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Li X, Li S, Xie P, Chen X, Chu Y, Chang H, Sun J, Li Q, Ren N, Ho SH. Advanced wastewater treatment with microalgae-indigenous bacterial interactions. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 20:100374. [PMID: 38283868 PMCID: PMC10821166 DOI: 10.1016/j.ese.2023.100374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/30/2024]
Abstract
Microalgal-indigenous bacterial wastewater treatment (MBWT) emerges as a promising approach for the concurrent removal of nitrogen (N) and phosphorus (P). Despite its potential, the prevalent use of MBWT in batch systems limits its broader application. Furthermore, the success of MBWT critically depends on the stable self-adaptation and synergistic interactions between microalgae and indigenous bacteria, yet the underlying biological mechanisms are not fully understood. Here we explore the viability and microbial dynamics of a continuous flow microalgae-indigenous bacteria advanced wastewater treatment system (CFMBAWTS) in processing actual secondary effluent, with a focus on varying hydraulic retention times (HRTs). The research highlights a stable, mutually beneficial relationship between indigenous bacteria and microalgae. Microalgae and indigenous bacteria can create an optimal environment for each other by providing essential cofactors (like iron, vitamins, and indole-3-acetic acid), oxygen, dissolved organic matter, and tryptophan. This collaboration leads to effective microbial growth, enhanced N and P removal, and energy generation. The study also uncovers crucial metabolic pathways, functional genes, and patterns of microbial succession. Significantly, the effluent NH4+-N and P levels complied with the Chinese national Class-II, Class-V, Class-IA, and Class-IB wastewater discharge standards when the HRT was reduced from 15 to 6 h. Optimal results, including the highest rates of CO2 fixation (1.23 g L-1), total energy yield (32.35 kJ L-1), and the maximal lipid (33.91%) and carbohydrate (41.91%) content, were observed at an HRT of 15 h. Overall, this study not only confirms the feasibility of CFMBAWTS but also lays a crucial foundation for enhancing our understanding of this technology and propelling its practical application in wastewater treatment plants.
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Affiliation(s)
- Xue Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Shengnan Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Peng Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Xi Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yuhao Chu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Haixing Chang
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Jian Sun
- Central Southern China Municipal Engineering Design and Research Institute Co., Ltd, Wuhan, 430010, PR China
| | - Qing Li
- Central Southern China Municipal Engineering Design and Research Institute Co., Ltd, Wuhan, 430010, PR China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
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2
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Macdonald JFH, Pérez-García P, Schneider YKH, Blümke P, Indenbirken D, Andersen JH, Krohn I, Streit WR. Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation. Sci Rep 2024; 14:10237. [PMID: 38702505 PMCID: PMC11068906 DOI: 10.1038/s41598-024-60978-8] [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: 11/13/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Enzymatic degradation of algae cell wall carbohydrates by microorganisms is under increasing investigation as marine organic matter gains more value as a sustainable resource. The fate of carbon in the marine ecosystem is in part driven by these degradation processes. In this study, we observe the microbiome dynamics of the macroalga Fucus vesiculosus in 25-day-enrichment cultures resulting in partial degradation of the brown algae. Microbial community analyses revealed the phylum Pseudomonadota as the main bacterial fraction dominated by the genera Marinomonas and Vibrio. More importantly, a metagenome-based Hidden Markov model for specific glycosyl hydrolyses and sulphatases identified Bacteroidota as the phylum with the highest potential for cell wall degradation, contrary to their low abundance. For experimental verification, we cloned, expressed, and biochemically characterised two α-L-fucosidases, FUJM18 and FUJM20. While protein structure predictions suggest the highest similarity to a Bacillota origin, protein-protein blasts solely showed weak similarities to defined Bacteroidota proteins. Both enzymes were remarkably active at elevated temperatures and are the basis for a potential synthetic enzyme cocktail for large-scale algal destruction.
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Affiliation(s)
- Jascha F H Macdonald
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Pablo Pérez-García
- Institute for General Microbiology, Molecular Microbiology, Kiel University, Kiel, Germany
| | - Yannik K-H Schneider
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Patrick Blümke
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Hamburg, Germany
| | - Jeanette H Andersen
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ines Krohn
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany.
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
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3
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Yang S, Zhou H, Pang Z, Wang Y, Chao J. Microbial community structure and diversity attached to the periphyton in different urban aquatic habitats. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:445. [PMID: 38607460 DOI: 10.1007/s10661-024-12599-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
Periphyton is a complex community composed of diverse prokaryotes and eukaryotes; understanding the characteristics of microbial communities within periphyton becomes crucial for biogeochemical cycles and energy dynamics of aquatic ecosystems. To further elucidate the community characteristics of periphyton across varied aquatic habitats, including unpolluted ecologically restored lakes, aquaculture ponds, and areas adjacent to domestic and industrial wastewater treatment plant outfalls, we explored the composition and diversity of prokaryotic and eukaryotic communities in periphyton by employing Illumina MiSeq sequencing. Our findings indicated that the prokaryotic communities were predominantly composed of Proteobacteria (40.92%), Bacteroidota (21.01%), and Cyanobacteria (10.12%), whereas the eukaryotic communities were primarily characterized by the dominance of Bacillariophyta (24.09%), Chlorophyta (20.83%), and Annelida (15.31%). Notably, Flavobacterium emerged as a widely distributed genus among the prokaryotic community. Unclassified_Tobrilidae exhibited higher abundance in unpolluted ecologically restored lakes. Chaetogaster and Nais were enriched in aquaculture ponds and domestic wastewater treatment plant outfall area, respectively, while Surirella and Gomphonema dominated industrial sewage treatment plant outfall area. The alpha diversity of eukaryotes was higher in unpolluted ecologically restored lakes. pH and nitrogen content (NO 2 - - N ,NO 3 - - N , and TN) significantly explained the variations for prokaryotic and eukaryotic community structures, respectively. Eukaryotic communities exhibited a more pronounced response to habitat variations compared to prokaryotic communities. Moreover, the association networks revealed an intensive positive correlation between dominant Bacillariophyta and Bacteroidota. This study provided useful data for identifying keystone species and understanding their ecological functions.
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Affiliation(s)
- Songnan Yang
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, People's Republic of China
| | - Huiping Zhou
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, People's Republic of China.
| | - Zhongzheng Pang
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, People's Republic of China
| | - Yiqun Wang
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, People's Republic of China
| | - Jianying Chao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, People's Republic of China.
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4
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Bergmann L, Balzer Le S, Hageskal G, Preuss L, Han Y, Astafyeva Y, Loevenich S, Emmann S, Perez-Garcia P, Indenbirken D, Katzowitsch E, Thümmler F, Alawi M, Wentzel A, Streit WR, Krohn I. New dienelactone hydrolase from microalgae bacterial community-Antibiofilm activity against fish pathogens and potential applications for aquaculture. Sci Rep 2024; 14:377. [PMID: 38172513 PMCID: PMC10764354 DOI: 10.1038/s41598-023-50734-9] [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: 07/27/2023] [Accepted: 12/24/2023] [Indexed: 01/05/2024] Open
Abstract
Biofilms are resistant to many traditional antibiotics, which has led to search for new antimicrobials from different and unique sources. To harness the potential of aquatic microbial resources, we analyzed the meta-omics datasets of microalgae-bacteria communities and mined them for potential antimicrobial and quorum quenching enzymes. One of the most interesting candidates (Dlh3), a dienelactone hydrolase, is a α/β-protein with predicted eight α-helices and eight β-sheets. When it was applied to one of the major fish pathogens, Edwardsiella anguillarum, the biofilm development was reproducibly inhibited by up to 54.5%. The transcriptome dataset in presence of Dlh3 showed an upregulation in functions related to self-defense like active genes for export mechanisms and transport systems. The most interesting point regarding the biotechnological potential for aquaculture applications of Dlh3 are clear evidence of biofilm inhibition and that health and division of a relevant fish cell model (CHSE-214) was not impaired by the enzyme.
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Affiliation(s)
- Lutgardis Bergmann
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Simone Balzer Le
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Gunhild Hageskal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Lena Preuss
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yuchen Han
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yekaterina Astafyeva
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Simon Loevenich
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Sarah Emmann
- Molecular Microbiology, Institute for General Microbiology, Kiel University, Kiel, Germany
| | - Pablo Perez-Garcia
- Molecular Microbiology, Institute for General Microbiology, Kiel University, Kiel, Germany
| | | | - Elena Katzowitsch
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Fritz Thümmler
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Ines Krohn
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany.
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5
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Bucheli J, Cella H, Nader C, Oliveira CYB, Bastolla CLV, Lopes RG, Pereira GDV, Karam J, Derner RB. Bacterial assemblages structure in intensive cultivations of the microalga Tetradesmus obliquus. J Basic Microbiol 2023; 63:1440-1450. [PMID: 37596061 DOI: 10.1002/jobm.202300362] [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: 06/26/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/20/2023]
Abstract
The present study shows the characterization of the bacterial communities associated with different systems during the cultivation of the microalga Tetradesmus obliquus. For that, sequential cultivation was performed in three different systems: (1) Photobioreactor bench-scale; (2) flat-panel photobioreactor; and (3) thin-layer cascade. Cultures were monitored daily for growth parameters and biomass samples were collected for characterization of bacterial communities using metagenomic. A total of 195,177 reads were produced, resulting in the identification of 72 OTUs. In the grouping of bacterial communities, 3 phyla, 6 classes, 28 families, and 35 taxa were found. The bacteria Brevundimonas and Porphyrobacter had a higher relative abundance compared with other taxa found. These taxa were present in all cultivation systems forming a possible core community. Bacterial communities associated with different cultivation systems of the microalga T. obliquus showed an increase in taxa richness and diversity in the super-intensive and intensive systems.
