1
|
Dutta S, Kothari S, Singh D, Ghosh S, Narayan Sarangi A, Sanjita Behera S, Prajapati S, Kumar Sinha P, Prusty A, Tripathy S. Novel oceanic cyanobacterium isolated from Bangaram island with profound acid neutralizing ability is proposed as Leptolyngbya iicbica sp. nov. strain LK. Mol Phylogenet Evol 2024; 197:108092. [PMID: 38723790 DOI: 10.1016/j.ympev.2024.108092] [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] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 05/04/2024] [Indexed: 05/19/2024]
Abstract
An acid-neutralizing, filamentous, non-heterocytous, marine cyanobacterium named 'LK' has been isolated from the seashore of Bangaram Island, an atoll of Lakshadweep, India, and is described here as a novel species. LK has been characterized using morphological, ecological, and genomic features. Based on 16S rRNA, whole-genome sequencing, and marker gene-based analysis, LK has been identified as a new species. LK clustered with Leptolyngbya-like strains belonging to the LPP group but diverged from Leptolyngbya sensu stricto, indicating the polyphyletic nature of the Leptolyngbya genus. Leptolyngbya sp. SIOISBB and Halomicronema sp. CCY15110 were identified as LK's two closest phylogenetic neighbors in various phylogenetic studies. The analysis of 16S rRNA, ITS secondary structures, and genome relatedness indices such as AAI, ANI, and gANI strongly support LK as a novel species of the Leptolyngbya genus. The mechanism behind acid neutralization in LK has been delineated, attributing it to a surface phenomenon most likely due to the presence of salts of calcium, magnesium, sodium, and potassium. We name LK as Leptolyngbya iicbica strain LK which is a novel species with prominent acidic pH-neutralizing properties.
Collapse
Affiliation(s)
- Subhajeet Dutta
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shreya Kothari
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Smruti Sanjita Behera
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Molecular Genetics Division, CSIR Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Satish Prajapati
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Prasanta Kumar Sinha
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Asharani Prusty
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
2
|
Zhang T, Zhou K, Wang Y, Xu J, Zheng Q, Luo T, Jiao N. Genomic insights into the adaptation of Synechococcus to the coastal environment on Xiamen. Front Microbiol 2023; 14:1292150. [PMID: 38059125 PMCID: PMC10696648 DOI: 10.3389/fmicb.2023.1292150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
Synechococcus are widely distributed in the global ocean, from the pelagic zone to coastal waters. However, little is known about Synechococcus in coastal seawater due to limitations in isolation and culture conditions. In this study, a combination of metagenomic sequencing technology, flow cytometry sorting, and multiple displacement amplification was used to investigate Synechococcus in the coastal seawater of Xiamen Island. The results revealed 18 clades of Synechococcus and diverse metabolic genes that appear to contribute to their adaptation to the coastal environment. Intriguingly, some metabolic genes related to the metabolism of carbohydrates, energy, nucleotides, and amino acids were found in 89 prophage regions that were detected in 16,258 Synechococcus sequences. The detected metabolic genes can enable prophages to contribute to the adaptation of Synechococcus hosts to the coastal marine environment. The detection of prophages also suggests that the cyanophages have infected Synechococcus. On the other hand, the identification of 773 genes associated with antiviral defense systems indicates that Synechococcus in Xiamen have evolved genetic traits in response to cyanophage infection. Studying the community diversity and functional genes of Synechococcus provides insights into their role in environmental adaptation and marine ecosystems.
