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Liu Q, Wu H, Huang C, Lin H, Li W, Zhao X, Li Z, Lv S. Microbial compositions, ecological networks, and metabolomics in sediments of black-odour water in Dongguan, China. ENVIRONMENTAL RESEARCH 2022; 210:112918. [PMID: 35181306 DOI: 10.1016/j.envres.2022.112918] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/29/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
Black-odour water with organic compounds and heavy metals caused by domestic and industrial activities has aroused people's attention in recent years, yet little is known about the ecological effects on aquatic organisms, especially microorganisms in sediments. To explore the response of microbial communities to environmental factors, the community and metabolites of nine river sediments with different pollution in Dongguan city, China were investigated using 16S rRNA gene sequencing and liquid chromatography tandem-mass. The results revealed that the composition and structure of sedimentary microbial communities significantly changed in rivers with varying pollution levels. Cyanobacteria were the most abundant organisms in the sediment of black-odorous rivers, while the relative abundance of Thaumarchaeota was gradually increased with the river quality gets better. The relative abundance of organic acids (including amino acids), alcohols, esters, and ketones associated with microbial metabolism in sediments of polluted rivers was increased. The 16S rRNA gene sequencing-based molecular ecological network analysis indicated that the interactions amongst bacteria were enhanced in severely contaminated communities. Sphingomonadaceae and Cyanobacteria have important roles in bacterial community structures of polluted rivers and those with ongoing treatment. The correlation analysis showed significant metal resistance and/or tolerance of the following bacteria species Thalassiosira weissflogii, Aminicenantes bacterium clone OPB95, 'Candidatus Halomonas phosphatis', and archaeal species Methanolinea and unidentified Thermoplasmata. These results indicated that sedimentary microbial communities may shift in composition and structure, as well as their interaction network, to adapt and resist environmental contamination and promote restoration.
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Affiliation(s)
- Qian Liu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Haowen Wu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Cong Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Hui Lin
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Wei Li
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - XiuFang Zhao
- Ecological Science Institute, LingNan Eco & Culture-Tourism Co.Ltd., Dongguan, 523125, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Sihao Lv
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China.
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Garcia CA, Baer SE, Garcia NS, Rauschenberg S, Twining BS, Lomas MW, Martiny AC. Nutrient supply controls particulate elemental concentrations and ratios in the low latitude eastern Indian Ocean. Nat Commun 2018; 9:4868. [PMID: 30451846 PMCID: PMC6242840 DOI: 10.1038/s41467-018-06892-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 09/14/2018] [Indexed: 11/17/2022] Open
Abstract
Variation in ocean C:N:P of particulate organic matter (POM) has led to competing hypotheses for the underlying drivers. Each hypothesis predicts C:N:P equally well due to regional co-variance in environmental conditions and biodiversity. The Indian Ocean offers a unique positive temperature and nutrient supply relationship to test these hypotheses. Here we show how elemental concentrations and ratios vary over daily and regional scales. POM concentrations were lowest in the southern gyre, elevated across the equator, and peaked in the Bay of Bengal. Elemental ratios were highest in the gyre, but approached Redfield proportions northwards. As Prochlorococcus dominated the phytoplankton community, biodiversity changes could not explain the elemental variation. Instead, our data supports the nutrient supply hypothesis. Finally, gyre dissolved iron concentrations suggest extensive iron stress, leading to depressed ratios compared to other gyres. We propose a model whereby differences in iron supply and N2-fixation influence C:N:P levels across ocean gyres.
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Affiliation(s)
- Catherine A Garcia
- Department of Earth System Science, University of California at Irvine, Irvine, CA, 92617, USA
| | - Steven E Baer
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
- Maine Maritime Academy, Castine, ME, 04420, USA
| | - Nathan S Garcia
- Department of Earth System Science, University of California at Irvine, Irvine, CA, 92617, USA
| | - Sara Rauschenberg
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | | | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Adam C Martiny
- Department of Earth System Science, University of California at Irvine, Irvine, CA, 92617, USA.
- Department of Ecology and Evolution, University of California at Irvine, Irvine, CA, 92617, USA.
