1
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Korn R, Berg C, Bersier LF, Gray SM, Thallinger GG. Habitat conditions and not moss composition mediate microbial community structure in Swiss peatlands. Environ Microbiol 2024; 26:e16631. [PMID: 38757479 DOI: 10.1111/1462-2920.16631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Peatlands, one of the oldest ecosystems, globally store significant amounts of carbon and freshwater. However, they are under severe threat from human activities, leading to changes in water, nutrient and temperature regimes in these delicate systems. Such shifts can trigger a substantial carbon flux into the atmosphere and diminish the water-holding capacity of peatlands. Microbes associated with moss in peatlands play a crucial role in providing these ecosystem services, which are at risk due to global change. Therefore, understanding the factors influencing microbial composition and function is vital. Our study focused on five peatlands along an altitudinal gradient in Switzerland, where we sampled moss on hummocks containing Sarracenia purpurea. Structural equation modelling revealed that habitat condition was the primary predictor of community structure and directly influenced other environmental variables. Interestingly, the microbial composition was not linked to the local moss species identity. Instead, microbial communities varied significantly between sites due to differences in acidity levels and nitrogen availability. This finding was also mirrored in a co-occurrence network analysis, which displayed a distinct distribution of indicator species for acidity and nitrogen availability. Therefore, peatland conservation should take into account the critical habitat characteristics of moss-associated microbial communities.
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Affiliation(s)
- Rachel Korn
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | - Sarah M Gray
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gerhard G Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
- OMICS Center Graz, BioTechMed, Graz, Austria
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2
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Song X, Zhao Y, Xie L, Zhang G, Wei Z, Gao W, Dong G, Li J. Origin, distribution and spatial characteristics of dissolved organic matter in the Heilongjiang River. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118881. [PMID: 37659372 DOI: 10.1016/j.jenvman.2023.118881] [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: 05/18/2023] [Revised: 08/13/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
The Heilongjiang River Basin is a vast area with significant DOM sources and composition differences. The mechanism of DOM degradation under spatial variation remains unclear. This research investigated the degradation characteristics of DOM in different watersheds of the Heilongjiang River. DOM levels were higher in midstream waters, while DOM degradation rates were higher in midstream and downstream waters. The parallel factor analysis (PARAFAC) results showed that the upstream amino acid fraction was significantly depleted, the midstream was dominated by the degradation of DOM of terrestrial origin, and the downstream humic acid fraction was decreased considerably. Gene sequencing results indicated that the upstream, middle, and downstream water bodies' microbial community composition and structure differed significantly. The network analysis results revealed microorganisms in upstream water bodies mainly utilized amino acid-like substances and small molecule humic acids. Microorganisms in the middle and lower reaches of the water column were characterized by the utilization of humic acid-like fractions. In this study, we further screened the key driving microorganisms (e.g., Flavobacterium and Lacibacter) responsible for the difference in the DOM utilization function of upstream-to-midstream and midstream-to-downstream microorganisms in the Heilongjiang River. These findings will help identify the cycling process of DOM under spatial variation and predict the succession pattern of microbial communities.
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Affiliation(s)
- Xinyu Song
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, 150080, China; College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
| | - Lina Xie
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Guogang Zhang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Zimin Wei
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China.
| | - Wenfang Gao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Guanhong Dong
- Mudanjiang Natural Resources Comprehensive Survey Center, China Geological Survey, Mudanjiang, 157000, China
| | - Jinxuan Li
- Mudanjiang Natural Resources Comprehensive Survey Center, China Geological Survey, Mudanjiang, 157000, China
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3
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Barbosa AB, Mosley BA, Galvão HM, Domingues RB. Short-Term Effects of Climate Change on Planktonic Heterotrophic Prokaryotes in a Temperate Coastal Lagoon: Temperature Is Good, Ultraviolet Radiation Is Bad, and CO 2 Is Neutral. Microorganisms 2023; 11:2559. [PMID: 37894217 PMCID: PMC10609585 DOI: 10.3390/microorganisms11102559] [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: 08/30/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Planktonic heterotrophic prokaryotes (HProks) are a pivotal functional group in marine ecosystems and are highly sensitive to environmental variability and climate change. This study aimed to investigate the short-term effects of increasing carbon dioxide (CO2), ultraviolet radiation (UVR), and temperature on natural assemblages of HProks in the Ria Formosa coastal lagoon during winter. Two multi-stressor microcosm experiments were used to evaluate the isolated and combined effects of these environmental changes on HProk abundance, production, growth, and mortality rates. The isolated and combined effects of increased CO2 on HProks were not significant. However, HProk production, cellular activity, instantaneous growth rate, and mortality rate were negatively influenced by elevated UVR and positively influenced by warming. Stronger effects were detected on HProk mortality in relation to specific growth rate, leading to higher HProk net growth rates and abundance under elevated UVR and lower values under warming conditions.
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Affiliation(s)
| | | | | | - Rita B. Domingues
- CIMA—Centre for Marine and Environmental Research & ARNET—Infrastructure Network in Aquatic Research, Campus de Gambelas, University of Algarve, 8005-139 Faro, Portugal
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4
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Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies. Biotechniques 2022; 73:183-191. [PMID: 36189957 PMCID: PMC9623733 DOI: 10.2144/btn-2022-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Coastal environments are dynamic and can vary widely on short- or long-term scales depending on location and weather. Incubation equipment that reflects these changes through programmable gradient light and temperature cycles would permit more precise in vitro coastal microbiome studies. Here we present an open-source incubation environment that mimics in situ conditions for in vitro coastal microbiome studies using a modified shaking water bath that has fully customizable temperature and light gradients that can also mimic real-time field conditions. We compared coastal microbial community profiles incubated in situ and in our build mimicking field conditions over 48 h. Analyses of congruence indicated significant overlap (p > 0.2) between microbial communities incubated in situ and in vitro at each time point.
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5
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Berggren M, Guillemette F, Bieroza M, Buffam I, Deininger A, Hawkes JA, Kothawala DN, LaBrie R, Lapierre JF, Murphy KR, Al-Kharusi ES, Rulli MPD, Hensgens G, Younes H, Wünsch UJ. Unified understanding of intrinsic and extrinsic controls of dissolved organic carbon reactivity in aquatic ecosystems. Ecology 2022; 103:e3763. [PMID: 35612376 PMCID: PMC9540823 DOI: 10.1002/ecy.3763] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/18/2022] [Indexed: 11/15/2022]
Abstract
Despite our growing understanding of the global carbon cycle, scientific consensus on the drivers and mechanisms that control dissolved organic carbon (DOC) turnover in aquatic systems is lacking, hampered by the mismatch between research that approaches DOC reactivity from either intrinsic (inherent chemical properties) or extrinsic (environmental context) perspectives. Here we propose a conceptual view of DOC reactivity in which the combination of intrinsic and extrinsic factors controls turnover rates and determines which reactions will occur. We review three major types of reactions (biological, photochemical, and flocculation) from an intrinsic chemical perspective and further define the environmental features that modulate the expression of chemically inherent reactivity potential. Finally, we propose hypotheses of how extrinsic and intrinsic factors together shape patterns in DOC turnover across the land‐to‐ocean continuum, underscoring that there is no intrinsic DOC reactivity without environmental context. By acknowledging the intrinsic–extrinsic control duality, our framework intends to foster improved modeling of DOC reactivity and its impact on ecosystem services.
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Affiliation(s)
- Martin Berggren
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - François Guillemette
- Département des sciences de l'environnement, Université du Québec à Trois-Rivières, Canada.,Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, Canada
| | - Magdalena Bieroza
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ishi Buffam
- Department of Landscape Architecture, Planning and Management, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Anne Deininger
- Norwegian Institute for Water Research (NIVA), Oslo, Norway.,Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway
| | - Jeffrey A Hawkes
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Dolly N Kothawala
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Richard LaBrie
- Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, Canada.,Département des Sciences biologiques, Université de Montréal, Montréal, Canada
| | - Jean-François Lapierre
- Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, Canada.,Département des Sciences biologiques, Université de Montréal, Montréal, Canada
| | - Kathleen R Murphy
- Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Enass S Al-Kharusi
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Mayra P D Rulli
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Geert Hensgens
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Hani Younes
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Urban J Wünsch
- Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
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6
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Garcia-Lopez E, Ruiz-Blas F, Sanchez-Casanova S, Peña Perez S, Martin-Cerezo ML, Cid C. Microbial Communities in Volcanic Glacier Ecosystems. Front Microbiol 2022; 13:825632. [PMID: 35547132 PMCID: PMC9084427 DOI: 10.3389/fmicb.2022.825632] [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: 11/30/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Glaciers constitute a polyextremophilic environment characterized by low temperatures, high solar radiation, a lack of nutrients, and low water availability. However, glaciers located in volcanic regions have special characteristics, since the volcanic foci provide them with heat and nutrients that allow the growth of microbial communities highly adapted to this environment. Most of the studies on these glacial ecosystems have been carried out in volcanic environments in the northern hemisphere, including Iceland and the Pacific Northwest. To better know, the microbial diversity of the underexplored glacial ecosystems and to check what their specific characteristics were, we studied the structure of bacterial communities living in volcanic glaciers in Deception Island, Antarctica, and in the Kamchatka peninsula. In addition to geographic coordinates, many other glacier environmental factors (like volcanic activity, altitude, temperature, pH, or ice chemical composition) that can influence the diversity and distribution of microbial communities were considered in this study. Finally, using their taxonomic assignments, an attempt was made to compare how different or similar are the biogeochemical cycles in which these microbiomes are involved.
