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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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2
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Tinguely C, Paulméry M, Terrettaz C, Gonzalez D. Diurnal cycles drive rhythmic physiology and promote survival in facultative phototrophic bacteria. ISME COMMUNICATIONS 2023; 3:125. [PMID: 38001234 PMCID: PMC10674011 DOI: 10.1038/s43705-023-00334-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023]
Abstract
Bacteria have evolved many strategies to spare energy when nutrients become scarce. One widespread such strategy is facultative phototrophy, which helps heterotrophs supplement their energy supply using light. Our knowledge of the impact that such behaviors have on bacterial fitness and physiology is, however, still limited. Here, we study how a representative of the genus Porphyrobacter, in which aerobic anoxygenic phototrophy is ancestral, responds to different light regimes under nutrient limitation. We show that bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime. Under dark-light alternance, our bacterial model presents a diphasic life history dependent on phototrophy: during dark phases, the cells inhibit DNA replication and part of the population lyses and releases nutrients, while subsequent light phases allow for the recovery and renewed growth of the surviving cells. We correlate these cyclic variations with a pervasive pattern of rhythmic transcription which reflects global changes in diurnal metabolic activity. Finally, we demonstrate that, compared to either a phototrophy mutant or a bacteriochlorophyll a overproducer, the wild type strain is better adapted to natural environments, where regular dark-light cycles are interspersed with additional accidental dark episodes. Overall, our results highlight the importance of light-induced biological rhythms in a new model of aerobic anoxygenic phototroph representative of an ecologically important group of environmental bacteria.
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Affiliation(s)
- Camille Tinguely
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mélanie Paulméry
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Céline Terrettaz
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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3
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Kim W, Kim M, Park W. Unlocking the mystery of lysine toxicity on Microcystis aeruginosa. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130932. [PMID: 36860069 DOI: 10.1016/j.jhazmat.2023.130932] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Lysine toxicity on certain groups of bacterial cells has been recognized for many years, but the detailed molecular mechanisms that drive this phenomenon have not been elucidated. Many cyanobacteria including Microcystis aeruginosa cannot efficiently export and degrade lysine, although they have evolved to maintain a single copy of the lysine uptake system through which arginine or ornithine can also be transported into the cytoplasm. Autoradiographic analysis using 14C-l-lysine confirmed that lysine was competitively uptaken into cells with arginine or ornithine, which explained the arginine or ornithine-mediated alleviation of lysine toxicity in M. aeruginosa. A relatively non-specific MurE amino acid ligase could incorporate l-lysine into the 3rd position of UDP-N-acetylmuramyl-tripeptide by replacing meso-diaminopimelic acid during the stepwise addition of amino acids on peptidoglycan (PG) biosynthesis. However, further transpeptidation was blocked because lysine substitution at the pentapeptide of the cell wall inhibited the activity of transpeptidases. The leaky PG structure caused irreversible damage to the photosynthetic system and membrane integrity. Collectively, our results suggest that a lysine-mediated coarse-grained PG network and the absence of concrete septal PG lead to the death of slow-growing cyanobacteria.
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Affiliation(s)
- Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea.
