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Pereira-García C, Del Amo EH, Vigués N, Rey-Velasco X, Rincón-Tomás B, Pérez-Cruz C, Sanz-Sáez I, Hu H, Bertilsson S, Pannier A, Soltmann U, Sánchez P, Acinas SG, Bravo AG, Alonso-Sáez L, Sánchez O. Unmasking the physiology of mercury detoxifying bacteria from polluted sediments. J Hazard Mater 2024; 467:133685. [PMID: 38335604 DOI: 10.1016/j.jhazmat.2024.133685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Marine sediments polluted from anthropogenic activities can be major reservoirs of toxic mercury species. Some microorganisms in these environments have the capacity to detoxify these pollutants, by using the mer operon. In this study, we characterized microbial cultures isolated from polluted marine sediments growing under diverse environmental conditions of salinity, oxygen availability and mercury tolerance. Specific growth rates and percentage of mercury removal were measured in batch cultures for a selection of isolates. A culture affiliated with Pseudomonas putida (MERCC_1942), which contained a mer operon as well as other genes related to metal resistances, was selected as the best candidate for mercury elimination. In order to optimize mercury detoxification conditions for strain MERCC_1942 in continuous culture, three different dilution rates were tested in bioreactors until the cultures achieved steady state, and they were subsequently exposed to a mercury spike; after 24 h, strain MERCC_1942 removed up to 76% of the total mercury. Moreover, when adapted to high growth rates in bioreactors, this strain exhibited the highest specific mercury detoxification rates. Finally, an immobilization protocol using the sol-gel technology was optimized. These results highlight that some sediment bacteria show capacity to detoxify mercury and could be used for bioremediation applications.
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Affiliation(s)
- Carla Pereira-García
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Elena H Del Amo
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut d'Ecologia Aquàtica, Facultat de Ciències, Universitat de Girona, 17003 Girona, Spain
| | - Núria Vigués
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Xavier Rey-Velasco
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Blanca Rincón-Tomás
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Carla Pérez-Cruz
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain; Instituto de Diagnóstico Ambiental y Estudios del Agua (IDAEA-CSIC), Barcelona, Spain
| | - Haiyan Hu
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Angela Pannier
- GMBU e.V., Department of Functional Coatings, D-01454 Radeberg, Germany
| | - Ulrich Soltmann
- GMBU e.V., Department of Functional Coatings, D-01454 Radeberg, Germany
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Andrea G Bravo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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2
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Rincón-Tomás B, Lanzén A, Sánchez P, Estupiñán M, Sanz-Sáez I, Bilbao ME, Rojo D, Mendibil I, Pérez-Cruz C, Ferri M, Capo E, Abad-Recio IL, Amouroux D, Bertilsson S, Sánchez O, Acinas SG, Alonso-Sáez L. Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota. J Hazard Mater 2024; 465:133120. [PMID: 38101011 DOI: 10.1016/j.jhazmat.2023.133120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/10/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments.
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Affiliation(s)
- Blanca Rincón-Tomás
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain; Grupo Inv. Geología Aplicada a Recursos Marinos y Ambientes Extremos, Instituto Geológico y Minero de España (IGME-CSIC), 28003 Madrid, Spain.
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Pablo Sánchez
- Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Mónica Estupiñán
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Isabel Sanz-Sáez
- Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - M Elisabete Bilbao
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Diana Rojo
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Iñaki Mendibil
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Carla Pérez-Cruz
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Marta Ferri
- Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Eric Capo
- Dep. Ecology and Environmental Science, Umeå University, 907 36 Umeå, Sweden
| | - Ion L Abad-Recio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - David Amouroux
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux (IPREM), Pau, France
| | - Stefan Bertilsson
- Dep. Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Olga Sánchez
- Dep. Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona (UAB), 08192 Bellaterra, Spain
| | - Silvia G Acinas
- Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain.
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3
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Alonso-Sáez L, Palacio AS, Cabello AM, Robaina-Estévez S, González JM, Garczarek L, López-Urrutia Á. Transcriptional Mechanisms of Thermal Acclimation in Prochlorococcus. mBio 2023:e0342522. [PMID: 37052490 DOI: 10.1128/mbio.03425-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30°C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17°C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones. IMPORTANCE Prochlorococcus is a major marine primary producer with a global impact on atmospheric CO2 fixation. This cyanobacterium is widely distributed across the temperate ocean, but virtually absent at latitudes above 40° for yet unknown reasons. Temperature has been suggested as a major limiting factor, but the exact mechanisms behind Prochlorococcus thermal growth restriction remain unexplored. This study brings us closer to understanding how Prochlorococcus functions under challenging temperature conditions, by focusing on its transcriptional response after long-term acclimation from its optimum to its thermal thresholds. Our results show that the drop in Prochlorococcus growth rate under cold conditions was paralleled by a transcriptional suppression of the photosynthetic machinery during daytime and a loss in the organism's regulatory capacity to maintain circadian expression patterns. Notably, warm temperature induced a marked shrinkage of the organism's cellular transcript inventory, which may also induce regulatory imbalances in the future functioning of this cyanobacterium.
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Affiliation(s)
- Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Antonio S Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ana M Cabello
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, IEO-CSIC, Gijón, Asturias, Spain
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4
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Labban A, Palacio AS, García FC, Hadaidi G, Ansari MI, López-Urrutia Á, Alonso-Sáez L, Hong PY, Morán XAG. Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain. Front Microbiol 2021; 12:612732. [PMID: 34040590 PMCID: PMC8141594 DOI: 10.3389/fmicb.2021.612732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24-34°C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94-1.38 d-1, was very similar (0.34 ± 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38-24.4 d-1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.
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Affiliation(s)
- Abbrar Labban
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Antonio S. Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Francisca C. García
- Environment and Sustainability Institute, University of Exeter, Penryn, United Kingdom
| | - Ghaida Hadaidi
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohd I. Ansari
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Gijón, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Gijón, Spain
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5
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Castillo YM, Forn I, Yau S, Morán XAG, Alonso-Sáez L, Arandia-Gorostidi N, Vaqué D, Sebastián M. Seasonal dynamics of natural Ostreococcus viral infection at the single cell level using VirusFISH. Environ Microbiol 2021; 23:3009-3019. [PMID: 33817943 DOI: 10.1111/1462-2920.15504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/03/2021] [Indexed: 11/28/2022]
Abstract
Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free-living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral-host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral-host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Ostreococcus were predominantly found during summer and autumn at surface and 50 m depth, in coastal, mid-shelf and shelf waters, representing up to 21% of the picoeukaryotic communities. Viral infection was only detected in surface waters, and its impact was variable but highest from May to July and November to December, when up to half of the population was infected. Metatranscriptomic data available from the mid-shelf station unveiled that the Ostreococcus population was dominated by the species O. lucimarinus. This work represents a proof of concept that the VirusFISH technique can be used to quantify the impact of viruses on targeted populations of key microbes from complex natural communities.