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Affiliation(s)
- Eva Garcia-Lopez
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
| | - Fatima Ruiz-Blas
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - Sonia Peña Perez
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - Cristina Cid
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
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7
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Jiang C, Zhang S, Wang J, Xia X. The inhibitory effects of sunlight on nitrogen removal in riverine overlying water with suspended particles. CHEMOSPHERE 2022; 295:133941. [PMID: 35150703 DOI: 10.1016/j.chemosphere.2022.133941] [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: 12/18/2021] [Revised: 01/30/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Overlying water with suspended particles is a hot spot for nitrogen removal in river systems. Although light exposure affects nitrogen transformations and nitrogen removal in some environments, such effects have rarely been explored and quantified in riverine overlying water. Herein, we examined the difference between dark and light conditions in the community composition and abundance of nitrogen transformation microbes in simulated overlying water by high-throughput sequencing and qPCR. Moreover, 15N-labeling techniques were used to investigate variation in nitrogen removal rates (N2 and N2O) as well as nitrification rates between dark and light conditions. We found apparent differences in the bacterial community between light and dark microcosms. The abundance of Cyanobacteria was greatly elevated in light microcosms, with the diazotroph nifH gene abundance being 7.4-fold higher in the light microcosm (P < 0.01). However, due to the vulnerability of some specifies to UV damage, the diazotroph species richness was reduced. The abundances of ammonia-oxidizing archaeal amoA, ammonia-oxidizing bacterial amoA, and denitrifying nirS genes were 80.1%, 46.3%, and 50.7% lower in the light microcosm, respectively, owing to the differential inhibition of sunlight exposure on these microbes. Both 15N-N2 and 15N-N2O were significantly produced regardless of conditions with or without light. Due to the combined effects of reduced nitrification and denitrification, as well as potentially enhanced nitrogen fixation, the accumulated amounts of 15N-N2 and 15N-N2O were 6.2% and 44.8% lower, respectively, in the light microcosm. This study quantifies the inhibitory effect of sunlight exposure on nitrogen removal in riverine overlying water and reveals the underlying mechanisms, providing insights into our understanding of nitrogen transformations in river systems.
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Affiliation(s)
- Chenrun Jiang
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China
| | - Sibo Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Junfeng Wang
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China
| | - Xinghui Xia
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China.
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8
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Piwosz K, Villena-Alemany C, Mujakić I. Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake. THE ISME JOURNAL 2022; 16:1046-1054. [PMID: 34802055 PMCID: PMC8941148 DOI: 10.1038/s41396-021-01142-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023]
Abstract
Lakes are a significant component of the global carbon cycle. Respiration exceeds net primary production in most freshwater lakes, making them a source of CO2 to the atmosphere. Driven by heterotrophic microorganisms, respiration is assumed to be unaffected by light, thus it is measured in the dark. However, photoheterotrophs, such as aerobic anoxygenic photoheterotrophic (AAP) bacteria that produce ATP via photochemical reactions, substantially reduce respiration in the light. They are an abundant and active component of bacterioplankton, but their photoheterotrophic contribution to microbial community metabolism remains unquantified. We showed that the community respiration rate in a freshwater lake was reduced by 15.2% (95% confidence interval (CI): 6.6-23.8%) in infrared light that is usable by AAP bacteria but not by primary producers. Moreover, significantly higher assimilation rates of glucose (18.1%; 7.8-28.4%), pyruvate (9.5%; 4.2-14.8%), and leucine (5.9%; 0.1-11.6%) were measured in infrared light. At the ecosystem scale, the amount of CO2 from respiration unbalanced by net primary production was by 3.69 × 109 g CO2 lower over these two sampling seasons when measured in the infrared light. Our results demonstrate that dark measurements of microbial activity significantly bias the carbon fluxes, providing a new paradigm for their quantification in aquatic environments.
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Affiliation(s)
- Kasia Piwosz
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981, Třeboň, Czechia. .,National Marine Fisheries Research Institute, 81-332, Gdynia, Poland.
| | - Cristian Villena-Alemany
- grid.418095.10000 0001 1015 3316Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia ,grid.14509.390000 0001 2166 4904Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Izabela Mujakić
- grid.418095.10000 0001 1015 3316Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia ,grid.14509.390000 0001 2166 4904Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
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9
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Aguilar P, Vila I, Sommaruga R. Bacterioplankton Zonation Does Exist in High Elevation, Polymictic Lakes. Front Microbiol 2022; 13:764566. [PMID: 35250918 PMCID: PMC8891803 DOI: 10.3389/fmicb.2022.764566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/25/2022] [Indexed: 01/04/2023] Open
Abstract
The assessment of distribution patterns or zonation of planktonic microbes along the water column is a crucial step to interpret their function in the ecosystem. In lakes without seasonal thermal stratification or polymictic systems such as high elevation tropical lakes, planktonic bacterial taxa are probably homogeneously distributed in the water column in contrast to what is known for thermally stratified lakes. However, we know little about bacterial distribution patterns in polymictic lakes and their relation to environmental gradients other than temperature. Here we assessed the diversity, microdiversity, and bacterial community composition at different discrete depths in three high elevation lakes (4,400-4,550 m above sea level) from the Andean plateau to test whether bacterial zonation patterns exist along the water column. For this objective, we analyzed bulk DNA and the putatively active fraction (cDNA) of the 16S rRNA gene. Although a clear gradient of temperature and oxygen was not detected along the water column, a significant vertical spatial zonation of the bacterial communities was present in two out of the three lakes, with microdiversity contributing to such pattern. Our results provide a reference for understanding how changing environmental conditions could affect high elevation aquatic ecosystems, particularly when warming is amplified with elevation, accelerating changes in hydrological regimes and biodiversity. Finally, our results highlight the importance of incorporating the whole water column in ecological studies of aquatic ecosystems lacking temporal or permanent thermal stratification.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Núcleo Milenio INVASAL, Concepción, Chile
| | - Irma Vila
- Núcleo Milenio INVASAL, Concepción, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
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10
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Morán XAG, García FC, Røstad A, Silva L, Al-Otaibi N, Irigoien X, Calleja ML. Diel dynamics of dissolved organic matter and heterotrophic prokaryotes reveal enhanced growth at the ocean's mesopelagic fish layer during daytime. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150098. [PMID: 34508930 DOI: 10.1016/j.scitotenv.2021.150098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/12/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Contrary to epipelagic waters, where biogeochemical processes closely follow the light and dark periods, little is known about diel cycles in the ocean's mesopelagic realm. Here, we monitored the dynamics of dissolved organic matter (DOM) and planktonic heterotrophic prokaryotes every 2 h for one day at 0 and 550 m (a depth occupied by vertically migrating fishes during light hours) in oligotrophic waters of the central Red Sea. We additionally performed predator-free seawater incubations of samples collected from the same site both at midnight and at noon. Comparable in situ variability in microbial biomass and dissolved organic carbon concentration suggests a diel supply of fresh DOM in both layers. The presence of fishes in the mesopelagic zone during daytime likely promoted a sustained, longer growth of larger prokaryotic cells. The specific growth rates were consistently higher in the noon experiments from both depths (surface: 0.34 vs. 0.18 d-1, mesopelagic: 0.16 vs. 0.09 d-1). Heterotrophic prokaryotes in the mesopelagic layer were also more efficient at converting extant DOM into new biomass. These results suggest that the ocean's twilight zone receives a consistent diurnal supply of labile DOM from the diel vertical migration of fishes, enabling an unexpectedly active community of heterotrophic prokaryotes.
