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Piwosz K, Villena-Alemany C, Całkiewicz J, Mujakić I, Náhlík V, Dean J, Koblížek M. Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon. FEMS Microbiol Ecol 2024; 100:fiae090. [PMID: 38886127 PMCID: PMC11229431 DOI: 10.1093/femsec/fiae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/10/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ > 800 nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation, but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.
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Affiliation(s)
- Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, 81-332 Gdynia, Poland
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czechia
| | - Joanna Całkiewicz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, 81-332 Gdynia, Poland
| | - Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czechia
| | - Vít Náhlík
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Aquaculture and Protection of Waters, University of South Bohemia, 389 25 České Budějovice, Czechia
| | - Jason Dean
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
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Villena‐Alemany C, Mujakić I, Porcal P, Koblížek M, Piwosz K. Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:60-71. [PMID: 36507772 PMCID: PMC10103773 DOI: 10.1111/1758-2229.13131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/19/2022] [Indexed: 05/20/2023]
Abstract
Aerobic anoxygenic photoheterotrophic (AAP) bacteria represent a functional group of prokaryotic organisms that harvests light energy using bacteriochlorophyll-containing photosynthetic reaction centers. They represent an active and rapidly growing component of freshwater bacterioplankton, with the highest numbers observed usually in summer. Species diversity of freshwater AAP bacteria has been studied before in lakes, but its seasonal dynamics remain unknown. In this report, we analysed temporal changes in the composition of the phototrophic community in an oligo-mesotrophic freshwater lake using amplicon sequencing of the pufM marker gene. The AAP community was dominated by phototrophic Gammaproteobacteria and Alphaproteobacteria, with smaller contribution of phototrophic Chloroflexota and Gemmatimonadota. Phototrophic Eremiobacteriota or members of Myxococcota were not detected. Interestingly, some AAP taxa, such as Limnohabitans, Rhodoferax, Rhodobacterales or Rhizobiales, were permanently present over the sampling period, while others, such as Sphingomonadales, Rhodospirillales or Caulobacterales appeared only transiently. The environmental factors that best explain the seasonal changes in AAP community were temperature, concentrations of oxygen and dissolved organic matter.
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Affiliation(s)
- Cristian Villena‐Alemany
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Izabela Mujakić
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Petr Porcal
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
- Department of Hydrochemistry and Ecosystem Modelling, Biology Centre of the Czech Academy of SciencesInstitute of HydrobiologyČeské BudějoviceCzechia
| | - Michal Koblížek
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine EcologyNational Marine Fisheries Research InstituteGdyniaPoland
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Bélisle AC, Gauthier S, Asselin H. Integrating Indigenous and scientific perspectives on environmental changes: Insights from boreal landscapes. PEOPLE AND NATURE 2022. [DOI: 10.1002/pan3.10399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Annie Claude Bélisle
- Institut de recherche sur les forêts Université du Québec en Abitibi‐Témiscamingue Rouyn‐Noranda Québec Canada
- Conseil de la Première Nation Abitibiwinni, Territoire et environnement Pikogan Québec Canada
| | - Sylvie Gauthier
- Natural Resources Canada Canadian Forest Service, Laurentian Forestry Centre Québec City Québec Canada
| | - Hugo Asselin
- School of Indigenous Studies Université du Québec en Abitibi‐Témiscamingue Rouyn‐Noranda Québec Canada
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Kuzyk SB, Ma X, Yurkov V. Seasonal Dynamics of Lake Winnipeg’s Microbial Communities Reveal Aerobic Anoxygenic Phototrophic Populations Coincide with Sunlight Availability. Microorganisms 2022; 10:microorganisms10091690. [PMID: 36144291 PMCID: PMC9501198 DOI: 10.3390/microorganisms10091690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/12/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
In this first comprehensive study of Lake Winnipeg’s microbial communities, limnetic and littoral euphotic zones were examined during each season from 2016 through 2020. Classical cultivation and modern high-throughput sequencing techniques provided quantification and identification of key phototrophic populations, including aerobic anoxygenic phototrophs (AAP). Annual dynamics found total heterotrophs reached 4.23 × 106 CFU/g in littoral sands, and 7.69 × 104 CFU/mL in summer littoral waters on oligotrophic media, higher counts than for copiotrophic compositions. Limnetic numbers inversely dipped to 4.34 × 103 CFU/mL midsummer. Cultured AAP did not follow heterotrophic trends, instead peaking during the spring in both littoral and limnetic waters as 19.1 and 4.7% of total copiotrophs, or 3.9 and 4.9% of oligotrophs, decreasing till autumn each year. Complementary observations came from environmental 16S V4 rRNA gene analysis, as AAP made up 1.49 and 1.02% of the littoral and limnetic sequenced communities in the spring, declining with seasonal progression. Spatial and temporal fluctuations of microbes compared to environmental factors exposed photosynthetic populations to independently and regularly fluctuate in the ecosystem. Oxygenic phototrophic numbers expectantly matched the midsummer peak of Chl a and b, oxygenic photosynthesis related carbon fixation, and water temperature. Independently, AAP particularly colonized spring littoral areas more than limnetic, and directly corresponded to habitat conditions that specifically promoted growth: the requirement of light and organic material.