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Affiliation(s)
- Yaiza M Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Sheree Yau
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Xosé Anxelu G Morán
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Laura Alonso-Sáez
- Centro Oceanográfico de Gijón/Xixón, IEO, Gijón/Xixón, Spain.,AZTI Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Spain
| | - Néstor Arandia-Gorostidi
- Centro Oceanográfico de Gijón/Xixón, IEO, Gijón/Xixón, Spain.,Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Institute of Oceanography and Global Change (IOCAG), University of Las Palmas de Gran Canaria (ULPGC), Telde, Spain
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6
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Palacio AS, Cabello AM, García FC, Labban A, Morán XAG, Garczarek L, Alonso-Sáez L, López-Urrutia Á. Changes in Population Age-Structure Obscure the Temperature-Size Rule in Marine Cyanobacteria. Front Microbiol 2020; 11:2059. [PMID: 32983043 PMCID: PMC7485217 DOI: 10.3389/fmicb.2020.02059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 08/05/2020] [Indexed: 11/13/2022] Open
Abstract
The temperature-size Rule (TSR) states that there is a negative relationship between ambient temperature and body size. This rule has been independently evaluated for different phases of the life cycle in multicellular eukaryotes, but mostly for the average population in unicellular organisms. We acclimated two model marine cyanobacterial strains (Prochlorococcus marinus MIT9301 and Synechococcus sp. RS9907) to a gradient of temperatures and measured the changes in population age-structure and cell size along their division cycle. Both strains displayed temperature-dependent diel changes in cell size, and as a result, the relationship between temperature and average cell size varied along the day. We computed the mean cell size of new-born cells in order to test the prediction of the TSR on a single-growth stage. Our work reconciles previous inconsistent results when testing the TSR on unicellular organisms, and shows that when a single-growth stage is considered the predicted negative response to temperature is revealed.
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Affiliation(s)
- Antonio S. Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ana María Cabello
- Spanish Institute of Oceanography (IEO), Oceanographic Center of Malaga, Málaga, Spain
| | - Francisca C. García
- Environment and Sustainability Institute, University of Exeter, Exeter, United Kingdom
| | - Abbrar Labban
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
| | - Xosé Anxelu G. Morán
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
- Spanish Institute of Oceanography (IEO), Oceanographic Center of Gijón/Xixón, Gijón, Spain
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Roscoff, France
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ángel López-Urrutia
- Spanish Institute of Oceanography (IEO), Oceanographic Center of Gijón/Xixón, Gijón, Spain
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7
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Zarandona I, Estupiñán M, Pérez C, Alonso-Sáez L, Guerrero P, de la Caba K. Chitosan Films Incorporated with Exopolysaccharides from Deep Seawater Alteromonas Sp. Mar Drugs 2020; 18:md18090447. [PMID: 32867255 PMCID: PMC7551391 DOI: 10.3390/md18090447] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/20/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
Two Alteromonas sp. strains isolated from deep seawater were grown to promote the production of exopolysaccharides (EPS, E611 and E805), which were incorporated into chitosan solutions to develop films. The combination of the major marine polysaccharides (chitosan and the isolated bacterial EPS) resulted in the formation of homogenous, transparent, colorless films, suggesting good compatibility between the two components of the film-forming formulation. With regards to optical properties, the films showed low values of gloss, in the range of 5-10 GU, indicating the formation of non-glossy and rough surfaces. In addition to the film surface, both showed hydrophobic character, with water contact angles higher than 100 º, regardless of EPS addition. Among the two EPS under analysis, chitosan films with E805 showed better mechanical performance, leading to resistant, flexible, easy to handle films.
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Affiliation(s)
- Iratxe Zarandona
- BIOMAT research group, University of the Basque Country (UPV/EHU), Escuela de Ingeniería de Gipuzkoa, Plaza de Europa 1, 20018 Donostia-San Sebastián, Spain;
| | - Mónica Estupiñán
- AZTI Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain; (M.E.); (C.P.); (L.A.-S.)
| | - Carla Pérez
- AZTI Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain; (M.E.); (C.P.); (L.A.-S.)
| | - Laura Alonso-Sáez
- AZTI Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain; (M.E.); (C.P.); (L.A.-S.)
| | - Pedro Guerrero
- BIOMAT research group, University of the Basque Country (UPV/EHU), Escuela de Ingeniería de Gipuzkoa, Plaza de Europa 1, 20018 Donostia-San Sebastián, Spain;
- Correspondence: (P.G.); (K.d.l.C.)
| | - Koro de la Caba
- BIOMAT research group, University of the Basque Country (UPV/EHU), Escuela de Ingeniería de Gipuzkoa, Plaza de Europa 1, 20018 Donostia-San Sebastián, Spain;
- Correspondence: (P.G.); (K.d.l.C.)
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8
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Arandia-Gorostidi N, González JM, Huete-Stauffer TM, Ansari MI, Morán XAG, Alonso-Sáez L. Light supports cell-integrity and growth rates of taxonomically diverse coastal photoheterotrophs. Environ Microbiol 2020; 22:3823-3837. [PMID: 32643243 DOI: 10.1111/1462-2920.15158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/29/2020] [Accepted: 07/06/2020] [Indexed: 11/28/2022]
Abstract
Despite the widespread distribution of proteorhodopsin (PR)-containing bacteria in the oceans, the use of light-derived energy to promote bacterial growth has only been shown in a few bacterial isolates, and there is a paucity of data describing the metabolic effects of light on environmental photoheterotrophic taxa. Here, we assessed the effects of light on the taxonomic composition, cell integrity and growth responses of microbial communities in monthly incubations between spring and autumn under different environmental conditions. The photoheterotrophs expressing PR in situ were dominated by Pelagibacterales and SAR116 in July and November, while members of Euryarchaeota, Gammaproteobacteria and Bacteroidetes dominated the PR expression in spring. Cell-membrane integrity decreased under dark conditions throughout most of the assessment, with maximal effects in summer, under low-nutrient conditions. A positive effect of light on growth was observed in one incubation (out of nine), coinciding with a declining phytoplankton bloom. Light-enhanced growth was found in Gammaproteobacteria (Alteromonadales) and Bacteroidetes (Polaribacter and Tenacibaculum). Unexpectedly, some Pelagibacterales also exhibited higher growth rates under light conditions. We propose that the energy harvested by PRs helps to maintain cell viability in dominant coastal photoheterotrophic oligotrophs while promoting the growth of some widespread taxa benefiting from the decline of phytoplankton blooms.
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Affiliation(s)
- Nestor Arandia-Gorostidi
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Tamara M Huete-Stauffer
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohd I Ansari
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G Morán
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Laura Alonso-Sáez
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Bizkaia, 48395, Spain
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9
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Lanzén A, Mendibil I, Borja Á, Alonso-Sáez L. A microbial mandala for environmental monitoring: Predicting multiple impacts on estuarine prokaryote communities of the Bay of Biscay. Mol Ecol 2020; 30:2969-2987. [PMID: 32479653 DOI: 10.1111/mec.15489] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/08/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023]
Abstract
Routine monitoring of benthic biodiversity is critical for managing and understanding the anthropogenic impacts on marine, transitional and freshwater ecosystems. However, traditional reliance on morphological identification generally makes it cost-prohibitive to increase the scale of monitoring programmes. Metabarcoding of environmental DNA has clear potential to overcome many of the problems associated with traditional monitoring, with prokaryotes and other microorganisms showing particular promise as bioindicators. However, due to the limited knowledge regarding the ecological roles and responses of environmental microorganisms to different types of pressure, the use of de novo approaches is necessary. Here, we use two such approaches for the prediction of multiple impacts present in estuaries and coastal areas of the Bay of Biscay based on microbial communities. The first (Random Forests) is a machine learning method while the second (Threshold Indicator Taxa Analysis and quantile regression splines) is based on de novo identification of bioindicators. Our results show that both methods overlap considerably in the indicator taxa identified, but less for sequence variants. Both methods also perform well in spite of the complexity of the studied ecosystem, providing predictive models with strong correlation to reference values and fair to good agreement with ecological status groups. The ability to predict several specific types of pressure is especially appealing. The cross-validated models and biotic indices developed can be directly applied to predict the environmental status of estuaries in the same geographical region, although more work is needed to evaluate and improve them for use in new regions or habitats.