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Affiliation(s)
- Xosé Anxelu G Morán
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia.
| | - Francisca C García
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia; Environment and Sustainability Institute, University of Exeter, TR10 9FE Penryn, United Kingdom
| | - Anders Røstad
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia
| | - Luis Silva
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia
| | - Najwa Al-Otaibi
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia; Department of Biology, College of Science, Taif University, Al-Hawiya 888, Saudi Arabia
| | | | - Maria Ll Calleja
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Science & Engineering Division, 23955-6900 Thuwal, Saudi Arabia; Max Planck Institute for Chemistry, 55128 Mainz, Germany
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11
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Silva L, Calleja ML, Ivetic S, Huete-Stauffer T, Roth F, Carvalho S, Morán XAG. Heterotrophic bacterioplankton responses in coral- and algae-dominated Red Sea reefs show they might benefit from future regime shift. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141628. [PMID: 32896805 DOI: 10.1016/j.scitotenv.2020.141628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/06/2020] [Accepted: 08/09/2020] [Indexed: 06/11/2023]
Abstract
In coral reefs, dissolved organic matter (DOM) cycling is a critical process for sustaining ecosystem functioning. However, global and local stressors have caused persistent shifts from coral- to algae-dominated benthic communities. The influence of such phase shifts on DOM nature and its utilization by heterotrophic bacterioplankton remains poorly studied. Every second month for one year, we retrieved seawater samples enriched in DOM produced by coral- and algae-dominated benthic communities in a central Red Sea reef during a full annual cycle. Seawater incubations were conducted in the laboratory under in situ temperature and light conditions by inoculating enriched DOM samples with bacterial assemblages collected in the surrounding waters. Dissolved organic carbon (DOC) concentrations were higher in the warmer months (May-September) in both communities, resulting in higher specific growth rates and bacterial growth efficiencies (BGE). However, these high summer values were significantly enhanced in algal-DOM relative to coral-DOM, suggesting the potential for bacterioplankton biomass increase in reefs with algae replacing healthy coral cover under warmer conditions. The potential exacerbation of heterotrophic bacterial activity in the ongoing widespread regime shift from coral- to algae-dominated communities may have detrimental consequences for the overall health of tropical coral reefs.
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Affiliation(s)
- Luis Silva
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia.
| | - Maria Ll Calleja
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia; Department of Climate Geochemistry, Max Planck Institute for Chemistry (MPIC), Hahn-Meitner-Weg 1, 55128 Mainz, Germany
| | | | - Tamara Huete-Stauffer
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Florian Roth
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia; Baltic Sea Centre, Stockholm University, 11418 Stockholm, Sweden; Tvärminne Zoological Station, University of Helsinki, 00100 Helsinki, Finland
| | - Susana Carvalho
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Xosé Anxelu G Morán
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
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12
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Sánchez O, Ferrera I, Mabrito I, Gazulla CR, Sebastián M, Auladell A, Marín-Vindas C, Cardelús C, Sanz-Sáez I, Pernice MC, Marrasé C, Sala MM, Gasol JM. Seasonal impact of grazing, viral mortality, resource availability and light on the group-specific growth rates of coastal Mediterranean bacterioplankton. Sci Rep 2020; 10:19773. [PMID: 33188261 PMCID: PMC7666142 DOI: 10.1038/s41598-020-76590-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/19/2020] [Indexed: 11/25/2022] Open
Abstract
Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups display the highest growth rates, contributing to the recycling of organic matter to a much greater extent than what their abundances alone would predict.
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Affiliation(s)
- Olga Sánchez
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, 29640, Fuengirola, Málaga, Spain. .,Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain.
| | - Isabel Mabrito
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain
| | - Carlota R Gazulla
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.,Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain.,Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria (ULPGC), Telde, 35214, Spain
| | - Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Carolina Marín-Vindas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain.,Escuela de Ciencias Biológicas, Universidad Nacional, Heredia, 40101, Costa Rica
| | - Clara Cardelús
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Massimo C Pernice
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Cèlia Marrasé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - M Montserrat Sala
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
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13
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Haynes VN, Ward JE. The interactive effects of titanium dioxide nanoparticles and light on heterotrophic bacteria and microalgae associated with marine aggregates in nearshore waters. MARINE ENVIRONMENTAL RESEARCH 2020; 161:105146. [PMID: 32942211 DOI: 10.1016/j.marenvres.2020.105146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/28/2020] [Accepted: 09/06/2020] [Indexed: 06/11/2023]
Abstract
Titanium dioxide nanoparticles (n-TiO2) are emerging contaminants and the ecological impact of these materials to the nearshore environment is largely unknown. The reactivity of n-TiO2 increases with light exposure, and the photocatalytic effects have been shown on cultures of bacteria and microalgae in the laboratory. The purpose of this study was to assess the response of natural bacterial and microalgal communities associated with marine aggregates to n-TiO2 under conditions similar to those found in the photic zone of nearshore waters. Nano and bulk TiO2 particles were incorporated into marine aggregates over 4 days under two light conditions: 6:18 and 0:24 (hours light:dark). The abundance and metabolic response of heterotrophic bacteria and viability of microalgae associated with aggregates were assessed. Although the proportion of living microalgae was unchanged, the abundance, total metabolic activity and functional diversity of heterotrophic bacteria were significantly altered by irradiated n-TiO2.
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Affiliation(s)
- Vena N Haynes
- University of Connecticut, Department of Marine Sciences, 1080 Shennecossett Road, Groton, CT, 06340, USA.
| | - J Evan Ward
- University of Connecticut, Department of Marine Sciences, 1080 Shennecossett Road, Groton, CT, 06340, USA.
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14
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Martinez-Varela A, Casas G, Piña B, Dachs J, Vila-Costa M. Large Enrichment of Anthropogenic Organic Matter Degrading Bacteria in the Sea-Surface Microlayer at Coastal Livingston Island (Antarctica). Front Microbiol 2020; 11:571983. [PMID: 33013806 PMCID: PMC7516020 DOI: 10.3389/fmicb.2020.571983] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/14/2020] [Indexed: 01/04/2023] Open
Abstract
The composition of bacteria inhabiting the sea-surface microlayer (SML) is poorly characterized globally and yet undescribed for the Southern Ocean, despite their relevance for the biogeochemistry of the surface ocean. We report the abundances and diversity of bacteria inhabiting the SML and the subsurface waters (SSL) determined from a unique sample set from a polar coastal ecosystem (Livingston Island, Antarctica). From early to late austral summer (January–March 2018), we consistently found a higher abundance of bacteria in the SML than in the SSL. The SML was enriched in some Gammaproteobacteria genus such as Pseudoalteromonas, Pseudomonas, and Colwellia, known to degrade a wide range of semivolatile, hydrophobic, and surfactant-like organic pollutants. Hydrocarbons and other synthetic chemicals including surfactants, such as perfluoroalkyl substances (PFAS), reach remote marine environments by atmospheric transport and deposition and by oceanic currents, and are known to accumulate in the SML. Relative abundances of specific SML-enriched bacterial groups were significantly correlated to concentrations of PFASs, taken as a proxy of hydrophobic anthropogenic pollutants present in the SML and its stability. Our observations provide evidence for an important pollutant-bacteria interaction in the marine SML. Given that pollutant emissions have increased during the Anthropocene, our results point to the need to assess chemical pollution as a factor modulating marine microbiomes in the contemporaneous and future oceans.
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Affiliation(s)
- Alícia Martinez-Varela
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Gemma Casas
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Benjamin Piña
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, Institut de Diagnóstic Ambiental i Estudis de l'aigua, Consejo Superior de Investigaciones Científicas (IDAEA-CSIC), Barcelona, Spain
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15
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Light and Primary Production Shape Bacterial Activity and Community Composition of Aerobic Anoxygenic Phototrophic Bacteria in a Microcosm Experiment. mSphere 2020; 5:5/4/e00354-20. [PMID: 32611696 PMCID: PMC7333569 DOI: 10.1128/msphere.00354-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Phytoplankton is a key component of aquatic microbial communities, and metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon (DOC). Yet, the impact of primary production on bacterial activity and community composition remains largely unknown, as, for example, in the case of aerobic anoxygenic phototrophic (AAP) bacteria that utilize both phytoplankton-derived DOC and light as energy sources. Here, we studied how reduction of primary production in a natural freshwater community affects the bacterial community composition and its activity, focusing primarily on AAP bacteria. The bacterial respiration rate was the lowest when photosynthesis was reduced by direct inhibition of photosystem II and the highest in ambient light condition with no photosynthesis inhibition, suggesting that it was limited by carbon availability. However, bacterial assimilation rates of leucine and glucose were unaffected, indicating that increased bacterial growth efficiency (e.g., due to photoheterotrophy) can help to maintain overall bacterial production when low primary production limits DOC availability. Bacterial community composition was tightly linked to light intensity, mainly due to the increased relative abundance of light-dependent AAP bacteria. This notion shows that changes in bacterial community composition are not necessarily reflected by changes in bacterial production or growth and vice versa. Moreover, we demonstrated for the first time that light can directly affect bacterial community composition, a topic which has been neglected in studies of phytoplankton-bacteria interactions.IMPORTANCE Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously.
