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Xu S, Liu Y, Zhang J. Transcriptomic mechanisms for the promotion of cyanobacterial growth against eukaryotic microalgae by a ternary antibiotic mixture. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:58881-58891. [PMID: 35377122 DOI: 10.1007/s11356-022-20041-3] [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: 07/07/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
This study evaluated the responses of a mixed culture of two cyanobacterial species (Microcystis aeruginosa and Synechocystis sp.) and two eukaryotic microalgal species (Raphidocelis subcapitata and Tetradesmus obliquus) to a mixture of three frequently detected antibiotics (tetracycline, ciprofloxacin and sulfamethoxazole) at environmentally relevant exposure doses of 60-300 ng/L. Mixed antibiotics selectively stimulated (p < 0.05) the growth and photosynthetic activity as well as generated transcriptomic responses in cyanobacteria without disrupting co-existing eukaryotic microalgae. Mixed antibiotics stimulated the growth of M. aeruginosa through the regulation of genes related to ribosome, photosynthesis, redox homeostasis, quorum sensing and nutrient metabolism. The proportion of M. aeruginosa among the four phytoplankton species in the mixed-culture system was increased from 33% to 38-44% under antibiotic exposure, which promoted the dominance of M. aeruginosa. Up-regulation of carbon catabolism-related genes contributed to the increased growth of Synechocystis sp. under antibiotic exposure. Since the antibiotic-stimulated growth rate of Synechocystis sp. was still lower than that of M. aeruginosa, the proportion of Synechocystis sp. in the mixed-culture system remained stable. Synechocystis sp. was less adaptive to antibiotic exposure than M. aeruginosa, due to a lower number of up-regulated ribosomal genes and photosynthesis-related genes. Antibiotic exposure reduced the proportions of two eukaryotic microalgal species in the mixed-culture system through a selective promotion of cyanobacterial competitiveness against eukaryotic microalgae, which may facilitate the formation of cyanobacteria bloom.
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Affiliation(s)
- Sijia Xu
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, People's Republic of China
| | - Ying Liu
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Jian Zhang
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, People's Republic of China
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Poliner E, Busch AWU, Newton L, Kim YU, Clark R, Gonzalez-Martinez SC, Jeong BR, Montgomery BL, Farré EM. Aureochromes maintain polyunsaturated fatty acid content in Nannochloropsis oceanica. PLANT PHYSIOLOGY 2022; 189:906-921. [PMID: 35166829 PMCID: PMC9157131 DOI: 10.1093/plphys/kiac052] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/12/2022] [Indexed: 05/05/2023]
Abstract
Nannochloropsis oceanica, like other stramenopile microalgae, is rich in long-chain polyunsaturated fatty acids (LC-PUFAs) such as eicosapentaenoic acid (EPA). We observed that fatty acid desaturases (FADs) involved in LC-PUFA biosynthesis were among the strongest blue light-induced genes in N. oceanica CCMP1779. Blue light was also necessary for maintaining LC-PUFA levels in CCMP1779 cells, and growth under red light led to a reduction in EPA content. Aureochromes are stramenopile-specific proteins that contain a light-oxygen-voltage (LOV)-sensing domain that associates with a flavin mononucleotide and is able to sense blue light. These proteins also contain a basic leucine zipper DNA-binding motif and can act as blue light-regulated transcription factors by associating with an E-box like motif, which we found enriched in the promoters of blue light-induced genes. We demonstrated that, in vitro, two CCMP1779 aureochromes were able to absorb blue light. Moreover, the loss or reduction of the expression of any of the three aureochrome genes led to a decrease in the blue light-specific induction of several FADs in CCMP1779. EPA content was also significantly reduced in NoAUREO2 and NoAUREO4 mutants. Taken together, our results indicate that aureochromes mediate blue light-dependent regulation of LC-PUFA content in N. oceanica CCMP1779 cells.