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Affiliation(s)
- Jaimet Bucheli
- Laboratory of Algae Cultivation, Aquaculture Department, Center for Agrarian Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Herculano Cella
- Laboratory of Algae Cultivation, Aquaculture Department, Center for Agrarian Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Camila Nader
- Laboratory of Algae Cultivation, Aquaculture Department, Center for Agrarian Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Carlos Yure B Oliveira
- Laboratory of Phycology, Botany Department, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Camila Lisarb V Bastolla
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Rafael Garcia Lopes
- Laboratory of Algae Cultivation, Aquaculture Department, Center for Agrarian Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Gabriella do Vale Pereira
- Laboratory of Algae Cultivation, Aquaculture Department, Center for Agrarian Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - João Karam
- Laboratory of Algae Cultivation, Aquaculture Department, Center for Agrarian Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Roberto Bianchini Derner
- Laboratory of Algae Cultivation, Aquaculture Department, Center for Agrarian Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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6
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Pushpakumara BLDU, Tandon K, Willis A, Verbruggen H. The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis. MICROBIAL ECOLOGY 2023; 86:2032-2046. [PMID: 37002423 PMCID: PMC10497448 DOI: 10.1007/s00248-023-02209-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.
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Affiliation(s)
| | - Kshitij Tandon
- School of Biosciences, University of Melbourne, Victoria, 3010, Australia
| | - Anusuya Willis
- Australian National Algae Culture Collection, CSIRO, Tasmania, 7000, Victoria, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Victoria, 3010, Australia
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7
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Vale F, Sousa CA, Sousa H, Simões LC, McBain AJ, Simões M. Bacteria and microalgae associations in periphyton-mechanisms and biotechnological opportunities. FEMS Microbiol Rev 2023; 47:fuad047. [PMID: 37586879 DOI: 10.1093/femsre/fuad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
Phototrophic and heterotrophic microorganisms coexist in complex and dynamic structures called periphyton. These structures shape the biogeochemistry and biodiversity of aquatic ecosystems. In particular, microalgae-bacteria interactions are a prominent focus of study by microbial ecologists and can provide biotechnological opportunities for numerous applications (i.e. microalgal bloom control, aquaculture, biorefinery, and wastewater bioremediation). In this review, we analyze the species dynamics (i.e. periphyton formation and factors determining the prevalence of one species over another), coexisting communities, exchange of resources, and communication mechanisms of periphytic microalgae and bacteria. We extend periphyton mathematical modelling as a tool to comprehend complex interactions. This review is expected to boost the applicability of microalgae-bacteria consortia, by drawing out knowledge from natural periphyton.
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Affiliation(s)
- Francisca Vale
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Cátia A Sousa
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Henrique Sousa
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Lúcia C Simões
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory in Biotechnology, Bioengineering and Microelectromechanical Systems, Braga/Guimarães, Portugal
| | - Andrew J McBain
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, United Kingdom
| | - Manuel Simões
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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8
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Molina-Aulestia DT, de Carvalho JC, de Melo Pereira GV, da Silva Vale A, de Carvalho DP, Soccol VT, Soccol CR. Fine resolution analysis of bacterial communities associated with Neochloris oleoabundans culture and insights into terpenes as contamination control agents. World J Microbiol Biotechnol 2023; 39:192. [PMID: 37166608 DOI: 10.1007/s11274-023-03641-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023]
Abstract
Biological contamination is one of the main bottlenecks in microalgae production, reducing quality and productivity and sometimes leading to the complete loss of the cultures. Selecting terpenes can be a pathway toward eco-friendly contamination control in microalgae cultures. This work evaluated the presence of bacterial contaminants in N. oleoabundans cultures through HTS and 16 S analysis and their susceptibility to six natural terpenes (α-pinene, β-pinene, limonene, trans-cinnamaldehyde, linalool, and eugenol). The principal phyla identified were Proteobacteria, Bacteroidetes, and Actinobacteria, and based on these data, 89 bacterial isolates of seven genera were obtained (36 Aureimonas sp., 27 Microbacterium sp., 5 Pseudomonas sp., 9 Bacillus sp., 14 Shinella sp., 1 Brevundimonas sp., and 1 Exiguobacterium sp.) at 25ºC in the presence of light. It was possible to observe that Beta-pinene 50 mg L- 1 only inhibited Bacillus sp. In contrast, Alpha-pinene, Linalool, and Trans-cinnamaldehyde, at a concentration of 6.25 mg L- 1 efficiently inhibited most isolates. The inhibition percentages found were 79-99%.
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Affiliation(s)
| | - Júlio César de Carvalho
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, Curitiba, 81531-980, PR, Brazil.
| | | | - Alexander da Silva Vale
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, Curitiba, 81531-980, PR, Brazil
| | - Dão Pedro de Carvalho
- Federal Institute of Education, Science and Technology of Paraná (IFPR), Londrina, PR, Brazil
| | - Vanete Thomaz Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, Curitiba, 81531-980, PR, Brazil
| | - Carlos Ricardo Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, Curitiba, 81531-980, PR, Brazil
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9
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Pushpakumara BLDU, Tandon K, Willis A, Verbruggen H. Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks. Sci Rep 2023; 13:2743. [PMID: 36797257 PMCID: PMC9935533 DOI: 10.1038/s41598-023-27816-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 02/18/2023] Open
Abstract
Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.
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Affiliation(s)
| | - Kshitij Tandon
- School of Biosciences, University of Melbourne, Melbourne, VIC, Australia
| | - Anusuya Willis
- Australian National Algae Culture Collection, CSIRO, Hobart, TAS, 7000, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, VIC, Australia.
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10
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Macdonald JFH, Krohn I, Streit WR. Screening Metagenomes for Algae Cell Wall Carbohydrates Degrading Hydrolases in Enrichment Cultures. Methods Mol Biol 2023; 2555:125-137. [PMID: 36306083 DOI: 10.1007/978-1-0716-2795-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Sustainable use of natural products is one of the key challenges for the future. An increasing focus is on marine organic matter, mostly algae. New biotechnological tools for processing high amounts of micro- and macroalgae are necessary for efficient industrial degradation of marine matter. Secreted glycosyl hydrolases can be enriched and tested on the specific algae cell wall polymers of all algae groups (Rhodophyta; Phaeophyceae; Chlorophyta/Charophyta). Metagenomic analyses established new possibilities to screen algae-associated microbiomes for novel degrading enzymes in combination with sequence-based function prediction.
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Affiliation(s)
- Jascha F H Macdonald
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany.
| | - Ines Krohn
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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11
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Barnum TP, Coates JD. Chlorine redox chemistry is widespread in microbiology. THE ISME JOURNAL 2023; 17:70-83. [PMID: 36202926 PMCID: PMC9751292 DOI: 10.1038/s41396-022-01317-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/07/2022]
Abstract
Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (ClO2-) by converting it to chloride (Cl-) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species. Cld was abundant in metagenomes from various terrestrial habitats. About 5% of bacterial and archaeal genera contain a microorganism encoding Cld in its genome, and within some genera Cld is highly conserved. Cld has been subjected to extensive horizontal gene transfer. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (ClO4-) or chlorate (ClO3-), indicating that in situ (per)chlorate reduction does not only occur through specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.
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Affiliation(s)
- Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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12
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Synergy between microalgae and microbiome in polluted waters. Trends Microbiol 2023; 31:9-21. [PMID: 35985939 DOI: 10.1016/j.tim.2022.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
Abstract
Microalga-microbiome interactions are central to both health and disease of aquatic environments. Despite impressive advances in deciphering how microorganisms participate in and impact aquatic ecosystems, the evolution and ecological involvement of microalgae and the microbiome in polluted waters are typically studied independently. Here, the phycosphere (i.e., the consortia of microalgae and the related microbiome) is regarded as an independent and integrated life form, and we summarize the survival strategies exhibited by this symbiont when exposed to anthropogenic pollution. We highlight the cellular strategies and discuss the modulation at the transcriptional and population levels, which reciprocally alters community structure or genome composition for medium-term acclimation or long-term adaptation. We propose a 'PollutantBiome' concept to help the understanding of microalga-microbiome interactions and development of beneficial microbial synthetic communities for pollutant remediation.
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13
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Emiliania huxleyi-Bacteria Interactions under Increasing CO 2 Concentrations. Microorganisms 2022; 10:microorganisms10122461. [PMID: 36557715 PMCID: PMC9786219 DOI: 10.3390/microorganisms10122461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
The interactions established between marine microbes, namely phytoplankton-bacteria, are key to the balance of organic matter export to depth and recycling in the surface ocean. Still, their role in the response of phytoplankton to rising CO2 concentrations is poorly understood. Here, we show that the response of the cosmopolitan Emiliania huxleyi (E. huxleyi) to increasing CO2 is affected by the coexistence with bacteria. Specifically, decreased growth rate of E. huxleyi at enhanced CO2 concentrations was amplified in the bloom phase (potentially also related to nutrient concentrations) and with the coexistence with Idiomarina abyssalis (I. abyssalis) and Brachybacterium sp. In addition, enhanced CO2 concentrations also affected E. huxleyi's cellular content estimates, increasing organic and decreasing inorganic carbon, in the presence of I. abyssalis, but not Brachybacterium sp. At the same time, the bacterial isolates only survived in coexistence with E. huxleyi, but exclusively I. abyssalis at present CO2 concentrations. Bacterial species or group-specific responses to the projected CO2 rise, together with the concomitant effect on E. huxleyi, might impact the balance between the microbial loop and the export of organic matter, with consequences for atmospheric carbon dioxide.