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16
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Ruiz-González C, Garcia-Chaves MC, Ferrera I, Niño-García JP, Del Giorgio PA. Taxonomic differences shape the responses of freshwater aerobic anoxygenic phototrophic bacterial communities to light and predation. Mol Ecol 2020; 29:1267-1283. [PMID: 32147876 DOI: 10.1111/mec.15404] [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: 12/09/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/29/2022]
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are a phylogenetically diverse and ubiquitous group of prokaryotes that use organic matter but can harvest light using bacteriochlorophyll a. Although the factors regulating AAP ecology have long been investigated through field surveys, the few available experimental studies have considered AAPs as a group, thus disregarding the potential differential responses between taxonomically distinct AAP assemblages. Here, we used sequencing of the pufM gene to describe the diversity of AAPs in 10 environmentally distinct temperate lakes, and to investigate the taxonomic responses of AAP communities in these lakes when subjected to similar experimental manipulations of light and predator removal. The studied communities were clearly dominated by Limnohabitans AAP but presented a clear taxonomic segregation between lakes presumably driven by local conditions, which was maintained after experimental manipulations. Predation reduction (but not light exposure) caused significant compositional shifts across most assemblages, but the magnitude of these changes could not be clearly related to changes in bulk AAP abundances or taxonomic richness of AAP assemblages during experiments. Only a few operational taxonomic units, which differed taxonomically between lakes, were found to respond positively during experimental treatments. Our results highlight that different freshwater AAP communities respond differently to similar control mechanisms, highlighting that in-depth knowledge on AAP diversity is essential to understand the ecology and potential role of these photoheterotrophs.
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Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Maria Carolina Garcia-Chaves
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada.,Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Isabel Ferrera
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Málaga, Spain
| | - Juan Pablo Niño-García
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada.,Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Paul A Del Giorgio
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
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17
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Song N, Jiang HL. Coordinated photodegradation and biodegradation of organic matter from macrophyte litter in shallow lake water: Dual role of solar irradiation. WATER RESEARCH 2020; 172:115516. [PMID: 31986394 DOI: 10.1016/j.watres.2020.115516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/31/2019] [Accepted: 01/15/2020] [Indexed: 05/20/2023]
Abstract
Eutrophication and climate warming cause macrophytes to spread rapidly in shallow lakes. The accumulation of excess decayed litter in lake water can improve the particulate organic matter content and lead to ecological deterioration. While decomposition of macrophyte litters in aquatic ecosystems is generally assumed to be biologically driven, photodegradation has been largely overlooked. In this study, the potential contribution of photodegradation to the decomposition of organic matter from macrophyte litter in a shallow lake was investigated under two types of light radiation: laboratory incubation light and natural solar radiation. Results showed that the combined photo- and biodegradation treatment removed more litter mass compared to solely photodegradation or biodegradation for over 108 days. More reactive oxygen species (ROS) were produced during litter degradation in lake water under the combined photo- and biodegradation treatments in comparison to other treatments. Removal efficiency of litter was doubled in the presence of ROS compared when ROS were captured. Additionally, NMR analysis revealed that lignin guaiacyl units were preferentially lost and the litter became more refractory under the combined photo oxidation and microbial degradation after 108 days. High-throughput sequencing analysis further indicated that solar irradiation stimulates the growth of bacteria (Treponema and Magnetospirillum) and fungi (Aspergillus) that have the ability to degrade aromatic compounds. Altogether, both ROS and specific microorganisms played important role in promoting litter degradation in lake water under light irradiation. Therefore, the role of solar radiation in particulate organic matter decomposition needs to be considered for a more accurate prediction of carbon dynamics in aquatic ecosystems.
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Affiliation(s)
- Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - He-Long Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China.
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18
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Song N, Bai L, Xu H, Jiang HL. The composition difference of macrophyte litter-derived dissolved organic matter by photodegradation and biodegradation: Role of reactive oxygen species on refractory component. CHEMOSPHERE 2020; 242:125155. [PMID: 31669998 DOI: 10.1016/j.chemosphere.2019.125155] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 09/27/2019] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
The overgrowth of macrophytes has become serious due to increasing eutrophication in shallow lakes. The primary degradation processes of macrophytes litter, including photodegradation and biodegradation, induce considerable patchiness in the concentration and bioavailability of dissolved organic matter (DOM). In this study we investigated the composition evolution of DOM derived from emergent aquatic plant litter, Phragmites australis, in microbial degradation, photodegradation, and the combination of bio- and photo-degradation. Results revealed that the effects of photo- and biodegradation on the composition difference of macrophyte litter-derived DOM during short- and long-term degradation phase were different. Although large changes in DOM were observed after five days of incubation, the abundance and chemical composition were similar in the three treatments. However, more concentration of DOM was produced by combined photo- and biodegradation at the long-term degradation phase, and the composition of DOM showed less lignin-like formulae, as well as less condensed aromatic and aromatic compounds when compared to sole treatments. More reactive oxygen species (ROS) were found under the combined treatments, thus the contents of refractory components (condensed aromatic- and aromatic compound groups) were reduced. This study provide deeper insight into the fate of DOM and relevant biogeochemical processes in eutrophic lakes.
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Affiliation(s)
- Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Leilei Bai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Huacheng Xu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - He-Long Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
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19
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Durán-Romero C, Medina-Sánchez JM, Carrillo P. Uncoupled phytoplankton-bacterioplankton relationship by multiple drivers interacting at different temporal scales in a high-mountain Mediterranean lake. Sci Rep 2020; 10:350. [PMID: 31941977 PMCID: PMC6962384 DOI: 10.1038/s41598-019-57269-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/19/2019] [Indexed: 01/22/2023] Open
Abstract
Global-change stressors act under different timing, implying complexity and uncertainty in the study of interactive effects of multiple factors on planktonic communities. We manipulated three types of stressors acting in different time frames in an in situ experiment: ultraviolet radiation (UVR); phosphorus (P) concentration; temperature (T) in an oligotrophic Mediterranean high-mountain lake. The aim was to examine how the sensitivity of phytoplankton and bacterioplankton to UVR and their trophic relationship change under nutrient acclimation and abrupt temperature shifts. Phytoplankton and bacteria showed a common pattern of metabolic response to UVR × P addition interaction, with an increase in their production rates, although evidencing an inhibitory UVR effect on primary production (PP) but stimulatory on bacterial production (HBP). An abrupt T shift in plankton acclimated to UVR and P addition decreased the values of PP, evidencing an inhibitory UVR effect, whereas warming increased HBP and eliminated the UVR effect. The weakening of commensalistic and predatory relationship between phyto- and bacterioplankton under all experimental conditions denotes the negative effects of present and future global-change conditions on planktonic food webs towards impairing C flux within the microbial loop.
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20
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Gómez-Consarnau L, Needham DM, Weber PK, Fuhrman JA, Mayali X. Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria. Front Microbiol 2019; 10:1204. [PMID: 31214143 PMCID: PMC6558058 DOI: 10.3389/fmicb.2019.01204] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/13/2019] [Indexed: 11/13/2022] Open
Abstract
Light plays a central role on primary productivity of aquatic systems. Yet, its potential impact on the degradation of photosynthetically produced biomass is not well understood. We investigated the patterns of light-induced particle breakdown and bacterial assimilation of detrital C and N using 13C and 15N labeled freeze-thawed diatom cells incubated in laboratory microcosms with a marine microbial community freshly collected from the Pacific Ocean. Particles incubated in the dark resulted in increased bacterial counts and dissolved organic carbon concentrations compared to those incubated in the light. Light also influenced the attached and free-living microbial community structure as detected by 16S rRNA gene amplicon sequencing. For example, Sphingobacteriia were enriched on dark-incubated particles and taxa from the family Flavobacteriaceae and the genus Pseudoalteromonas were numerically enriched on particles in the light. Isotope incorporation analysis by phylogenetic microarray and NanoSIMS (a method called Chip-SIP) identified free-living and attached microbial taxa able to incorporate N and C from the particles. Some taxa, including members of the Flavobacteriaceae and Cryomorphaceae, exhibited increased isotope incorporation in the light, suggesting the use of photoheterotrophic metabolisms. In contrast, some members of Oceanospirillales and Rhodospirillales showed decreased isotope incorporation in the light, suggesting that their heterotrophic metabolism, particularly when occurring on particles, might increase at night or may be inhibited by sunlight. These results show that light influences particle degradation and C and N incorporation by attached bacteria, suggesting that the transfer between particulate and free-living phases are likely affected by external factors that change with the light regime, such as time of day, water column depth and season.
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Affiliation(s)
- Laura Gómez-Consarnau
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, CA, United States
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21
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Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JÉ, Vik D, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB. Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell 2019; 177:1109-1123.e14. [PMID: 31031001 PMCID: PMC6525058 DOI: 10.1016/j.cell.2019.03.040] [Citation(s) in RCA: 384] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/05/2019] [Accepted: 03/20/2019] [Indexed: 01/04/2023]
Abstract
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Nádia Conceição-Neto
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium; Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK
| | - Ben Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Mathieu Ardyna
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, Evry 91057, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Céline Dimier
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | | | - Joannie Ferland
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Directors' Research, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yunxiao Liu
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Claudie Marec
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, 28359 Bremen, Germany; MARUM, Bremen University, 28359 Bremen, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of Russian Academy of Sciences, 36 Nakhimovsky prosp, 117997 Moscow, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Jean-Éric Tremblay
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Marcel Babin
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Alexander I Culley
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8093 Zurich, Switzerland
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA.
