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Maréchal E. Marine and Freshwater Plants: Challenges and Expectations. FRONTIERS IN PLANT SCIENCE 2019; 10:1545. [PMID: 31824548 PMCID: PMC6883403 DOI: 10.3389/fpls.2019.01545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/05/2019] [Indexed: 05/05/2023]
Abstract
The past decades have seen an increasing interest on the biology of photosynthetic species living in aquatic environments, including diverse organisms collectively called "algae." If we consider the relative size of scientific communities, marine and freshwater plants have been overall less studied than terrestrial ones. The efforts put on land plants were motivated by agriculture and forestry, applications for human industry, easy access to terrestrial ecosystems, and convenient cultivation methods in fields or growth chambers. By contrast, the fragmentary knowledge on the biology of algae, the hope to find in this biodiversity inspiration for biotechnologies, and the emergency created by the environmental crisis affecting oceans, lakes, rivers, or melting glaciers, have stressed the importance to make up for lost time. Needed efforts embrace a broad spectrum of disciplines, from environmental and evolutionary sciences, to molecular and cell biology. In this multiscale view, functional genomics and ecophysiology occupy a pivotal position linking molecular and cellular analyses and ecosystem-level studies. Without pretending to be exhaustive and with few selected references, six grand challenges, requiring multidisciplinary approaches, are introduced below.
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Lima ARJ, Siqueira AS, de Vasconcelos JM, Pereira JS, de Azevedo JSN, Moraes PHG, Aguiar DCF, de Lima CPS, Vianez-Júnior JLSG, Nunes MRT, Xavier LP, Dall'Agnol LT, Goncalves EC. Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics. Front Microbiol 2018; 9:2811. [PMID: 30515147 PMCID: PMC6256058 DOI: 10.3389/fmicb.2018.02811] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/01/2018] [Indexed: 11/22/2022] Open
Abstract
Currently only four genome sequences for Limnothrix spp. are publicly available, and information on the genetic properties of cyanobacteria belonging to this genus is limited. In this study, we report the draft genome of Limnothrix sp. CACIAM 69d, isolated from the reservoir of a hydroelectric dam located in the Amazon ecosystem, from where cyanobacterial genomic data are still scarce. Comparative genomic analysis of Limnothrix revealed the presence of key enzymes in the cyanobacterial central carbon metabolism and how it is well equipped for environmental sulfur and nitrogen acquisition. Additionally, this work covered the analysis of Limnothrix CRISPR-Cas systems, pathways related to biosynthesis of secondary metabolites and assembly of extracellular polymeric substances and their exportation. A trans-AT PKS gene cluster was identified in two strains, possibly related to the novel toxin Limnothrixin biosynthesis. Overall, the draft genome of Limnothrix sp. CACIAM 69d adds new data to the small Limnothrix genome library and contributes to a growing representativeness of cyanobacterial genomes from the Amazon region. The comparative genomic analysis of Limnothrix made it possible to highlight unique genes for each strain and understand the overall features of their metabolism.
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Affiliation(s)
- Alex Ranieri Jerônimo Lima
- Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Andrei Santos Siqueira
- Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Janaina Mota de Vasconcelos
- Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - James Siqueira Pereira
- Laboratório de Biodiversidade Molecular, Universidade Federal Rural da Amazônia, Campus de Capanema, Capanema, Brazil
| | - Juliana Simão Nina de Azevedo
- Laboratório de Biodiversidade Molecular, Universidade Federal Rural da Amazônia, Campus de Capanema, Capanema, Brazil
| | | | | | | | | | | | - Luciana Pereira Xavier
- Laboratório de Biotecnologia de Enzimas e Biotransformações, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Leonardo Teixeira Dall'Agnol
- Grupo de Pesquisa em Biodiversidade, Bioprospecção e Biotecnologia, Universidade Federal do Maranhão, São Luís, Brazil
| | - Evonnildo Costa Goncalves
- Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
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Cornet L, Meunier L, Van Vlierberghe M, Léonard RR, Durieu B, Lara Y, Misztak A, Sirjacobs D, Javaux EJ, Philippe H, Wilmotte A, Baurain D. Consensus assessment of the contamination level of publicly available cyanobacterial genomes. PLoS One 2018; 13:e0200323. [PMID: 30044797 PMCID: PMC6059444 DOI: 10.1371/journal.pone.0200323] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022] Open
Abstract
Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.