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Ansari MI, Calleja MLI, Silva L, Viegas M, Ngugi DK, Huete-Stauffer TM, Morán XAG. High-Frequency Variability of Bacterioplankton in Response to Environmental Drivers in Red Sea Coastal Waters. Front Microbiol 2022; 13:780530. [PMID: 35432231 PMCID: PMC9009512 DOI: 10.3389/fmicb.2022.780530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Autotrophic and heterotrophic bacterioplankton are essential to the biogeochemistry of tropical ecosystems. However, the processes that govern their dynamics are not well known. We provide here a high-frequency assessment of bacterial community dynamics and concurrent environmental factors in Red Sea coastal waters. Weekly sampling of surface samples during a full annual cycle at an enclosed station revealed high variability in ecological conditions, which reflected in changes of major bacterioplankton communities. Temperature varied between 23 and 34°C during the sampling period. Autotrophic (Synechococcus, 1.7–16.2 × 104 cells mL−1) and heterotrophic bacteria (1.6–4.3 × 105 cells mL−1) showed two maxima in abundance in spring and summer, while minima were found in winter and autumn. Heterotrophic cells with high nucleic acid content (HNA) peaked in July, but their contribution to the total cell counts (35–60%) did not show a clear seasonal pattern. Actively respiring cells (CTC+) contributed between 4 and 51% of the total number of heterotrophic bacteria, while live cells (with intact membrane) consistently accounted for over 90%. Sequenced 16S rRNA amplicons revealed a predominance of Proteobacteria in summer and autumn (>40%) and a smaller contribution in winter (21–24%), with members of the Alphaproteobacteria class dominating throughout the year. The contribution of the Flavobacteriaceae family was highest in winter (21%), while the Rhodobacteraceae contribution was lowest (6%). Temperature, chlorophyll-a, and dissolved organic carbon concentration were the environmental variables with the greatest effects on bacterial abundance and diversity patterns.
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Affiliation(s)
- Mohd Ikram Ansari
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biosciences, Integral University, Lucknow, India
- *Correspondence: Mohd Ikram Ansari, ; Xosé Anxelu G. Morán,
| | - Maria LI. Calleja
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Climate Geochemistry, Max Planck Institute for Chemistry (MPIC), Mainz, Germany
| | - Luis Silva
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Miguel Viegas
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Kamanda Ngugi
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tamara Megan Huete-Stauffer
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G. Morán
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centro Oceanográfico de Gijón/Xixón (IEO, CSIC), Gijón/Xixón, Spain
- *Correspondence: Mohd Ikram Ansari, ; Xosé Anxelu G. Morán,
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Marois C, Girard C, Klanten Y, Vincent WF, Culley AI, Antoniades D. Local Habitat Filtering Shapes Microbial Community Structure in Four Closely Spaced Lakes in the High Arctic. Front Microbiol 2022; 13:779505. [PMID: 35222324 PMCID: PMC8873593 DOI: 10.3389/fmicb.2022.779505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is lacking for many ecosystems. The aim of this study was to characterize and compare the microbial communities of four closely spaced lakes in Stuckberry Valley (northern Ellesmere Island, Canadian Arctic Archipelago), in the coastal margin zone of the Last Ice Area, that differed in their physicochemical, morphological and catchment characteristics. We performed high-throughput amplicon sequencing of the V4 16S rRNA gene to provide inter- and intra-lake comparisons. Two deep (>25 m) and mostly oxygenated lakes showed highly similar community assemblages that were distinct from those of two shallower lakes (<10 m) with anoxic bottom waters. Proteobacteria, Verrucomicrobia, and Planctomycetes were the major phyla present in the four water bodies. One deep lake contained elevated proportions of Cyanobacteria and Thaumarchaeota that distinguished it from the others, while the shallow lakes had abundant communities of predatory bacteria, as well as microbes in their bottom waters that contribute to sulfur and methane cycles. Despite their proximity, our data suggest that local habitat filtering is the primary determinant of microbial diversity in these systems. This study provides the first detailed examination of the microbial assemblages of the Stuckberry lakes system, resulting in new insights into the microbial ecology of the High Arctic.