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Affiliation(s)
- Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Iñaki Mendibil
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
| | - Ángel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
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10
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Alonso-Sáez L, Morán XAG, González JM. Transcriptional Patterns of Biogeochemically Relevant Marker Genes by Temperate Marine Bacteria. Front Microbiol 2020; 11:465. [PMID: 32265888 PMCID: PMC7098952 DOI: 10.3389/fmicb.2020.00465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
Environmental microbial gene expression patterns remain largely unexplored, particularly at interannual time scales. We analyzed the variability in the expression of marker genes involved in ecologically relevant biogeochemical processes at a temperate Atlantic site over two consecutive years. Most of nifH transcripts, involved in nitrogen (N) fixation, were affiliated with the symbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa, suggesting a key role as N providers in this system. The expression of nifH and amoA (i.e., marker for ammonia oxidation) showed consistent maxima in summer and autumn, respectively, suggesting a temporal succession of these important N cycling processes. The patterns of expression of genes related to the oxidation of carbon monoxide (coxL) and reduced sulfur (soxB) were different from that of amoA, indicating alternate timings for these energy conservation strategies. We detected expression of alkaline phosphatases, induced under phosphorus limitation, in agreement with the reported co-limitation by this nutrient at the study site. In contrast, low-affinity phosphate membrane transporters (pit) typically expressed under phosphorus luxury conditions, were mainly detected in post-bloom conditions. Rhodobacteraceae dominated the expression of soxB, coxL and ureases, while Pelagibacteraceae dominated the expression of proteorhodopsins. Bacteroidetes and Gammaproteobacteria were major contributors to the uptake of inorganic nutrients (pit and amt transporters). Yet, in autumn, Thauma- and Euryarchaeota unexpectedly contributed importantly to the uptake of ammonia and phosphate, respectively. We provide new hints on the active players and potential dynamics of ecologically relevant functions in situ, highlighting the potential of metatranscriptomics to provide significant input to future omics-driven marine ecosystem assessment.
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Affiliation(s)
- Laura Alonso-Sáez
- Marine Research Division, AZTI, Sukarrieta, Spain.,Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía (IEO), Gijón/Xixón, Spain
| | - Xosé Anxelu G Morán
- Biological and Environmental Sciences and Engineering Division, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
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11
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Arandia-Gorostidi N, Alonso-Sáez L, Stryhanyuk H, Richnow HH, Morán XAG, Musat N. Warming the phycosphere: Differential effect of temperature on the use of diatom-derived carbon by two copiotrophic bacterial taxa. Environ Microbiol 2020; 22:1381-1396. [PMID: 32090403 DOI: 10.1111/1462-2920.14954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/25/2020] [Indexed: 11/28/2022]
Abstract
Heterotrophic bacteria associated with microphytoplankton, particularly those colonizing the phycosphere, are major players in the remineralization of algal-derived carbon. Ocean warming might impact dissolved organic carbon (DOC) uptake by microphytoplankton-associated bacteria with unknown biogeochemical implications. Here, by incubating natural seawater samples at three different temperatures, we analysed the effect of experimental warming on the abundance and C and N uptake activity of Rhodobacteraceae and Flavobacteria, two bacterial groups typically associated with microphytoplankton. Using a nano-scale secondary ion mass spectrometry (nanoSIMS) single-cell analysis, we quantified the temperature sensitivity of these two taxonomic groups to the uptake of algal-derived DOC in the microphytoplankton associated fraction with 13 C-bicarbonate and 15 N-leucine as tracers. We found that cell-specific 13 C uptake was similar for both groups (~0.42 fg C h-1 μm-3 ), but Rhodobacteraceae were more active in 15 N-leucine uptake. Due to the higher abundance of Flavobacteria associated with microphytoplankton, this group incorporated fourfold more carbon than Rhodobacteraceae. Cell-specific 13 C uptake was influenced by temperature, but no significant differences were found for 15 N-leucine uptake. Our results show that the contribution of Flavobacteria and Rhodobacteraceae to C assimilation increased up to sixfold and twofold, respectively, with an increase of 3°C above ambient temperature, suggesting that warming may differently affect the contribution of distinct copiotrophic bacterial taxa to carbon cycling.
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Affiliation(s)
- Nestor Arandia-Gorostidi
- Department of Earth System Science, Stanford University, Green Earth Sciences Building, 367 Panama St., Room 129, Stanford, CA, 94305-4216, USA.,Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Av. Príncipe de Asturias, 70 bis 33212, Gijón, Asturias, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research Unit, Txatxarramendi Irla s/n, 48395, Sukarrieta, Bizkaia, Spain
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Xosé Anxelu G Morán
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955, Thuwal, Saudi Arabia
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
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12
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Estupiñán M, Hernández I, Saitua E, Bilbao ME, Mendibil I, Ferrer J, Alonso-Sáez L. Novel Vibrio spp. Strains Producing Omega-3 Fatty Acids Isolated from Coastal Seawater. Mar Drugs 2020; 18:E99. [PMID: 32024040 PMCID: PMC7074563 DOI: 10.3390/md18020099] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/26/2022] Open
Abstract
Omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs), such as eicosapentaenoic acid (EPA) (20:5n-3) and docosahexaenoic acid (DHA) (22:6n-3), are considered essential for human health. Microorganisms are the primary producers of omega-3 fatty acids in marine ecosystems, representing a sustainable source of these lipids, as an alternative to the fish industry. Some marine bacteria can produce LC-PUFAs de novo via the Polyunsaturated Fatty Acid (Pfa) synthase/ Polyketide Synthase (PKS) pathway, which does not require desaturation and elongation of saturated fatty acids. Cultivation-independent surveys have revealed that the diversity of microorganisms harboring a molecular marker of the pfa gene cluster (i.e., pfaA-KS domain) is high and their potential distribution in marine systems is widespread, from surface seawater to sediments. However, the isolation of PUFA producers from marine waters has been typically restricted to deep or cold environments. Here, we report a phenotypic and genotypic screening for the identification of omega-3 fatty acid producers in free-living bacterial strains isolated from 5, 500, and 1000 m deep coastal seawater from the Bay of Biscay (Spain). We further measured EPA production in pelagic Vibrio sp. strains collected at the three different depths. Vibrio sp. EPA-producers and non-producers were simultaneously isolated from the same water samples and shared a high percentage of identity in their 16S rRNA genes, supporting the view that the pfa gene cluster can be horizontally transferred. Within a cluster of EPA-producers, we found intraspecific variation in the levels of EPA synthesis for isolates harboring different genetic variants of the pfaA-KS domain. The maximum production of EPA was found in a Vibrio sp. strain isolated from a 1000 m depth (average 4.29% ± 1.07 of total fatty acids at 10 °C, without any optimization of culturing conditions).
