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Koblížek M, Ferrera I, Kolářová E, Duhamel S, Popendorf KJ, Gasol JM, Van Mooy BAS. Growth and mortality of aerobic anoxygenic phototrophs in the North Pacific Subtropical Gyre. Appl Environ Microbiol 2024; 90:e0003224. [PMID: 38551354 PMCID: PMC11022572 DOI: 10.1128/aem.00032-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/08/2024] [Indexed: 04/18/2024] Open
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria harvest light energy using bacteriochlorophyll-containing reaction centers to supplement their mostly heterotrophic metabolism. While their abundance and growth have been intensively studied in coastal environments, much less is known about their activity in oligotrophic open ocean regions. Therefore, we combined in situ sampling in the North Pacific Subtropical Gyre, north of O'ahu island, Hawaii, with two manipulation experiments. Infra-red epifluorescence microscopy documented that AAP bacteria represented approximately 2% of total bacteria in the euphotic zone with the maximum abundance in the upper 50 m. They conducted active photosynthetic electron transport with maximum rates up to 50 electrons per reaction center per second. The in situ decline of bacteriochlorophyll concentration over the daylight period, an estimate of loss rates due to predation, indicated that the AAP bacteria in the upper 50 m of the water column turned over at rates of 0.75-0.90 d-1. This corresponded well with the specific growth rate determined in dilution experiments where AAP bacteria grew at a rate 1.05 ± 0.09 d-1. An amendment of inorganic nitrogen to obtain N:P = 32 resulted in a more than 10 times increase in AAP abundance over 6 days. The presented data document that AAP bacteria are an active part of the bacterioplankton community in the oligotrophic North Pacific Subtropical Gyre and that their growth was mostly controlled by nitrogen availability and grazing pressure.IMPORTANCEMarine bacteria represent a complex assembly of species with different physiology, metabolism, and substrate preferences. We focus on a specific functional group of marine bacteria called aerobic anoxygenic phototrophs. These photoheterotrophic organisms require organic carbon substrates for growth, but they can also supplement their metabolic needs with light energy captured by bacteriochlorophyll. These bacteria have been intensively studied in coastal regions, but rather less is known about their distribution, growth, and mortality in the oligotrophic open ocean. Therefore, we conducted a suite of measurements in the North Pacific Subtropical Gyre to determine the distribution of these organisms in the water column and their growth and mortality rates. A nutrient amendment experiment showed that aerobic anoxygenic phototrophs were limited by inorganic nitrogen. Despite this, they grew more rapidly than average heterotrophic bacteria, but their growth was balanced by intense grazing pressure.
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Affiliation(s)
- Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía (IEO-CSIC), Fuengirola, Málaga, Spain
| | - Eva Kolářová
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Solange Duhamel
- Department of Cellular and Molecular Biology, University of Arizona, Tucson, Arizona, USA
| | - Kimberly J. Popendorf
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, Florida, USA
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Benjamin A. S. Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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Brüwer JD, Orellana LH, Sidhu C, Klip HCL, Meunier CL, Boersma M, Wiltshire KH, Amann R, Fuchs BM. In situ cell division and mortality rates of SAR11, SAR86, Bacteroidetes, and Aurantivirga during phytoplankton blooms reveal differences in population controls. mSystems 2023; 8:e0128722. [PMID: 37195198 PMCID: PMC10308942 DOI: 10.1128/msystems.01287-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/21/2023] [Indexed: 05/18/2023] Open
Abstract
Net growth of microbial populations, that is, changes in abundances over time, can be studied using 16S rRNA fluorescence in situ hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, and the copiotrophic phylum Bacteroidetes, and its genus Aurantivirga. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8/day and Aurantivirga of up to 1.9/day differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9/day, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (-0.6 to 0.5/day) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within 1 day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom-up and top-down controls. IMPORTANCE The growth of a microbial population is often calculated from their numerical abundance over time. However, this does not take cell division and mortality rates into account, which are important for deriving ecological processes like bottom-up and top-down control. In this study, we determined growth by numerical abundance and calibrated microscopy-based methods to determine the frequency of dividing cells and subsequently calculate taxon-specific cell division rates in situ. The cell division and mortality rates of two oligotrophic (SAR11 and SAR86) and two copiotrophic (Bacteroidetes and Aurantivirga) taxa during two spring phytoplankton blooms showed a tight coupling for all four taxa throughout the blooms without any temporal offset. Unexpectedly, SAR11 showed high cell division rates days before the bloom while cell abundances remained constant, which is indicative of strong top-down control. Microscopy remains the method of choice to understand ecological processes like top-down and bottom-up control on a cellular level.