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Affiliation(s)
- Luc Cornet
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- UR Geology–Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Liège, Belgium
| | - Loïc Meunier
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Mick Van Vlierberghe
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Raphaël R. Léonard
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- InBioS–CIP, Macromolecular Crystallography, University of Liège, Liège, Belgium
| | - Benoit Durieu
- InBioS–CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Yannick Lara
- InBioS–CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Agnieszka Misztak
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- Intercollegiate Faculty of Biotechnology UG-MUG, Gdansk, Poland
| | - Damien Sirjacobs
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Emmanuelle J. Javaux
- UR Geology–Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Liège, Belgium
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, Moulis, France
| | - Annick Wilmotte
- InBioS–CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Denis Baurain
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- * E-mail:
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Huo D, Chen Y, Zheng T, Liu X, Zhang X, Yu G, Qiao Z, Li R. Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing. Front Microbiol 2018; 9:971. [PMID: 29867874 PMCID: PMC5962762 DOI: 10.3389/fmicb.2018.00971] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 04/25/2018] [Indexed: 11/17/2022] Open
Abstract
Microcystis is one of the most common and dominant bloom-forming cyanobacteria in freshwater worldwide. The method for genotype detection based on traditional molecular cloning is expensive and time consuming and generates a limited number of sequences. In this study, a high-throughput sequencing (HTS) method was developed to detect the internal transcribed spacer (ITS) regions between 16S and 23S rRNA region of Microcystis populations along a typical water system in Yuqiao Reservoir-Haihe River in Tianjin, northern China. A total of 629,341 reads were obtained and clustered into 2005 operational taxonomic units (OTUs). Analysis of alpha diversity indices showed that the Haihe River is more diverse than Yuqiao Reservoir. In general, the two water areas exhibit a clear differentiation pattern in OTU abundance, sharing genotypes from a small part of Yuqiao Reservoir with those in the Haihe River. Phylogenetic analysis further indicated the possible flexible evolution of Microcystis genotypes occurring in the research areas. This study provides the first exhaustive description of HTS method for detection of ITS region to evaluate Microcystis intra-species diversity and relationship.
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Affiliation(s)
- Da Huo
- National Demonstration Center for Experimental Aqua-ecology and Aquaculture Education, Department of Fisheries Sciences, Tianjin Agricultural University, Tianjin, China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Youxin Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Tao Zheng
- National Demonstration Center for Experimental Aqua-ecology and Aquaculture Education, Department of Fisheries Sciences, Tianjin Agricultural University, Tianjin, China
| | - Xiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xinyue Zhang
- National Demonstration Center for Experimental Aqua-ecology and Aquaculture Education, Department of Fisheries Sciences, Tianjin Agricultural University, Tianjin, China
| | - Gongliang Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhiyi Qiao
- National Demonstration Center for Experimental Aqua-ecology and Aquaculture Education, Department of Fisheries Sciences, Tianjin Agricultural University, Tianjin, China
| | - Renhui Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Desiderato JG, Alvarenga DO, Constancio MTL, Alves LMC, Varani AM. The genome sequence of Dyella jiangningensis FCAV SCS01 from a lignocellulose-decomposing microbial consortium metagenome reveals potential for biotechnological applications. Genet Mol Biol 2018; 41:507-513. [PMID: 29767666 PMCID: PMC6082245 DOI: 10.1590/1678-4685-gmb-2017-0155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/13/2017] [Indexed: 11/22/2022] Open
Abstract
Cellulose and its associated polymers are structural components of the plant cell
wall, constituting one of the major sources of carbon and energy in nature. The
carbon cycle is dependent on cellulose- and lignin-decomposing microbial
communities and their enzymatic systems acting as consortia. These microbial
consortia are under constant exploration for their potential biotechnological
use. Herein, we describe the characterization of the genome of Dyella
jiangningensis FCAV SCS01, recovered from the metagenome of a
lignocellulose-degrading microbial consortium, which was isolated from a
sugarcane crop soil under mechanical harvesting and covered by decomposing
straw. The 4.7 Mbp genome encodes 4,194 proteins, including 36 glycoside
hydrolases (GH), supporting the hypothesis that this bacterium may contribute to
lignocellulose decomposition. Comparative analysis among fully sequenced
Dyella species indicate that the genome synteny is not
conserved, and that D. jiangningensis FCAV SCS01 carries 372
unique genes, including an alpha-glucosidase and maltodextrin glucosidase coding
genes, and other potential biomass degradation related genes. Additional genomic
features, such as prophage-like, genomic islands and putative new biosynthetic
clusters were also uncovered. Overall, D. jiangningensis FCAV
SCS01 represents the first South American Dyella genome
sequenced and shows an exclusive feature among its genus, related to biomass
degradation.
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Affiliation(s)
- Joana G Desiderato
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
| | - Danillo O Alvarenga
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
| | - Milena T L Constancio
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
| | - Lucia M C Alves
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
| | - Alessandro M Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
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Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde. Toxins (Basel) 2018; 10:toxins10050186. [PMID: 29734762 PMCID: PMC5983242 DOI: 10.3390/toxins10050186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 01/12/2023] Open
Abstract
The Cape Verde islands are part of the African Sahelian arid belt that possesses an erratic rain pattern prompting the need for water reservoirs, which are now critical for the country’s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and the eutrophication of water bodies, particularly in reservoirs. To date, there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde. Our analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs. Faveta potentially toxic and bloom-forming Microcystis sp., dominated our samples, while a Cryptomonas green algae and Gammaproteobacteria dominated Saquinho and Poilão reservoirs. We reconstructed and assembled the Microcystis genome, extracted from the metagenome of bulk DNA from Faveta water. Phylogenetic analysis of Microcystis cf. aeruginosa CV01’s genome revealed its close relationship with other Microcystis genomes, as well as clustering with other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This survey reinforces the need to better understand the country’s microbial ecology as a whole of water reservoirs on the rise.