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14
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Astafyeva Y, Gurschke M, Streit WR, Krohn I. Interplay between the microalgae Micrasterias radians and its symbiont Dyadobacter sp. HH091. Front Microbiol 2022; 13:1006609. [PMID: 36312980 PMCID: PMC9606717 DOI: 10.3389/fmicb.2022.1006609] [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: 07/29/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Based on previous research, related to detailed insight into mutualistic collaboration of microalga and its microbiome, we established an artificial plant-bacteria system of the microalga Micrasterias radians MZCH 672 and the bacterial isolate Dyadobacter sp. HH091. The bacteria, affiliated with the phylum Bacteroidota, strongly stimulated growth of the microalga when it was added to axenic algal cultures. For further advances, we studied the isolate HH091 and its interaction with the microalga M. radians using transcriptome and extensive genome analyses. The genome of HH091 contains predicted polysaccharide utilizing gene clusters co-working with the type IX secretion system (T9SS) and conceivably involved in the algae-bacteria liaison. Here, we focus on characterizing the mechanism of T9SS, implementing the attachment and invasion of microalga by Dyadobacter sp. HH091. Omics analysis exposed T9SS genes: gldK, gldL, gldM, gldN, sprA, sprE, sprF, sprT, porU and porV. Besides, gld genes not considered as the T9SS components but required for gliding motility and protein secretion (gldA, gldB, gldD, gldF, gldG, gldH, gldI, gldJ), were also identified at this analysis. A first model of T9SS apparatus of Dyadobacter was proposed in a course of this research. Using the combination of fluorescence labeling of Dyadobacter sp. HH091, we examined the bacterial colonisation and penetration into the cell wall of the algal host M. radians MZCH 672.
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15
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Astafyeva Y, Gurschke M, Qi M, Bergmann L, Indenbirken D, de Grahl I, Katzowitsch E, Reumann S, Hanelt D, Alawi M, Streit WR, Krohn I. Microalgae and Bacteria Interaction-Evidence for Division of Diligence in the Alga Microbiota. Microbiol Spectr 2022; 10:e0063322. [PMID: 35913168 PMCID: PMC9430724 DOI: 10.1128/spectrum.00633-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/07/2022] [Indexed: 11/20/2022] Open
Abstract
Microalgae are one of the most dominant forms of life on earth that is tightly associated with a distinct and specialized microbiota. We have previously shown that the microbiota of Scenedesmus quadricauda harbors less than 10 distinct microbial species. Here, we provide evidence that dominant species are affiliated with the genera of Variovorax, Porphyrobacter, and Dyadobacter. Experimental and transcriptome-based evidence implies that within this multispecies interaction, Dyadobacter is a key to alga growth and fitness and is highly adapted to live in the phycosphere. While presumably under light conditions the alga provides the energy source to the bacteria, Dyadobacter produces and releases mainly a large variety of polysaccharides modifying enzymes. This is coherent with high-level expression of the T9SS in alga cocultures. The transcriptome data further imply that quorum-quenching proteins (QQ) and biosynthesis of vitamins B1, B2, B5, B6, and B9 are expressed by Dyadobacter at high levels in comparison to Variovorax and Porphyrobacter. Notably, Dyadobacter produces a significant number of leucine-rich repeat (LRR) proteins and enzymes involved in bacterial reactive oxygen species (ROS) tolerance. Complementary to this, Variovorax expresses the genes of the biosynthesis of vitamins B2, B5, B6, B7, B9, and B12, and Porphyrobacter is specialized in the production of vitamins B2 and B6. Thus, the shared currency between partners are vitamins, microalgae growth-promoting substances, and dissolved carbon. This work significantly enlarges our knowledge on alga-bacteria interaction and demonstrates physiological investigations of microalgae and associated bacteria, using microscopy observations, photosynthetic activity measurements, and flow cytometry. IMPORTANCE The current study gives a detailed insight into mutualistic collaboration of microalgae and bacteria, including the involvement of competitive interplay between bacteria. We provide experimental evidence that Gram-negative bacteria belonging to the Dyadobacter, Porphyrobacter, and Variovorax are the key players in a Scenedesmus quadricauda alga-bacteria interaction. We impart strong evidence that Dyadobacter produces and releases polysaccharides degradation enzymes and leucine-rich repeat proteins; Variovorax supplies the consortium with auxins and vitamin B12, while Porphyrobacter produces a broad spectrum of B vitamins. We show not only that the microalgae collaborate with the bacteria and vice versa but also that the bacteria interact with each other via quorum-sensing and secretion system mechanisms. The shared currency between partners appears to be vitamins, microalgae growth-promoting substances, and dissolved carbon.
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Affiliation(s)
- Yekaterina Astafyeva
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Marno Gurschke
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Minyue Qi
- University Medical Center Hamburg-Eppendorf, Bioinformatics Core, Hamburg, Germany
| | - Lutgardis Bergmann
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Imke de Grahl
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Plant Biochemistry and Infection Biology, Hamburg, Germany
| | - Elena Katzowitsch
- University of Würzburg, Core Unit Systems Medicine, Würzburg, Germany
| | - Sigrun Reumann
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Plant Biochemistry and Infection Biology, Hamburg, Germany
| | - Dieter Hanelt
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Aquatic Ecophysiology and Phycology, Hamburg, Germany
| | - Malik Alawi
- University Medical Center Hamburg-Eppendorf, Bioinformatics Core, Hamburg, Germany
| | - Wolfgang R. Streit
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Ines Krohn
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
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16
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Sethuraman A, Stancheva R, Sanders C, Caceres L, Castro D, Hausknecht-Buss H, Henry S, Johansen H, Kasler A, Lastor S, Massaro I, Mekuria I, Moron-Solano A, Read N, Vengerova G, Zhang A, Zhang X, Read B. Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California. G3 GENES|GENOMES|GENETICS 2022; 12:6593491. [PMID: 35639673 PMCID: PMC9258536 DOI: 10.1093/g3journal/jkac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 04/28/2022] [Indexed: 11/30/2022]
Abstract
Here, we report the discovery of a novel Sediminibacterium sequenced from laboratory cultures of freshwater stream cyanobacteria from sites in Southern California, grown in BG11 medium. Our genome-wide analyses reveal a highly contiguous and complete genome (97% BUSCO) that is placed within sediminibacterial clades in phylogenomic analyses. Functional annotation indicates the presence of genes that could be involved in mutualistic/commensal relationship with associated cyanobacterial hosts.
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Affiliation(s)
- Arun Sethuraman
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
- Department of Biological Sciences, California State University San Marcos , San Marcos, California USA 92096, USA
| | - Rosalina Stancheva
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
| | - Ciara Sanders
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
| | - Lakme Caceres
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
- Palomar College , San Marcos, CA 92069, USA
- University of San Diego , San Diego, CA 92110, USA
| | - David Castro
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
| | - Hannah Hausknecht-Buss
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
- Scripps College , Claremont, CA 91711, USA
| | - Simone Henry
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
- Scripps College , Claremont, CA 91711, USA
| | - Haven Johansen
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
- Western Washington University , Bellingham, WA 98225, USA
| | - Antolette Kasler
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
| | - Sandy Lastor
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
- Bay Path University , Long Meadow, MA 01106, USA
| | - Isabelle Massaro
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
| | - Immanuel Mekuria
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
| | - Andrea Moron-Solano
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
- University of California , Davis, Davis, CA 95616, USA
| | - Niki Read
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
| | - Gretchen Vengerova
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
- City College of San Francisco , San Francisco, CA 94112, USA
| | - Andrew Zhang
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
- Indiana University Bloomington , Bloomington, IN 47405, USA
| | - Xiaoyu Zhang
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
| | - Betsy Read
- Department of Biology, San Diego State University , San Diego, CA 92182, USA
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17
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Sadiq FA, Hansen MF, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, Zhang H. Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature. FEMS Microbiol Rev 2022; 46:6595875. [PMID: 35640890 DOI: 10.1093/femsre/fuac024] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022] Open
Abstract
The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.
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Affiliation(s)
- Faizan Ahmed Sadiq
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium
| | - Mads Frederik Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium.,Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, Private Bag, 11222, Palmerston North, New Zealand
| | - Wenwei Lu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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18
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Krohn I, Menanteau‐Ledouble S, Hageskal G, Astafyeva Y, Jouannais P, Nielsen JL, Pizzol M, Wentzel A, Streit WR. Health benefits of microalgae and their microbiomes. Microb Biotechnol 2022; 15:1966-1983. [PMID: 35644921 PMCID: PMC9249335 DOI: 10.1111/1751-7915.14082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/16/2022] Open
Abstract
Microalgae comprise a phylogenetically very diverse group of photosynthetic unicellular pro‐ and eukaryotic organisms growing in marine and other aquatic environments. While they are well explored for the generation of biofuels, their potential as a source of antimicrobial and prebiotic substances have recently received increasing interest. Within this framework, microalgae may offer solutions to the societal challenge we face, concerning the lack of antibiotics treating the growing level of antimicrobial resistant bacteria and fungi in clinical settings. While the vast majority of microalgae and their associated microbiota remain unstudied, they may be a fascinating and rewarding source for novel and more sustainable antimicrobials and alternative molecules and compounds. In this review, we present an overview of the current knowledge on health benefits of microalgae and their associated microbiota. Finally, we describe remaining issues and limitation, and suggest several promising research potentials that should be given attention.
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Affiliation(s)
- Ines Krohn
- Department of Microbiology and Biotechnology University of Hamburg Hamburg Germany
| | | | - Gunhild Hageskal
- Department of Biotechnology and Nanomedicine SINTEF Industry Trondheim Norway
| | - Yekaterina Astafyeva
- Department of Microbiology and Biotechnology University of Hamburg Hamburg Germany
| | | | - Jeppe Lund Nielsen
- Department for Chemistry and Bioscience Aalborg University Aalborg Denmark
| | - Massimo Pizzol
- Department of Planning Aalborg University Aalborg Denmark
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine SINTEF Industry Trondheim Norway
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology University of Hamburg Hamburg Germany
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19
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Krimech A, Helamieh M, Wulf M, Krohn I, Riebesell U, Cherifi O, Mandi L, Kerner M. Differences in adaptation to light and temperature extremes of Chlorella sorokiniana strains isolated from a wastewater lagoon. BIORESOURCE TECHNOLOGY 2022; 350:126931. [PMID: 35247554 DOI: 10.1016/j.biortech.2022.126931] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Presently, two Chlorella sorokiniana strains sampled during summer (CS-S) and winter (CS-W) from a maturation pond and isolated by dominance were studied on their behavior on temperature and light extremes in batch experiments. Although both strains showed no differences in their tolerance of temperatures up to 45 °C, the growth rates, pigment contents and fatty acid compositions in response to PAR at 700 and 1,500 µmol m-2sec-1 differed. CS-W was less affected by photoinhibition and maintained constantly high growth rates. High radiation resulted in both strains in an equivalent decrease of chlorophyll a and accessory pigments indicating that the latter did not function as a light filter. PUFAS (18:3 and 16:3) increased in CS-W at high radiation by > 60% and decreased in CS-S by 8 %. Results indicate that CS-W is highly favorable for mass cultivation particularly in outdoors, in which diurnal variations of solar radiation occur.