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Affiliation(s)
- Catherine Marois
- Département de Biochimie, Microbiologie et Bio-Informatique, Université Laval, Québec, QC, Canada
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Catherine Girard
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Yohanna Klanten
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Département de Géographie, Université Laval, Québec, QC, Canada
| | - Warwick F. Vincent
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-Informatique, Université Laval, Québec, QC, Canada
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Dermot Antoniades
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Département de Géographie, Université Laval, Québec, QC, Canada
- *Correspondence: Dermot Antoniades,
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Galachyants AD, Krasnopeev AY, Podlesnaya GV, Potapov SA, Sukhanova EV, Tikhonova IV, Zimens EA, Kabilov MR, Zhuchenko NA, Gorshkova AS, Suslova MY, Belykh OI. Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal. Microorganisms 2021; 9:842. [PMID: 33920057 PMCID: PMC8071047 DOI: 10.3390/microorganisms9040842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bacteria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity. We detected pufM-containing Alphaproteobacteria (orders Rhodobacterales, Rhizobiales, Rhodospirillales, and Sphingomonadales), Betaproteobacteria (order Burkholderiales), Gemmatimonadetes, and Planctomycetes. Rhodobacterales dominated all the studied biotopes. The diversity of rhodopsin-containing bacteria in neuston and plankton of Lake Baikal was comparable to other studied water bodies. Bacteroidetes along with Proteobacteria were the prevailing phyla, and Verrucomicrobia and Planctomycetes were also detected. The number of rhodopsin sequences unclassified to the phylum level was rather high: 29% in the water microbiomes and 22% in the epilithon. Diversity of rhodopsin-containing bacteria in epilithic biofilms was comparable with that in neuston and plankton at the phyla level. Unweighted pair group method with arithmetic mean (UPGMA) and non-metric multidimensional scaling (NMDS) analysis indicated a distinct discrepancy between epilithon and microbial communities of water (including neuston and plankton) in the 16S rRNA, pufM and rhodopsin genes.
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Affiliation(s)
- Agnia Dmitrievna Galachyants
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Andrey Yurjevich Krasnopeev
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Galina Vladimirovna Podlesnaya
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Sergey Anatoljevich Potapov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Elena Viktorovna Sukhanova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Irina Vasiljevna Tikhonova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Ekaterina Andreevna Zimens
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Marsel Rasimovich Kabilov
- Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Natalia Albertovna Zhuchenko
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Anna Sergeevna Gorshkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Maria Yurjevna Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Olga Ivanovna Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
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Abstract
Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota. They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes’ epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments. IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria. We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.
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9
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Kopejtka K, Tomasch J, Zeng Y, Selyanin V, Dachev M, Piwosz K, Tichý M, Bína D, Gardian Z, Bunk B, Brinkmann H, Geffers R, Sommaruga R, Koblížek M. Simultaneous Presence of Bacteriochlorophyll and Xanthorhodopsin Genes in a Freshwater Bacterium. mSystems 2020; 5:e01044-20. [PMID: 33361324 PMCID: PMC7762795 DOI: 10.1128/msystems.01044-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Photoheterotrophic bacteria represent an important part of aquatic microbial communities. There exist two fundamentally different light-harvesting systems: bacteriochlorophyll-containing reaction centers or rhodopsins. Here, we report a photoheterotrophic Sphingomonas strain isolated from an oligotrophic lake, which contains complete sets of genes for both rhodopsin-based and bacteriochlorophyll-based phototrophy. Interestingly, the identified genes were not expressed when cultured in liquid organic media. Using reverse transcription quantitative PCR (RT-qPCR), RNA sequencing, and bacteriochlorophyll a quantification, we document that bacteriochlorophyll synthesis was repressed by high concentrations of glucose or galactose in the medium. Coactivation of photosynthesis genes together with genes for TonB-dependent transporters suggests the utilization of light energy for nutrient import. The photosynthetic units were formed by ring-shaped light-harvesting complex 1 and reaction centers with bacteriochlorophyll a and spirilloxanthin as the main light-harvesting pigments. The identified rhodopsin gene belonged to the xanthorhodopsin family, but it lacks salinixanthin antenna. In contrast to bacteriochlorophyll, the expression of xanthorhodopsin remained minimal under all experimental conditions tested. Since the gene was found in the same operon as a histidine kinase, we propose that it might serve as a light sensor. Our results document that photoheterotrophic Sphingomonas bacteria use the energy of light under carbon-limited conditions, while under carbon-replete conditions, they cover all their metabolic needs through oxidative phosphorylation.IMPORTANCE Phototrophic organisms are key components of many natural environments. There exist two main phototrophic groups: species that collect light energy using various kinds of (bacterio)chlorophylls and species that utilize rhodopsins. Here, we present a freshwater bacterium Sphingomonas sp. strain AAP5 which contains genes for both light-harvesting systems. We show that bacteriochlorophyll-based reaction centers are repressed by light and/or glucose. On the other hand, the rhodopsin gene was not expressed significantly under any of the experimental conditions. This may indicate that rhodopsin in Sphingomonas may have other functions not linked to bioenergetics.