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Affiliation(s)
- Jan D. Brüwer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Helena C. L. Klip
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Cédric L. Meunier
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Maarten Boersma
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
- University of Bremen, Bremen, Germany
| | - Karen H. Wiltshire
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Wattenmeerstation, List auf Sylt, Bremerhaven, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Lineage-Specific Growth Curves Document Large Differences in Response of Individual Groups of Marine Bacteria to the Top-Down and Bottom-Up Controls. mSystems 2021; 6:e0093421. [PMID: 34581594 PMCID: PMC8547455 DOI: 10.1128/msystems.00934-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Marine bacterioplankton represent a diverse assembly of species differing largely in their abundance, physiology, metabolic activity, and role in microbial food webs. To analyze their sensitivity to bottom-up and top-down controls, we performed a manipulation experiment where grazers were removed, with or without the addition of phosphate. Using amplicon-reads normalization by internal standard (ARNIS), we reconstructed growth curves for almost 300 individual phylotypes. Grazer removal caused a rapid growth of most bacterial groups, which grew at rates of 0.6 to 3.5 day−1, with the highest rates (>4 day−1) recorded among Rhodobacteraceae, Oceanospirillales, Alteromonadaceae, and Arcobacteraceae. Based on their growth response, the phylotypes were divided into three basic groups. Most of the phylotypes responded positively to both grazer removal as well as phosphate addition. The second group (containing, e.g., Rhodobacterales and Rhizobiales) responded to the grazer removal but not to the phosphate addition. Finally, some clades, such as SAR11 and Flavobacteriaceae, responded only to phosphate amendment but not to grazer removal. Our results show large differences in bacterial responses to experimental manipulations at the phylotype level and document different life strategies of marine bacterioplankton. In addition, growth curves of 130 phylogroups of aerobic anoxygenic phototrophs were reconstructed based on changes of the functional pufM gene. The use of functional genes together with rRNA genes may significantly expand the scientific potential of the ARNIS technique. IMPORTANCE Growth is one of the main manifestations of life. It is assumed generally that bacterial growth is constrained mostly by nutrient availability (bottom-up control) and grazing (top-down control). Since marine bacteria represent a very diverse assembly of species with different metabolic properties, their growth characteristics also largely differ accordingly. Currently, the growth of marine microorganisms is typically evaluated using microscopy in combination with fluorescence in situ hybridization (FISH). However, these laborious techniques are limited in their throughput and taxonomical resolution. Therefore, we combined a classical manipulation experiment with next-generation sequencing to resolve the growth dynamics of almost 300 bacterial phylogroups in the coastal Adriatic Sea. The analysis documented that most of the phylogroups responded positively to both grazer removal and phosphate addition. We observed significant differences in growth kinetics among closely related species, which could not be distinguished by the classical FISH technique.
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Lu S, He R, Zhao D, Zeng J, Huang X, Li K, Yu Z, Wu QL. Effects of shading levels on the composition and co-occurrence patterns of bacterioplankton and epibiotic bacterial communities of Cabomba caroliniana. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147286. [PMID: 33932676 DOI: 10.1016/j.scitotenv.2021.147286] [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: 11/11/2020] [Revised: 03/31/2021] [Accepted: 04/17/2021] [Indexed: 06/12/2023]
Abstract
Epibiotic bacterial community colonized on the plant leaf plays important roles in promoting plant growth and nutrient absorption, but is sensitive to environmental changes. As one of the most important environmental factors affecting the growth of plants and photosynthetic microorganisms, light may affect the diversity, composition, and interactions of the epibiotic bacterial community. Submerged plants in the aquatic ecosystem may be more sensitive to light intensity variations compared to the terrestrial plants since they usually receive less light. However, the effects of light on the interactions between the submerged plants and their epibiotic microbial communities remain uncertain. Here we used the 16S rRNA gene high-throughput sequencing to investigate the diversity and composition of the bacterioplankton and epibiotic bacterial communities of the Cabomba caroliniana under four different shading levels. A total of 24 water and leaf samples were collected from the experimental microcosms near Lake Taihu. We found the epibiotic bacterial community possessed a higher diversity than that of the bacterioplankton community, although the alpha diversity of the bacterioplankton community was more susceptible to different levels of shading. SourceTracker analysis revealed that with the increase of shading, the colonization of bacterioplankton to epibiotic bacteria decreased. Network analysis showed that the bacterial community network at 50% shading level had the lowest modularity and highest clustering coefficient compared to the bacterial community networks of other shading levels. Our findings provided new understandings of the effects of different light intensities on the epibiotic bacterial communities of submerged macrophytes.