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Affiliation(s)
- Aafaf Krimech
- National Center for Studies and Research on Water and Energy, Cadi Ayyad University, Marrakech, Morocco; Laboratory of Water, Biodiversity, and Climate Change, Cadi Ayyad University, Marrakech, Morocco
| | - Mark Helamieh
- SSC Strategic Science Consult GmbH, Hamburg, Germany
| | - Melina Wulf
- SSC Strategic Science Consult GmbH, Hamburg, Germany
| | - Ines Krohn
- Universität Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Ulf Riebesell
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Biological Oceanography, Kiel, Germany
| | - Ouafa Cherifi
- National Center for Studies and Research on Water and Energy, Cadi Ayyad University, Marrakech, Morocco; Laboratory of Water, Biodiversity, and Climate Change, Cadi Ayyad University, Marrakech, Morocco
| | - Laila Mandi
- National Center for Studies and Research on Water and Energy, Cadi Ayyad University, Marrakech, Morocco; Laboratory of Water, Biodiversity, and Climate Change, Cadi Ayyad University, Marrakech, Morocco
| | - Martin Kerner
- SSC Strategic Science Consult GmbH, Hamburg, Germany.
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20
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Characterization of two microalgae consortia grown in industrial wastewater for biomass valorization. ALGAL RES 2022. [DOI: 10.1016/j.algal.2021.102628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Lian J, Steinert G, de Vree J, Meijer S, Heryanto C, Bosma R, Wijffels RH, Barbosa MJ, Smidt H, Sipkema D. Bacterial diversity in different outdoor pilot plant photobioreactor types during production of the microalga Nannochloropsis sp. CCAP211/78. Appl Microbiol Biotechnol 2022; 106:2235-2248. [PMID: 35166894 PMCID: PMC8930801 DOI: 10.1007/s00253-022-11815-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/22/2021] [Accepted: 01/29/2022] [Indexed: 11/25/2022]
Abstract
As large-scale outdoor production cannot be done in complete containment, cultures are (more) open for bacteria, which may affect the productivity and stability of the algae production process. We investigated the bacterial diversity in two indoor reactors and four pilot-scale outdoor reactors for the production of Nannochloropsis sp. CCAP211/78 spanning four months of operation from July to October. Illumina sequencing of 16S rRNA gene amplicons demonstrated that a wide variety of bacteria were present in all reactor types, with predominance of Bacteroidetes and Alphaproteobacteria. Bacterial communities were significantly different between all reactor types (except between the horizontal tubular reactor and the vertical tubular reactor) and also between runs in each reactor. Bacteria common to the majority of samples included one member of the Saprospiraceae family and one of the NS11-12_marine group (both Bacteroidetes). Hierarchical clustering analysis revealed two phases during the cultivation period separated by a major shift in bacterial community composition in the horizontal tubular reactor, the vertical tubular reactor and the raceway pond with a strong decrease of the Saprospiraceae and NS11-12_marine group that initially dominated the bacterial communities. Furthermore, we observed a less consistent pattern of bacterial taxa appearing in different reactors and runs, most of which belonging to the classes Deltaproteobacteria and Flavobacteriia. In addition, canonical correspondence analysis showed that the bacterial community composition was significantly correlated with the nitrate concentration. This study contributes to our understanding of bacterial diversity and composition in different types of outdoor reactors exposed to a range of dynamic biotic and abiotic factors. Key points • Reactor types had significantly different bacterial communities except HT and VT • The inoculum source and physiochemical factors together affect bacterial community • The bacterial family Saprospiraceae is positively correlated to microalgal growth.
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Affiliation(s)
- Jie Lian
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jeroen de Vree
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Sven Meijer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christa Heryanto
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Rouke Bosma
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, N8049, Bodø, Norway
| | - Maria J Barbosa
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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22
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Madhubalaji CK, Ravi S, Mudliar SN. Unraveling of Chlorella-associated bacterial load, diversity, and their imputed functions at high- and low-yield conditions through metagenome sequencing. JOURNAL OF PHYCOLOGY 2022; 58:133-145. [PMID: 34850388 DOI: 10.1111/jpy.13225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/04/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Chlorella-associated bacteria can have a significant influence on facilitating higher Chlorella biomass yield due to their symbiotic relationship. In this study, non-axenic Chlorella was cultivated in an airlift photobioreactor at high and low-yield conditions. The associated bacterial diversity was analyzed using 16S rRNA metagenome sequencing. At high-yield conditions, the bacterial load was observed in the range of 108 -1010 CFU · mL-1 , whereas at low-yield conditions, bacteria were more dominant and observed in the range of 1014 -1015 CFU · mL-1 . The majority of the bacterial species associated with Chlorella at high-yield conditions belongs to Proteobacteria and Bacteroidetes. Further, Bacteroidetes levels were decreased at low-yield conditions and were highly diversified with Planctomycetes, Firmicutes, and 18 others. Predicted functional genes indicated that Chlorella-associated bacteria have the enzymes involved in the metabolism and biosynthesis of B-complex vitamins (i.e., vitamin B12 , thiamin, biotin, pyridoxine, and riboflavin). A critical evaluation revealed that vitamin biosynthesis genes were more abundant at low-yield conditions; however, vitamin B12 transport genes (B12 transport ATP-binding protein, B12 substrate-binding transportation, and B12 permease protein) were less abundant, indicating even though vitamins production occurs, but their availability to Chlorella was limited due to the lack of vitamin transport genes. Further, at high yield, Chlorella-associated bacteria enabled higher growth by supplementing the vitamins. In contrast, at low-yield condition-an increased bacterial load, diversity, and limited vitamin transport functional genes affected the Chlorella yield. It can be inferred that Chlorella yield was significantly affected by three factors: associated bacterial load, diversity, and transport functional genes of vitamins.
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Affiliation(s)
- Chegu Krishnamurthi Madhubalaji
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysuru, 570020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarada Ravi
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysuru, 570020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sandeep N Mudliar
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysuru, 570020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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23
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Arbab S, Ullah H, Khan MIU, Khattak MNK, Zhang J, Li K, Hassan IU. Diversity and distribution of thermophilic microorganisms and their applications in biotechnology. J Basic Microbiol 2021; 62:95-108. [PMID: 34878177 DOI: 10.1002/jobm.202100529] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/16/2021] [Accepted: 11/27/2021] [Indexed: 11/07/2022]
Abstract
Hot springs ecosystem is the most ancient continuously inhabited ecosystem on earth which harbors diverse thermophilic bacteria and archaea distributed worldwide. Life in extreme environments is very challenging so there is a great potential biological dark matter and their adaptation to harsh environments eventually producing thermostable enzymes which are very vital for the welfare of mankind. There is an enormous need for a new generation of stable enzymes that can endure harsh conditions in industrial processes and can either substitute or complement conventional chemical processes. Here, we review at the variety and distribution of thermophilic microbes, as well as the different thermostable enzymes that help them survive at high temperatures, such as proteases, amylases, lipases, cellulases, pullulanase, xylanases, and DNA polymerases, as well as their special properties, such as high-temperature stability. We have documented the novel isolated thermophilic and hyperthermophilic microorganisms, as well as the discovery of their enzymes, demonstrating their immense potential in the scientific community and in industry.
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Affiliation(s)
- Safia Arbab
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China.,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hanif Ullah
- West China School of Nursing, Sichuan University, Chengdu, China
| | - Muhammad I U Khan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Muhammad N K Khattak
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Jiyu Zhang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China.,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ka Li
- West China School of Nursing, Sichuan University, Chengdu, China
| | - Inam Ul Hassan
- Department of Microbiology, Hazara University, Manshera, Pakistan
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24
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Krohn I, Bergmann L, Qi M, Indenbirken D, Han Y, Perez-Garcia P, Katzowitsch E, Hägele B, Lübcke T, Siry C, Riemann R, Alawi M, Streit WR. Deep (Meta)genomics and (Meta)transcriptome Analyses of Fungal and Bacteria Consortia From Aircraft Tanks and Kerosene Identify Key Genes in Fuel and Tank Corrosion. Front Microbiol 2021; 12:722259. [PMID: 34675897 PMCID: PMC8525681 DOI: 10.3389/fmicb.2021.722259] [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: 06/08/2021] [Accepted: 08/19/2021] [Indexed: 11/29/2022] Open
Abstract
Microbial contamination of fuels, associated with a wide variety of bacteria and fungi, leads to decreased product quality and can compromise equipment performance by biofouling or microbiologically influenced corrosion. Detection and quantification of microorganisms are critical in monitoring fuel systems for an early detection of microbial contaminations. To address these challenges, we have analyzed six metagenomes, one transcriptome, and more than 1,200 fluid and swab samples taken from fuel tanks or kerosene. Our deep metagenome sequencing and binning approaches in combination with RNA-seq data and qPCR methods implied a metabolic symbiosis between fungi and bacteria. The most abundant bacteria were affiliated with α-, β-, and γ-Proteobacteria and the filamentous fungi Amorphotheca. We identified a high number of genes, which are related to kerosene degradation and biofilm formation. Surprisingly, a large number of genes coded enzymes involved in polymer degradation and potential bio-corrosion processes. Thereby, the transcriptionally most active microorganisms were affiliated with the genera Methylobacteria, Pseudomonas, Kocuria, Amorpotheka, Aspergillus, Fusarium, and Penicillium. Many not yet cultured bacteria and fungi appeared to contribute to the biofilm transcriptional activities. The largest numbers of transcripts were observed for dehydrogenase, oxygenase, and exopolysaccharide production, attachment and pili/flagella-associated proteins, efflux pumps, and secretion systems as well as lipase and esterase activity.