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Teira E, Logares R, Gutiérrez‐Barral A, Ferrera I, Varela MM, Morán XAG, Gasol JM. Impact of grazing, resource availability and light on prokaryotic growth and diversity in the oligotrophic surface global ocean. Environ Microbiol 2019; 21:1482-1496. [DOI: 10.1111/1462-2920.14581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Eva Teira
- Departamento de Ecoloxía e Bioloxía AnimalUniversidade de Vigo Vigo Spain
| | - Ramiro Logares
- Departamento de Biologia Marina i OceanografiaInstitut de Ciències del Mar, CSIC Barcelona Catalonia Spain
| | | | - Isabel Ferrera
- Departamento de Biologia Marina i OceanografiaInstitut de Ciències del Mar, CSIC Barcelona Catalonia Spain
- Instituto Español de OceanografíaCentro Oceanográfico de Málaga Fuengirola Spain
| | - Marta M. Varela
- Instituto Español de OceanografíaCentro Oceanográfico de A Coruña A Coruña Spain
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Josep M. Gasol
- Departamento de Biologia Marina i OceanografiaInstitut de Ciències del Mar, CSIC Barcelona Catalonia Spain
- Centre for Marine Ecosystems ResearchEdith Cowan University Joondalup Western Australia Australia
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Reverey F, Ganzert L, Lischeid G, Ulrich A, Premke K, Grossart HP. Dry-wet cycles of kettle hole sediments leave a microbial and biogeochemical legacy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:985-996. [PMID: 29426223 DOI: 10.1016/j.scitotenv.2018.01.220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/20/2018] [Accepted: 01/22/2018] [Indexed: 06/08/2023]
Abstract
Understanding interrelations between an environment's hydrological past and its current biogeochemistry is necessary for the assessment of biogeochemical and microbial responses to changing hydrological conditions. The question how previous dry-wet events determine the contemporary microbial and biogeochemical state is addressed in this study. Therefore, sediments exposed to the atmosphere of areas with a different hydrological past within one kettle hole, i.e. (1) the predominantly inundated pond center, (2) the pond margin frequently desiccated for longer periods and (3) an intermediate zone, were incubated with the same rewetting treatment. Physicochemical and textural characteristics were related to structural microbial parameters regarding carbon and nitrogen turnover, i.e. abundance of bacteria and fungi, denitrifiers (targeted by the nirK und nirS functional genes) and nitrate ammonifiers (targeted by the nrfA functional gene). Our study reveals that, in combination with varying sediment texture, the hydrological history creates distinct microbial habitats with defined boundary conditions within the kettle hole, mainly driven by redox conditions, pH and organic matter (OM) composition. OM mineralization, as indicated by CO2-outgassing, was most efficient in exposed sediments with a less stable hydrological past. The potential for nitrogen retention via nitrate ammonification was highest in the hydrologically rather stable pond center, counteracting nitrogen loss due to denitrification. Therefore, the degree of hydrological stability is an important factor leaving a microbial and biogeochemical legacy, which determines carbon and nitrogen losses from small lentic freshwater systems in the long term run.
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Affiliation(s)
- Florian Reverey
- Leibniz Centre for Agricultural Landscape Research, Working Group: Small Water Bodies in Agricultural Landscapes, Eberswalder Str. 84, 15374 Müncheberg, Germany; Potsdam University, Institute of Earth and Environmental Science, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
| | - Lars Ganzert
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Experimental Limnology, Alte Fischerhütte 2, OT Neuglobsow, 16775 Stechlin, Germany
| | - Gunnar Lischeid
- Leibniz Centre for Agricultural Landscape Research, Working Group: Small Water Bodies in Agricultural Landscapes, Eberswalder Str. 84, 15374 Müncheberg, Germany; Potsdam University, Institute of Earth and Environmental Science, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research, Working Group: Microbial Biogeochemistry, Eberswalder Str. 84, 15374 Müncheberg, Germany
| | - Katrin Premke
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Chemical Analytics and Biogeochemistry, Müggelseedamm 310, 12587 Berlin, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Experimental Limnology, Alte Fischerhütte 2, OT Neuglobsow, 16775 Stechlin, Germany; Potsdam University, Institute for Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
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24
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Duhamel S, Van Wambeke F, Lefevre D, Benavides M, Bonnet S. Mixotrophic metabolism by natural communities of unicellular cyanobacteria in the western tropical South Pacific Ocean. Environ Microbiol 2018; 20:2743-2756. [PMID: 29573372 DOI: 10.1111/1462-2920.14111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 03/12/2018] [Accepted: 03/17/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria are major contributors to ocean biogeochemical cycling. However, mixotrophic metabolism and the relative importance of inorganic and organic carbon assimilation within the most abundant cyanobacteria are still poorly understood. We explore the ability of Prochlorococcus and Synechococcus to assimilate organic molecules with variable C:N:P composition and its modulation by light availability and photosynthetic impairment. We used a combination of radiolabelled molecules incubations with flow cytometry cell sorting to separate picoplankton groups from the western tropical South Pacific Ocean. Prochlorococcus and Synechococcus assimilated glucose, leucine and ATP at all stations, but cell-specific assimilation rates of N and P containing molecules were significantly higher than glucose. Incubations in the dark or with an inhibitor of photosystem II resulted in reduced assimilation rates. Light-enhanced cell-specific glucose uptake was generally higher for cyanobacteria (∼50%) than for the low nucleic acid fraction of bacterioplankton (LNA, ∼35%). Our results confirm previous findings, based mainly on cultures and genomic potentials, showing that Prochlorococcus and Synechococcus have a flexible mixotrophic metabolism, but demonstrate that natural populations remain primarily photoautotrophs. Our findings indicate that mixotrophy by marine cyanobacteria is more likely to be an adaptation to low inorganic nutrient availability rather than a facultative pathway for carbon acquisition.
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Affiliation(s)
- Solange Duhamel
- Lamont Doherty Earth Observatory, Division of Biology and Paleo Environment, PO Box 1000, 61 Route 9W, Palisades, NY 10964, USA
| | - France Van Wambeke
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Dominique Lefevre
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Mar Benavides
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.,Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 98848, Noumea, New Caledonia
| | - Sophie Bonnet
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.,Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 98848, Noumea, New Caledonia
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25
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Piwosz K, Kaftan D, Dean J, Šetlík J, Koblížek M. Nonlinear effect of irradiance on photoheterotrophic activity and growth of the aerobic anoxygenic phototrophic bacteriumDinoroseobacter shibae. Environ Microbiol 2017; 20:724-733. [DOI: 10.1111/1462-2920.14003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/10/2017] [Accepted: 11/17/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Kasia Piwosz
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - David Kaftan
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - Jason Dean
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - Jiří Šetlík
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - Michal Koblížek
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
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26
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Sánchez O, Koblížek M, Gasol JM, Ferrera I. Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:300-309. [PMID: 28401694 DOI: 10.1111/1758-2229.12535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Estimation of growth rates is crucial to understand the ecological role of prokaryotes and their contribution to marine biogeochemical cycling. However, there are only a few estimates for individual taxa. Two top-down (grazing) and bottom-up (phosphorus (P) availability) manipulation experiments were conducted under different light regimes in the NW Mediterranean Sea. Growth rate of different phylogenetic groups, including the Bacteroidetes, Rhodobacteraceae, SAR11, Gammaproteobacteria and its subgroups Alteromonadaceae and the NOR5/OM60 clade, were estimated from changes in cell numbers. Maximal growth rates were achieved in the P-amended treatments but when comparing values between treatments (response ratios), the response to predation removal was in general larger than to P-amendment. The Alteromonadaceae displayed the highest rates in both experiments followed by the Rhodobacteraceae, but all groups largely responded to filtration and P-amendment, even the SAR11 which presented low growth rates. Comparing light and dark treatments, growth rates were on average equal or higher in the dark than in the light for all groups, except for the Rhodobacteraceae and particularly the NOR5 clade, groups that contain photoheterotrophic species. These results are useful to evaluate the potential contributions of different bacterial types to biogeochemical processes under changing environmental conditions.
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Affiliation(s)
- Olga Sánchez
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, 08193, Spain
| | - Michal Koblížek
- Institute of Microbiology CAS, Center Algatech, 379 81 Třeboň, Czech Republic
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, E08003, Spain
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, E08003, Spain
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28
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Light enhances the growth rates of natural populations of aerobic anoxygenic phototrophic bacteria. ISME JOURNAL 2017; 11:2391-2393. [PMID: 28534877 DOI: 10.1038/ismej.2017.79] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/07/2017] [Accepted: 03/16/2017] [Indexed: 11/09/2022]
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are microorganisms that can harvest light energy using bacteriochlorophyll a to supplement their predominantly organotrophic metabolism. Growth enhancement by light has repeatedly been demonstrated in laboratory experiments with AAP isolates. However, the ecological advantage of light utilization is unclear, as it has never been proven in the natural environment. Here, we conducted manipulation experiments in the NW Mediterranean and found that AAP bacteria display high growth rates which are controlled to a large extent by intense grazing pressure and phosphorous availability. Foremost, we found that, contrarily to the bulk bacterioplakton, AAP bacteria display higher growth rates when incubated under light-dark cycles than in complete darkness. These results represent the first direct evidence that natural populations of marine AAP bacteria can be stimulated by light.