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Affiliation(s)
- Shijie Lu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China
| | - Rujia He
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, East Beijing Road 73, Nanjing 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, East Beijing Road 73, Nanjing 210008, China.
| | - Xiaolong Huang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, East Beijing Road 73, Nanjing 210008, China
| | - Kuanyi Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, East Beijing Road 73, Nanjing 210008, China
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, East Beijing Road 73, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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5
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Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea. Sci Rep 2021; 11:11186. [PMID: 34045659 PMCID: PMC8159981 DOI: 10.1038/s41598-021-90863-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/17/2021] [Indexed: 11/29/2022] Open
Abstract
Bacteria are an active and diverse component of pelagic communities. The identification of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profile, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classified the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more differentiated by depth than by area, with temperature and identified salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identified genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium-related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors affecting picoplankton in the open sea environment.
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6
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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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7
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Sebastián M, Forn I, Auladell A, Gómez-Letona M, Sala MM, Gasol JM, Marrasé C. Differential recruitment of opportunistic taxa leads to contrasting abilities in carbon processing by bathypelagic and surface microbial communities. Environ Microbiol 2020; 23:190-206. [PMID: 33089653 DOI: 10.1111/1462-2920.15292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/20/2020] [Indexed: 01/04/2023]
Abstract
Different factors affect the way dissolved organic matter (DOM) is processed in the ocean water column, including environmental conditions and the functional capabilities of the communities. Recent studies have shown that bathypelagic prokaryotes are metabolically flexible, but whether this versatility translates into a higher ability to process DOM has been barely explored. Here we performed a multifactorial transplant experiment to compare the growth, activity and changes in DOM quality in surface and bathypelagic waters inoculated with either surface or bathypelagic prokaryotic communities. The effect of nutrient additions to surface waters was also explored. Despite no differences in the cell abundance of surface and deep ocean prokaryotes were observed in any of the treatments, in surface waters with nutrients the heterotrophic production of surface prokaryotes rapidly decreased. Conversely, bathypelagic communities displayed a sustained production throughout the experiment. Incubations with surface prokaryotes always led to a significant accumulation of recalcitrant compounds, which did not occur with bathypelagic prokaryotes, suggesting they have a higher ability to process DOM. These contrasting abilities could be explained by the recruitment of a comparatively larger number of opportunistic taxa within the bathypelagic assemblages, which likely resulted in a broader community capability of substrate utilization.
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Affiliation(s)
- Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, 35214, Spain
| | - Irene Forn
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
| | - Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
| | - Markel Gómez-Letona
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, 35214, Spain
| | - M Montserrat Sala
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
| | - Cèlia Marrasé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, 08003, Spain
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8
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Girard EB, Kaliwoda M, Schmahl WW, Wörheide G, Orsi WD. Biodegradation of textile waste by marine bacterial communities enhanced by light. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:406-418. [PMID: 32410317 DOI: 10.1111/1758-2229.12856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
Knowledge of biofilm formation on pollutants in the marine realm is expanding, but how communities respond to substrates during colonization remains poorly understood. Here, we assess community assembly and respiration in response to two different micropollutants, virgin high-density polyethylene (HDPE) microbeads and textile fibres under different light settings. Raman characterization, high-throughput DNA sequencing data, quantitative PCR, and respiration measurements reveal how a stimulation of aerobic respiration by micropollutants is translated into selection for significantly different communities colonizing the substrates. Despite the lack of evidence for biodegradation of HDPE, an increased abundance and respiration of bacterial taxa closely related to hydrocarbonoclastic Kordiimonas spp. and Alteromonas spp. in the presence of textile waste highlights their biodegradation potential. Incubations with textile fibres exhibited significantly higher respiration rates in the presence of light, which could be partially explained by photochemical dissolution of the textile waste into smaller bioavailable compounds. Our results suggest that the development and increased respiration of these unique microbial communities may potentially play a role in the bioremediation of the relatively long-lived textile pollutants in marine habitats, and that the respiration of heterotrophic hydrocarbon-degrading bacteria colonizing marine pollutants can be stimulated by light.