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Affiliation(s)
- Mónica Estupiñán
- AZTI, Marine Research Division, Txatxarramendi Irla s/n, 48395 Sukarrieta, Spain; (M.E.); (M.E.B.); (I.M.)
| | - Igor Hernández
- AZTI, Food Research Division, Astondo Bidea, Building 609, 48160 Derio, Spain; (I.H.); (E.S.); (J.F.)
| | - Eduardo Saitua
- AZTI, Food Research Division, Astondo Bidea, Building 609, 48160 Derio, Spain; (I.H.); (E.S.); (J.F.)
| | - M. Elisabete Bilbao
- AZTI, Marine Research Division, Txatxarramendi Irla s/n, 48395 Sukarrieta, Spain; (M.E.); (M.E.B.); (I.M.)
| | - Iñaki Mendibil
- AZTI, Marine Research Division, Txatxarramendi Irla s/n, 48395 Sukarrieta, Spain; (M.E.); (M.E.B.); (I.M.)
| | - Jorge Ferrer
- AZTI, Food Research Division, Astondo Bidea, Building 609, 48160 Derio, Spain; (I.H.); (E.S.); (J.F.)
| | - Laura Alonso-Sáez
- AZTI, Marine Research Division, Txatxarramendi Irla s/n, 48395 Sukarrieta, Spain; (M.E.); (M.E.B.); (I.M.)
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13
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Arias-Jayo N, Abecia L, Alonso-Sáez L, Ramirez-Garcia A, Rodriguez A, Pardo MA. High-Fat Diet Consumption Induces Microbiota Dysbiosis and Intestinal Inflammation in Zebrafish. Microb Ecol 2018; 76:1089-1101. [PMID: 29736898 DOI: 10.1007/s00248-018-1198-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/27/2018] [Indexed: 05/26/2023]
Abstract
Energy-dense foods and overnutrition represent major starting points altering lipid metabolism, systemic inflammation and gut microbiota. The aim of this work was to investigate the effects of a high-fat diet (HFD) over a period of 25 days on intestinal microbiota and inflammation in zebrafish. Microbial composition of HFD-fed animals was analysed and compared to controls by 16S rRNA sequencing and quantitative PCR. The expression level on several genes related to inflammation was tested. Furthermore, microscopic assessment of the intestine was performed in both conditions. The consumption of the HFD resulted in microbial dysbiosis, characterised by an increase in the relative abundance of the phylum Bacteroidetes. Moreover, an emerging intestinal inflammation via NF-κβ activation was confirmed by the overexpression of several genes related to signalling receptors, antimicrobial metabolism and the inflammatory cascade. The intestinal barrier was also damaged, with an increase of goblet cell mucin production. This is the first study performed in zebrafish which suggests that the consumption of a diet enriched with 10% fat changes the intestinal microbial community composition, which was correlated with low-grade inflammation.
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Affiliation(s)
- Nerea Arias-Jayo
- Food research, Azti, Parque tecnológico de Bizkaia, Astondo Bidea 609, 48160, Derio, Spain.
| | - Leticia Abecia
- CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 801A, 48160, Derio, Spain
| | - Laura Alonso-Sáez
- Marine research, Azti, Txatxarramendi ugartea z/g, 48395, Txatxarramendi, Spain
| | - Andoni Ramirez-Garcia
- Departmento de Immunología, Microbiología y Parasitología, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), 48940, Leioa, Spain
| | - Alfonso Rodriguez
- St Luke's General Hospital, Freshford Road, Friarsinch, Kilkenny, R95 FY71, Ireland
| | - Miguel A Pardo
- Food research, Azti, Parque tecnológico de Bizkaia, Astondo Bidea 609, 48160, Derio, Spain
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14
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Arandia-Gorostidi N, Huete-Stauffer TM, Alonso-Sáez L, G Morán XA. Testing the metabolic theory of ecology with marine bacteria: different temperature sensitivity of major phylogenetic groups during the spring phytoplankton bloom. Environ Microbiol 2017; 19:4493-4505. [PMID: 28836731 DOI: 10.1111/1462-2920.13898] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/27/2022]
Abstract
Although temperature is a key driver of bacterioplankton metabolism, the effect of ocean warming on different bacterial phylogenetic groups remains unclear. Here, we conducted monthly short-term incubations with natural coastal bacterial communities over an annual cycle to test the effect of experimental temperature on the growth rates and carrying capacities of four phylogenetic groups: SAR11, Rhodobacteraceae, Gammaproteobacteria and Bacteroidetes. SAR11 was the most abundant group year-round as analysed by CARD-FISH, with maximum abundances in summer, while the other taxa peaked in spring. All groups, including SAR11, showed high temperature-sensitivity of growth rates and/or carrying capacities in spring, under phytoplankton bloom or post-bloom conditions. In that season, Rhodobacteraceae showed the strongest temperature response in growth rates, estimated here as activation energy (E, 1.43 eV), suggesting an advantage to outcompete other groups under warmer conditions. In summer E values were in general lower than 0.65 eV, the value predicted by the Metabolic Theory of Ecology (MTE). Contrary to MTE predictions, carrying capacity tended to increase with warming for all bacterial groups. Our analysis confirms that resource availability is key when addressing the temperature response of heterotrophic bacterioplankton. We further show that even under nutrient-sufficient conditions, warming differentially affected distinct bacterioplankton taxa.
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Affiliation(s)
- Nestor Arandia-Gorostidi
- Plankton Ecology and Pelagic Ecosystem Dynamics Division, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain
| | - Tamara Megan Huete-Stauffer
- Plankton Ecology and Pelagic Ecosystem Dynamics Division, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, Saudi Arabia
| | - Laura Alonso-Sáez
- Plankton Ecology and Pelagic Ecosystem Dynamics Division, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Marine Research Division, AZTI, Sukarrieta, Bizkaia, Spain
| | - Xosé Anxelu G Morán
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, Saudi Arabia
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15
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Arandia-Gorostidi N, Weber PK, Alonso-Sáez L, Morán XAG, Mayali X. Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment. ISME J 2016; 11:641-650. [PMID: 27922602 DOI: 10.1038/ismej.2016.156] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 09/21/2016] [Accepted: 10/05/2016] [Indexed: 11/09/2022]
Abstract
Quantifying the contribution of marine microorganisms to carbon and nitrogen cycles and their response to predicted ocean warming is one of the main challenges of microbial oceanography. Here we present a single-cell NanoSIMS isotope analysis to quantify C and N uptake by free-living and attached phytoplankton and heterotrophic bacteria, and their response to short-term experimental warming of 4 °C. Elevated temperature increased total C fixation by over 50%, a small but significant fraction of which was transferred to heterotrophs within 12 h. Cell-to-cell attachment doubled the secondary C uptake by heterotrophic bacteria and increased secondary N incorporation by autotrophs by 68%. Warming also increased the abundance of phytoplankton with attached heterotrophs by 80%, and promoted C transfer from phytoplankton to bacteria by 17% and N transfer from bacteria to phytoplankton by 50%. Our results indicate that phytoplankton-bacteria attachment provides an ecological advantage for nutrient incorporation, suggesting a mutualistic relationship that appears to be enhanced by temperature increases.