Collapse
Affiliation(s)
- Ting Zhang
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Kun Zhou
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Yanhui Wang
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Jinxin Xu
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Qiang Zheng
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Tingwei Luo
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Nianzhi Jiao
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| |
Collapse
|
3
|
Schluchter WM, Babin CH, Liu X, Bieller A, Shen G, Alvey RM, Bryant DA. Loss of Biliverdin Reductase Increases Oxidative Stress in the Cyanobacterium Synechococcus sp. PCC 7002. Microorganisms 2023; 11:2593. [PMID: 37894251 PMCID: PMC10608806 DOI: 10.3390/microorganisms11102593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Oxygenic photosynthesis requires metal-rich cofactors and electron-transfer components that can produce reactive oxygen species (ROS) that are highly toxic to cyanobacterial cells. Biliverdin reductase (BvdR) reduces biliverdin IXα to bilirubin, which is a potent scavenger of radicals and ROS. The enzyme is widespread in mammals but is also found in many cyanobacteria. We show that a previously described bvdR mutant of Synechocystis sp. PCC 6803 contained a secondary deletion mutation in the cpcB gene. The bvdR gene from Synechococcus sp. PCC 7002 was expressed in Escherichia coli, and recombinant BvdR was purified and shown to reduce biliverdin to bilirubin. The bvdR gene was successfully inactivated in Synechococcus sp. PCC 7002, a strain that is naturally much more tolerant of high light and ROS than Synechocystis sp. PCC 6803. The bvdR mutant strain, BR2, had lower total phycobiliprotein and chlorophyll levels than wild-type cells. As determined using whole-cell fluorescence at 77 K, the photosystem I levels were also lower than those in wild-type cells. The BR2 mutant had significantly higher ROS levels compared to wild-type cells after exposure to high light for 30 min. Together, these results suggest that bilirubin plays an important role as a scavenger for ROS in Synechococcus sp. PCC 7002. The oxidation of bilirubin by ROS could convert bilirubin to biliverdin IXα, and thus BvdR might be important for regenerating bilirubin. These results further suggest that BvdR is a key component of a scavenging cycle by which cyanobacteria protect themselves from the toxic ROS byproducts generated during oxygenic photosynthesis.
Collapse
Affiliation(s)
- Wendy M. Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Courtney H. Babin
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Xindi Liu
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Amori Bieller
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA (R.M.A.); (D.A.B.)
| | - Richard M. Alvey
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA (R.M.A.); (D.A.B.)
- Biology Department, Bloomington, Illinois Wesleyan University, Bloomington, IL 61702, USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA (R.M.A.); (D.A.B.)
| |
Collapse
|
4
|
Almeida PIND, Jesus HED, Pereira PHF, Vieira CED, Bianchini A, Martins CDMG, Santos HFD. The microbial profile of rivers and lagoons three years after the impact of the world's largest mining disaster (Fundão dam, Brazil). ENVIRONMENTAL RESEARCH 2023; 216:114710. [PMID: 36334830 DOI: 10.1016/j.envres.2022.114710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
The collapse of the Fundão tailings dam (Minas Gerais, Brazil) was the largest environmental disaster in Brazil's history and in the world mining industry. This disaster carried approximately 55 million m3 of iron ore tailings along the rivers and the lagoons of the Doce river basin. Although multiple studies assessed the impact on microbial communities in those rivers and lagoons right after the dam rupture, it is not known whether the microbiome in those environments remains impacted years after the disaster. Assessing the microbiome is very important to evaluate impacts and evaluate the health of the environment, due to the several ecological roles played by microorganisms. Here, we evaluated the impact of the dam failure on water and sediment bacteriome and archaeome by high-throughput next-generation sequencing. Samples were taken from two rivers and six lagoons during the dry and rainy seasons approximately three years post disturbance. The results showed a large number and abundance of microbial groups associated with the presence of heavy metals and mine tailings sediments. Some of these microorganisms were also reported in large abundance in the impacted rivers shortly after the Fundão dam rupture. Among the most abundant microorganisms in the Doce River, we can highlight the bacteria hgcI clade and the archaea Nitrososphera sp. in the water, and the bacteria Anaerolineaceae sp. in the sediment. These results suggest that the microbiome of the rivers and the lagoons in the Doce river basin remains severely impacted by the Fundão tailings dam failure even three years after the disaster. The presence of those microorganisms can also help to assess the occurrence of the Fundão dam sediment in other environments.