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Affiliation(s)
- Elsa B Girard
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
| | - Melanie Kaliwoda
- SNSB - Mineralogische Staatssammlung München, München, 80333, Germany
| | - Wolfgang W Schmahl
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- SNSB - Mineralogische Staatssammlung München, München, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, 80333, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
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9
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Xue CX, Zhang H, Lin HY, Sun Y, Luo D, Huang Y, Zhang XH, Luo H. Ancestral niche separation and evolutionary rate differentiation between sister marine flavobacteria lineages. Environ Microbiol 2020; 22:3234-3247. [PMID: 32390223 DOI: 10.1111/1462-2920.15065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/30/2022]
Abstract
Marine flavobacteria are specialists for polysaccharide degradation. They dominate in habitats enriched with polysaccharides, but are also prevalent in pelagic environments where polysaccharides are less available. These niches are likely occupied by distinct lineages, but evolutionary processes underlying their niche differentiation remain elusive. Here, genomic analyses and physiological assays indicate that the sister flavobacteria lineages Leeuwenhoekiella and Nonlabens likely explore polysaccharide-rich macroalgae and polysaccharide-poor pelagic niches respectively. Phylogenomic analyses inferred that the niche separation likely occurred anciently and coincided with increased sequence evolutionary rate in Nonlabens compared with Leeuwenhoekiella. Further analyses ruled out the known mechanisms likely driving evolutionary rate acceleration, including reduced selection efficiency, decreased generation time and increased mutation rate. In particular, the mutation rates were determined using an unbiased experimental method, which measures the present-day populations and may not reflect ancestral populations. These data collectively lead to a new hypothesis that an ancestral and transient mutation rate increase resulted in evolutionary rate increase in Nonlabens. This hypothesis was supported by inferring that gains and losses of genes involved in SOS response, a mechanism known to drive transiently increased mutation rate, coincided with evolutionary rate acceleration. Our analyses highlight the evolutionary mechanisms underlying niche differentiation of flavobacteria lineages.
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Affiliation(s)
- Chun-Xu Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.,Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - He-Yu Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Danli Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Yongjie Huang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China
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10
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Bock C, Jensen M, Forster D, Marks S, Nuy J, Psenner R, Beisser D, Boenigk J. Factors shaping community patterns of protists and bacteria on a European scale. Environ Microbiol 2020; 22:2243-2260. [PMID: 32202362 DOI: 10.1111/1462-2920.14992] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/18/2020] [Indexed: 01/19/2023]
Abstract
Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high-throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross-domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.
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Affiliation(s)
- Christina Bock
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Manfred Jensen
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Str. 14, 67663, Kaiserslautern, Germany
| | - Sabina Marks
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Julia Nuy
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Roland Psenner
- Lake and Glacier Research, Institute of Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Daniela Beisser
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Jens Boenigk
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
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11
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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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12
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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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13
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Morán XAG, Calvo-Díaz A, Arandia-Gorostidi N, Huete-Stauffer TM. Temperature sensitivities of microbial plankton net growth rates are seasonally coherent and linked to nutrient availability. Environ Microbiol 2018; 20:3798-3810. [PMID: 30159999 DOI: 10.1111/1462-2920.14393] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/24/2018] [Indexed: 11/27/2022]
Abstract
Recent work suggests that temperature effects on marine heterotrophic bacteria are strongly seasonal, but few attempts have been made to concurrently assess them across trophic levels. Here, we estimated the temperature sensitivities (using activation energies, E) of autotrophic and heterotrophic microbial plankton net growth rates over an annual cycle in NE Atlantic coastal waters. Phytoplankton grew in winter and late autumn (0.41 ± 0.16 SE d-1 ) and decayed in the remaining months (-0.42 ± 0.10 d-1 ). Heterotrophic microbes shared a similar seasonality, with positive net growth for bacteria (0.14-1.48 d-1 ), while nanoflagellates had higher values (> 0.4 d-1 ) in winter and spring relative to the rest of the year (-0.46 to 0.29 d-1 ). Net growth rates activation energies showed similar dynamics in the three groups (-1.07 to 1.51 eV), characterized by maxima in winter, minima in summer and resumed increases in autumn. Microbial plankton E values were significantly correlated with nitrate concentrations as a proxy for nutrient availability. Nutrient-sufficiency (i.e., > 1 μmol l-1 nitrate) resulted in significantly higher activation energies of phytoplankton and heterotrophic nanoflagellates relative to nutrient-limited conditions. We suggest that only within spatio-temporal windows of both moderate bottom-up and top-down controls will temperature have a major enhancing effect on microbial growth.
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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 Sciences and Engineering Division, Thuwal, Saudi Arabia
| | - Alejandra Calvo-Díaz
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía (IEO), Gijón/Xixón, Spain
| | - Nestor Arandia-Gorostidi
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía (IEO), Gijón/Xixón, Spain.,Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Tamara Megan Huete-Stauffer
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, Thuwal, Saudi Arabia.,Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía (IEO), Gijón/Xixón, Spain
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