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Affiliation(s)
- Nestor Arandia-Gorostidi
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain
| | - Peter K Weber
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Laura Alonso-Sáez
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,AZTI, Sukarrieta, Bizkaia, Spain
| | - Xosé Anxelu G Morán
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xavier Mayali
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, USA.,Oregon State University, Microbiology Department, Corvallis, OR, USA
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16
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Huete-Stauffer TM, Arandia-Gorostidi N, Alonso-Sáez L, Morán XAG. Experimental Warming Decreases the Average Size and Nucleic Acid Content of Marine Bacterial Communities. Front Microbiol 2016; 7:730. [PMID: 27242747 PMCID: PMC4876119 DOI: 10.3389/fmicb.2016.00730] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/02/2016] [Indexed: 12/16/2022] Open
Abstract
Organism size reduction with increasing temperature has been suggested as a universal response to global warming. Since genome size is usually correlated to cell size, reduction of genome size in unicells could be a parallel outcome of warming at ecological and evolutionary time scales. In this study, the short-term response of cell size and nucleic acid content of coastal marine prokaryotic communities to temperature was studied over a full annual cycle at a NE Atlantic temperate site. We used flow cytometry and experimental warming incubations, spanning a 6°C range, to analyze the hypothesized reduction with temperature in the size of the widespread flow cytometric bacterial groups of high and low nucleic acid content (HNA and LNA bacteria, respectively). Our results showed decreases in size in response to experimental warming, which were more marked in 0.8 μm pre-filtered treatment rather than in the whole community treatment, thus excluding the role of protistan grazers in our findings. Interestingly, a significant effect of temperature on reducing the average nucleic acid content (NAC) of prokaryotic cells in the communities was also observed. Cell size and nucleic acid decrease with temperature were correlated, showing a common mean decrease of 0.4% per °C. The usually larger HNA bacteria consistently showed a greater reduction in cell and NAC compared with their LNA counterparts, especially during the spring phytoplankton bloom period associated to maximum bacterial growth rates in response to nutrient availability. Our results show that the already smallest planktonic microbes, yet with key roles in global biogeochemical cycling, are likely undergoing important structural shrinkage in response to rising temperatures.
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Affiliation(s)
- Tamara M Huete-Stauffer
- Plankton Ecology and Pelagic Ecosystem Dynamics, Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía Gijón/Xixón, Spain
| | - Nestor Arandia-Gorostidi
- Plankton Ecology and Pelagic Ecosystem Dynamics, Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía Gijón/Xixón, Spain
| | - Laura Alonso-Sáez
- Plankton Ecology and Pelagic Ecosystem Dynamics, Centro Oceanográfico de Gijón/Xixón, Instituto Español de OceanografíaGijón/Xixón, Spain; Marine Research Division, AZTISukarrieta, Spain
| | - Xosé Anxelu G Morán
- Plankton Ecology and Pelagic Ecosystem Dynamics, Centro Oceanográfico de Gijón/Xixón, Instituto Español de OceanografíaGijón/Xixón, Spain; Division of Biological and Environmental Sciences and Engineering, Red Sea Research Center, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
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17
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Morán XAG, Alonso-Sáez L, Nogueira E, Ducklow HW, González N, López-Urrutia Á, Díaz-Pérez L, Calvo-Díaz A, Arandia-Gorostidi N, Huete-Stauffer TM. More, smaller bacteria in response to ocean's warming? Proc Biol Sci 2016; 282:rspb.2015.0371. [PMID: 26063843 PMCID: PMC4590472 DOI: 10.1098/rspb.2015.0371] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterotrophic bacteria play a major role in organic matter cycling in the ocean. Although the high abundances and relatively fast growth rates of coastal surface bacterioplankton make them suitable sentinels of global change, past analyses have largely overlooked this functional group. Here, time series analysis of a decade of monthly observations in temperate Atlantic coastal waters revealed strong seasonal patterns in the abundance, size and biomass of the ubiquitous flow-cytometric groups of low (LNA) and high nucleic acid (HNA) content bacteria. Over this relatively short period, we also found that bacterioplankton cells were significantly smaller, a trend that is consistent with the hypothesized temperature-driven decrease in body size. Although decadal cell shrinking was observed for both groups, it was only LNA cells that were strongly coherent, with ecological theories linking temperature, abundance and individual size on both the seasonal and interannual scale. We explain this finding because, relative to their HNA counterparts, marine LNA bacteria are less diverse, dominated by members of the SAR11 clade. Temperature manipulation experiments in 2012 confirmed a direct effect of warming on bacterial size. Concurrent with rising temperatures in spring, significant decadal trends of increasing standing stocks (3% per year) accompanied by decreasing mean cell size (−1% per year) suggest a major shift in community structure, with a larger contribution of LNA bacteria to total biomass. The increasing prevalence of these typically oligotrophic taxa may severely impact marine food webs and carbon fluxes by an overall decrease in the efficiency of the biological pump.
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Affiliation(s)
- Xosé Anxelu G Morán
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia Instituto Español de Oceanografía, Centro Oceanográfico de Xixón, Xixón, Asturies 33212, Spain
| | - Laura Alonso-Sáez
- Instituto Español de Oceanografía, Centro Oceanográfico de Xixón, Xixón, Asturies 33212, Spain Marine Research Division, AZTI Tecnalia, Sukarrieta, Bizkaia 48395, Spain
| | - Enrique Nogueira
- Instituto Español de Oceanografía, Centro Oceanográfico de Xixón, Xixón, Asturies 33212, Spain
| | - Hugh W Ducklow
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA
| | - Natalia González
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid 28933, Spain
| | - Ángel López-Urrutia
- Instituto Español de Oceanografía, Centro Oceanográfico de Xixón, Xixón, Asturies 33212, Spain
| | - Laura Díaz-Pérez
- Instituto Español de Oceanografía, Centro Oceanográfico de Xixón, Xixón, Asturies 33212, Spain
| | - Alejandra Calvo-Díaz
- Instituto Español de Oceanografía, Centro Oceanográfico de Xixón, Xixón, Asturies 33212, Spain
| | | | - Tamara M Huete-Stauffer
- Instituto Español de Oceanografía, Centro Oceanográfico de Xixón, Xixón, Asturies 33212, Spain
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18
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García FC, Alonso-Sáez L, Morán XAG, López-Urrutia Á. Seasonality in molecular and cytometric diversity of marine bacterioplankton: the re-shuffling of bacterial taxa by vertical mixing. Environ Microbiol 2015; 17:4133-42. [DOI: 10.1111/1462-2920.12984] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 07/10/2015] [Accepted: 07/10/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Francisca C. García
- Instituto Español de Oceanografía; Centro Oceanográfico de Gijón/Xixón; 33212 Gijón/Xixón Spain
| | - Laura Alonso-Sáez
- Instituto Español de Oceanografía; Centro Oceanográfico de Gijón/Xixón; 33212 Gijón/Xixón Spain
| | - Xosé Anxelu G. Morán
- Instituto Español de Oceanografía; Centro Oceanográfico de Gijón/Xixón; 33212 Gijón/Xixón Spain
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering; King Abdullah University of Science and Technology; 23955-6500 Thuwal Saudi Arabia
| | - Ángel López-Urrutia