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29
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Hernández KL, Yannicelli B, Olsen LM, Dorador C, Menschel EJ, Molina V, Remonsellez F, Hengst MB, Jeffrey WH. Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano. Front Microbiol 2016; 7:1857. [PMID: 27920763 PMCID: PMC5118629 DOI: 10.3389/fmicb.2016.01857] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/04/2016] [Indexed: 11/13/2022] Open
Abstract
In high altitude environments, extreme levels of solar radiation and important differences of ionic concentrations over narrow spatial scales may modulate microbial activity. In Salar de Huasco, a high-altitude wetland in the Andean mountains, the high diversity of microbial communities has been characterized and associated with strong environmental variability. Communities that differed in light history and environmental conditions, such as nutrient concentrations and salinity from different spatial locations, were assessed for bacterial secondary production (BSP, 3H-leucine incorporation) response from short-term exposures to solar radiation. We sampled during austral spring seven stations categorized as: (a) source stations, with recently emerged groundwater (no-previous solar exposure); (b) stream running water stations; (c) stations connected to source waters but far downstream from source points; and (d) isolated ponds disconnected from ground sources or streams with a longer isolation and solar exposure history. Very high values of 0.25 μE m-2 s-1, 72 W m-2 and 12 W m-2 were measured for PAR, UVA, and UVB incident solar radiation, respectively. The environmental factors measured formed two groups of stations reflected by principal component analyses (near to groundwater sources and isolated systems) where isolated ponds had the highest BSP and microbial abundance (35 microalgae taxa, picoeukaryotes, nanoflagellates, and bacteria) plus higher salinities and PO43- concentrations. BSP short-term response (4 h) to solar radiation was measured by 3H-leucine incorporation under four different solar conditions: full sun, no UVB, PAR, and dark. Microbial communities established in waters with the longest surface exposure (e.g., isolated ponds) had the lowest BSP response to solar radiation treatments, and thus were likely best adapted to solar radiation exposure contrary to ground source waters. These results support our light history (solar exposure) hypothesis where the more isolated the community is from ground water sources, the better adapted it is to solar radiation. We suggest that factors other than solar radiation (e.g., salinity, PO43-, NO3-) are also important in determining microbial productivity in heterogeneous environments such as the Salar de Huasco.
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Affiliation(s)
- Klaudia L Hernández
- Centro de Investigación Marina Quintay CIMARQ, Facultad de Ecología y Recursos Naturales, Universidad Andres BelloSantiago, Chile; Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de ChileValdivia, Chile
| | - Beatriz Yannicelli
- Centro de Estudios Avanzados en Zonas AridasLa Serena, Chile; Facultad de Ciencias del Mar, Universidad Católica del NorteCoquimbo, Chile; Ecology and Sustainable Management of Oceanic Islands, Universidad Católica del Norte, CoquimboCoquimbo, Chile; Centro Universitario de la Región Este, Universidad de la RepúblicaRocha, Uruguay
| | | | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile; Centro de Biotecnología y BioingenieríaSantiago, Chile
| | - Eduardo J Menschel
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de ChileValdivia, Chile; Programa de Postgrado en Oceanografía, Departamento de Oceanografía, Universidad de ConcepciónConcepción, Chile; Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (FONDAP-IDEAL), Universidad Austral de ChileValdivia-Punta Arenas, Chile
| | - Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha Valparaíso, Chile
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte Antofagasta, Chile
| | - Martha B Hengst
- Centro de Biotecnología y BioingenieríaSantiago, Chile; Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del NorteAntofagasta, Chile
| | - Wade H Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola FL, USA
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30
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Molina V, Hernández K, Dorador C, Eissler Y, Hengst M, Pérez V, Harrod C. Bacterial Active Community Cycling in Response to Solar Radiation and Their Influence on Nutrient Changes in a High-Altitude Wetland. Front Microbiol 2016; 7:1823. [PMID: 27909430 PMCID: PMC5112256 DOI: 10.3389/fmicb.2016.01823] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/31/2016] [Indexed: 01/08/2023] Open
Abstract
Microbial communities inhabiting high-altitude spring ecosystems are subjected to extreme changes in solar irradiance and temperature throughout the diel cycle. Here, using 16S rRNA gene tag pyrosequencing (cDNA) we determined the composition of actively transcribing bacteria from spring waters experimentally exposed through the day (morning, noon, and afternoon) to variable levels of solar radiation and light quality, and evaluated their influence on nutrient recycling. Solar irradiance, temperature, and changes in nutrient dynamics were associated with changes in the active bacterial community structure, predominantly by Cyanobacteria, Verrucomicrobia, Proteobacteria, and 35 other Phyla, including the recently described Candidate Phyla Radiation (e.g., Parcubacteria, Gracilibacteria, OP3, TM6, SR1). Diversity increased at noon, when the highest irradiances were measured (3.3-3.9 H', 1125 W m-2) compared to morning and afternoon (0.6-2.8 H'). This shift was associated with a decrease in the contribution to pyrolibraries by Cyanobacteria and an increase of Proteobacteria and other initially low frequently and rare bacteria phyla (< 0.5%) in the pyrolibraries. A potential increase in the activity of Cyanobacteria and other phototrophic groups, e.g., Rhodobacterales, was observed and associated with UVR, suggesting the presence of photo-activated repair mechanisms to resist high levels of solar radiation. In addition, the percentage contribution of cyanobacterial sequences in the afternoon was similar to those recorded in the morning. The shifts in the contribution by Cyanobacteria also influenced the rate of change in nitrate, nitrite, and phosphate, highlighted by a high level of nitrate accumulation during hours of high radiation and temperature associated with nitrifying bacteria activity. We did not detect ammonia or nitrite oxidizing bacteria in situ, but both functional groups (Nitrosomona and Nitrospira) appeared mainly in pyrolibraries generated from dark incubations. In total, our results reveal that both the structure and the diversity of the active bacteria community was extremely dynamic through the day, and showed marked shifts in composition that influenced nutrient recycling, highlighting how abiotic variation affects potential ecosystem functioning.
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Affiliation(s)
- Verónica Molina
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa AnchaValparaíso, Chile
| | - Klaudia Hernández
- Centro de Investigación Marina Quintay, Facultad de Ecología y Recursos Naturales, Universidad Andres BelloValparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, AntofagastaChile
- Centre for Biotechnology and BioengineeringSantiago, Chile
| | - Yoanna Eissler
- Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de ValparaísoValparaíso, Chile
| | - Martha Hengst
- Centre for Biotechnology and BioengineeringSantiago, Chile
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del NorteAntofagasta, Chile
| | - Vilma Pérez
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, AntofagastaChile
- Centre for Biotechnology and BioengineeringSantiago, Chile
| | - Chris Harrod
- Fish and Stable Isotope Ecology Laboratory, Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile
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31
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Saharan dust inputs and high UVR levels jointly alter the metabolic balance of marine oligotrophic ecosystems. Sci Rep 2016; 6:35892. [PMID: 27775100 PMCID: PMC5075918 DOI: 10.1038/srep35892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/06/2016] [Indexed: 01/13/2023] Open
Abstract
The metabolic balance of the most extensive bioma on the Earth is a controversial topic of the global-change research. High ultraviolet radiation (UVR) levels by the shoaling of upper mixed layers and increasing atmospheric dust deposition from arid regions may unpredictably alter the metabolic state of marine oligotrophic ecosystems. We performed an observational study across the south-western (SW) Mediterranean Sea to assess the planktonic metabolic balance and a microcosm experiment in two contrasting areas, heterotrophic nearshore and autotrophic open sea, to test whether a combined UVR × dust impact could alter their metabolic balance at mid-term scales. We show that the metabolic state of oligotrophic areas geographically varies and that the joint impact of UVR and dust inputs prompted a strong change towards autotrophic metabolism. We propose that this metabolic response could be accentuated with the global change as remote-sensing evidence shows increasing intensities, frequencies and number of dust events together with variations in the surface UVR fluxes on SW Mediterranean Sea. Overall, these findings suggest that the enhancement of the net carbon budget under a combined UVR and dust inputs impact could contribute to boost the biological pump, reinforcing the role of the oligotrophic marine ecosystems as CO2 sinks.
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Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology. Microbiol Mol Biol Rev 2016; 80:929-54. [PMID: 27630250 DOI: 10.1128/mmbr.00003-16] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of "heterotrophic" bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.