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Flynn KJ, Skibinski DOF, Lindemann C. Effects of growth rate, cell size, motion, and elemental stoichiometry on nutrient transport kinetics. PLoS Comput Biol 2018; 14:e1006118. [PMID: 29702650 PMCID: PMC5942848 DOI: 10.1371/journal.pcbi.1006118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 05/09/2018] [Accepted: 03/29/2018] [Indexed: 12/17/2022] Open
Abstract
Nutrient acquisition is a critical determinant for the competitive advantage for auto- and osmohetero- trophs alike. Nutrient limited growth is commonly described on a whole cell basis through reference to a maximum growth rate (Gmax) and a half-saturation constant (KG). This empirical application of a Michaelis-Menten like description ignores the multiple underlying feedbacks between physiology contributing to growth, cell size, elemental stoichiometry and cell motion. Here we explore these relationships with reference to the kinetics of the nutrient transporter protein, the transporter rate density at the cell surface (TRD; potential transport rate per unit plasma-membrane area), and diffusion gradients. While the half saturation value for the limiting nutrient increases rapidly with cell size, significant mitigation is afforded by cell motion (swimming or sedimentation), and by decreasing the cellular carbon density. There is thus potential for high vacuolation and high sedimentation rates in diatoms to significantly decrease KG and increase species competitive advantage. Our results also suggest that Gmax for larger non-diatom protists may be constrained by rates of nutrient transport. For a given carbon density, cell size and TRD, the value of Gmax/KG remains constant. This implies that species or strains with a lower Gmax might coincidentally have a competitive advantage under nutrient limited conditions as they also express lower values of KG. The ability of cells to modulate the TRD according to their nutritional status, and hence change the instantaneous maximum transport rate, has a very marked effect upon transport and growth kinetics. Analyses and dynamic models that do not consider such modulation will inevitably fail to properly reflect competitive advantage in nutrient acquisition. This has important implications for the accurate representation and predictive capabilities of model applications, in particular in a changing environment.
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Affiliation(s)
- Kevin J. Flynn
- Biosciences, Swansea University, Swansea, United Kingdom
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Anderson TR, Hessen DO, Boersma M, Urabe J, Mayor DJ. Will Invertebrates Require Increasingly Carbon-Rich Food in a Warming World? Am Nat 2017; 190:725-742. [PMID: 29166161 DOI: 10.1086/694122] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Elevated temperature causes metabolism and respiration to increase in poikilothermic organisms. We hypothesized that invertebrate consumers will therefore require increasingly carbon-rich diets in a warming environment because the increased energetic demands are primarily met using compounds rich in carbon, that is, carbohydrates and lipids. Here, we test this hypothesis using a new stoichiometric model that has carbon (C) and nitrogen (N) as currencies. Model predictions did not support the hypothesis, indicating instead that the nutritional requirements of invertebrates, at least in terms of food quality expressed as C∶N ratio, may change little, if at all, at elevated temperature. Two factors contribute to this conclusion. First, invertebrates facing limitation by nutrient elements such as N have, by default, excess C in their food that can be used to meet the increased demand for energy in a warming environment, without recourse to extra dietary C. Second, increased feeding at elevated temperature compensates for the extra demands of metabolism to the extent that, when metabolism and intake scale equally with temperature (have the same Q10), the relative requirement for dietary C and N remains unaltered. Our analysis demonstrates that future climate-driven increases in the C∶N ratios of autotroph biomass will likely exacerbate the stoichiometric mismatch between nutrient-limited invertebrate grazers and their food, with important consequences for C sequestration and nutrient cycling in ecosystems.