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Moss NA, Leao T, Glukhov E, Gerwick L, Gerwick WH. Collection, Culturing, and Genome Analyses of Tropical Marine Filamentous Benthic Cyanobacteria. Methods Enzymol 2018; 604:3-43. [PMID: 29779657 DOI: 10.1016/bs.mie.2018.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Decreasing sequencing costs has sparked widespread investigation of the use of microbial genomics to accelerate the discovery and development of natural products for therapeutic uses. Tropical marine filamentous cyanobacteria have historically produced many structurally novel natural products, and therefore present an excellent opportunity for the systematic discovery of new metabolites via the information derived from genomics and molecular genetics. Adequate knowledge transfer and institutional know-how are important to maintain the capability for studying filamentous cyanobacteria due to their unusual microbial morphology and characteristics. Here, we describe workflows, procedures, and commentary on sample collection, cultivation, genomic DNA generation, bioinformatics tools, and biosynthetic pathway analysis concerning filamentous cyanobacteria.
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Affiliation(s)
- Nathan A Moss
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States
| | - Tiago Leao
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States
| | - Evgenia Glukhov
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States
| | - Lena Gerwick
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States.
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Vu CHT, Lee HG, Chang YK, Oh HM. Axenic cultures for microalgal biotechnology: Establishment, assessment, maintenance, and applications. Biotechnol Adv 2018; 36:380-396. [DOI: 10.1016/j.biotechadv.2017.12.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/27/2017] [Accepted: 12/28/2017] [Indexed: 02/06/2023]
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Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium [corrected] Strains from a Freshwater Ecosystem. GENOME ANNOUNCEMENTS 2018; 6:6/5/e00009-18. [PMID: 29437085 PMCID: PMC5794932 DOI: 10.1128/genomea.00009-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Freshwater ecosystems represent 0.01% of the water on Earth, but they support 6% of global biodiversity that is still mostly uncharacterized. Here, we describe the genome sequences of three strains belonging to novel species in the Pseudomonas, Flavobacterium, and Sediminibacterium genera recovered from a water sample of Lake Garda, Italy.
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Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community. Appl Environ Microbiol 2017; 83:AEM.01068-17. [PMID: 28754701 DOI: 10.1128/aem.01068-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/19/2017] [Indexed: 11/20/2022] Open
Abstract
The cyanobacterial culture HT-58-2 was originally described as a strain of Tolypothrix nodosa with the ability to produce tolyporphins, which comprise a family of distinct tetrapyrrole macrocycles with reported efflux pump inhibition properties. Upon reviving the culture from what was thought to be a nonextant collection, studies of culture conditions, strain characterization, phylogeny, and genomics have been undertaken. Here, HT-58-2 was shown by 16S rRNA analysis to closely align with Brasilonema strains and not with Tolypothrix isolates. Light, fluorescence, and scanning electron microscopy revealed cyanobacterium filaments that are decorated with attached bacteria and associated with free bacteria. Metagenomic surveys of HT-58-2 cultures revealed a diversity of bacteria dominated by Erythrobacteraceae, 97% of which are Porphyrobacter species. A dimethyl sulfoxide washing procedure was found to yield enriched cyanobacterial DNA (presumably by removing community bacteria) and sequence data sufficient for genome assembly. The finished, closed HT-58-2Cyano genome consists of 7.85 Mbp (42.6% G+C) and contains 6,581 genes. All genes for biosynthesis of tetrapyrroles (e.g., heme, chlorophyll a, and phycocyanobilin) and almost all for cobalamin were identified dispersed throughout the chromosome. Among the 6,177 protein-encoding genes, coding sequences (CDSs) for all but two of the eight enzymes for conversion of glutamic acid to protoporphyrinogen IX also were found within one major gene cluster. The cluster also includes 10 putative genes (and one hypothetical gene) encoding proteins with domains for a glycosyltransferase, two cytochrome P450 enzymes, and a flavin adenine dinucleotide (FAD)-binding protein. The composition of the gene cluster suggests a possible role in tolyporphin biosynthesis.IMPORTANCE A worldwide search more than 25 years ago for cyanobacterial natural products with anticancer activity identified a culture (HT-58-2) from Micronesia that produces tolyporphins. Tolyporphins are tetrapyrroles, like chlorophylls, but have several profound structural differences that reside outside the bounds of known biosynthetic pathways. To begin probing the biosynthetic origin and biological function of tolyporphins, our research has focused on studying the cyanobacterial strain, about which almost nothing has been previously reported. We find that the HT-58-2 culture is composed of the cyanobacterium and a community of associated bacteria, complicating the question of which organisms make tolyporphins. Elucidation of the cyanobacterial genome revealed an intriguing gene cluster that contains tetrapyrrole biosynthesis genes and a collection of unknown genes, suggesting that the cluster may be responsible for tolyporphin production. Knowledge of the genome and the gene cluster sharply focuses research to identify related cyanobacterial producers of tolyporphins and delineate the tolyporphin biosynthetic pathway.
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