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Affiliation(s)
- Eric Poliner
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan, USA
| | - Andrea W U Busch
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Young Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Rachel Clark
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | | | - Byeong-Ryool Jeong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandon Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QiBEBT), Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Beronda L Montgomery
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Author for correspondence: (E.M.F.)
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Perera IA, Abinandan S, Subashchandrabose SR, Venkateswarlu K, Cole N, Naidu R, Megharaj M. Extracellular Polymeric Substances Drive Symbiotic Interactions in Bacterial‒Microalgal Consortia. MICROBIAL ECOLOGY 2022; 83:596-607. [PMID: 34132846 DOI: 10.1007/s00248-021-01772-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
The importance of several factors that drive the symbiotic interactions between bacteria and microalgae in consortia has been well realised. However, the implication of extracellular polymeric substances (EPS) released by the partners remains unclear. Therefore, the present study focused on the influence of EPS in developing consortia of a bacterium, Variovorax paradoxus IS1, with a microalga, Tetradesmus obliquus IS2 or Coelastrella sp. IS3, all isolated from poultry slaughterhouse wastewater. The bacterium increased the specific growth rates of microalgal species significantly in the consortia by enhancing the uptake of nitrate (88‒99%) and phosphate (92‒95%) besides accumulating higher amounts of carbohydrates and proteins. The EPS obtained from exudates, collected from the bacterial or microalgal cultures, contained numerous phytohormones, vitamins, polysaccharides and amino acids that are likely involved in interspecies interactions. The addition of EPS obtained from V. paradoxus IS1 to the culture medium doubled the growth of both the microalgal strains. The EPS collected from T. obliquus IS2 significantly increased the growth of V. paradoxus IS1, but there was no apparent change in bacterial growth when it was cultured in the presence of EPS from Coelastrella sp. IS3. These observations indicate that the interaction between V. paradoxus IS1 and T. obliquus IS2 was mutualism, while commensalism was the interaction between the bacterial strain and Coelastrella sp. IS3. Our present findings thus, for the first time, unveil the EPS-induced symbiotic interactions among the partners involved in bacterial‒microalgal consortia.
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Affiliation(s)
- Isiri Adhiwarie Perera
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| | - Sudharsanam Abinandan
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, NSW, 2308, Australia
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, NSW, 2308, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, 515003, India
| | - Nicole Cole
- Analytical and Biomolecular Research Facility (ABRF), The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, NSW, 2308, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia.
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, NSW, 2308, Australia.
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Calhoun S, Bell TAS, Dahlin LR, Kunde Y, LaButti K, Louie KB, Kuftin A, Treen D, Dilworth D, Mihaltcheva S, Daum C, Bowen BP, Northen TR, Guarnieri MT, Starkenburg SR, Grigoriev IV. A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology. Commun Biol 2021; 4:333. [PMID: 33712730 PMCID: PMC7955037 DOI: 10.1038/s42003-021-01859-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Microalgae efficiently convert sunlight into lipids and carbohydrates, offering bio-based alternatives for energy and chemical production. Improving algal productivity and robustness against abiotic stress requires a systems level characterization enabled by functional genomics. Here, we characterize a halotolerant microalga Scenedesmus sp. NREL 46B-D3 demonstrating peak growth near 25 °C that reaches 30 g/m2/day and the highest biomass accumulation capacity post cell division reported to date for a halotolerant strain. Functional genomics analysis revealed that genes involved in lipid production, ion channels and antiporters are expanded and expressed. Exposure to temperature stress shifts fatty acid metabolism and increases amino acids synthesis. Co-expression analysis shows that many fatty acid biosynthesis genes are overexpressed with specific transcription factors under cold stress. These and other genes involved in the metabolic and regulatory response to temperature stress can be further explored for strain improvement.