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Affiliation(s)
- Karel Kopejtka
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Jürgen Tomasch
- Research Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
| | - Yonghui Zeng
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
- Department of Environmental Science, Aarhus University, Aarhus, Denmark
| | - Vadim Selyanin
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Marko Dachev
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Kasia Piwosz
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Martin Tichý
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - David Bína
- Institute of Plant Molecular Biology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Institute of Parasitology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Zdenko Gardian
- Institute of Plant Molecular Biology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Institute of Parasitology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Henner Brinkmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Robert Geffers
- Research Group Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ruben Sommaruga
- Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
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10
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Zhang H, Wang Y, Huang T, Liu K, Huang X, Ma B, Li N, Sekar R. Mixed-culture aerobic anoxygenic photosynthetic bacterial consortia reduce nitrate: Core species dynamics, co-interactions and assessment in raw water of reservoirs. BIORESOURCE TECHNOLOGY 2020; 315:123817. [PMID: 32683291 DOI: 10.1016/j.biortech.2020.123817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Three consortia of mixed-culture Aerobic Anoxygenic Photosynthetic Bacteria (AAPB) with excellent aerobic denitrifying ability were isolated from drinking water source reservoirs. The results showed that the removal of dissolved organic carbon (DOC) and nitrate nitrogen (NO3--N) by mixed-culture AAPB were higher than 90% and 99%, respectively. The Illumina MiSeq sequencing of pufM gene revealed that the dominant genera and their relative abundance changed over the culture periods. Sphingomonas sanxanigenens was the most dominant species observed at 9 h, whereas at 48 h, the most abundant species was Rhodobacter blasticus. A network analysis demonstrated that the co-interactions among the different genera were complex and variable. Mixed-culture AAPB removed more than 30% of NO3--N and 25% of DOC from the source water and this study suggests that mixed-culture AAPB can be regarded as a latent denitrifying microbial inoculum in the reservoir raw water treatment.
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Affiliation(s)
- Haihan Zhang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Yan Wang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Kaiwen Liu
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ben Ma
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Nan Li
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Raju Sekar
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
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11
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Szabó-Tugyi N, Vörös L, V-Balogh K, Botta-Dukát Z, Bernát G, Schmera D, Somogyi B. Aerobic anoxygenic phototrophs are highly abundant in hypertrophic and polyhumic waters. FEMS Microbiol Ecol 2020; 95:5530753. [PMID: 31291460 DOI: 10.1093/femsec/fiz104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 07/08/2019] [Indexed: 01/20/2023] Open
Abstract
Aerobic anoxygenic phototrophs (AAPs) are a group of photoheterotrophic bacteria common in natural waters. Here, AAP abundance and contribution to total bacterial abundance and biomass were investigated to test whether the trophic status of a lake or content of coloured dissolved organic matter (CDOM) play a role in determining AAP distribution and abundance in shallow inland lakes, with special focus on hypertrophic and polyhumic waters. Twenty-six different shallow lakes in Hungary were monitored. AAP abundance and biomass were determined by epifluorescence microscopy. The lakes exhibit a broad range of CDOM (2-7000 mg Pt L-1) and phytoplankton biomass (2-1200 μg L-1 chlorophyll a concentration). Very high AAP abundance (up to 3 × 107 cells mL-1) was observed in polyhumic and hypertrophic shallow lakes. AAP abundance was influenced by phytoplankton biomass and CDOM content, and these effects were interrelated. As determined, 40 μg L-1 chlorophyll a and 52 mg Pt L-1 CDOM are threshold levels above which these effects have a synergistic relationship. Hence, the observed high AAP abundance in some soda pans is a consequence of combined hypertrophy and high CDOM content. AAP contribution was influenced by total suspended solids (TSS) content: the success of AAP cells could be explained by high TSS levels, which might be explained by the decrease of their selective grazing control.
