in the translational and clinical fields in the future.
Collapse
Affiliation(s)
- Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA; Alliance Pharma. Inc., Malvern, PA, 19355, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
| |
Collapse
|
17
|
Affiliation(s)
- Keke Hu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Tho D. K. Nguyen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Pieter E. Oomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
- ParaMedir B.V., 1e Energieweg 13, 9301 LK Roden, The Netherlands
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| |
Collapse
|
18
|
Olofsson M, Klawonn I, Karlson B. Nitrogen fixation estimates for the Baltic Sea indicate high rates for the previously overlooked Bothnian Sea. AMBIO 2021; 50:203-214. [PMID: 32314265 PMCID: PMC7708615 DOI: 10.1007/s13280-020-01331-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/22/2019] [Accepted: 03/20/2020] [Indexed: 05/05/2023]
Abstract
Dense blooms of diazotrophic filamentous cyanobacteria are formed every summer in the Baltic Sea. We estimated their contribution to nitrogen fixation by combining two decades of cyanobacterial biovolume monitoring data with recently measured genera-specific nitrogen fixation rates. In the Bothnian Sea, estimated nitrogen fixation rates were 80 kt N year-1, which has doubled during recent decades and now exceeds external loading from rivers and atmospheric deposition of 69 kt year-1. The estimated contribution to the Baltic Proper was 399 kt N year-1, which agrees well with previous estimates using other approaches and is greater than the external input of 374 kt N year-1. Our approach can potentially be applied to continuously estimate nitrogen loads via nitrogen fixation. Those estimates are crucial for ecosystem adaptive management since internal nitrogen loading may counteract the positive effects of decreased external nutrient loading.
Collapse
Affiliation(s)
- Malin Olofsson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Sven Källfelts Gata 15, 426 71 Västra Frölunda, Gothenburg, Sweden
- Present Address: Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Isabell Klawonn
- Department of Experimental Limnology, IGB-Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, OT Neuglobsow, Stechlin, 16775 Berlin, Germany
| | - Bengt Karlson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Sven Källfelts Gata 15, 426 71 Västra Frölunda, Gothenburg, Sweden
| |
Collapse
|
19
|
Zilius M, Samuiloviene A, Stanislauskienė R, Broman E, Bonaglia S, Meškys R, Zaiko A. Depicting Temporal, Functional, and Phylogenetic Patterns in Estuarine Diazotrophic Communities from Environmental DNA and RNA. MICROBIAL ECOLOGY 2021; 81:36-51. [PMID: 32803362 DOI: 10.1007/s00248-020-01562-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Seasonally nitrogen-limited and phosphorus-replete temperate coastal waters generally host dense and diverse diazotrophic communities. Despite numerous studies in marine systems, little is known about diazotrophs and their functioning in oligohaline estuarine environments. Here we applied a combination of nifH transcript and metagenomic shotgun sequencing approaches to investigate temporal shifts in taxonomic composition and nifH activity of size-fractionated diazotrophic communities in a shallow and mostly freshwater coastal lagoon. Patterns in active nifH phylotypes exhibited a clear seasonal succession, which reflected their different tolerances to temperature change and nitrogen (N) availability. Thus, in spring, heterotrophic diazotrophs (Proteobacteria) dominated the nifH phylotypes, while increasing water temperature and depletion of inorganic N fostered heterocystous Cyanobacteria in summer. Metagenomic data demonstrated four main N-cycling pathways and three of them with a clear seasonal pattern: denitrification (spring) → N2 fixation (summer) → assimilative NO3- reduction (fall), with NH4+ uptake into cells occurring across all seasons. Although a substantial denitrification signal was observed in spring, it could have originated from the re-suspended benthic rather than planktonic community. Our results contribute to a better understanding of the realized genetic potential of pelagic N2 fixation and its seasonal dynamics in oligohaline estuarine ecosystems, which are natural coastal biogeochemical reactors.
Collapse
Affiliation(s)
- Mindaugas Zilius
- Marine Research Institute, Klaipeda University, 92294, Klaipeda, Lithuania.