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Affiliation(s)
- Ines Krohn
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Lutgardis Bergmann
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Minyue Qi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniela Indenbirken
- Virus Genomics, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Yuchen Han
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Pablo Perez-Garcia
- Institute of General Microbiology, Molecular Microbiology, Kiel University, Kiel, Germany
| | - Elena Katzowitsch
- Faculty of Medicine, Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | | | - Tim Lübcke
- T/TQ-MN, Lufthansa Technik AG HAM, Hamburg, Germany
| | | | - Ralf Riemann
- T/TQ-MN, Lufthansa Technik AG HAM, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
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25
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Abstract
Microalgal cultures are often maintained in xenic conditions, i.e., with associated bacteria, and many studies indicate that these communities both are complex and have significant impacts on the physiology of the target photoautotroph. Here, we investigated the structure and stability of microbiomes associated with a diverse sampling of diatoms during long-term maintenance in serial batch culture. We found that, counter to our initial expectation, evenness diversity increased with time since cultivation, driven by a decrease in dominance by the most abundant taxa in each culture. We also found that the site from which and time at which a culture was initially collected had a stronger impact on microbiome structure than the diatom species; however, some bacterial taxa were commonly present in most cultures despite having widely geographically separated collection sites. Our results support the conclusion that stochastic initial conditions (i.e., the local microbial community at the collection site) are important for the long-term structure of these microbiomes, but deterministic forces such as negative frequency dependence and natural selection exerted by the diatom are also at work. IMPORTANCE Natural microbial communities are extremely complex, with many more species coexisting in the same place than there are different resources to support them. Understanding the forces that allow this high level of diversity has been a central focus of ecological and evolutionary theory for many decades. Here, we used stock cultures of diatoms, which were maintained for years in continuous growth alongside populations of bacteria, as proxies for natural communities. We show that the bacterial communities remained relatively stable for years, and there is evidence that ecological forces worked to stabilize coexistence instead of favoring competition and exclusion. We also show evidence that, despite some important regional differences in bacterial communities, there was a globally present core microbiome potentially selected for in these diatom cultures. Understanding interactions between bacteria and diatoms is important both for basic ecological science and for practical science, such as industrial biofuel production.
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26
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Mattsson L, Sörenson E, Capo E, Farnelid HM, Hirwa M, Olofsson M, Svensson F, Lindehoff E, Legrand C. Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System. Front Bioeng Biotechnol 2021; 9:651895. [PMID: 33968914 PMCID: PMC8100445 DOI: 10.3389/fbioe.2021.651895] [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: 01/11/2021] [Accepted: 03/23/2021] [Indexed: 01/22/2023] Open
Abstract
Functionally uniform monocultures have remained the paradigm in microalgal cultivation despite the apparent challenges to avoid invasions by other microorganisms. A mixed microbial consortium approach has the potential to optimize and maintain biomass production despite of seasonal changes and to be more resilient toward contaminations. Here we present a 3-year outdoor production of mixed consortia of locally adapted microalgae and bacteria in cold temperate latitude. Microalgal consortia were cultivated in flat panel photobioreactors using brackish Baltic Sea water and CO2 from a cement factory (Degerhamn, Cementa AB, Heidelberg Cement Group) as a sustainable CO2 source. To evaluate the ability of the microbial consortia to maintain stable biomass production while exposed to seasonal changes in both light and temperature, we tracked changes in the microbial community using molecular methods (16S and 18S rDNA amplicon sequencing) and monitored the biomass production and quality (lipid, protein, and carbohydrate content) over 3 years. Despite changes in environmental conditions, the mixed consortia maintained stable biomass production by alternating between two different predominant green microalgae (Monoraphidium and Mychonastes) with complementary tolerance to temperature. The bacterial population was few taxa co-occured over time and the composition did not have any connection to the shifts in microalgal taxa. We propose that a locally adapted and mixed microalgal consortia, with complementary traits, can be useful for optimizing yield of commercial scale microalgal cultivation.
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Affiliation(s)
- Lina Mattsson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eva Sörenson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eric Capo
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Hanna Maria Farnelid
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Maurice Hirwa
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.,Axis Communications, Lund, Sweden
| | | | - Fredrik Svensson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Elin Lindehoff
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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27
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Toward the Enhancement of Microalgal Metabolite Production through Microalgae-Bacteria Consortia. BIOLOGY 2021; 10:biology10040282. [PMID: 33915681 PMCID: PMC8065533 DOI: 10.3390/biology10040282] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
Abstract
Engineered mutualistic consortia of microalgae and bacteria may be a means of assembling a novel combination of metabolic capabilities with potential biotechnological advantages. Microalgae are promising organisms for the sustainable production of metabolites of commercial interest, such as lipids, carbohydrates, pigments, and proteins. Several studies reveal that microalgae growth and cellular storage of these metabolites can be enhanced significantly by co-cultivation with growth-promoting bacteria. This review summarizes the state of the art of microalgae-bacteria consortia for the production of microalgal metabolites. We discuss the current knowledge on microalgae-bacteria mutualism and the mechanisms of bacteria to enhance microalgae metabolism. Furthermore, the potential routes for a microalgae-bacteria biorefinery are outlined in an attempt to overcome the economic failures and negative energy balances of the existing production processes.
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28
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Menaa F, Wijesinghe PAUI, Thiripuranathar G, Uzair B, Iqbal H, Khan BA, Menaa B. Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions. Mar Drugs 2020; 18:md18120641. [PMID: 33327517 PMCID: PMC7764995 DOI: 10.3390/md18120641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023] Open
Abstract
Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)–microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.
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Affiliation(s)
- Farid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
- Correspondence: or
| | - P. A. U. I. Wijesinghe
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Gobika Thiripuranathar
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan;
| | - Haroon Iqbal
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China;
| | - Barkat Ali Khan
- Department of Pharmacy, Gomal University, Dera Ismail Khan 29050, Pakistan;
| | - Bouzid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
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29
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Kumar Awasthi M, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E, Liu T, Kumar S, Pandey A, Singh L, Zhang Z. Metagenomics for taxonomy profiling: tools and approaches. Bioengineered 2020; 11:356-374. [PMID: 32149573 PMCID: PMC7161568 DOI: 10.1080/21655979.2020.1736238] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/25/2022] Open
Abstract
The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - B. Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, South Korea
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongyu Chen
- Institute of Biology, Freie Universität Berlin Altensteinstr, Berlin, Germany
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - Ekta Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
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30
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Chernikova TN, Bargiela R, Toshchakov SV, Shivaraman V, Lunev EA, Yakimov MM, Thomas DN, Golyshin PN. Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata. Front Microbiol 2020; 11:572931. [PMID: 33193176 PMCID: PMC7655873 DOI: 10.3389/fmicb.2020.572931] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/01/2020] [Indexed: 12/26/2022] Open
Abstract
Marine hydrocarbon-degrading bacteria play an important role in natural petroleum biodegradation processes and were initially associated with man-made oil spills or natural seeps. There is no full clarity though on what, in the absence of petroleum, their natural niches are. Few studies pointed at some marine microalgae that produce oleophilic compounds (alkanes, long-chain fatty acids, and alcohols) as potential natural hosts of these bacteria. We established Dansk crude oil-based enrichment cultures with photobioreactor-grown marine microalgae cultures Pavlova lutheri and Nannochloropsis oculata and analyzed the microbial succession using cultivation and SSU (16S) rRNA amplicon sequencing. We found that petroleum enforced a strong selection for members of Alpha- and Gamma-proteobacteria in both enrichment cultures with the prevalence of Alcanivorax and Marinobacter spp., well-known hydrocarbonoclastic bacteria. In total, 48 non-redundant bacterial strains were isolated and identified to represent genera Alcanivorax, Marinobacter, Thalassospira, Hyphomonas, Halomonas, Marinovum, Roseovarius, and Oleibacter, which were abundant in sequencing reads in both crude oil enrichments. Our assessment of public databases demonstrated some overlaps of geographical sites of isolation of Nannochloropsis and Pavlova with places of molecular detection and isolation of Alcanivorax and Marinobacter spp. Our study suggests that these globally important hydrocarbon-degrading bacteria are associated with P. lutheri and N. oculata.