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Affiliation(s)
- Nóra Szabó-Tugyi
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | - Lajos Vörös
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | - Katalin V-Balogh
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | | | - Gábor Bernát
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | - Dénes Schmera
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | - Boglárka Somogyi
- MTA Centre for Ecological Research, Balaton Limnological Institute
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12
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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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13
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Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria. Sci Rep 2019; 9:18766. [PMID: 31822744 PMCID: PMC6904477 DOI: 10.1038/s41598-019-55210-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/25/2019] [Indexed: 01/21/2023] Open
Abstract
The anoxygenic phototrophic bacteria (APB) are an active component of aquatic microbial communities. While DNA-based studies have delivered a detailed picture of APB diversity, they cannot provide any information on the activity of individual species. Therefore, we focused on the expression of a photosynthetic gene by APB communities in two freshwater lakes (Cep lake and the Římov Reservoir) in the Czech Republic. First, we analyzed expression levels of pufM during the diel cycle using RT-qPCR. The transcription underwent a strong diel cycle and was inhibited during the day in both lakes. Then, we compared DNA- (total) and RNA-based (active) community composition by sequencing pufM amplicon libraries. We observed large differences in expression activity among different APB phylogroups. While the total APB community in the Římov Reservoir was dominated by Betaproteobacteria, Alphaproteobacteria prevailed in the active library. A different situation was encountered in the oligotrophic lake Cep where Betaproteobacteria (order Burkholderiales) dominated both the DNA and RNA libraries. Interestingly, in Cep lake we found smaller amounts of highly active uncultured phototrophic Chloroflexi, as well as phototrophic Gemmatimonadetes. Despite the large diversity of APB communities, light repression of pufM expression seems to be a common feature of all aerobic APB present in the studied lakes.
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14
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Seasonal dynamics of aerobic anoxygenic phototrophs in freshwater lake Vlkov. Folia Microbiol (Praha) 2019; 64:705-710. [DOI: 10.1007/s12223-019-00735-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 07/15/2019] [Indexed: 11/25/2022]
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15
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Echeverría-Vega A, Chong G, Serrano AE, Guajardo M, Encalada O, Parro V, Blanco Y, Rivas L, Rose KC, Moreno-Paz M, Luque JA, Cabrol NA, Demergasso CS. Watershed-Induced Limnological and Microbial Status in Two Oligotrophic Andean Lakes Exposed to the Same Climatic Scenario. Front Microbiol 2018; 9:357. [PMID: 29556224 PMCID: PMC5844981 DOI: 10.3389/fmicb.2018.00357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 02/14/2018] [Indexed: 12/04/2022] Open
Abstract
Laguna Negra and Lo Encañado are two oligotrophic Andean lakes forming part of the system fed by meltwater from distinct glacial tongues of the Echaurren glacier in central Chile, which is in a recession period. The recent increase in temperature and decline in precipitation have led to an increase of glacial meltwater and sediments entering these lakes. Although the lacustrine systems are also hydrogeologically connected, the limnology of the lakes is strongly controlled by the surface processes related to the respective sub-watersheds and hydrology. Watershed characteristics (area and length, slope, lithology, resistance to erosion, among others) affect the chemical and physical characteristics of both lakes (e.g., nutrient concentration and turbidity). We studied physical and chemical variables and performed 16S rRNA amplicon sequencing to determine the specific microbial signature of the lakes. The transparency, temperature, turbidity and concentrations of chlorophyll-a, dissolved organic matter, nutrients and the total number of cells, revealed the different status of both lakes at the time of sampling. The predominant bacterial groups in both lakes were Proteobacteria, Verrucomicrobia, and Bacteroidetes. Interestingly, the contribution of phototrophs was significantly higher in LN compared to LE (13 and 4% respectively) and the major fraction corresponded to Anoxygenic Phototrophs (AP) represented by Chloroflexi, Alpha, and Betaproteobacteria. Multivariate analyses showed that the nutrient levels and the light availability of both lakes, which finally depend on the hydrological characteristics of the respective watersheds, explain the differential community composition/function. The abundance of a diverse photoheterotrophic bacterioplankton community suggests that the ability to utilize solar energy along with organic and inorganic substrates is a key function in these oligotrophic mountain lakes.