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Ribeiro CMR, Maia AS, Ribeiro AR, Couto C, Almeida AA, Santos M, Tiritan ME. Anthropogenic pressure in a Portuguese river: Endocrine-disrupting compounds, trace elements and nutrients. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2016; 51:1043-1052. [PMID: 27411033 DOI: 10.1080/10934529.2016.1198622] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Natural organic compounds such as phytoestrogens and phytosterols found in various plants, as well as mycotoxins produced by fungi, can be found in aquatic environments. The aim of this study was to investigate the occurrence of three different classes of natural estrogenic compounds, i.e., phytoestrogens, phytosterols and mycotoxins, in estuarine water samples from the Ave River estuary. For that, water samples were collected at five sampling points distributed along the estuary at low tide, during 1 year, processed by solid-phase extraction (SPE) and analyzed by gas chromatography coupled to mass spectrometry (GC-MS). To correlate the presence of phytoestrogens and phytosterols in the estuarine water, local flora was collected on riverside. Trace elements content and physicochemical parameters such as nutrients and dissolved oxygen were also determined seasonally at each sampling point, to give insights for the evaluation of water quality and anthropogenic pressure. Both phytoestrogens and phytosterols showed a seasonal variation, with the highest values observed in spring and summer and the lowest in winter. Daidzein (DAID) was found up to 404.0 ng L(-1) in spring and coumestrol (COUM) was found up to 165.0 ng L(-1) in summer. The mycotoxin deoxynivalenol (DON) was ubiquitously determined with values ranging from 59.5 to 642.4 ng L(-1). Nutrients and metals distribution and concentration varied among sampling stations and seasons. This study revealed for the first time the presence of mycotoxins, various classes of phytoestrogens and stigmasterol (STG) in estuarine water from the Ave River (Portugal), and the evaluation of the water quality confirmed that this estuary is still highly impacted by anthropogenic activities.
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Affiliation(s)
- Cláudia M R Ribeiro
- a CESPU, Institute of Research and Advanced Training in Health Sciences and Technologies , Gandra , Portugal
- b Interdisciplinary Centre for Marine and Environmental Research (CIIMAR / CIMAR), University of Porto , Porto , Portugal
| | - Alexandra S Maia
- a CESPU, Institute of Research and Advanced Training in Health Sciences and Technologies , Gandra , Portugal
- c Catholic University of Portugal, CBQF - Centre for Biotechnology and Fine Chemistry - Associated Laboratory, Faculty of Biotechnology (ESB) , Porto , Portugal
| | - Ana R Ribeiro
- a CESPU, Institute of Research and Advanced Training in Health Sciences and Technologies , Gandra , Portugal
- d Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculty of Engineering, University of Porto , Porto , Portugal
| | - Cristina Couto
- a CESPU, Institute of Research and Advanced Training in Health Sciences and Technologies , Gandra , Portugal
- e LLQAV/REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto , Porto , Portugal
| | - Agostinho A Almeida
- e LLQAV/REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto , Porto , Portugal
| | - Mariana Santos
- a CESPU, Institute of Research and Advanced Training in Health Sciences and Technologies , Gandra , Portugal
| | - Maria E Tiritan
- a CESPU, Institute of Research and Advanced Training in Health Sciences and Technologies , Gandra , Portugal
- b Interdisciplinary Centre for Marine and Environmental Research (CIIMAR / CIMAR), University of Porto , Porto , Portugal
- f Faculty of Pharmacy, University of Porto, Laboratory of Organic and Pharmaceutical, Department of Chemical Sciences, University of Porto , Porto , Portugal
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Flynn KJ, Clark DR, Wheeler G. The role of coccolithophore calcification in bioengineering their environment. Proc Biol Sci 2016; 283:rspb.2016.1099. [PMID: 27358373 PMCID: PMC4936047 DOI: 10.1098/rspb.2016.1099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/08/2016] [Indexed: 11/12/2022] Open
Abstract
Coccolithophorids are enigmatic plankton that produce calcium carbonate coccoliths, which over geological time have buried atmospheric CO2 into limestone, changing both the atmosphere and geology of the Earth. However, the role of coccoliths for the proliferation of these organisms remains unclear; suggestions include roles in anti-predation, enhanced photosynthesis and sun-screening. Here we test the hypothesis that calcification stabilizes the pH of the seawater proximate to the organisms, providing a level of acidification countering the detrimental basification that occurs during net photosynthesis. Such bioengineering provides a more stable pH environment for growth and fits the empirical evidence for changes in rates of calcification under different environmental conditions. Under this scenario, simulations suggest that the optimal production ratio of inorganic to organic particulate C (PIC : POCprod) will be lower (by approx. 20%) with ocean acidification and that overproduction of coccoliths in a future acidified ocean, where pH buffering is weaker, presents a risk to calcifying cells.