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4
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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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Abstract
Improving the availability of representative isolates from the coral microbiome is essential for investigating symbiotic mechanisms and applying beneficial microorganisms to improve coral health. However, few studies have explored the diversity of bacteria which can be isolated from a single species. Here, we isolated a total of 395 bacterial strains affiliated with 49 families across nine classes from the coral Pocillopora damicornis. Identification results showed that most of the strains represent potential novel bacterial species or genera. We also sequenced and assembled the genomes of 118 of these isolates, and then the putative functions of these isolates were identified based on genetic signatures derived from the genomes and this information was combined with isolate-specific phenotypic data. Genomic information derived from the isolates identified putative functions including nitrification and denitrification, dimethylsulfoniopropionate transformation, and supply of fixed carbon, amino acids, and B vitamins which may support their eukaryotic partners. Furthermore, the isolates contained genes associated with chemotaxis, biofilm formation, quorum sensing, membrane transport, signal transduction, and eukaryote-like repeat-containing and cell-cell attachment proteins, all of which potentially help the bacterium establish association with the coral host. Our work expands on the existing culture collection of coral-associated bacteria and provides important information on the metabolic potential of these isolates which can be used to refine understanding of the role of bacteria in coral health and are now available to be applied to novel strategies aimed at improving coral resilience through microbiome manipulation. IMPORTANCE Microbes underpin the health of corals which are the building blocks of diverse and productive reef ecosystems. Studying the culturable fraction of coral-associated bacteria has received less attention in recent times than using culture-independent molecular methods. However, the genomic and phenotypic characterization of isolated strains allows assessment of their functional role in underpinning coral health and identification of beneficial microbes for microbiome manipulation. Here, we isolated 395 bacterial strains from tissues of Pocillopora damicornis with many representing potentially novel taxa and therefore providing a significant contribution to coral microbiology through greatly enlarging the existing cultured coral-associated bacterial bank. Through analysis of the genomes obtained in this study for the coral-associated bacteria and coral host, we elucidate putative metabolic linkages and symbiotic establishment. The results of this study will help to elucidate the role of specific isolates in coral health and provide beneficial microbes for efforts aimed at improving coral health.
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Piwosz K, Villena-Alemany C, Mujakić I. Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake. THE ISME JOURNAL 2022; 16:1046-1054. [PMID: 34802055 PMCID: PMC8941148 DOI: 10.1038/s41396-021-01142-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023]
Abstract
Lakes are a significant component of the global carbon cycle. Respiration exceeds net primary production in most freshwater lakes, making them a source of CO2 to the atmosphere. Driven by heterotrophic microorganisms, respiration is assumed to be unaffected by light, thus it is measured in the dark. However, photoheterotrophs, such as aerobic anoxygenic photoheterotrophic (AAP) bacteria that produce ATP via photochemical reactions, substantially reduce respiration in the light. They are an abundant and active component of bacterioplankton, but their photoheterotrophic contribution to microbial community metabolism remains unquantified. We showed that the community respiration rate in a freshwater lake was reduced by 15.2% (95% confidence interval (CI): 6.6-23.8%) in infrared light that is usable by AAP bacteria but not by primary producers. Moreover, significantly higher assimilation rates of glucose (18.1%; 7.8-28.4%), pyruvate (9.5%; 4.2-14.8%), and leucine (5.9%; 0.1-11.6%) were measured in infrared light. At the ecosystem scale, the amount of CO2 from respiration unbalanced by net primary production was by 3.69 × 109 g CO2 lower over these two sampling seasons when measured in the infrared light. Our results demonstrate that dark measurements of microbial activity significantly bias the carbon fluxes, providing a new paradigm for their quantification in aquatic environments.
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Affiliation(s)
- Kasia Piwosz
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981, Třeboň, Czechia. .,National Marine Fisheries Research Institute, 81-332, Gdynia, Poland.
| | - Cristian Villena-Alemany
- grid.418095.10000 0001 1015 3316Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia ,grid.14509.390000 0001 2166 4904Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Izabela Mujakić
- grid.418095.10000 0001 1015 3316Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia ,grid.14509.390000 0001 2166 4904Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
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7
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Reis PCJ, Thottathil SD, Prairie YT. The role of methanotrophy in the microbial carbon metabolism of temperate lakes. Nat Commun 2022; 13:43. [PMID: 35013226 PMCID: PMC8748455 DOI: 10.1038/s41467-021-27718-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/07/2021] [Indexed: 11/30/2022] Open
Abstract
Previous stable isotope and biomarker evidence has indicated that methanotrophy is an important pathway in the microbial loop of freshwater ecosystems, despite the low cell abundance of methane-oxidizing bacteria (MOB) and the low methane concentrations relative to the more abundant dissolved organic carbon (DOC). However, quantitative estimations of the relative contribution of methanotrophy to the microbial carbon metabolism of lakes are scarce, and the mechanism allowing methanotrophy to be of comparable importance to DOC-consuming heterotrophy remained elusive. Using incubation experiments, microscopy, and multiple water column profiles in six temperate lakes, we show that MOB play a much larger role than their abundances alone suggest because of their larger cell size and higher specific activity. MOB activity is tightly constrained by the local methane:oxygen ratio, with DOC-rich lakes with large hypolimnetic volume fraction showing a higher carbon consumption through methanotrophy than heterotrophy at the whole water column level. Our findings suggest that methanotrophy could be a critical microbial carbon consumption pathway in many temperate lakes, challenging the prevailing view of a DOC-centric microbial metabolism in these ecosystems.