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Bryant JA, Aylward FO, Eppley JM, Karl DM, Church MJ, DeLong EF. Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre. THE ISME JOURNAL 2016; 10:1308-22. [PMID: 26645474 PMCID: PMC5029195 DOI: 10.1038/ismej.2015.221] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 10/07/2015] [Accepted: 10/25/2015] [Indexed: 11/09/2022]
Abstract
Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces.
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Affiliation(s)
- Jessica A Bryant
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology, Cambridge, MA, USA
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
| | - Frank O Aylward
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
| | - Matthew J Church
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
| | - Edward F DeLong
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology, Cambridge, MA, USA
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
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Barsotti F, Brigante M, Sarakha M, Maurino V, Minero C, Vione D. Photochemical processes induced by the irradiation of 4-hydroxybenzophenone in different solvents. Photochem Photobiol Sci 2016; 14:2087-96. [PMID: 26463252 DOI: 10.1039/c5pp00214a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The singlet and triplet excited states of 4-hydroxybenzophenone (4BPOH) undergo deprotonation in the presence of water to produce the anionic ground-state, causing fluorescence quenching and photoactivity inhibition. The same process does not take place in an aprotic solvent such as acetonitrile. In acetonitrile, 4BPOH is fluorescent (interestingly, one of its fluorescence peaks overlaps with peak C of humic substances), it yields singlet oxygen upon irradiation and induces the triplet-sensitised transformation of phenol (with a rate constant of (6.6 ± 0.3) × 10(7) M(-1) s(-1) (μ ± σ) between phenol itself and a triplet 4BPOH). The 4BPOH shows an intermediate behaviour in a partially protic solvent such as 2-propanol, where some deprotonation of the excited states is observed. In acetonitrile/2-propanol mixtures (at least up to 50% of 2-propanol) there is also some evidence of alcohol oxidation by the 4BPOH triplet state, while the experimental data are silent concerning such a possibility in pure 2-propanol. Considering that benzophenones are important components of chromophoric dissolved organic matter (CDOM) in surface waters, the present findings could have significance for the photoactivity of the hydrophilic surface layers vs. the hydrophobic cores of CDOM.
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Affiliation(s)
- Francesco Barsotti
- Dipartimento di Chimica, Università di Torino, Via P. Giuria 5, 10125 Torino, Italy
| | - Marcello Brigante
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France
| | - Mohamed Sarakha
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France
| | - Valter Maurino
- Dipartimento di Chimica, Università di Torino, Via P. Giuria 5, 10125 Torino, Italy
| | - Claudio Minero
- Dipartimento di Chimica, Università di Torino, Via P. Giuria 5, 10125 Torino, Italy
| | - Davide Vione
- Dipartimento di Chimica, Università di Torino, Via P. Giuria 5, 10125 Torino, Italy and Centro NatRisk, Via L. Da Vinci 44, 10095 Grugliasco (TO), Italy.
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Bacosa HP, Liu Z, Erdner DL. Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters. Front Microbiol 2015; 6:1325. [PMID: 26648916 PMCID: PMC4664628 DOI: 10.3389/fmicb.2015.01325] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/11/2015] [Indexed: 01/06/2023] Open
Abstract
Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 days under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters.
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Affiliation(s)
- Hernando P Bacosa
- Marine Science Institute, The University of Texas at Austin Port Aransas, TX, USA
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin Port Aransas, TX, USA
| | - Deana L Erdner
- Marine Science Institute, The University of Texas at Austin Port Aransas, TX, USA
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Ruiz-González C, Salazar G, Logares R, Proia L, Gasol JM, Sabater S. Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River. Front Microbiol 2015; 6:1293. [PMID: 26635761 PMCID: PMC4659902 DOI: 10.3389/fmicb.2015.01293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/06/2015] [Indexed: 11/13/2022] Open
Abstract
Deductions about the ecology of high taxonomic bacterial ranks (i.e., phylum, class, order) are often based on their abundance patterns, yet few studies have quantified how accurately variations in abundance of these bacterial groups represent the dynamics of the taxa within them. Using 454-pyrosequencing of the 16S rRNA gene, we investigated whether the changes in abundance of six dominant bacterial classes (Actinobacteria, Beta-/Alpha-/Gamma-proteobacteria, Flavobacteria, and Sphingobacteria) along a large dam-regulated river are reflected by those of their constituent Operational Taxonomic Units (OTUs; 97% similarity level). The environmental impact generated by the reservoirs promoted clear compositional shifts in all bacterial classes that resulted from changes in the abundance of individual OTUs rather than from the appearance of new taxa along the river. Abundance patterns at the class level represented the dynamics of only a small but variable proportion of their constituting OTUs, which were not necessarily the most abundant ones. Within most classes, we detected sub-groups of OTUs showing contrasting responses to reservoir-induced environmental changes. Overall, we show that the patterns observed at the class level fail to capture the dynamics of a significant fraction of their constituent members, calling for caution when the ecological attributes of high-ranks are to be interpreted.
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Affiliation(s)
- Clara Ruiz-González
- Institute of Aquatic Ecology, University of Girona Girona, Spain ; Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC) Barcelona, Spain ; Département des Sciences Biologiques, Université du Québec à Montréal Montréal, QC, Canada
| | - Guillem Salazar
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC) Barcelona, Spain
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC) Barcelona, Spain
| | - Lorenzo Proia
- Institute of Aquatic Ecology, University of Girona Girona, Spain ; Catalan Institute for Water Research, Scienfitic and Technological Parc of the University of Girona Girona, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC) Barcelona, Spain
| | - Sergi Sabater
- Institute of Aquatic Ecology, University of Girona Girona, Spain ; Catalan Institute for Water Research, Scienfitic and Technological Parc of the University of Girona Girona, Spain
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Sample dilution and bacterial community composition influence empirical leucine-to-carbon conversion factors in surface waters of the world's oceans. Appl Environ Microbiol 2015; 81:8224-32. [PMID: 26407885 DOI: 10.1128/aem.02454-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/15/2015] [Indexed: 11/20/2022] Open
Abstract
The transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu(-1) and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean.
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Sarmento H, Casamayor EO, Auguet JC, Vila-Costa M, Felip M, Camarero L, Gasol JM. Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes. Front Microbiol 2015; 6:361. [PMID: 25999921 PMCID: PMC4419848 DOI: 10.3389/fmicb.2015.00361] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/09/2015] [Indexed: 11/13/2022] Open
Abstract
Sharp boundaries in the physical environment are usually associated with abrupt shifts in organism abundance, activity, and diversity. Aquatic surface microlayers (SML) form a steep gradient between two contrasted environments, the atmosphere and surface waters, where they regulate the gas exchange between both environments. They usually harbor an abundant and active microbial life: the neuston. Few ecosystems are subjected to such a high UVR regime as high altitude lakes during summer. Here, we measured bulk estimates of heterotrophic activity, community structure and single-cell physiological properties by flow cytometry in 19 high-altitude remote Pyrenean lakes and compared the biological processes in the SML with those in the underlying surface waters. Phototrophic picoplankton (PPP) populations, were generally present in high abundances and in those lakes containing PPP populations with phycoerythrin (PE), total PPP abundance was higher at the SML. Heterotrophic nanoflagellates (HNF) were also more abundant in the SML. Bacteria in the SML had lower leucine incorporation rates, lower percentages of “live” cells, and higher numbers of highly-respiring cells, likely resulting in a lower growth efficiency. No simple and direct linear relationships could be found between microbial abundances or activities and environmental variables, but factor analysis revealed that, despite their physical proximity, microbial life in SML and underlying waters was governed by different and independent processes. Overall, we demonstrate that piconeuston in high altitude lakes has specific features different from those of the picoplankton, and that they are highly affected by potential stressful environmental factors, such as high UVR radiation.
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Affiliation(s)
- Hugo Sarmento
- Institut de Ciències del Mar, ICM-Consejo Superior de Investigaciones Científicas Barcelona, Spain ; Laboratory of Microbial Processes and Biodiversity, Department of Hydrobiology, Federal University of São Carlos São Carlos, Brazil
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Limnological Observatory of the Pyrenees, Centre d'Estudis Avançats de Blanes, CEAB-Consejo Superior de Investigaciones Científicas Blanes, Spain
| | - Jean-Christophe Auguet
- Integrative Freshwater Ecology Group, Limnological Observatory of the Pyrenees, Centre d'Estudis Avançats de Blanes, CEAB-Consejo Superior de Investigaciones Científicas Blanes, Spain
| | - Maria Vila-Costa
- Integrative Freshwater Ecology Group, Limnological Observatory of the Pyrenees, Centre d'Estudis Avançats de Blanes, CEAB-Consejo Superior de Investigaciones Científicas Blanes, Spain
| | - Marisol Felip
- Department of Environmental Chemistry, IDAEA-CSIC Barcelona, Spain ; Centre de Recerca d'Alta Muntanya, Universitat de Barcelona Lleida, Spain
| | - Lluís Camarero
- Integrative Freshwater Ecology Group, Limnological Observatory of the Pyrenees, Centre d'Estudis Avançats de Blanes, CEAB-Consejo Superior de Investigaciones Científicas Blanes, Spain ; Centre de Recerca d'Alta Muntanya, Universitat de Barcelona Lleida, Spain
| | - Josep M Gasol
- Institut de Ciències del Mar, ICM-Consejo Superior de Investigaciones Científicas Barcelona, Spain
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Fauteux L, Cottrell MT, Kirchman DL, Borrego CM, Garcia-Chaves MC, del Giorgio PA. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes. PLoS One 2015; 10:e0124035. [PMID: 25927833 PMCID: PMC4415779 DOI: 10.1371/journal.pone.0124035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/10/2015] [Indexed: 11/19/2022] Open
Abstract
There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.