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Affiliation(s)
| | - Guillermo Chong
- Departamento de Ciencias Geológicas, Universidad Católica de Norte, Antofagasta, Chile
| | - Antonio E Serrano
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Mariela Guajardo
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | - Olga Encalada
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Luis Rivas
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Kevin C Rose
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - José A Luque
- Departamento de Ciencias Geológicas, Universidad Católica de Norte, Antofagasta, Chile.,Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Nathalie A Cabrol
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States.,Space Science Division, NASA Ames Research Center, Moffett Field, CA, United States
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16
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Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans. Appl Environ Microbiol 2017; 84:AEM.02116-17. [PMID: 29030444 DOI: 10.1128/aem.02116-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/07/2017] [Indexed: 11/20/2022] Open
Abstract
The genus Limnohabitans (Comamonadaceae, Betaproteobacteria) is a common and a highly active component of freshwater bacterioplanktonic communities. To date, the genus has been considered to contain only heterotrophic species. In this study, we detected the photosynthesis genes pufLM and bchY in 28 of 46 strains from three Limnohabitans lineages. The pufM sequences obtained are very closely related to environmental pufM sequences detected in various freshwater habitats, indicating the ubiquity and potential importance of photoheterotrophic Limnohabitans in nature. Additionally, we sequenced and analyzed the genomes of 5 potentially photoheterotrophic Limnohabitans strains, to gain further insights into their phototrophic capacity. The structure of the photosynthesis gene cluster turned out to be highly conserved within the genus Limnohabitans and also among all potentially photosynthetic Betaproteobacteria strains. The expression of photosynthetic complexes was detected in a culture of Limnohabitans planktonicus II-D5T using spectroscopic and pigment analyses. This was further verified by a novel combination of infrared microscopy and fluorescent in situ hybridization.IMPORTANCE The data presented document that the capacity to perform anoxygenic photosynthesis is common among the members of the genus Limnohabitans, indicating that they may have a novel role in freshwater habitats.
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17
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Šantić D, Šestanović S, Vrdoljak A, Šolić M, Kušpilić G, Ninčević Gladan Ž, Koblížek M. Distribution of aerobic anoxygenic phototrophs in the Eastern Adriatic Sea. MARINE ENVIRONMENTAL RESEARCH 2017; 130:134-141. [PMID: 28760621 DOI: 10.1016/j.marenvres.2017.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 06/07/2023]
Abstract
The spatial patterns of aerobic anoxygenic phototrophs abundances were investigated, for the first time, in the Adriatic Sea. Also, the spatial patterns of the whole picoplankton community as well as the environmental factors that potentially influence these patterns were highlighted. AAP abundances was in average 66.9 ± 66.8 × 103 cell mL-1, and their proportion in total bacteria was 7.3 ± 4.3%. These values are in the upper range of AAP abundances observed in marine environments. Multivariate analyses proved that environmental factors influenced the picoplankton community interdependently. Chl a was the main driving factor for the picoplankton community, accounting for 33.3% of picoplankton community variance, followed by NO2- (17.9% of variance explained) and temperature (14.2% of variance explained). Chl a showed stronger correlation with AAPs, non-pigmented bacteria and Picoeucaryotes than with cyanobacteria. Abundance of cyanobacteria was stronger correlated to salinity and the N:P ratio than to nutrient concentrations.
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Affiliation(s)
- Danijela Šantić
- Laboratory of Marine Microbiology, Institute of Oceanography and Fisheries, Šetalište I. Meštrovića 63, Split, Croatia.
| | - Stefanija Šestanović
- Laboratory of Marine Microbiology, Institute of Oceanography and Fisheries, Šetalište I. Meštrovića 63, Split, Croatia.
| | - Ana Vrdoljak
- Laboratory of Marine Microbiology, Institute of Oceanography and Fisheries, Šetalište I. Meštrovića 63, Split, Croatia.
| | - Mladen Šolić
- Laboratory of Marine Microbiology, Institute of Oceanography and Fisheries, Šetalište I. Meštrovića 63, Split, Croatia.
| | - Grozdan Kušpilić
- Laboratory of Chemical Oceanography and Sedimentology of the Sea, Institute of Oceanography and Fisheries, Šetalište I. Meštrovića 63, Split, Croatia.
| | - Živana Ninčević Gladan
- Laboratory of Plankton and Shellfish Toxicity, Institute of Oceanography and Fisheries, Šetalište I. Meštrovića 63, Split, Croatia.