| | | | - Rūta Stanislauskienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Elias Broman
- Baltic Sea Center, Stockholm University, Stockholm, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Stefano Bonaglia
- Marine Research Institute, Klaipeda University, 92294, Klaipeda, Lithuania
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
- Department of Biology, University of Southern Denmark, 5230, Odense, Denmark
- Department of Marine Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, 7042 Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 92019, Auckland, New Zealand
| |
Collapse
|
20
|
Xiao M, Hamilton DP, Chuang A, Burford MA. Intra-population strain variation in phosphorus storage strategies of the freshwater cyanobacterium Raphidiopsis raciborskii. FEMS Microbiol Ecol 2020; 96:5837077. [DOI: 10.1093/femsec/fiaa092] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/12/2020] [Indexed: 01/10/2023] Open
Abstract
ABSTRACT
Several cyanobacteria, including diazotrophic Raphidiopsis raciborskii, can form harmful blooms when dissolved inorganic phosphorus concentrations are very low. We hypothesized that R. raciborskii strains would vary in phosphorus (P) allocations to cell growth and storage, providing resilience of populations to continuously low or variable P supplies. We tested this hypothesis using six toxic strains (producing cylindrospermopsins) isolated from a field population using batch monocultures with and without P and dissolved inorganic nitrogen (DIN). Treatments replete with DIN, irrespective of P addition, had similar exponential growth rates for individual strains. P storage capacity varied 4-fold among strains and was significantly higher in DIN-free treatments than in replete treatments. P was stored by all R. raciborskii strains, in preference to allocation to increase growth rates. P stores decreased with increased growth rate across strains, but weeere not related to the time to P starvation in P-free treatments. The storage capacity of R. raciborskii, combined with strategies to efficiently uptake P, means that P controls may not control R. raciborskii populations in the short term. Intra-population strain variation in P storage capacity will need to be reflected in process-based models to predict blooms of R. raciborskii and other cyanobacteria adapted to low-P conditions.
Collapse
Affiliation(s)
- Man Xiao
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - David P Hamilton
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Ann Chuang
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Michele A Burford
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| |
Collapse
|
21
|
Environmental drivers of metabolic heterogeneity in clonal microbial populations. Curr Opin Biotechnol 2020; 62:202-211. [DOI: 10.1016/j.copbio.2019.11.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/15/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023]
|
22
|
Mayali X. NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:449-467. [PMID: 31299167 DOI: 10.1146/annurev-marine-010419-010714] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
One major objective of aquatic microbial ecology is to understand the distribution of microbial populations over space and time and in response to environmental factors. Perhaps more importantly, it is crucial to quantify how those microbial cells affect biogeochemical processes of interest, such as primary production, nitrogen cycling, or the breakdown of pollutants. One valuable approach to link microbial identity to activity is to carry out incubations with stable-isotope-labeled substrates and then quantify the isotope incorporation by individual microbial cells using nanoscale secondary ion mass spectrometry (NanoSIMS). This review summarizes recent efforts in this field, highlights novel methods, describes studies investigating rare metabolisms as well as widespread microbial activity, and hopes to provide a framework to increase the use and capabilities of NanoSIMS for microbial biogeochemical studies in the future.
Collapse
Affiliation(s)
- Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA;
| |
Collapse
|
23
|
Microfluidic Single-Cell Analytics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:159-189. [PMID: 32737554 DOI: 10.1007/10_2020_134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
What is the impact of cellular heterogeneity on process performance? How do individual cells contribute to averaged process productivity? Single-cell analysis is a key technology for answering such key questions of biotechnology, beyond bulky measurements with populations. The analysis of cellular individuality, its origins, and the dependency of process performance on cellular heterogeneity has tremendous potential for optimizing biotechnological processes in terms of metabolic, reaction, and process engineering. Microfluidics offer unmatched environmental control of the cellular environment and allow massively parallelized cultivation of single cells. However, the analytical accessibility to a cell's physiology is of crucial importance for obtaining the desired information on the single-cell production phenotype. Highly sensitive analytics are required to detect and quantify the minute amounts of target analytes and small physiological changes in a single cell. For their application to biotechnological questions, single-cell analytics must evolve toward the measurement of kinetics and specific rates of the smallest catalytic unit, the single cell. In this chapter, we focus on an introduction to the latest single-cell analytics and their application for obtaining physiological parameters in a biotechnological context from single cells. We present and discuss recent advancements in single-cell analytics that enable the analysis of cell-specific growth, uptake, and production kinetics, as well as the gene expression and regulatory mechanisms at a single-cell level.
Collapse
|
24
|
Tan Y, Li J, Zhang L, Chen M, Zhang Y, An R. Mechanism Underlying Flow Velocity and Its Corresponding Influence on the Growth of Euglena gracilis, a Dominant Bloom Species in Reservoirs. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16234641. [PMID: 31766587 PMCID: PMC6926883 DOI: 10.3390/ijerph16234641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/01/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
The effects of hydrodynamics on algae growth have received considerable attention, and flow velocity is one of the most frequently discussed factors. For Euglena gracilis, which aggregates resources and is highly resistant to environmental changes, the mechanism underlying the impact of flow velocity on its growth is poorly understood. Experiments were conducted to examine the response of algae growth to different velocities, and several enzymes were tested to determine their physiological mechanisms. Significant differences in the growth of E. gracilis were found at different flow velocities, and this phenomenon is unique compared to the growth of other algal species. With increasing flow velocity and time, the growth of E. gracilis is gradually inhibited. In particular, we found that the pioneer enzyme is peroxidase (POD) and that the main antioxidant enzyme is catalase (CAT) when E. gracilis experiences flow velocity stress. Hysteresis between total phosphorus (TP) consumption and alkaline phosphatase (AKP) synthesis was observed. Under experimental control conditions, the results indicate that flow velocities above 0.1 m/s may inhibit growth and that E. gracilis prefers a relatively slow or even static flow velocity, and this finding could be beneficial for the control of E. gracilis blooms.
