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Torpee S, Kantachote D, Sukhoom A, Tantirungkij M. Culture optimization to enhance carotenoid production of a selected purple nonsulfur bacterium and its activity against acute hepatopancreatic necrosis disease-causing Vibrio parahaemolyticus. Biotechnol Appl Biochem 2022; 69:2422-2436. [PMID: 34841569 DOI: 10.1002/bab.2292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
Purple nonsulfur bacteria (PNSB) were investigated for their carotenoid production and anti-vibrio activity against acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio parahaemolyticus. To test carotenoid production, selected strains were cultivated in basic isolation medium (BIM), glutamate acetate medium, G5 medium and artificial acetic acid wastewater (AAW) medium. From 144 PNSB, Rhodopseudomonas palustris KTSSG46 was selected to produce carotenoids under microaerobic light conditions in BIM. When the culture medium was optimized, strain KTSSG46 grown in BIM modified with l-glutamate at 1 g/L more effectively inhibited AHPND-causing V. parahaemolyticus strains than standard BIM with 1 g/L (NH4 )2 SO4 . BIM was further modified with 1.23 g/L MgSO4 ·7H2 O and carotenoid production increased 40.22%. Carotenoid production at day 2 by strain KTSSG46 grown in BIM modified with l-glutamate at 1 and 1.23 g/L MgSO4 ·7H2 O was the same as production in BIM modified with monosodium glutamate (MSG). Culture supernatants from all BIM formulations showed similar activity against the resistant AHPND strain SR2. Based on high-performance liquid chromatography, carotenoids of strain KTSSG46 might be canthaxanthin. Grown in BIM modified with MSG, strain KTSSG46 could produce inexpensive carotenoids and release anti-vibrio compounds that, applied as shrimp feed additive, would prevent AHPND strains.
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Affiliation(s)
- Salwa Torpee
- Department of Microbiology, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| | - Duangporn Kantachote
- Department of Microbiology, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| | - Ampaitip Sukhoom
- Department of Microbiology, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| | - Manee Tantirungkij
- Research and Academic Service Center, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
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2
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Aguilar-Cruz Y, Milke F, Leinberger J, Poehlein A, Zotz G, Brinkhoff T. Diversity and putative metabolic function of prokaryotic communities in tank bromeliads along an elevation gradient in tropical Mexico. Front Microbiol 2022; 13:945488. [PMID: 36312956 PMCID: PMC9608151 DOI: 10.3389/fmicb.2022.945488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/13/2022] [Indexed: 12/02/2022] Open
Abstract
Tank bromeliads are unique canopy microhabitats that offer freshwater and organic nutrient-rich substrates in the Neotropics. In them it is possible to thoroughly characterize environmental factors and species composition of terrestrial and aquatic biota. Therefore, these plants have been used as natural models to study how communities are distributed and assembled. Here we used amplicon sequencing of the 16S rRNA gene and their functional annotations to study the diversity and metabolic potential of prokaryotic communities in tank bromeliads in five different forests along an elevation gradient in tropical Mexico. Furthermore, we analyzed the effects of vegetation type and environmental factors inside the tanks on prokaryotic composition. We found a high prokaryotic diversity in tank bromeliads along the elevation gradient. Prokaryotes commonly observed in acidic environments rich in organic carbon, and the potential pathogen Pasteurella multocida, were present in all samples, but few amplicon sequence variants were shared between forests. The prokaryotic composition was affected by forest type, and comparisons against null models suggest that it was shaped by non-neutral processes. Furthermore, prokaryotic community changes significantly covaried with tank water temperature, pH, and inorganic carbon. We found a high diversity of putative metabolic groups dominated by chemoheterotrophs and fermenters, but taxonomic groups involved in nitrogen and sulfur cycling were also present in all samples. These results suggest that tank bromeliads promote taxonomic and metabolic diversity of the prokaryotic community at a local and regional scale and play an important role in the biogeochemistry of forest canopies in the Neotropics.