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Affiliation(s)
- Paula C J Reis
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada.
| | - Shoji D Thottathil
- Department of Environmental Science, SRM University AP, Amaravati, Andhra Pradesh, 522 502, India
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
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8
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Ding Y, Nie L, Yang XC, Li Y, Huo YY, Li Z, Gao Y, Cui HL, Li J, Xu XW. Mechanism and Structural Insights Into a Novel Esterase, E53, Isolated From Erythrobacter longus. Front Microbiol 2022; 12:798194. [PMID: 35069500 PMCID: PMC8767022 DOI: 10.3389/fmicb.2021.798194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Esterases are a class of enzymes that split esters into an acid and an alcohol in a chemical reaction with water, having high potential in pharmaceutical, food and biofuel industrial applications. To advance the understanding of esterases, we have identified and characterized E53, an alkalophilic esterase from a marine bacterium Erythrobacter longus. The crystal structures of wild type E53 and three variants were solved successfully using the X-ray diffraction method. Phylogenetic analysis classified E53 as a member of the family IV esterase. The enzyme showed highest activity against p-nitrophenyl butyrate substrate at pH 8.5-9.5 and 40°C. Based on the structural feature, the catalytic pocket was defined as R1 (catalytic center), R2 (pocket entrance), and R3 (end area of pocket) regions. Nine variants were generated spanning R1-R3 and thorough functional studies were performed. Detailed structural analysis and the results obtained from the mutagenesis study revealed that mutations in the R1 region could regulate the catalytic reaction in both positive and negative directions; expanding the bottleneck in R2 region has improved the enzymatic activity; and R3 region was associated with the determination of the pH pattern of E53. N166A in R3 region showed reduced activity only under alkaline conditions, and structural analysis indicated the role of N166 in stabilizing the loop by forming a hydrogen bond with L193 and G233. In summary, the systematic studies on E53 performed in this work provide structural and functional insights into alkaliphilic esterases and further our knowledge of these enzymes.
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Affiliation(s)
- Yi Ding
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | | | - Xiao-Chen Yang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Yang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Ying-Yi Huo
- Teaching Center of Biological Experiments, Zhejiang University, Hangzhou, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Gao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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9
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Yang H, Hu C. Soil Chemistry and Nutrients Influence the Distribution of Aerobic Anoxygenic Phototrophic Bacteria and Eukaryotic Phototrophic Microorganisms of Physical Soil Crusts at Different Elevations on the Tibetan Plateau. MICROBIAL ECOLOGY 2022; 83:100-113. [PMID: 33733304 DOI: 10.1007/s00248-021-01734-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Photosynthetic microorganisms are widely distributed in the soil and play an important role in plant-free soil crusts. However, the distribution and environmental drivers of phototrophic microbial communities in physical soil crusts, where the abundance of cyanobacteria is low, are scarcely understood. Here, we performed high-throughput sequencing of pufM and 18S rRNA genes in soil crusts at different elevations on the Tibetan Plateau and used the data combined with environmental variables to analyze the diversity and structure of phototrophic microbial communities. We found that the dominant taxa of aerobic anoxygenic phototrophic bacteria (AAPB) and eukaryotic phototrophic microorganisms (EPM) were shown to shift with elevation. The phototrophic microbial diversity showed a single-peak pattern, with the lowest diversity of AAPB and highest diversity of EPM at middle elevations. Moreover, the elevation and soil property determined the phototrophic microbial community. Soil salts, especially Cl-, were the most important for AAPB. Likewise, soil nutrients, especially carbon, were the most important for EPM. The relationship between high-abundance taxa and environmental variables showed that Rhizobiales was significantly negatively correlated with salt ions and positively correlated with chlorophyll. Rhodobacterales showed the strongest and significant positive associations with Cl-. Chlorophyceae and Bacillariophyceae were positively correlated with CO32-. These results indicated that salinity and soil nutrients affected the diversity and structure of microbial communities. This study contributes to our understanding of the diversity, composition, and structure of photosynthetic microorganisms in physical soil crusts and helps in developing new approaches for controlling desertification and salinization and improving the desert ecological environment.