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology CAS, 379 81 Trebon, Czech Republic.
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18
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Ferrera I, Sarmento H, Priscu JC, Chiuchiolo A, González JM, Grossart HP. Diversity and Distribution of Freshwater Aerobic Anoxygenic Phototrophic Bacteria across a Wide Latitudinal Gradient. Front Microbiol 2017; 8:175. [PMID: 28275369 PMCID: PMC5320280 DOI: 10.3389/fmicb.2017.00175] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/24/2017] [Indexed: 11/13/2022] Open
Abstract
Aerobic anoxygenic phototrophs (AAPs) have been shown to exist in numerous marine and brackish environments where they are hypothesized to play important ecological roles. Despite their potential significance, the study of freshwater AAPs is in its infancy and limited to local investigations. Here, we explore the occurrence, diversity and distribution of AAPs in lakes covering a wide latitudinal gradient: Mongolian and German lakes located in temperate regions of Eurasia, tropical Great East African lakes, and polar permanently ice-covered Antarctic lakes. Our results show a widespread distribution of AAPs in lakes with contrasting environmental conditions and confirm that this group is composed of different members of the Alpha- and Betaproteobacteria. While latitude does not seem to strongly influence AAP abundance, clear patterns of community structure and composition along geographic regions were observed as indicated by a strong macro-geographical signal in the taxonomical composition of AAPs. Overall, our results suggest that the distribution patterns of freshwater AAPs are likely driven by a combination of small-scale environmental conditions (specific of each lake and region) and large-scale geographic factors (climatic regions across a latitudinal gradient).
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Affiliation(s)
- Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain; Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland FisheriesStechlin, Germany
| | - Hugo Sarmento
- Department of Hydrobiology, Universidade Federal de São Carlos São Carlos, Brazil
| | - John C Priscu
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Amy Chiuchiolo
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - José M González
- Department of Microbiology, University of La Laguna La Laguna, Spain
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland FisheriesStechlin, Germany; Department of Biochemistry and Biology, Potsdam UniversityPotsdam, Germany
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19
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Lehours AC, Jeune AHL, Aguer JP, Céréghino R, Corbara B, Kéraval B, Leroy C, Perrière F, Jeanthon C, Carrias JF. Unexpectedly high bacteriochlorophyll a concentrations in neotropical tank bromeliads. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:689-698. [PMID: 27264016 DOI: 10.1111/1758-2229.12426] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The contribution of bacteriochlorophyll a (BChl a) to photosynthetically driven electron transport is generally low in aquatic and terrestrial systems. Here, we provide evidence that anoxygenic bacterial phototrophy is widespread and substantial in water retained by tank bromeliads of a primary rainforest in French Guiana. An analysis of the water extracted from 104 randomly selected tank bromeliads using infrared fluorimetry suggested the overall presence of abundant anoxygenic phototrophic bacterial populations. We found that purple bacteria dominated these populations responsible for unusually high BChl a/chlorophyll a ratios (>50%). Our data suggest that BChl a-based phototrophy in tank bromeliads can have significant effects on the ecology of tank-bromeliad ecosystems and on the carbon and energy fluxes in Neotropical forests.
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Affiliation(s)
- Anne-Catherine Lehours
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, 63000, France
- CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, 63178, Aubière, France
| | - Anne-Hélène Le Jeune
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, 63000, France
- CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, 63178, Aubière, France
| | - Jean-Pierre Aguer
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, 63000, France
- CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, 63178, Aubière, France
| | - Régis Céréghino
- Toulouse Université, INP, Université Paul Sabatier, EcoLab, Toulouse, F31062, France
- UMR CNRS 5245, EcoLab, Toulouse, 31062, France
| | - Bruno Corbara
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, 63000, France
- CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, 63178, Aubière, France
| | - Benoit Kéraval
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, 63000, France
- CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, 63178, Aubière, France
| | - Céline Leroy
- IRD, UMR AMAP (botAnique et Modélisation de l'Architecture des Plantes et des végétations), Boulevard de la Lironde, TA A-51/PS2, Montpellier, 34398, France
- EcofoG (Ecologie des Forêts de Guyane, UMR 8172), Campus Agronomique, 97379 Kourou, France
| | - Fanny Perrière
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, 63000, France
- CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, 63178, Aubière, France
| | - Christian Jeanthon