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Affiliation(s)
- Yonatan Aguilar-Cruz
- Functional Ecology of Plants, Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- *Correspondence: Yonatan Aguilar-Cruz, ; Felix Milke,
| | - Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- *Correspondence: Yonatan Aguilar-Cruz, ; Felix Milke,
| | - Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Gerhard Zotz
- Functional Ecology of Plants, Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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3
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Carrias JF, Gerphagnon M, Rodríguez-Pérez H, Borrel G, Loiseau C, Corbara B, Céréghino R, Mary I, Leroy C. Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem. FEMS Microbiol Ecol 2020; 96:5807077. [PMID: 32175561 DOI: 10.1093/femsec/fiaa045] [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: 09/05/2019] [Accepted: 03/13/2020] [Indexed: 12/23/2022] Open
Abstract
Despite the growing number of investigations on microbial succession during the last decade, most of our knowledge on primary succession of bacteria in natural environments comes from conceptual models and/or studies of chronosequences. Successional patterns of litter-degrading bacteria remain poorly documented, especially in undisturbed environments. Here we conducted an experiment with tank bromeliads as natural freshwater microcosms to assess major trends in bacterial succession on two leaf-litter species incubated with or without animal exclusion. We used amplicon sequencing and a co-occurrence network to assess changes in bacterial community structure according to treatments. Alpha-diversity and community complexity displayed the same trends regardless of the treatments, highlighting that primary succession of detrital-bacteria is subject to resource limitation and biological interactions, much like macro-organisms. Shifts in bacterial assemblages along the succession were characterized by an increase in uncharacterized taxa and potential N-fixing bacteria, the latter being involved in positive co-occurrence between taxa. These findings support the hypothesis of interdependence between taxa as a significant niche-based process shaping bacterial communities during the advanced stage of succession.
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Affiliation(s)
- Jean-François Carrias
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Mélanie Gerphagnon
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Héctor Rodríguez-Pérez
- UMR EcoFoG, CNRS, CIRAD, INRA, AgroParisTech, Université des Antilles, Université de Guyane, 97310 Kourou, France
| | - Guillaume Borrel
- Institut Pasteur, Department of Microbiology, Unité de Biologie Évolutive de la Cellule Microbienne, Paris, France
| | - Camille Loiseau
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Bruno Corbara
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Régis Céréghino
- Ecolab, Laboratoire Ecologie Fonctionnelle et Environnement, CNRS, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse, France
| | - Isabelle Mary
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Céline Leroy
- UMR EcoFoG, CNRS, CIRAD, INRA, AgroParisTech, Université des Antilles, Université de Guyane, 97310 Kourou, France.,AMAP, IRD, CIRAD, CNRS, INRA, Université Montpellier, Montpellier, France
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Simão TLL, Utz LRP, Dias R, Giongo A, Triplett EW, Eizirik E. Remarkably Complex Microbial Community Composition in Bromeliad Tank Waters Revealed by eDNA Metabarcoding. J Eukaryot Microbiol 2020; 67:593-607. [PMID: 32562451 DOI: 10.1111/jeu.12814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/04/2020] [Accepted: 06/04/2020] [Indexed: 11/29/2022]
Abstract
To investigate patterns of biotic community composition at different spatial scales and biological contexts, we used environmental DNA metabarcoding to characterize eukaryotic and prokaryotic assemblages present in the phytotelmata of three bromeliad species (Aechmea gamosepala, Vriesea friburgensis, and Vriesea platynema) at a single Atlantic Forest site in southern Brazil. We sampled multiple individuals per species and multiple tanks from each individual, totalizing 30 samples. We observed very high levels of diversity in these communities, and remarkable variation across individuals and even among tanks from the same individual. The alpha diversity was higher for prokaryotes than eukaryotes, especially for A. gamosepala and V. platynema samples. Some biotic components appeared to be species-specific, while most of the biota was shared among species, but varied substantially in frequency among samples. Interestingly, V. friburgensis communities (which were sampled at nearby locations) tended to be more heterogeneous across samples, for both eukaryotes and prokaryotes. The opposite was true for V. platynema, whose samples were more broadly spaced but whose communities were more similar to each other. Our results indicate that additional attention should be devoted to within-individual heterogeneity when assessing bromeliad phytotelmata biodiversity, and highlight the complexity of the biotic assemblages gathered in these unique habitats.