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Affiliation(s)
- Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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10
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Duan X, Guo C, Zhang C, Li H, Zhou Y, Gao H, Xia X, He H, McMinn A, Wang M. Effect of East Asian atmospheric particulate matter deposition on bacterial activity and community structure in the oligotrophic Northwest Pacific. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 283:117088. [PMID: 33857882 DOI: 10.1016/j.envpol.2021.117088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Large amounts of anthropogenic East Asian (EA) particulate matters (PM), containing inorganic nutrients and organic matter, are deposited in the oligotrophic Northwest Pacific Ocean. However, the effects of such deposition on marine microbes remain unclear. In this study, the effect of EA PM deposition on marine bacteria was assessed by five on-board microcosm experiments, conducted in oligotrophic basins of the South China Sea. The addition of EA PM to the sampling water induced a clear shift in bacterial community composition from prevailing oligotrophs (i.e., SAR 11 clade, Prochlorococcus, AEGEAN-169 marine group) to less common copiotrophs (i.e., Alteromonas, Ruegeria, Flavobacteriaceae) and thus a slight increase in bacterial diversity. The shift to more active community composition, as well as stimulation of PM nutrients, resulted in a large increase in cell-specific and bulk bacterial production. In contrast, there were only minor changes in bacterial abundance, possibly due to increased top-down mortality. The EA PM also exhibited a stronge toxic effect on pico-cyanobacteria, leading to a significant decrease in their proportion. Moreover, the responses of bacterial metabolism and community composition exhibited significant relationships with the hydrographic condition of the locations. Stronger promotion effects of the EA PM on bacterial production and community shift from oligotrophs to copiotrophs was demonstrated at the more oligotrophic sites with lower chlorophyll a concentrations. These results suggest that PM deposition from polluted areas has the potential to alter the typical oligotrophic microbiomes and change the net metabolic balance of the bacterial community. These will then influence the dynamics of carbon flow in microbial food webs and biogeochemical cycles, especially with the trend of global warming and expansion of low-chlorophyll regions.
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Affiliation(s)
- Xueping Duan
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Chao Zhang
- Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China
| | - Hongbo Li
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Yao Zhou
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Huiwang Gao
- Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hui He
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
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11
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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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12
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Farhan Ul Haque M, Xu HJ, Murrell JC, Crombie A. Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review. MICROBIOLOGY (READING, ENGLAND) 2020; 166:894-908. [PMID: 33085587 PMCID: PMC7660913 DOI: 10.1099/mic.0.000977] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.