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Affiliation(s)
- Tatyana N Chernikova
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,CEB-Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | | | | | - Evgenii A Lunev
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Michail M Yakimov
- Institute for Marine Biological Resources and Biotechnology of the National Research Council, IRBIM-CNR, Messina, Italy
| | - David N Thomas
- School of Ocean Sciences, Bangor University, Menai Bridge, United Kingdom
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,CEB-Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
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31
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Oriano M, Zorzetto L, Guagliano G, Bertoglio F, van Uden S, Visai L, Petrini P. The Open Challenge of in vitro Modeling Complex and Multi-Microbial Communities in Three-Dimensional Niches. Front Bioeng Biotechnol 2020; 8:539319. [PMID: 33195112 PMCID: PMC7606986 DOI: 10.3389/fbioe.2020.539319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 09/28/2020] [Indexed: 12/03/2022] Open
Abstract
The comprehension of the underlying mechanisms of the interactions within microbial communities represents a major challenge to be faced to control their outcome. Joint efforts of in vitro, in vivo and ecological models are crucial to controlling human health, including chronic infections. In a broader perspective, considering that polymicrobial communities are ubiquitous in nature, the understanding of these mechanisms is the groundwork to control and modulate bacterial response to any environmental condition. The reduction of the complex nature of communities of microorganisms to a single bacterial strain could not suffice to recapitulate the in vivo situation observed in mammals. Furthermore, some bacteria can adapt to various physiological or arduous environments embedding themselves in three-dimensional matrices, secluding from the external environment. Considering the increasing awareness that dynamic complex and dynamic population of microorganisms (microbiota), inhabiting different apparatuses, regulate different health states and protect against pathogen infections in a fragile and dynamic equilibrium, we underline the need to produce models to mimic the three-dimensional niches in which bacteria, and microorganisms in general, self-organize within a microbial consortium, strive and compete. This review mainly focuses, as a case study, to lung pathology-related dysbiosis and life-threatening diseases such as cystic fibrosis and bronchiectasis, where the co-presence of different bacteria and the altered 3D-environment, can be considered as worst-cases for chronic polymicrobial infections. We illustrate the state-of-art strategies used to study biofilms and bacterial niches in chronic infections, and multispecies ecological competition. Although far from the rendering of the 3D-environments and the polymicrobial nature of the infections, they represent the starting point to face their complexity. The increase of knowledge respect to the above aspects could positively affect the actual healthcare scenario. Indeed, infections are becoming a serious threat, due to the increasing bacterial resistance and the slow release of novel antibiotics on the market.
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Affiliation(s)
- Martina Oriano
- Molecular Medicine Department (DMM), Center for Health Technologies (CHT), UdR INSTM, University of Pavia, Pavia, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Zorzetto
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Giuseppe Guagliano
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta” and UdR INSTM Politecnico di Milano, Milan, Italy
| | - Federico Bertoglio
- Molecular Medicine Department (DMM), Center for Health Technologies (CHT), UdR INSTM, University of Pavia, Pavia, Italy
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatic, Department of Biotechnology, Braunschweig, Germany
| | - Sebastião van Uden
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta” and UdR INSTM Politecnico di Milano, Milan, Italy
| | - Livia Visai
- Molecular Medicine Department (DMM), Center for Health Technologies (CHT), UdR INSTM, University of Pavia, Pavia, Italy
- Department of Occupational Medicine, Toxicology and Environmental Risks, Istituti Clinici Scientifici (ICS) Maugeri, IRCCS, Pavia, Italy
| | - Paola Petrini
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta” and UdR INSTM Politecnico di Milano, Milan, Italy
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32
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Haberkorn I, Walser J, Helisch H, Böcker L, Belz S, Schuppler M, Fasoulas S, Mathys A. Characterization of Chlorella vulgaris (Trebouxiophyceae) associated microbial communities 1. JOURNAL OF PHYCOLOGY 2020; 56:1308-1322. [PMID: 32428976 PMCID: PMC7687158 DOI: 10.1111/jpy.13026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Microalgae exhibit extensive potential for counteracting imminent challenges in the nutraceutical, pharmaceutical, and biomaterial sectors, but lack economic viability. Biotechnological systems for contamination control could advance the economic viability of microalgal feedstock, but the selection of suitable strains that sustainably promote microalgal productivity remains challenging. In this study, total diversity in phototrophic Chlorella vulgaris cultures was assessed by amplicon sequencing comparing cultures subjected to five different cultivation conditions. Overall, 12 eukaryotic and 53 prokaryotic taxa were identified; Alphaproteobacteria (36.7%) dominated the prokaryotic and C. vulgaris (97.2%) the eukaryotic community. Despite altering cultivation conditions, 2 eukaryotic and 40 prokaryotic taxa remained stably associated with C. vulgaris; diversity between systems did not significantly differ (P > 0.05). Among those, 20 cultivable taxa were isolated and identified by 16S rDNA sequencing. Subsequently, controlled co-cultures were investigated showing stable associations of C. vulgaris with Sphingopyxis sp. and Pseudomonas sp.. Out-competition of C. vulgaris due to ammonium or phosphate limitation was not observed, despite significantly elevated growth of Sphingopyxis sp. and Tistrella sp.. (P < 0.05). Nevertheless, C. vulgaris growth was impaired by Tistrella sp.. Hence, the study provides a selection of stable indigenous prokaryotes and eukaryotes for artificially tailoring microbial biocenoses. Following a bottom-up approach, it provides a base for controlled co-cultures and thus the establishment of even more complex biocenoses using interkingdom assemblages. Such assemblages can benefit from functional richness for improved nutrient utilization, as well as bacterial load control, which can enhance microalgal feedstock production through improved culture stability and productivity.
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Affiliation(s)
- Iris Haberkorn
- Laboratory of Sustainable Food ProcessingInstitute of Food, Nutrition and HealthSwiss Federal Institute of Technology (ETH)Schmelzbergstrasse 98092ZürichSwitzerland
| | - Jean‐Claude Walser
- Genetic Diversity CentreSwiss Federal Institute of Technology (ETH)Universitätsstrasse 168092ZürichSwitzerland
| | - Harald Helisch
- Institute of Space System EngineeringUniversity of StuttgartPfaffenwaldring 2970569StuttgartGermany
| | - Lukas Böcker
- Laboratory of Sustainable Food ProcessingInstitute of Food, Nutrition and HealthSwiss Federal Institute of Technology (ETH)Schmelzbergstrasse 98092ZürichSwitzerland
| | - Stefan Belz
- Institute of Space System EngineeringUniversity of StuttgartPfaffenwaldring 2970569StuttgartGermany
| | - Markus Schuppler
- Laboratory of Food MicrobiologyInstitute of Food, Nutrition and HealthSwiss Federal Institute of Technology (ETH)Schmelzbergstrasse 78092ZürichSwitzerland
| | - Stefanos Fasoulas
- Institute of Space System EngineeringUniversity of StuttgartPfaffenwaldring 2970569StuttgartGermany
| | - Alexander Mathys
- Laboratory of Sustainable Food ProcessingInstitute of Food, Nutrition and HealthSwiss Federal Institute of Technology (ETH)Schmelzbergstrasse 98092ZürichSwitzerland
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Xia P, Yan D, Sun R, Song X, Lin T, Yi Y. Community composition and correlations between bacteria and algae within epiphytic biofilms on submerged macrophytes in a plateau lake, southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138398. [PMID: 32335447 DOI: 10.1016/j.scitotenv.2020.138398] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
Epiphytic biofilms are complex matrix-enclosed communities comprising large numbers of bacteria and algae, which play an important role in the biogeochemical cycles in aquatic systems. However, little is known about the correlations that occur between these communities or the relative impact of environmental factors on their composition. In this study, epiphytic biofilms on three different aquatic plants were sampled in a typical plateau lake (Caohai, southwest China) in July and November of 2018. Bacterial diversity was assessed using Miseq sequencing approaches and algal communities were assessed using light microscopy. Gammaproteobacteria (54.64%), Bacteroidetes (17.50%) and Firmicutes (13.99%) were the dominant bacterial taxa and Chlorophyta (47.62%), Bacillariophyta (28.57%) and Euglenophyta (19.05%) were the dominant algae. The alpha diversity values of the epiphytic bacterial and algal communities were greater during the macrophyte decline period (November) than during the growth period (July). Microbial community composition was significantly affected by abiotic factors (water temperature, NH4+, pH or TP) and biotic factors (algae or bacteria). Interestingly, in July and November, the epiphytic algal community dissimilarity was stronger than that observed for bacterial community dissimilarity, suggesting that bacterial community dissimilarity may increase more slowly with environmental change than algal community dissimilarity. Furthermore, association network analysis revealed complex correlations between algal biomass and bacteria phylotype, and that 67.83% of correlations were positive and 32.17% were negative. This may indicate that facilitative correlations between algae and bacteria are predominant in epiphytic biofilms. These results provide new information on algal-bacterial correlations as well as the possible mechanisms that drive variations in the microbial community in epiphytic biofilms in freshwater lakes.
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Affiliation(s)
- Pinhua Xia
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China
| | - Dingbo Yan
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China
| | - Rongguo Sun
- College of Chemistry and Material, Guizhou Normal University, Guiyang, PR China
| | - Xu Song
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China
| | - Tao Lin
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China
| | - Yin Yi
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China; The State Key Laboratory of Southwest Karst Mountain Biodiversity Conservation of Forestry and Grassland Administration, Guizhou Normal University, Guiyang, 550001, PR China.
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Gubelit YI, Grossart HP. New Methods, New Concepts: What Can Be Applied to Freshwater Periphyton? Front Microbiol 2020; 11:1275. [PMID: 32670226 PMCID: PMC7328189 DOI: 10.3389/fmicb.2020.01275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the "Black Queen Hypothesis") derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.
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Affiliation(s)
- Yulia I. Gubelit
- Laboratory of Freshwater Hydrobiology, Zoological Institute, Russian Academy of Science, Saint Petersburg, Russia
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute for Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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Draft Genome Sequence of the Green Alga Scenedesmus acuminatus SAG 38.81. Microbiol Resour Announc 2020; 9:9/24/e01278-19. [PMID: 32527781 PMCID: PMC7291106 DOI: 10.1128/mra.01278-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Scenedesmus acuminatus, also known as Tetradesmus acuminatus, is a promising green microalga for sustainable production of microalga products, including valuable compounds such as astaxanthin, β-carotene, and lutein, polysaccharides such as β-glucan, and polyunsaturated fatty acids. Here, we report the draft whole-genome sequence of Scenedesmus acuminatus SAG 38.81.