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Affiliation(s)
- Taiz L L Simão
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Av. Ipiranga, 6681, prédio 12., Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
| | - Laura R P Utz
- Laboratório de Ecologia Aquática, Escola de Ciências da Saúde e da Vida, PUCRS, Av. Ipiranga, 6681, prédio 12., Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
| | - Raquel Dias
- Department of Integrative Structural and Computational Biology, Scripps Research Translational Institute, 3344 North Torrey Pines Court, Suite 300, La Jolla, California, 92037, USA
| | - Adriana Giongo
- Instituto do Petróleo e Recursos Naturais, PUCRS, Av. Ipiranga 6681, prédio 96J, Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, 1052 Museum Road, P.O. Box 110700, Gainesville, Florida, 32608, USA
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Av. Ipiranga, 6681, prédio 12., Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
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5
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Louca S, Jacques SMS, Pires APF, Leal JS, González AL, Doebeli M, Farjalla VF. Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions. Environ Microbiol 2017; 19:3132-3151. [PMID: 28488752 DOI: 10.1111/1462-2920.13788] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/24/2017] [Indexed: 11/27/2022]
Abstract
Phytotelmata in tank-forming Bromeliaceae plants are regarded as potential miniature models for aquatic ecology, but detailed investigations of their microbial communities are rare. Hence, the biogeochemistry in bromeliad tanks remains poorly understood. Here we investigate the structure of bacterial and archaeal communities inhabiting the detritus within the tanks of two bromeliad species, Aechmea nudicaulis and Neoregelia cruenta, from a Brazilian sand dune forest. We used metagenomic sequencing for functional community profiling and 16S sequencing for taxonomic profiling. We estimated the correlation between functional groups and various environmental variables, and compared communities between bromeliad species. In all bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions, including all denitrification steps, ammonification, sulfate respiration, methanogenesis, reductive acetogenesis and anoxygenic phototrophy. Overall, CO2 reducers dominated in abundance over sulfate reducers, and anoxygenic phototrophs largely outnumbered oxygenic photoautotrophs. Functional community structure correlated strongly with environmental variables, between and within a single bromeliad species. Methanogens and reductive acetogens correlated with detrital volume and canopy coverage, and exhibited higher relative abundances in N. cruenta. A comparison of bromeliads to freshwater lake sediments and soil from around the world, revealed stark differences in terms of taxonomic as well as functional microbial community structure.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Saulo M S Jacques
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Ecologia e Evolução, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aliny P F Pires
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana S Leal
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Angélica L González
- Biology Department & Center for Computational & Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Vinicius F Farjalla
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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6
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Pires APF, Leal JDS, Peeters ETHM. Rainfall changes affect the algae dominance in tank bromeliad ecosystems. PLoS One 2017; 12:e0175436. [PMID: 28422988 PMCID: PMC5396887 DOI: 10.1371/journal.pone.0175436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/27/2017] [Indexed: 11/18/2022] Open
Abstract
Climate change and biodiversity loss have been reported as major disturbances in the biosphere which can trigger changes in the structure and functioning of natural ecosystems. Nonetheless, empirical studies demonstrating how both factors interact to affect shifts in aquatic ecosystems are still unexplored. Here, we experimentally test how changes in rainfall distribution and litter diversity affect the occurrence of the algae-dominated condition in tank bromeliad ecosystems. Tank bromeliads are miniature aquatic ecosystems shaped by the rainwater and allochthonous detritus accumulated in the bases of their leaves. Here, we demonstrated that changes in the rainfall distribution were able to reduce the chlorophyll-a concentration in the water of bromeliad tanks affecting significantly the occurrence of algae-dominated conditions. On the other hand, litter diversity did not affect the algae dominance irrespective to the rainfall scenario. We suggest that rainfall changes may compromise important self-reinforcing mechanisms responsible for maintaining high levels of algae on tank bromeliads ecosystems. We summarized these results into a theoretical model which suggests that tank bromeliads may show two different regimes, determined by the bromeliad ability in taking up nutrients from the water and by the total amount of light entering the tank. We concluded that predicted climate changes might promote regime shifts in tropical aquatic ecosystems by shaping their structure and the relative importance of other regulating factors.
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Affiliation(s)
- Aliny Patricia Flauzino Pires
- Departamento de Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Fundação Brasileira para o Desenvolvimento Sustentável, Rio de Janeiro, Brazil
- Brazilian Research Network on Climate Change—Rede Clima, Instituto Nacional de Pesquisas Espaciais, São José dos Campos, São Paulo, Brazil
| | - Juliana da Silva Leal
- Departamento de Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Edwin T. H. M. Peeters
- Department of Environmental Sciences, Aquatic Ecology and Water Quality Management Group, Wageningen University, Wageningen, The Netherlands
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