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Affiliation(s)
- Kevin J Flynn
- College of Science, Swansea University, Swansea SA2 8PP, UK
| | - Darren R Clark
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | - Glen Wheeler
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
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Tan W, Adebusuyi AA. Proton and nutrient balanced medium for scalable, practical pH control in high-density Chlorella vulgaris cultures. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.02.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Flynn KJ, Clark DR, Mitra A, Fabian H, Hansen PJ, Glibert PM, Wheeler GL, Stoecker DK, Blackford JC, Brownlee C. Ocean acidification with (de)eutrophication will alter future phytoplankton growth and succession. Proc Biol Sci 2015; 282:20142604. [PMID: 25716793 PMCID: PMC4375859 DOI: 10.1098/rspb.2014.2604] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human activity causes ocean acidification (OA) though the dissolution of anthropogenically generated CO2 into seawater, and eutrophication through the addition of inorganic nutrients. Eutrophication increases the phytoplankton biomass that can be supported during a bloom, and the resultant uptake of dissolved inorganic carbon during photosynthesis increases water-column pH (bloom-induced basification). This increased pH can adversely affect plankton growth. With OA, basification commences at a lower pH. Using experimental analyses of the growth of three contrasting phytoplankton under different pH scenarios, coupled with mathematical models describing growth and death as functions of pH and nutrient status, we show how different conditions of pH modify the scope for competitive interactions between phytoplankton species. We then use the models previously configured against experimental data to explore how the commencement of bloom-induced basification at lower pH with OA, and operating against a background of changing patterns in nutrient loads, may modify phytoplankton growth and competition. We conclude that OA and changed nutrient supply into shelf seas with eutrophication or de-eutrophication (the latter owing to pollution control) has clear scope to alter phytoplankton succession, thus affecting future trophic dynamics and impacting both biogeochemical cycling and fisheries.
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Affiliation(s)
- Kevin J Flynn
- Centre for Sustainable Aquatic Research, Swansea University, Swansea SA2 8PP, UK
| | - Darren R Clark
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | - Aditee Mitra
- Centre for Sustainable Aquatic Research, Swansea University, Swansea SA2 8PP, UK
| | - Heiner Fabian
- Centre for Sustainable Aquatic Research, Swansea University, Swansea SA2 8PP, UK
| | - Per J Hansen
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Patricia M Glibert
- University of Maryland Center for Environmental Science, Horn Point Laboratory, PO Box 775, Cambridge, MD 21613, USA
| | - Glen L Wheeler
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK Marine Biological Association, Citadel Hill, Plymouth PL1 2PB, UK
| | - Diane K Stoecker
- University of Maryland Center for Environmental Science, Horn Point Laboratory, PO Box 775, Cambridge, MD 21613, USA
| | | | - Colin Brownlee
- Marine Biological Association, Citadel Hill, Plymouth PL1 2PB, UK
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A simple separation method for downstream biochemical analysis of aquatic microbes. J Microbiol Methods 2015; 111:78-86. [PMID: 25655777 DOI: 10.1016/j.mimet.2015.01.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 02/02/2023]
Abstract
In order to study the chemical composition of aquatic microbes it is necessary to obtain completely separated fractions of subpopulations. Size separation by filtration is usually unsuccessful because the smaller group of organisms contaminates the larger fractions due to being trapped on filter surfaces of nominally much larger pore sizes. Here we demonstrate that a simple sucrose density separation method allowed us to separate microorganisms of even subtle size differences and to determine their bulk biochemical composition (proteins, polysaccharides+nucleic acids, and lipids). Both autotrophs and heterotrophs (through anaplerotic pathways) were labeled with (14)C-bicarbonate for biochemical fractionation. We provided proof of concept that eukaryotic microbes could be cleanly separated from prokaryotes in cultures and in field samples, enabling detection of differences in their biochemical makeup. We explored methodological issues regarding separation mechanisms, fixation, and pre-concentration via tangential flow filtration of oligotrophic marine waters where abundances of microorganisms are comparably low. By selecting an appropriate centrifugal force, two processes (i.e., isopycnal and rate-zonal separation) can be exploited simultaneously resulting in finely-separated density fractions, which also resulted in size separation. Future applications of this method include exploration of the stoichiometric, biochemical and genetic differences among subpopulations of microbes in a wide variety of aquatic environments.
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