Collapse
Affiliation(s)
- Yi Tan
- Institute of Ecology and Environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu 610065, China; (Y.T.); (J.L.); (R.A.)
| | - Jia Li
- Institute of Ecology and Environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu 610065, China; (Y.T.); (J.L.); (R.A.)
| | - Linglei Zhang
- Institute of Ecology and Environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu 610065, China; (Y.T.); (J.L.); (R.A.)
- Correspondence: (L.Z.); (M.C.); Tel.: +86-189-8210-0418 (L.Z.); +86-151-9663-6869 (M.C.)
| | - Min Chen
- Institute of Ecology and Environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu 610065, China; (Y.T.); (J.L.); (R.A.)
- Correspondence: (L.Z.); (M.C.); Tel.: +86-189-8210-0418 (L.Z.); +86-151-9663-6869 (M.C.)
| | - Yaowen Zhang
- Department of Architectural Engineering, Urban Vocational College of Sichuan, Chengdu 610110, China;
| | - Ruidong An
- Institute of Ecology and Environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu 610065, China; (Y.T.); (J.L.); (R.A.)
| |
Collapse
|
25
|
Barchewitz T, Guljamow A, Meissner S, Timm S, Henneberg M, Baumann O, Hagemann M, Dittmann E. Non-canonical localization of RubisCO under high-light conditions in the toxic cyanobacterium Microcystis aeruginosa PCC7806. Environ Microbiol 2019; 21:4836-4851. [PMID: 31637830 DOI: 10.1111/1462-2920.14837] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/11/2019] [Accepted: 10/18/2019] [Indexed: 01/25/2023]
Abstract
The frequent production of the hepatotoxin microcystin (MC) and its impact on the lifestyle of bloom-forming cyanobacteria are poorly understood. Here, we report that MC interferes with the assembly and the subcellular localization of RubisCO, in Microcystis aeruginosa PCC7806. Immunofluorescence, electron microscopic and cellular fractionation studies revealed a pronounced heterogeneity in the subcellular localization of RubisCO. At high cell density, RubisCO particles are largely separate from carboxysomes in M. aeruginosa and relocate to the cytoplasmic membrane under high-light conditions. We hypothesize that the binding of MC to RubisCO promotes its membrane association and enables an extreme versatility of the enzyme. Steady-state levels of the RubisCO CO2 fixation product 3-phosphoglycerate are significantly higher in the MC-producing wild type. We also detected noticeable amounts of the RubisCO oxygenase reaction product secreted into the medium that may support the mutual interaction of M. aeruginosa with its heterotrophic microbial community.
Collapse
Affiliation(s)
- Tino Barchewitz
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Arthur Guljamow
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Sven Meissner
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Stefan Timm
- Department of Plant Physiology, Institute Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Manja Henneberg
- Department of Plant Physiology, Institute Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Otto Baumann
- Department of Zoophysiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Elke Dittmann
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| |
Collapse
|
26
|
Phosphate availability affects fixed nitrogen transfer from diazotrophs to their epibionts. ISME JOURNAL 2019; 13:2701-2713. [PMID: 31249392 PMCID: PMC6794295 DOI: 10.1038/s41396-019-0453-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/20/2019] [Accepted: 05/17/2019] [Indexed: 12/02/2022]
Abstract
Dinitrogen (N2) fixation is a major source of external nitrogen (N) to aquatic ecosystems and therefore exerts control over productivity. Studies have shown that N2 -fixers release freshly fixed N into the environment, but the causes for this N release are largely unclear. Here, we show that the availability of phosphate can directly affect the transfer of freshly fixed N to epibionts in filamentous, diazotrophic cyanobacteria. Stable-isotope incubations coupled to single-cell analyses showed that <1% and ~15% of freshly fixed N was transferred to epibionts of Aphanizomenon and Nodularia, respectively, at phosphate scarcity during a summer bloom in the Baltic Sea. When phosphate was added, the transfer of freshly fixed N to epibionts dropped to about half for Nodularia, whereas the release from Aphanizomenon increased slightly. At the same time, the growth rate of Nodularia roughly doubled, indicating that less freshly fixed N was released and was used for biomass production instead. Phosphate scarcity and the resulting release of freshly fixed N could explain the heavy colonization of Nodularia filaments by microorganisms during summer blooms. As such, the availability of phosphate may directly affect the partitioning of fixed N2 in colonies of diazotrophic cyanobacteria and may impact the interactions with their microbiome.
Collapse
|