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Affiliation(s)
| | - Hui-Juan Xu
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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13
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Light and Primary Production Shape Bacterial Activity and Community Composition of Aerobic Anoxygenic Phototrophic Bacteria in a Microcosm Experiment. mSphere 2020; 5:5/4/e00354-20. [PMID: 32611696 PMCID: PMC7333569 DOI: 10.1128/msphere.00354-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Phytoplankton is a key component of aquatic microbial communities, and metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon (DOC). Yet, the impact of primary production on bacterial activity and community composition remains largely unknown, as, for example, in the case of aerobic anoxygenic phototrophic (AAP) bacteria that utilize both phytoplankton-derived DOC and light as energy sources. Here, we studied how reduction of primary production in a natural freshwater community affects the bacterial community composition and its activity, focusing primarily on AAP bacteria. The bacterial respiration rate was the lowest when photosynthesis was reduced by direct inhibition of photosystem II and the highest in ambient light condition with no photosynthesis inhibition, suggesting that it was limited by carbon availability. However, bacterial assimilation rates of leucine and glucose were unaffected, indicating that increased bacterial growth efficiency (e.g., due to photoheterotrophy) can help to maintain overall bacterial production when low primary production limits DOC availability. Bacterial community composition was tightly linked to light intensity, mainly due to the increased relative abundance of light-dependent AAP bacteria. This notion shows that changes in bacterial community composition are not necessarily reflected by changes in bacterial production or growth and vice versa. Moreover, we demonstrated for the first time that light can directly affect bacterial community composition, a topic which has been neglected in studies of phytoplankton-bacteria interactions.IMPORTANCE Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously.
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14
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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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15
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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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16
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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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17
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Vigneron A, Cruaud P, Mohit V, Martineau MJ, Culley AI, Lovejoy C, Vincent WF. Multiple Strategies for Light-Harvesting, Photoprotection, and Carbon Flow in High Latitude Microbial Mats. Front Microbiol 2018; 9:2881. [PMID: 30564204 PMCID: PMC6288179 DOI: 10.3389/fmicb.2018.02881] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/09/2018] [Indexed: 12/27/2022] Open
Abstract
Microbial mats are ubiquitous in polar freshwater ecosystems and sustain high concentrations of biomass despite the extreme seasonal variations in light and temperature. Here we aimed to resolve genomic adaptations for light-harvesting, bright-light protection, and carbon flow in mats that undergo seasonal freeze-up. To bracket a range of communities in shallow water habitats, we sampled cyanobacterial mats in the thawed littoral zone of two lakes situated at the northern and southern limits of the Canadian Arctic permafrost zone. We applied a multiphasic approach using pigment profiles from high performance liquid chromatography, Illumina MiSeq sequencing of the 16S and 18S rRNA genes, and metagenomic analysis. The mats shared a taxonomic and functional core microbiome, dominated by oxygenic cyanobacteria with light-harvesting and photoprotective pigments, bacteria with bacteriochlorophyll, and bacteria with light-driven Type I rhodopsins. Organisms able to use light for energy related processes represented up to 85% of the total microbial community, with 15–30% attributable to cyanobacteria and 55–70% attributable to other bacteria. The proportion of genes involved in anaplerotic CO2 fixation was greater than for genes associated with oxygenic photosynthesis. Diverse heterotrophic bacteria, eukaryotes (including metazoans and fungi) and viruses co-occurred in both communities. The results indicate a broad range of strategies for capturing sunlight and CO2, and for the subsequent flow of energy and carbon in these complex, light-driven microbial ecosystems.