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Nitschke MR, Fidalgo C, Simões J, Brandão C, Alves A, Serôdio J, Frommlet JC. Symbiolite formation: a powerful in vitro model to untangle the role of bacterial communities in the photosynthesis-induced formation of microbialites. THE ISME JOURNAL 2020; 14:1533-1546. [PMID: 32203119 PMCID: PMC7242451 DOI: 10.1038/s41396-020-0629-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/21/2020] [Accepted: 02/28/2020] [Indexed: 11/09/2022]
Abstract
Microbially induced calcification is an ancient, community-driven mineralisation process that produces different types of microbialites. Symbiolites are photosynthesis-induced microbialites, formed by calcifying co-cultures of dinoflagellates from the family Symbiodiniaceae and bacteria. Symbiolites encase the calcifying community as endolithic cells, pointing at an autoendolithic niche of symbiotic dinoflagellates, and provide a rare opportunity to study the role of bacteria in bacterial-algal calcification, as symbiodiniacean cultures display either distinct symbiolite-producing (SP) or non-symbiolite-producing (NP) phenotypes. Using Illumina sequencing, we found that the bacterial communities of SP and NP cultures differed significantly in the relative abundance of 23 genera, 14 families, and 2 phyla. SP cultures were rich in biofilm digesters from the phylum Planctomycetes and their predicted metagenomes were enriched in orthologs related to biofilm formation. In contrast, NP cultures were dominated by biofilm digesters from the Bacteroidetes, and were inferred as enriched in proteases and nucleases. Functional assays confirmed the potential of co-cultures and bacterial isolates to produce biofilms and point at acidic polysaccharides as key stimulators for mineral precipitation. Hence, bacteria appear to influence symbiolite formation primarily through their biofilm-producing and modifying activity and we anticipate that symbiolite formation, as a low-complexity in vitro model, will significantly advance our understanding of photosynthesis-induced microbial calcification processes.
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Affiliation(s)
- Matthew R Nitschke
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Cátia Fidalgo
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - João Simões
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Cláudio Brandão
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Artur Alves
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - João Serôdio
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jörg C Frommlet
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.
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Maghembe R, Damian D, Makaranga A, Nyandoro SS, Lyantagaye SL, Kusari S, Hatti-Kaul R. Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae. Antibiotics (Basel) 2020; 9:antibiotics9050229. [PMID: 32375367 PMCID: PMC7277505 DOI: 10.3390/antibiotics9050229] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/10/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
"Omics" represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and 'blind'-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism's inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.
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Affiliation(s)
- Reuben Maghembe
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
| | - Donath Damian
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
| | - Abdalah Makaranga
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- International Center for Genetic Engineering and Biotechnology (ICGEB), Omics of Algae Group, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Stephen Samwel Nyandoro
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania;
| | - Sylvester Leonard Lyantagaye
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biochemistry, Mbeya College of Health and Allied Sciences, University of Dar es Salaam, P.O. Box 608, Mbeya, Tanzania
| | - Souvik Kusari
- Institute of Environmental Research (INFU), Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
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38
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Paquette AJ, Sharp CE, Schnurr PJ, Allen DG, Short SM, Espie GS. Dynamic changes in community composition of Scenedesmus-seeded artificial, engineered microalgal biofilms. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Rambo IM, Dombrowski N, Constant L, Erdner D, Baker BJ. Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus. Environ Microbiol 2019; 22:1764-1783. [PMID: 31775181 DOI: 10.1111/1462-2920.14878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 11/13/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.
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Affiliation(s)
- Ian M Rambo
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA.,NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Lauren Constant
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Deana Erdner
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
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40
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Characterisation of bacteria from the cultures of a Chlorella strain isolated from textile wastewater and their growth enhancing effects on the axenic cultures of Chlorella vulgaris in low nutrient media. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101666] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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Biological contamination and its chemical control in microalgal mass cultures. Appl Microbiol Biotechnol 2019; 103:9345-9358. [PMID: 31720774 DOI: 10.1007/s00253-019-10193-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/29/2019] [Accepted: 10/07/2019] [Indexed: 12/18/2022]
Abstract
Microalgae are versatile sources of bioproducts, a solution for many environmental problems. However, and despite its importance, one of the main problems in large-scale cultures-the presence of contaminants-is rarely systematically approached. Contamination, or the presence of undesirable organisms in a culture, is deleterious for the culture and frequently leads to culture crashes. To avoid contamination, closed systems can be used; however, for very large-scale open systems, contamination is unavoidable and remediation procedures are necessary-ranging from physicochemical treatment to addition of biocidal substances. In all cases, early detection and culture monitoring are paramount. This article describes the biological contaminants, contamination mechanisms, and control systems used in open and closed cultures, discussing the latest advances and techniques in the area. It also discusses the complex interactions of algae with other microorganisms that can be expected in cultivation systems.
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42
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Li L, Jeon Y, Lee SH, Ryu H, Santo Domingo JW, Seo Y. Dynamics of the physiochemical and community structures of biofilms under the influence of algal organic matter and humic substances. WATER RESEARCH 2019; 158:136-145. [PMID: 31026675 PMCID: PMC6563348 DOI: 10.1016/j.watres.2019.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 04/04/2019] [Accepted: 04/07/2019] [Indexed: 05/22/2023]
Abstract
Increased loading of algal organic matter (AOM) during harmful algal blooms not only burdens water treatment processes but also challenges safe drinking water delivery. While organic constituents promote biofilm growth in drinking water distribution systems (DWDS), the effects of AOM on biofilm formation in DWDS are not well understood. Herein, three parallel biofilm reactors were used to assess and compare how treated AOM- and humic substance (HS)-impacted bulk water, and R2A medium (a control) affect biofilm development for 168 days. The 16S rRNA gene sequencing analysis revealed that the bacterial communities in biofilms were clustered with the organic matter types in bulk water, where Family Comamonadaceae was the most dominant but showed different temporal dynamics depending on the organic matter characteristics in bulk water. Higher diversity was observed in the biofilms grown in AOM-impacted bulk water (BFAOM) than biofilms grown in HS-impacted (BFHS) and R2A-impacted bulk water (BFR2A) as the biofilms matured. In addition, some taxa (e.g., Rhodobacteraceae and Sphingomonadaceae) were enriched in BFAOM compared to BFHS and BFR2A. The biofilm image analysis results indicated that compared to BFHS, BFAOM and BFR2A had relatively thinner and heterogeneous physical structures with lower amounts of cell biomass, extracellular polymeric substances (EPS), and higher EPS protein/polysaccharide ratios. Overall, this study revealed how AOM- and HS-impacted bulk water shape the physiochemical and community structures of biofilms, which can provide insights into assessing biofilm-associated risks and optimizing disinfection practices for biofilm control in DWDS.
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Affiliation(s)
- Lei Li
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH, USA
| | - Youchul Jeon
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH, USA
| | - Sang-Hoon Lee
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH, USA
| | - Hodon Ryu
- Water Systems Division, National Risk Management Research Laboratory, U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA
| | - Jorge W Santo Domingo
- Water Systems Division, National Risk Management Research Laboratory, U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA
| | - Youngwoo Seo
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH, USA; Department of Chemical Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH, USA.
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Mangal V, Stenzler BR, Poulain AJ, Guéguen C. Aerobic and Anaerobic Bacterial Mercury Uptake is Driven by Algal Organic Matter Composition and Molecular Weight. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:157-165. [PMID: 30516365 DOI: 10.1021/acs.est.8b04909] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The biological mobilization of mercury (Hg) into microbes capable of Hg methylation is one of the limiting steps in the formation of the neurotoxin methylmercury (MeHg). Although algal dissolved organic matter (DOM) has been associated with increased MeHg production, the relationship between bacterial Hg uptake and algal DOM remains unexplored. In this study, we aimed to address how the quantity and quality of DOM, freshly harvested from several algae, affected the bacterial uptake of Hg with the use of a biosensor capable of functioning both aerobically and anaerobically. We combined biosensor measurements with high-resolution mass spectrometry and field-flow fractionation to elucidate how DOM composition and molecular weight influenced microbial Hg uptake. We showed that freshly harvested DOM from Chlorophyte and Euglena mutabilis strongly inhibited aerobic and anaerobic Hg uptake, whereas DOM harvested from Euglena gracilis did not exhibit this same pronounced effect. Once fractionated, we found that amino acids and polyamines, most abundant in Euglena gracilis DOM, were positively correlated to increase Hg uptake, suggesting that these molecules are potentially underappreciated ligands affecting Hg bioavailability. As water quality is affected by eutrophication, algal community assemblages will change, leading to variations in the nature of autochthonous DOM released in aquatic systems. Our results highlight that variations in the emergent properties of DOM originating from varying algal species can have a profound effect on bacterial Hg uptake and thus methylation.
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Affiliation(s)
- Vaughn Mangal
- Environmental and Life Sciences Graduate program , Trent University , 1600 West Bank Drive Peterborough ON Canada , K9J 7B8
| | - Benjamin R Stenzler
- Biology Department , University of Ottawa , 30 Marie Curie , Ottawa ON Canada , K1N 6N5
| | - Alexandre J Poulain
- Biology Department , University of Ottawa , 30 Marie Curie , Ottawa ON Canada , K1N 6N5
| | - Celine Guéguen
- Chemistry Department , Trent University , 1600 West Bank Drive Peterborough ON Canada , K9J 7B8
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Zhang S, Merino N, Okamoto A, Gedalanga P. Interkingdom microbial consortia mechanisms to guide biotechnological applications. Microb Biotechnol 2018; 11:833-847. [PMID: 30014573 PMCID: PMC6116752 DOI: 10.1111/1751-7915.13300] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 01/01/2023] Open
Abstract
Microbial consortia are capable of surviving diverse conditions through the formation of synergistic population-level structures, such as stromatolites, microbial mats and biofilms. Biotechnological applications are poised to capitalize on these unique interactions. However, current artificial co-cultures constructed for societal benefits, including biosynthesis, agriculture and bioremediation, face many challenges to perform as well as natural consortia. Interkingdom microbial consortia tend to be more robust and have higher productivity compared with monocultures and intrakingdom consortia, but the control and design of these diverse artificial consortia have received limited attention. Further, feasible research techniques and instrumentation for comprehensive mechanistic insights have only recently been established for interkingdom microbial communities. Here, we review these recent advances in technology and our current understanding of microbial interaction mechanisms involved in sustaining or developing interkingdom consortia for biotechnological applications. Some of the interactions among members from different kingdoms follow similar mechanisms observed for intrakingdom microbial consortia. However, unique interactions in interkingdom consortia, including endosymbiosis or interkingdom-specific cell-cell interactions, provide improved mitigation to external stresses and inhibitory compounds. Furthermore, antagonistic interactions among interkingdom species can promote fitness, diversification and adaptation, along with the production of beneficial metabolites and enzymes for society. Lastly, we shed light on future research directions to develop study methods at the level of metabolites, genes and meta-omics. These potential research methods could lead to the control and utilization of highly diverse microbial communities.