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Affiliation(s)
- Lisa Fauteux
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
| | - Matthew T. Cottrell
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd., Lewes, DE 19958, United States of America
| | - David L. Kirchman
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd., Lewes, DE 19958, United States of America
| | - Carles M. Borrego
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus de Montilivi, E-17071, Girona, Spain
| | - Maria Carolina Garcia-Chaves
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
| | - Paul A. del Giorgio
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
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Amado AM, Cotner JB, Cory RM, Edhlund BL, McNeill K. Disentangling the interactions between photochemical and bacterial degradation of dissolved organic matter: amino acids play a central role. MICROBIAL ECOLOGY 2015; 69:554-566. [PMID: 25351141 DOI: 10.1007/s00248-014-0512-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 10/08/2014] [Indexed: 06/04/2023]
Abstract
Photochemical and bacterial degradation are important pathways to carbon mineralization and can be coupled in dissolved organic matter (DOM) decomposition. However, details of several mechanisms of the coupled photochemical and biological processing of DOM remain too poorly understood to achieve accurate predictions of the impact of these processes on DOM fate and reactivity. The aim of this study was to evaluate how photochemical degradation of amino acids affects bacterial metabolism and whether or not photochemical degradation of DOM competes for amino acids with biological processes. We examined the interactions between photochemical and bacterial degradation dynamics using a mixture of 18 amino acids and examined their dynamics and turnover rates within a larger pool of allochthonous or autochthonous DOM. We observed that photochemical exposure of DOM containing amino acids led to delayed biomass production (even though the final biomass did not differ), most likely due to a need for upregulation of biosynthetic pathways for amino acids that were damaged by photochemically produced reactive oxygen species (ROS). This response was most pronounced in bacterial communities where the abundance of photosensitive amino acids was highest (amended treatments and autochthonous DOM) and least pronounced when the abundance of these amino acids was low (unamended and allochthonous DOM), likely because these bacteria already had these biosynthetic pathways functioning. We observed both a cost and benefit associated with photochemical exposure of DOM. We observed a cost associated with photochemically produced ROS that partially degrade key amino acids and a benefit associated with an increase in the availability of other compounds in the DOM. Bacteria growing on DOM sources that are low in labile amino acids, such as those in terrestrially influenced environments, experience more of the benefits associated with photochemical exposure, whereas bacteria growing in more amino acid-rich environments, such as eutrophic and less terrestrially influenced waters, experience a higher cost due to the increased necessity of salvage pathways for these essential amino acids. Finally, we propose a conceptual model whereby the effects of DOM photochemical degradation on microbial metabolism result from the balance between two mechanisms: One is dependent on the DOM sources, and the other is dependent on the DOM concentration in natural systems.
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Affiliation(s)
- André M Amado
- Department of Ecology, Evolution and Behavior, University of Minnesota, Twin Cities, Saint Paul, MN, 55455, USA,
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Fernández-Zenoff MV, Estévez MC, Farías ME. Diurnal variation in bacterioplankton composition and DNA damage in the microbial community from an Andean oligotrophic lake. Rev Argent Microbiol 2015; 46:358-62. [PMID: 25576421 DOI: 10.1016/s0325-7541(14)70095-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 10/02/2014] [Indexed: 10/24/2022] Open
Abstract
Laguna Azul is an oligotrophic lake situated at 4,560 m above sea level and subject to a high level of solar radiation. Bacterioplankton community composition (BCC) was analysed by denaturing gradient gel electrophoresis and the impact of solar ultraviolet radiation was assessed by measuring cyclobutane pyrimidine dimers (CPD). Furthermore, pure cultures of Acinetobacter johnsonii A2 and Rhodococcus sp. A5 were exposed simultaneously and CPD accumulation was studied. Gel analyses generated a total of 7 sequences belonging to Alpha-proteobacteria (1 band), Beta-proteobacteria (1 band), Bacteroidetes (2 bands), Actinobacteria (1 band), and Firmicutes (1 band). DGGE profiles showed minimal changes in BCC and no CPD was detected even though a high level of damage was found in biodosimeters. A. johnsonii A2 showed low level of DNA damage while Rhodococcus sp. A5 exhibited high resistance since no CPD were detected under natural UV-B exposure, suggesting that the bacterial community is well adapted to this highly solar irradiated environment.
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Affiliation(s)
- María V Fernández-Zenoff
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina; Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina.
| | - María C Estévez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | - María E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
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McEnroe NA, Williams CJ, Xenopoulos MA, Porcal P, Frost PC. Distinct optical chemistry of dissolved organic matter in urban pond ecosystems. PLoS One 2013; 8:e80334. [PMID: 24348908 PMCID: PMC3865342 DOI: 10.1371/journal.pone.0080334] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 10/02/2013] [Indexed: 12/03/2022] Open
Abstract
Urbanization has the potential to dramatically alter the biogeochemistry of receiving freshwater ecosystems. We examined the optical chemistry of dissolved organic matter (DOM) in forty-five urban ponds across southern Ontario, Canada to examine whether optical characteristics in these relatively new ecosystems are distinct from other freshwater systems. Dissolved organic carbon (DOC) concentrations ranged from 2 to 16 mg C L-1 across the ponds with an average value of 5.3 mg C L-1. Excitation-emission matrix (EEM) spectroscopy and parallel factor analysis (PARAFAC) modelling showed urban pond DOM to be characterized by microbial-like and, less importantly, by terrestrial derived humic-like components. The relatively transparent, non-humic DOM in urban ponds was more similar to that found in open water, lake ecosystems than to rivers or wetlands. After irradiation equivalent to 1.7 days of natural solar radiation, DOC concentrations, on average, decreased by 38% and UV absorbance decreased by 25%. Irradiation decreased the relative abundances of terrestrial humic-like components and increased protein-like aspects of the DOM pool. These findings suggest that high internal production and/or prolonged exposure to sunlight exerts a distinct and significant influence on the chemistry of urban pond DOM, which likely reduces its chemical similarity with upstream sources. These properties of urban pond DOM may alter its biogeochemical role in these relatively novel aquatic ecosystems.
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Affiliation(s)
- Nicola A. McEnroe
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | | | | | - Petr Porcal
- Biology Centre of the Academy of Science of the Czech Republic, v.v.i., Institute of Hydrobiology, České Budějovice, Czech Republic
| | - Paul C. Frost
- Department of Biology, Trent University, Peterborough, Ontario, Canada
- * E-mail:
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Hunting ER, White CM, van Gemert M, Mes D, Stam E, van HG, der Geest, Kraak MHS, Admiraal W. UV radiation and organic matter composition shape bacterial functional diversity in sediments. Front Microbiol 2013; 4:317. [PMID: 24194736 PMCID: PMC3809517 DOI: 10.3389/fmicb.2013.00317] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/07/2013] [Indexed: 11/17/2022] Open
Abstract
UV radiation and organic matter (OM) composition are known to influence the species composition of bacterioplankton communities. Potential effects of UV radiation on bacterial communities residing in sediments remain completely unexplored to date. However, it has been demonstrated that UV radiation can reach the bottom of shallow waters and wetlands and alter the OM composition of the sediment, suggesting that UV radiation may be more important for sediment bacteria than previously anticipated. It is hypothesized here that exposure of shallow OM-containing sediments to UV radiation induces OM source-dependant shifts in the functional composition of sediment bacterial communities. This study therefore investigated the combined influence of both UV radiation and OM composition on bacterial functional diversity in laboratory sediments. Two different OM sources, labile and recalcitrant OM, were used and metabolic diversity was measured with Biolog GN. Radiation exerted strong negative effects on the metabolic diversity in the treatments containing recalcitrant OM, more than in treatments containing labile OM. The functional composition of the bacterial community also differed significantly between the treatments. Our findings demonstrate that a combined effect of UV radiation and OM composition shapes the functional composition of microbial communities developing in sediments, hinting that UV radiation may act as an important sorting mechanism for bacterial communities and driver for bacterial functioning in shallow waters and wetlands.
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Affiliation(s)
- Ellard R Hunting
- Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands ; National Institute for Public Health and the Environment Bilthoven, Netherlands
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