- Instituto Español de Oceanografía; Centro Oceanográfico de Gijón/Xixón; 33212 Gijón/Xixón Spain
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Alonso-Sáez L, Díaz-Pérez L, Morán XAG. The hidden seasonality of the rare biosphere in coastal marine bacterioplankton. Environ Microbiol 2015; 17:3766-80. [DOI: 10.1111/1462-2920.12801] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 01/31/2015] [Accepted: 02/01/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Laura Alonso-Sáez
- Instituto Español de Oceanografía; Centro Oceanográfico de Xixón; 33212 Xixón Spain
- AZTI; Marine Research Division; 48395 Sukarrieta Spain
| | - Laura Díaz-Pérez
- Instituto Español de Oceanografía; Centro Oceanográfico de Xixón; 33212 Xixón Spain
| | - Xosé Anxelu G. Morán
- Instituto Español de Oceanografía; Centro Oceanográfico de Xixón; 33212 Xixón Spain
- Red Sea Research Center; King Abdullah University of Science and Technology; 23955-6900 Thuwal Saudi Arabia
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Alonso-Sáez L, Zeder M, Harding T, Pernthaler J, Lovejoy C, Bertilsson S, Pedrós-Alió C. Winter bloom of a rare betaproteobacterium in the Arctic Ocean. Front Microbiol 2014; 5:425. [PMID: 25191307 PMCID: PMC4138443 DOI: 10.3389/fmicb.2014.00425] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/28/2014] [Indexed: 11/13/2022] Open
Abstract
Extremely low abundance microorganisms (members of the "rare biosphere") are believed to include dormant taxa, which can sporadically become abundant following environmental triggers. Yet, microbial transitions from rare to abundant have seldom been captured in situ, and it is uncertain how widespread these transitions are. A bloom of a single ribotype (≥99% similarity in the 16S ribosomal RNA gene) of a widespread betaproteobacterium (Janthinobacterium sp.) occurred over 2 weeks in Arctic marine waters. The Janthinobacterium population was not detected microscopically in situ in January and early February, but suddenly appeared in the water column thereafter, eventually accounting for up to 20% of bacterial cells in mid February. During the bloom, this bacterium was detected at open water sites up to 50 km apart, being abundant down to more than 300 m. This event is one of the largest monospecific bacterial blooms reported in polar oceans. It is also remarkable because Betaproteobacteria are typically found only in low abundance in marine environments. In particular, Janthinobacterium were known from non-marine habitats and had previously been detected only in the rare biosphere of seawater samples, including the polar oceans. The Arctic Janthinobacterium formed mucilagenous monolayer aggregates after short (ca. 8 h) incubations, suggesting that biofilm formation may play a role in maintaining rare bacteria in pelagic marine environments. The spontaneous mass occurrence of this opportunistic rare taxon in polar waters during the energy-limited season extends current knowledge of how and when microbial transitions between rare and abundant occur in the ocean.
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Affiliation(s)
- Laura Alonso-Sáez
- Limnology and Science for Life Laboratory, Department of Ecology and Genetics, Uppsala University Uppsala, Sweden
| | - Michael Zeder
- Limnological Station, Institute of Plant Biology, University of Zurich Kilchberg, Switzerland
| | - Tommy Harding
- Département de Biologie, Université Laval Québec, QC, Canada
| | - Jakob Pernthaler
- Limnological Station, Institute of Plant Biology, University of Zurich Kilchberg, Switzerland
| | - Connie Lovejoy
- Département de Biologie, Université Laval Québec, QC, Canada
| | - Stefan Bertilsson
- Limnology and Science for Life Laboratory, Department of Ecology and Genetics, Uppsala University Uppsala, Sweden
| | - Carlos Pedrós-Alió
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC Barcelona, Spain
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Galand PE, Alonso-Sáez L, Bertilsson S, Lovejoy C, Casamayor EO. Contrasting activity patterns determined by BrdU incorporation in bacterial ribotypes from the Arctic Ocean in winter. Front Microbiol 2013; 4:118. [PMID: 23750155 PMCID: PMC3657686 DOI: 10.3389/fmicb.2013.00118] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/26/2013] [Indexed: 11/13/2022] Open
Abstract
The winter Arctic Ocean is one of the most unexplored marine environments from a microbiological perspective. Heterotrophic bacteria maintain their activity at a baseline level during the extremely low-energy conditions of the winter, but little is known about the specific phylotypes that have the potential to survive and grow in such harsh environment. In this study, we aimed at identifying actively growing ribotypes in winter Arctic Ocean seawater cultures by experimental incubations with the thymidine analog bromodeoxyuridine (BrdU), followed by immunocapturing, terminal restriction fragment length polymorphism fingerprinting, cloning, and sequencing the 16S rRNA gene. We incubated water collected at different months over the Arctic winter and showed that the actively growing bacterial fraction, taking up BrdU, represented only a subset of the total community. Among the BrdU-labeled bacterial taxa we identified the Flavobacteria Polaribacter, the Alphaproteobacteria SAR11, the Gammaproteobacteria Arctic 96B-16 cluster and, predominately, members of Colwellia spp. Interestingly, Colwellia sequences formed three clusters (93 and 97% pairwise 16S rRNA identity) that contributed in contrasting ways to the active communities in the incubations. Polaribacter, Arctic 96B-16 and one cluster of Colwellia were more abundant in the active community represented by the BrdU-labeled DNA. In contrast, SAR11 and two other Colwellia clusters were underrepresented in the BrdU-labeled community compared to total communities. Despite the limitation of the long incubations needed to label slow growing arctic communities, the BrdU approach revealed the potential for active growth in low-energy conditions in some relevant groups of polar bacteria, including Polaribacter and Arctic 96B-16. Moreover, under similar incubation conditions, the growth of different Colwellia ribotypes varied, suggesting that related clusters of Colwellia may have distinct metabolic features.
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Affiliation(s)
- Pierre E Galand
- Biogeodynamics and Biodiversity Group, Centre d'Estudis Avançats de Blanes, Centre d'Estudis Avançats de Blanes-Consejo Superior de Investigaciones Científicas Blanes, Spain ; UPMC Univ Paris 06 France ; CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls Banyuls sur Mer, France
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Abstract
Archaea are abundant in polar oceans but important ecological aspects of this group remain enigmatic, such as patterns of diversity and biogeography. Here, we provide the first high-throughput sequencing population study of Antarctic archaea based on 198 bp fragments of the 16S rRNA gene, targeting different water masses across the Amundsen and Ross Seas. Our results suggest that archaeal community composition is strongly shaped by hydrography and significantly influenced by environmental parameters. Archaeal communities from cold continental shelf waters (SW) of the Ross Sea were similar over depth with a single thaumarchaeal phylotype dominating Antarctic surface waters (AASW) and deeper SW (contributing up to 80% of reads). However, this phylotype contributed less than 8% of reads in circumpolar deep waters (CDW). A related thaumarchaeon (98% identity) was almost absent in AASW, but contributed up to 30% of reads in CDW, suggesting ecological differentiation of closely related phylotypes. Significantly higher archaeal richness and evenness were observed in CDW, with Shannon indices (c. 2.5) twice as high as for AASW, and high contributions of Group II Euryarchaeota. Based on these results, we suggest that CDW is a hotspot of archaeal diversity and may play an important role in the dispersal of archaeal phylotypes to other oceanic water masses.