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Affiliation(s)
- Shu Zhang
- Global Research Center for Environment and Energy based on Nanomaterials ScienceNational Institute for Material Science1‐1 NamikiTsukubaIbarakiJapan
- Department of Molecular Microbiology and ImmunologyNorris Comprehensive Cancer CenterUniversity of Southern California1441 Eastlake StreetLos AngelesCA90033USA
- Present address:
Section of Infection and ImmunityHerman Ostrow School of DentistryUniversity of Southern CaliforniaCA90089‐0641USA
| | - Nancy Merino
- Earth‐Life Science InstituteTokyo Institute of Technology, 2‐12‐1‐I7E‐323Ookayama, Meguro‐kuTokyo 152‐8550Japan
- Department of Earth SciencesUniversity of Southern California, 835 Bloom Walk, SHS 562Los AngelesCA 90089‐0740USA
| | - Akihiro Okamoto
- Global Research Center for Environment and Energy based on Nanomaterials ScienceNational Institute for Material Science1‐1 NamikiTsukubaIbarakiJapan
| | - Phillip Gedalanga
- Department of Health ScienceCalifornia State University Fullerton, 800 North State College BoulevardFullertonCA 92831‐3599USA
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Lian J, Wijffels RH, Smidt H, Sipkema D. The effect of the algal microbiome on industrial production of microalgae. Microb Biotechnol 2018; 11:806-818. [PMID: 29978601 PMCID: PMC6116740 DOI: 10.1111/1751-7915.13296] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/10/2018] [Accepted: 06/11/2018] [Indexed: 12/22/2022] Open
Abstract
Microbes are ubiquitously distributed, and they are also present in algae production systems. The algal microbiome is a pivotal part of the alga holobiont and has a key role in modulating algal populations in nature. However, there is a lack of knowledge on the role of bacteria in artificial systems ranging from laboratory flasks to industrial ponds. Coexisting microorganisms, and predominantly bacteria, are often regarded as contaminants in algal research, but recent studies manifested that many algal symbionts not only promote algal growth but also offer advantages in downstream processing. Because of the high expectations for microalgae in a bio‐based economy, better understanding of benefits and risks of algal–microbial associations is important for the algae industry. Reducing production cost may be through applying specific bacteria to enhance algae growth at large scale as well as through preventing the growth of a broad spectrum of algal pathogens. In this review, we highlight the latest studies of algae–microbial interactions and their underlying mechanisms, discuss advantages of large‐scale algal–bacterial cocultivation and extend such knowledge to a broad range of biotechnological applications.
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Affiliation(s)
- Jie Lian
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Rene H Wijffels
- Bioprocess Engineering Group, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands.,Faculty of Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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Richter LV, Mansfeldt CB, Kuan MM, Cesare AE, Menefee ST, Richardson RE, Ahner BA. Altered Microbiome Leads to Significant Phenotypic and Transcriptomic Differences in a Lipid Accumulating Chlorophyte. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6854-6863. [PMID: 29750518 DOI: 10.1021/acs.est.7b06581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Given the challenges facing the economically favorable production of products from microalgae, understanding factors that might impact productivity rates including growth rates and accumulation of desired products, for example, triacylglycerols (TAG) for biodiesel feedstock, remains critical. Although operational parameters such as media composition and reactor design can clearly effect growth rates, the role of microbe-microbe interactions is just beginning to be elucidated. In this study an oleaginous marine algae Chlorella spp. C596 culture is shown to be better described as a microbial community. Perturbations to this microbial community showed a significant impact on phenotypes including sustained differences in growth rate and TAG accumulation of 2.4 and 2.5 fold, respectively. Characterization of the associated community using Illumina 16S rRNA amplicon and random shotgun transcriptomic analyses showed that the fast growth rate correlated with two specific bacterial species ( Ruegeria and Rhodobacter spp). The transcriptomic response of the Chlorella species revealed that the slower growing algal consortium C596-S1 upregulated genes associated with photosynthesis and resource scavenging and decreased the expression of genes associated with transcription and translation relative to the initial C596-R1. Our studies advance the appreciation of the effects microbiomes can have on algal growth in bioreactors and suggest that symbiotic interactions are involved in a range of critical processes including nitrogen, carbon cycling, and oxidative stress.
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Affiliation(s)
- Lubna V Richter
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Cresten B Mansfeldt
- School of Civil and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Michael M Kuan
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Alexandra E Cesare
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Stephen T Menefee
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Ruth E Richardson
- School of Civil and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Beth A Ahner
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
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47
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Bengtsson MM, Wagner K, Schwab C, Urich T, Battin TJ. Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels. Mol Ecol 2018; 27:2913-2925. [PMID: 29679511 PMCID: PMC6055792 DOI: 10.1111/mec.14696] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/15/2018] [Accepted: 02/09/2018] [Indexed: 01/08/2023]
Abstract
Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbour an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found that under light limitation‐dominant phototrophs, including diatoms and cyanobacteria, displayed a remarkable plasticity in their photosynthetic machinery manifested as higher abundance of messenger RNAs (mRNAs) involved in photosynthesis and chloroplast ribosomal RNA. Under higher light availability, bacterial mRNAs involved in phosphorus metabolism, mainly from Betaproteobacteria and Cyanobacteria, increased, likely compensating for nutrient depletion in thick biofilms with high biomass. Consumers, including diverse ciliates, displayed community shifts indicating preferential grazing on algae instead of bacteria under higher light. For the first time, we show that the functional integrity of stream biofilms under variable light availability is maintained by structure–function adaptations on several trophic levels. Our findings shed new light on complex biofilms, or “microbial jungles”, where in analogy to forests, diverse and multitrophic level communities lend stability to ecosystem functioning. This multitrophic level perspective, coupling metatranscriptomics to process measurements, could advance understanding of microbial‐driven ecosystems beyond biofilms, including planktonic and soil environments. https://doi.org/10.1111/mec.14733
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Affiliation(s)
- Mia M Bengtsson
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Department of Limnology and Oceanography, University of Vienna, Vienna, Austria
| | - Karoline Wagner
- Department of Limnology and Oceanography, University of Vienna, Vienna, Austria
| | - Clarissa Schwab
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Tom J Battin
- Stream Biofilm and Ecosystem Research Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), ENAC, Lausanne, Switzerland
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48
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Lee PA, Martinez KJ, Letcher PM, Corcoran AA, Ryan RA. A novel predatory bacterium infecting the eukaryotic alga Nannochloropsis. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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49
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Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation. PLoS One 2018; 13:e0195862. [PMID: 29659617 PMCID: PMC5901992 DOI: 10.1371/journal.pone.0195862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/31/2018] [Indexed: 11/27/2022] Open
Abstract
The experimental set-up of this study mimicked recirculating aquaculture systems (RAS) where water quality parameters such as dissolved oxygen, pH, temperature, and turbidity were controlled and wastes produced by fish and feeding were converted to inorganic forms. A key process in the RAS was the conversion of ammonia to nitrite and nitrite to nitrate through nitrification. It was hypothesized that algae inclusion in RAS would improve the ammonia removal from the water; thereby improving RAS water quality and stability. To test this hypothesis, the stability of the microbiota community composition in a freshwater RAS with (RAS+A) or without algae (RAS-A) was challenged by introducing an acute pH drop (from pH 7 to 4 during three hours) to the system. Stigeoclonium nanum, a periphytic freshwater microalga was used in this study. No significant effect of the algae presence was found on the resistance to the acute pH drop on ammonia conversion to nitrite and nitrite conversion to nitrate. Also the resilience of the ammonia conversion to the pH drop disruption was not affected by the addition of algae. This could be due to the low biomass of algae achieved in the RAS. However, with regard to the conversion step of nitrite to nitrate, RAS+A was significantly more resilient than RAS-A. In terms of overall bacterial communities, the composition and predictive function of the bacterial communities was significantly different between RAS+A and RAS-A.
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Fulbright SP, Robbins-Pianka A, Berg-Lyons D, Knight R, Reardon KF, Chisholm ST. Bacterial community changes in an industrial algae production system. ALGAL RES 2018; 31:147-156. [PMID: 29785358 DOI: 10.1016/j.algal.2017.09.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities. Therefore, the richness, structure, and composition of bacterial communities were characterized in closed photobioreactor cultivations of Nannochloropsis salina in F/2 medium at different scales, across nine months spanning late summer-early spring, and during a sequence of serially inoculated cultivations. Using 16S rRNA sequence data from 275 samples, bacterial communities in small, medium, and large cultures were shown to be significantly different. Larger systems contained richer bacterial communities compared to smaller systems. Relationships between bacterial communities and algae growth were complex. On one hand, blooms of a specific bacterial type were observed in three abnormal, poorly performing replicate cultivations, while on the other, notable changes in the bacterial community structures were observed in a series of serial large-scale batch cultivations that had similar growth rates. Bacteria common to the majority of samples were identified, including a single OTU within the class Saprospirae that was found in all samples. This study contributes important information for crop protection in algae systems, and demonstrates the complex ecosystems that need to be understood for consistent, successful industrial algae cultivation. This is the first study to profile bacterial communities during the scale-up process of industrial algae systems.
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