- Marine Phototrophic Prokaryotes Team 29680 Roscoff, CNRS, Station Biologique de Roscoff, France
- Oceanic Plankton Group, Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Jean-François Carrias
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, 63000, France
- CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, 63178, Aubière, France
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20
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Cepáková Z, Hrouzek P, Žišková E, Nuyanzina-Boldareva E, Šorf M, Kozlíková-Zapomělová E, Salka I, Grossart HP, Koblížek M. High turnover rates of aerobic anoxygenic phototrophs in European freshwater lakes. Environ Microbiol 2016; 18:5063-5071. [PMID: 27485742 DOI: 10.1111/1462-2920.13475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/21/2016] [Indexed: 11/30/2022]
Abstract
Aerobic Anoxygenic Phototrophic (AAP) bacteria are bacteriochlorophyll (BChl) a -containing organisms which use light energy to supplement their predominantly heterotrophic metabolism. Here, we investigated mortality and growth rates of AAP bacteria in three different freshwater lakes in Central Europe: the mountain lake Plešné, the oligo-mesotrophic Lake Stechlin and the forest pond Huntov. The mortality of AAP bacteria was estimated from diel changes of BChl a fluorescence. Net and gross growth rates were calculated from the increases in AAP cell numbers. The gross growth rates of AAP bacteria ranged from 0.38 to 5.6 d-1 , with the highest values observed during summer months. Simultaneously, the rapidly growing AAP cells have to cope with an intense grazing pressure by both zooplankton and protists. The presented results document that during the day, gross growth usually surpased mortality. Our results indicate that AAP bacteria utilize light energy under natural conditions to maintain rapid growth rates, which are balanced by a generally intense grazing pressure.
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Affiliation(s)
- Zuzana Cepáková
- Center Algatech, Institute of Microbiology CAS, Třeboň, 37981, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | - Pavel Hrouzek
- Center Algatech, Institute of Microbiology CAS, Třeboň, 37981, Czech Republic
| | - Eva Žišková
- Center Algatech, Institute of Microbiology CAS, Třeboň, 37981, Czech Republic
| | | | - Michal Šorf
- Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | | | - Ivette Salka
- Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, 16775, Germany
| | - Hans-Peter Grossart
- Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, 16775, Germany.,Inst for Biochemistry and Biology, Potsdam University, 14469 Potsdam, Maulbeerallee 2, Germany
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology CAS, Třeboň, 37981, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
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Lew S, Lew M, Koblížek M. Influence of selected environmental factors on the abundance of aerobic anoxygenic phototrophs in peat-bog lakes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:13853-13863. [PMID: 27032635 PMCID: PMC4943989 DOI: 10.1007/s11356-016-6521-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
Aerobic anoxygenic phototrophs (AAPs) are photoheterotrophic prokaryotes that are widespread in many limnic and marine environments. So far, little is known about their distribution in peat-bog lakes. Seventeen peat-bog lakes were sampled during three summer seasons 2009, 2011, and 2012, and the vertical distribution of AAPs was determined by infrared epifluorescence microscopy. The analysis demonstrated that in the surface layers of the studied lakes, AAP abundance ranged from 0.3 to 12.04 × 10(5) cells mL(-1), which represents <1 to 18.3 % of the total bacteria. The vertical distribution of AAPs confirmed their presence in the upper parts of the water column with minimum numbers in the anoxic bottom waters. We have shown that the AAP abundance was significantly positively correlated with the water pH, and the highest proportion of photoheterotrophs was found in peat-bog lakes with a pH between 6.7 and 7.6. Our results demonstrated an influence of water acidity on the abundance of AAPs, which may reflect a fundamental difference in the microbial composition between acidic and pH neutral peat-bog lakes.
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Affiliation(s)
- Sylwia Lew
- />Faculty of Biology and Biotechnology, University of Warmia and Mazury in Poland, Oczapowskiego 1a, 10-957 Olsztyn, Poland
| | - Marcin Lew
- />Faculty of Veterinary Medicine, University of Warmia and Mazury in Poland, Oczapowskiego 2, 10-957 Olsztyn, Poland
| | - Michal Koblížek
- />Institute of Microbiology CAS, Center Algatech, 37981 Třeboň, Czech Republic
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Single-cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production. ISME JOURNAL 2016; 10:1579-88. [PMID: 26771928 DOI: 10.1038/ismej.2015.242] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/18/2015] [Accepted: 11/20/2015] [Indexed: 11/08/2022]
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance.
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23
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Koblížek M. Ecology of aerobic anoxygenic phototrophs in aquatic environments. FEMS Microbiol Rev 2015; 39:854-70. [DOI: 10.1093/femsre/fuv032] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2015] [Indexed: 11/13/2022] Open
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