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Affiliation(s)
- Laura Alonso-Sáez
- Department of Ecology and Genetics, Limnology. Uppsala University. Norbyvägen 18D, SE-75236 Uppsala, Sweden
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Morán XAG, Alonso-Sáez L. Independence of bacteria on phytoplankton? Insufficient support for Fouilland & Mostajir's (2010) suggested new concept. FEMS Microbiol Ecol 2011; 78:203-5; author reply 206-9. [PMID: 21732956 DOI: 10.1111/j.1574-6941.2011.01167.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Morán XAG, Alonso-Sáez L. Independence of bacteria on phytoplankton? Insufficient support for Fouilland & Mostajir's (2010) suggested new concept. FEMS Microbiol Ecol 2011. [PMID: 21732956 DOI: 10.1111/j.1574‐6941.2011.01167.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
In a recent review, Fouilland & Mostajir questioned the direct dependence of bacterioplankton on phytoplankton based on a dataset of total primary production (particulate plus dissolved) and bacterial carbon demand (bacterial production plus respiration) estimated rates. We point out two problems for this interpretation. Firstly, there is considerable uncertainty in the authors' application of conversion factors to raw data and modelled rates so that the shape of the scatterplots can be substantially altered. Secondly, the current conceptual view of dissolved organic carbon lability and its temporal and spatial variations still provides enough support for the accepted paradigm.
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Llirós M, Alonso-Sáez L, Gich F, Plasencia A, Auguet O, Casamayor EO, Borrego CM. Active bacteria and archaea cells fixing bicarbonate in the dark along the water column of a stratified eutrophic lagoon. FEMS Microbiol Ecol 2011; 77:370-84. [DOI: 10.1111/j.1574-6941.2011.01117.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Alonso-Sáez L, Pinhassi J, Pernthaler J, Gasol JM. Leucine-to-carbon empirical conversion factor experiments: does bacterial community structure have an influence? Environ Microbiol 2011; 12:2988-97. [PMID: 20561017 DOI: 10.1111/j.1462-2920.2010.02276.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The suitability of applying empirical conversion factors (eCFs) to determine bacterial biomass production remains unclear because seawater cultures are usually overtaken by phylotypes that are not abundant in situ. While eCFs vary across environments, it has not been tested whether differences in eCFs are driven by changes in bacterial community composition or by in situ environmental conditions. We carried out seawater cultures throughout a year to analyse the correlation between eCFs and bacterial community structure, analysed by catalysed reporter deposition fluorescence in situ hybridization. Gammaproteobacteria usually dominated seawater cultures, but their abundance exhibited a wide range (25-73% of cell counts) and significantly increased with inorganic nutrient enrichment. Flavobacteria were less abundant but increased up to 40% of cells counts in winter seawater cultures, when in situ chlorophyll a was high. The correlations between eCFs and the abundance of the main broad phylogenetic groups (Gamma-, Alphaproteobacteria and Flavobacteria) were significant, albeit weak, while more specific groups (Alteromonadaceae and Rhodobacteraceae) were not significantly correlated. Our results show that the frequent development of the fast-growing group Alteromonadaceae in seawater cultures does not strongly drive the observed variations in eCFs. Rather, the results imply that environmental conditions and the growth of specific phylotypes interact to determine eCFs.
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Affiliation(s)
- Laura Alonso-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, 08003-Barcelona, Catalunya, Spain.
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Gantner S, Andersson AF, Alonso-Sáez L, Bertilsson S. Novel primers for 16S rRNA-based archaeal community analyses in environmental samples. J Microbiol Methods 2010; 84:12-8. [PMID: 20940022 DOI: 10.1016/j.mimet.2010.10.001] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 09/30/2010] [Accepted: 10/01/2010] [Indexed: 11/30/2022]
Abstract
Next generation sequencing technologies for in depth analyses of complex microbial communities rely on rational primer design based on up-to-date reference databases. Most of the 16S rRNA-gene based analyses of environmental Archaea community composition use PCR primers developed from small data sets several years ago, making an update long overdue. Here we present a new set of archaeal primers targeting the 16S rRNA gene designed from 8500 aligned archaeal sequences in the SILVA database. The primers 340F-1000R showed a high archaeal specificity (<1% bacteria amplification) covering 93 and 97% of available sequences for Crenarchaeota and Euryarchaeota respectively. In silico tests of the primers revealed at least 38% higher coverage for Archaea compared to other commonly used primers. Empirical tests with clone libraries confirmed the high specificity of the primer pair to Archaea in three biomes: surface waters in the Arctic Ocean, the pelagic zone of a temperate lake and a methanogenic bioreactor. The clone libraries featured both Euryarchaeota and Crenarchaeota in variable proportions and revealed dramatic differences in the archaeal community composition and minimal phylogenetic overlap between samples.
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Affiliation(s)
- Stephan Gantner
- Department of Ecology & Genetics, Limnology, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
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Alonso-Sáez L, Sánchez O, Gasol JM, Balagué V, Pedrós-Alio C. Winter-to-summer changes in the composition and single-cell activity of near-surface Arctic prokaryotes. Environ Microbiol 2008; 10:2444-54. [PMID: 18557769 DOI: 10.1111/j.1462-2920.2008.01674.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We collected surface samples in Franklin Bay (Western Arctic) from ice-covered to ice-free conditions, to determine seasonal changes in the identity and in situ activity of the prokaryotic assemblages. Catalysed reported fluorescence in situ hybridization was used to quantify the abundance of different groups, and combined with microautoradiography to determine the fraction of active cells taking up three substrates: glucose, amino acids and ATP. In surface waters, Archaea accounted for 16% of the total cell count in winter, but decreased to almost undetectable levels in summer, when Bacteria made up 97% of the total cell count. Alphaproteobacteria were the most abundant group followed by Bacteroidetes (average of 34% and 14% of total cell counts respectively). Some bacterial groups appearing in low abundances (< 10% of total cell counts), such as Betaproteobacteria, Roseobacter and Gammaproteobacteria, showed a high percentage of active cells. By contrast, more abundant groups, such as SAR11 or Bacteroidetes, had a lower percentage of active cells in the uptake of the substrates tested. Archaea showed low heterotrophic activity throughout the year. In comparison with temperate oceans, the percentage of active Bacteria in the uptake of the substrates was relatively high, even during the winter season.
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Affiliation(s)
- Laura Alonso-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, 08003-Barcelona, Catalunya, Spain.
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Alonso-Sáez L, Balagué V, Sà EL, Sánchez O, González JM, Pinhassi J, Massana R, Pernthaler J, Pedrós-Alió C, Gasol JM. Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH. FEMS Microbiol Ecol 2007; 60:98-112. [PMID: 17250750 DOI: 10.1111/j.1574-6941.2006.00276.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
We combined denaturing gradient gel electrophoresis (DGGE), catalysed reporter deposition-FISH (CARD-FISH) and clone libraries to investigate the seasonality of the bacterial assemblage composition in north-west Mediterranean coastal waters. DGGE analysis indicated that bacterial diversity changed gradually throughout the year, although with a clear distinction of the summer period. Alphaproteobacteria were the dominant group on an annual basis [29% of the DAPI (4',6-diamidino-2-phenylindole) counts by CARD-FISH, and 70% of the bacterial clones]. The SAR11 clade was most abundant during spring and summer (>20% of DAPI counts), while the Roseobacter clade was abundant primarily in winter and spring (up to 7% of DAPI counts). The phylum Bacteroidetes constituted the second most important group and was quantitatively uniform throughout the year (average 11% of the DAPI counts). Gammaproteobacteria showed a peak during summer (8% of DAPI counts), when most of them belonged to the NOR5 cluster. Clone libraries and CARD-FISH showed reasonable agreement in the quantitative proportions of Bacteroidetes and Gammaproteobacteria, but Alphaproteobacteria were overrepresented in clone libraries. Sequencing of the most predominant DGGE bands failed to detect the SAR11 group despite their high abundance. The combination of the three molecular approaches allowed a comprehensive assessment of seasonal changes in bacterial diversity.