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Affiliation(s)
- Adrien Vigneron
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Perrine Cruaud
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada
| | - Vani Mohit
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Marie-Josée Martineau
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada
| | - Alexander I Culley
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada
| | - Connie Lovejoy
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Warwick F Vincent
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
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18
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Props R, Schmidt ML, Heyse J, Vanderploeg HA, Boon N, Denef VJ. Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels. Environ Microbiol 2017; 20:521-534. [DOI: 10.1111/1462-2920.13953] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 09/30/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Ruben Props
- Center for Microbial Ecology and Technology (CMET); Ghent University, Coupure Links 653; 9000 Gent Belgium
- Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200; 2400 Mol Belgium
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI USA
| | - Marian L. Schmidt
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI USA
| | - Jasmine Heyse
- Center for Microbial Ecology and Technology (CMET); Ghent University, Coupure Links 653; 9000 Gent Belgium
| | | | - Nico Boon
- Center for Microbial Ecology and Technology (CMET); Ghent University, Coupure Links 653; 9000 Gent Belgium
| | - Vincent J. Denef
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI USA
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19
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Light enhances the growth rates of natural populations of aerobic anoxygenic phototrophic bacteria. ISME JOURNAL 2017; 11:2391-2393. [PMID: 28534877 DOI: 10.1038/ismej.2017.79] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/07/2017] [Accepted: 03/16/2017] [Indexed: 11/09/2022]
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are microorganisms that can harvest light energy using bacteriochlorophyll a to supplement their predominantly organotrophic metabolism. Growth enhancement by light has repeatedly been demonstrated in laboratory experiments with AAP isolates. However, the ecological advantage of light utilization is unclear, as it has never been proven in the natural environment. Here, we conducted manipulation experiments in the NW Mediterranean and found that AAP bacteria display high growth rates which are controlled to a large extent by intense grazing pressure and phosphorous availability. Foremost, we found that, contrarily to the bulk bacterioplakton, AAP bacteria display higher growth rates when incubated under light-dark cycles than in complete darkness. These results represent the first direct evidence that natural populations of marine AAP bacteria can be stimulated by light.
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20
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Liu Q, Wu YH, Cheng H, Xu L, Wang CS, Xu XW. Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434. Stand Genomic Sci 2017; 12:32. [PMID: 28496940 PMCID: PMC5424368 DOI: 10.1186/s40793-017-0243-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/27/2017] [Indexed: 11/26/2022] Open
Abstract
The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as well as grow under aerobic conditions. It is the type species of the genus Porphyrobacter. Here we describe the characteristics of the strain DSM 9434, including the genome sequence and annotation, synthesis of BChl a, and metabolic pathways of the organism. The genome of strain DSM 9434 comprises 3,090,363 bp and contains 2,902 protein-coding genes, 47 tRNA genes and 6 rRNA genes. Strain DSM 9434 encodes 46 genes which participate in BChl a synthesis and this investigation shed light on the evolution and functional implications regarding bacteriochlorophyll synthesis.
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Affiliation(s)
- Qian Liu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 36th Baochubei Road, Hangzhou, 310012 People's Republic of China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 36th Baochubei Road, Hangzhou, 310012 People's Republic of China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 36th Baochubei Road, Hangzhou, 310012 People's Republic of China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 36th Baochubei Road, Hangzhou, 310012 People's Republic of China.,College of Life Sciences, Zhejiang University, Hangzhou, 310058 People's Republic of China
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 36th Baochubei Road, Hangzhou, 310012 People's Republic of China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 36th Baochubei Road, Hangzhou, 310012 People's Republic of China
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21
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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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22
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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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23
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Hirose S, Matsuura K, Haruta S. Phylogenetically Diverse Aerobic Anoxygenic Phototrophic Bacteria Isolated from Epilithic Biofilms in Tama River, Japan. Microbes Environ 2016; 31:299-306. [PMID: 27453124 PMCID: PMC5017807 DOI: 10.1264/jsme2.me15209] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates were classified into 14 groups in 8 operational taxonomic units (OTUs) and distributed in the orders Rhodospirillales, Rhodobacterales, and Sphingomonadales of Alphaproteobacteria and in Betaproteobacteria. Physiological analyses confirmed that none of the representative isolates from any of the groups grew under anaerobic phototrophic conditions. Seven isolates in 4 OTUs showed a 16S rRNA gene sequence identity of 98.0% or less with any established species, suggesting the presence of previously undescribed species of AAP bacteria. Six isolates in 2 other OTUs had the closest relatives, which have not been reported to be AAP bacteria. Physiological comparisons among the isolates revealed differences in preferences for nutrient concentrations, BChl contents, and light-harvesting proteins. These results suggest that diverse and previously unknown AAP bacteria inhabit river biofilms.
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Affiliation(s)
- Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University
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