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Affiliation(s)
- Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tisza Ann Szeremy Bell
- Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Division of Biological Sciences, Genome Core, University of Montana, Missoula, MT, USA
| | - Lukas R Dahlin
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Yuliya Kunde
- Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine B Louie
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrea Kuftin
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Treen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Dilworth
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sirma Mihaltcheva
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin P Bowen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Shawn R Starkenburg
- Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
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Torres S, Lama C, Mantecón L, Flemetakis E, Infante C. Selection and validation of reference genes for quantitative real-time PCR in the green microalgae Tetraselmis chui. PLoS One 2021; 16:e0245495. [PMID: 33444403 PMCID: PMC7808622 DOI: 10.1371/journal.pone.0245495] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/30/2020] [Indexed: 01/08/2023] Open
Abstract
Quantitative real-time reverse transcription PCR (RT-qPCR) is a highly sensitive technique that can be applied to analyze how genes are modulated by culture conditions, but identification of appropriate reference genes for normalization is a critical factor to be considered. For this reason, the expression stability of 18 candidate reference genes was evaluated for the green microalgae Tetraselmis chui using the widely employed algorithms geNorm, NormFinder, BestKeeper, the comparative ΔCT method, and RefFinder. Microalgae samples were collected from large scale outdoor photobioreactors during the growing phase (OUT_GP), and during the semi-continuous phase at different times of the day (OUT_DC). Samples from standard indoor cultures under highly controlled conditions (IND) were also collected to complement the other data. Different rankings for the candidate reference genes were obtained depending on the culture conditions and the algorithm employed. After comparison of the achieved ranks with the different methods, the references genes selected for samples from specific culture conditions were ALD and EFL in OUT_GP, RPL32 and UBCE in OUT_DC, and cdkA and UBCE in IND. Moreover, the genes EFL and cdkA or EFL and UBCE appeared as appropriate combinations for pools generated from all samples (ALL). Examination in the OUT_DC cultures of genes encoding the large and small subunits of ADP-glucose pyrophosphorylase (AGPL and AGPS, respectively) confirmed the reliability of the identified reference genes, RPL32 and UBCE. The present study represents a useful contribution for studies of gene expression in T. chui, and also represents the first step to set-up an RT-qPCR platform for quality control of T. chui biomass production in industrial facilities.
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Affiliation(s)
- Sonia Torres
- Fitoplancton Marino, S.L., El Puerto de Santa María, Cádiz, Spain
| | - Carmen Lama
- Fitoplancton Marino, S.L., El Puerto de Santa María, Cádiz, Spain
| | - Lalia Mantecón
- Fitoplancton Marino, S.L., El Puerto de Santa María, Cádiz, Spain
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Carlos Infante
- Fitoplancton Marino, S.L., El Puerto de Santa María, Cádiz, Spain
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León-Saiki GM, Carreres BM, Remmers IM, Wijffels RH, Martins dos Santos VA, van der Veen D, Schaap PJ, Suarez-Diez M, Martens DE. Evaluation of diurnal responses of Tetradesmus obliquus under nitrogen limitation. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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An assessment of heterotrophy and mixotrophy in Scenedesmus and its utilization in wastewater treatment. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101911] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation. Sci Data 2019; 6:254. [PMID: 31685817 PMCID: PMC6828702 DOI: 10.1038/s41597-019-0263-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/11/2019] [Indexed: 11/08/2022] Open
Abstract
The RDF data model facilitates integration of diverse data available in structured and semi-structured formats. To obtain a coherent RDF graph the chosen ontology must be consistently applied. However, addition of new diverse data causes the ontology to evolve, which could lead to accumulation of unintended erroneous composites. Thus, there is a need for a gate keeping system that compares the intended content described in the ontology with the actual content of the resource. The Empusa code generator facilitates creation of composite RDF resources from disparate sources. Empusa can convert a schema into an associated application programming interface (API), that can be used to perform data consistency checks and generates Markdown documentation to make persistent URLs resolvable. Using Empusa consistency is ensured within and between the ontology and the content of the resource. As an illustration of the potential of Empusa, we present the Genome Biology Ontology Language (GBOL). GBOL uses and extends current ontologies to provide a formal representation of genomic entities, along with their properties, relations and provenance.
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