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Affiliation(s)
- Laura Alonso-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar CSIC, 08003-Barcelona, Catalunya, Spain.
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Alonso-Sáez L, Gasol JM. Seasonal variations in the contributions of different bacterial groups to the uptake of low-molecular-weight compounds in northwestern Mediterranean coastal waters. Appl Environ Microbiol 2007; 73:3528-35. [PMID: 17400772 PMCID: PMC1932672 DOI: 10.1128/aem.02627-06] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed the contributions of different heterotrophic bacterial groups to the uptake of several low-molecular weight compounds during a seasonal cycle on the northwestern Mediterranean coast (Blanes Bay Microbial Observatory). The bacterial assemblage structure had been shown to change substantially year-round for this site, but whether changes in the activities of the different bacterial groups also occurred on the seasonal scale was unknown. Microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization was used to analyze the patterns of glucose, amino acid, and ATP uptake by different bacterial groups. Gammaproteobacteria and Bacteroidetes were not very active in the uptake of glucose at any time of the year (<10% of cells were active) compared to Alphaproteobacteria (generally >20% of cells were active). Dissolved free amino acids were taken up considerably by Alphaproteobacteria and Gammaproteobacteria but not by Bacteroidetes. Relatively high percentages of cells of the three broad phylogenetic groups actively took up ATP, which could be related to the important phosphorous limitation of bacterial production during most of the year in Blanes Bay. The contribution of SAR11 to the uptake of the monomers was variable year-round, generally with fewer than 30% of the cells being active. By contrast, Roseobacter were highly overrepresented in the uptake of all the substrates throughout all the year, with more than 50% of cells being active in all the samples and for all substrates. Our results suggest that substantial changes in the activity of some phylogenetic groups of bacteria occur throughout the year.
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Affiliation(s)
- Laura Alonso-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, 08003 Barcelona, Spain
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Alonso-Sáez L, Gasol JM, Lefort T, Hofer J, Sommaruga R. Effect of natural sunlight on bacterial activity and differential sensitivity of natural bacterioplankton groups in northwestern Mediterranean coastal waters. Appl Environ Microbiol 2006; 72:5806-13. [PMID: 16957198 PMCID: PMC1563624 DOI: 10.1128/aem.00597-06] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the effects of natural sunlight on heterotrophic marine bacterioplankton in short-term experiments. We used a single-cell level approach involving flow cytometry combined with physiological probes and microautoradiography to determine sunlight effects on the activity and integrity of the cells. After 4 h of sunlight exposure, most bacterial cells maintained membrane integrity and viability as assessed by the simultaneous staining with propidium iodide and SYBR green I. In contrast, a significant inhibition of heterotrophic bacterial activity was detected, measured by 5-cyano-2,3 ditolyl tetrazolium chloride reduction and leucine incorporation. We applied microautoradiography combined with catalyzed reporter deposition-fluorescence in situ hybridization to test the sensitivity of the different bacterial groups naturally occurring in the Northwestern Mediterranean to sunlight. Members of the Gammaproteobacteria and Bacteroidetes groups appeared to be highly resistant to solar radiation, with small changes in activity after exposure. On the contrary, Alphaproteobacteria bacteria were more sensitive to radiation as measured by the cell-specific incorporation of labeled amino acids, leucine, and ATP. Within Alphaproteobacteria, bacteria belonging to the Roseobacter group showed higher resistance than members of the SAR11 cluster. The activity of Roseobacter was stimulated by exposure to photosynthetic available radiation compared to the dark treatment. Our results suggest that UV radiation can significantly affect the in situ single-cell activity of bacterioplankton and that naturally dominating phylogenetic bacterial groups have different sensitivity to natural levels of incident solar radiation.
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Affiliation(s)
- Laura Alonso-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, 08003 Barcelona, Spain
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Pinhassi J, Simó R, González JM, Vila M, Alonso-Sáez L, Kiene RP, Moran MA, Pedrós-Alió C. Dimethylsulfoniopropionate turnover is linked to the composition and dynamics of the bacterioplankton assemblage during a microcosm phytoplankton bloom. Appl Environ Microbiol 2006; 71:7650-60. [PMID: 16332737 PMCID: PMC1317407 DOI: 10.1128/aem.71.12.7650-7660.2005] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Processing of the phytoplankton-derived organic sulfur compound dimethylsulfoniopropionate (DMSP) by bacteria was studied in seawater microcosms in the coastal Gulf of Mexico (Alabama). Modest phytoplankton blooms (peak chlorophyll a [Chl a] concentrations of approximately 2.5 microg liter(-1)) were induced in nutrient-enriched microcosms, while phytoplankton biomass remained low in unamended controls (Chl a concentrations of approximately 0.34 microg liter(-1)). Particulate DMSP concentrations reached 96 nM in the enriched microcosms but remained approximately 14 nM in the controls. Bacterial biomass production increased in parallel with the increase in particulate DMSP, and nutrient limitation bioassays in the initial water showed that enrichment with DMSP or glucose caused a similar stimulation of bacterial growth. Concomitantly, increased bacterial consumption rate constants of dissolved DMSP (up to 20 day(-1)) and dimethylsulfide (DMS) (up to 6.5 day(-1)) were observed. Nevertheless, higher DMSP S assimilation efficiencies and higher contribution of DMSP to bacterial S demand were found in the controls compared to the enriched microcosms. This indicated that marine bacterioplankton may rely more on DMSP as a source of S under oligotrophic conditions than under the senescence phase of phytoplankton blooms. Phylogenetic analysis of the bacterial assemblages in all microcosms showed that the DMSP-rich algal bloom favored the occurrence of various Roseobacter members, flavobacteria (Bacteroidetes phylum), and oligotrophic marine Gammaproteobacteria. Our observations suggest that the composition of the bacterial assemblage and the relative contribution of DMSP to the overall dissolved organic sulfur/organic matter pool control how efficiently bacteria assimilate DMSP S and thereby potentially divert it from DMS production.
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Affiliation(s)
- Jarone Pinhassi
- Marine Microbiology, Department of Biology and Environmental Sciences, University of Kalmar, SE-39182 Kalmar, Sweden.
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Sommaruga R, Hofer JS, Alonso-Sáez L, Gasol JM. Differential sunlight sensitivity of picophytoplankton from surface Mediterranean Coastal Waters. Appl Environ Microbiol 2005; 71:2154-7. [PMID: 15812050 PMCID: PMC1082567 DOI: 10.1128/aem.71.4.2154-2157.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We tested the sensitivity of coastal picophytoplankton exposed to natural sunlight in short-term experiments. Cell abundance and cell-specific chlorophyll fluorescence were significantly reduced in Prochlorococcus spp. but not in Synechococcus, whereas picoeukaryotes had an intermediate response. These results are the first direct evidence of a differential sensitivity to sunlight of these ubiquitous marine members of unicellular phytoplankton.
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Affiliation(s)
- Ruben Sommaruga
- Laboratory of Aquatic Photobiology and Plankton Ecology, Institute of Zoology and Limnology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.
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