Collapse
Affiliation(s)
- Pedro Ivo Neves de Almeida
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ, 24210-201, Brazil
| | - Hugo Emiliano de Jesus
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ, 24210-201, Brazil
| | - Pedro Henrique Freitas Pereira
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ, 24210-201, Brazil
| | - Carlos Eduardo Delfino Vieira
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, FURG. Av. Itália, S/n, Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Adalto Bianchini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, FURG. Av. Itália, S/n, Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Camila De Martinez Gaspar Martins
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, FURG. Av. Itália, S/n, Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Henrique Fragoso Dos Santos
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ, 24210-201, Brazil.
| |
Collapse
|
5
|
Tang J, Yao D, Zhou H, Du L, Daroch M. Reevaluation of Parasynechococcus-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11081060. [PMID: 35448788 PMCID: PMC9024877 DOI: 10.3390/plants11081060] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 05/28/2023]
Abstract
Morphologically similar to Synechococcus, a large number of Parasynechococcus strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 Synechococcus-like strains were reevaluated using a combination of 16S rRNA phylogeny and genomic approach, identifying 54 strains as Parasynechococcus-like strains and showing considerably intragenus genetic divergence among the subclades identified. Further, bioinformatics analysis disclosed diversified patterns of distribution, abundance, density, and diversity of microsatellites (SSRs) and compound microsatellites (CSSRs) in genomes of these Parasynechococcus-like strains. Variations of SSRs and CSSRs were observed amongst phylotypes and subclades. Both SSRs and CSSRs were in particular unequally distributed among genomes. Dinucleotide SSRs were the most widespread, while the genomes showed two patterns in the second most abundant repeat type (mononucleotide or trinucleotide SSRs). Both SSRs and CSSRs were predominantly observed in coding regions. These two types of microsatellites showed positive correlation with genome size (p < 0.01) but negative correlation with GC content (p < 0.05). Additionally, the motif (A)n, (AG)n and (AGC)n was a major one in the corresponding category. Meanwhile, distinctive motifs of CSSRs were found in 39 genomes. This study characterizes SSRs and CSSRs in genomes of Parasynechococcus-like strains and will be useful as a prerequisite for future studies regarding their distribution, function, and evolution. Moreover, the identified SSRs may facilitate fast acclimation of Parasynechococcus-like strains to fluctuating environments and contribute to the extensive distribution of Parasynechococcus species in global marine environments.
Collapse
Affiliation(s)
- Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China; (J.T.); (D.Y.); (H.Z.); (L.D.)
| | - Dan Yao
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China; (J.T.); (D.Y.); (H.Z.); (L.D.)
| | - Huizhen Zhou
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China; (J.T.); (D.Y.); (H.Z.); (L.D.)
| | - Lianming Du
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China; (J.T.); (D.Y.); (H.Z.); (L.D.)
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Road, Shenzhen 518055, China
| |
Collapse
|
6
|
Johansen JR, González-Resendiz L, Escobar-Sánchez V, Segal-Kischinevzky C, Martínez-Yerena J, Hernández-Sánchez J, Hernández-Pérez G, León-Tejera H. When will taxonomic saturation be achieved? A case study in Nunduva and Kyrtuthrix (Rivulariaceae, Cyanobacteria). JOURNAL OF PHYCOLOGY 2021; 57:1699-1720. [PMID: 34289115 DOI: 10.1111/jpy.13201] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
A number of heterocytous, mat-forming, tapering cyanobacteria in Rivulariaceae have recently been observed in both the Atlantic and Pacific coasts in the rocky intertidal and supratidal zones. These belong to the genera Nunduva, Kyrtuthrix, and Phyllonema and have been the subject of several recent studies. Herein, two new species of Nunduva (N. komarkovae and N. sanagustinensis) and two new species of Kyrtuthrix (K. munecosensis and K. totonaca) are characterized and described from the coasts of Mexico. Genetic separation based on the 16S-23S ITS region was pronounced (>10% in all comparisons). Morphological differences between all existing species in these two genera were also observed, but the group is morphologically complex, and these taxa are considered pseudocryptic. Nunduva and Kyrtuthrix remain morphologically and phylogenetically separate even with the addition of new species. However, how long will this remain the case? Many new genera and species of cyanobacteria have recently been described. Will the taxonomy of cyanobacteria eventually become saturated? Will we start to see multiple populations for the same cryptic species, or will future taxonomists collapse multiple species into fewer species, or multiple genera into single genera. The description of even more Nunduva and Kyrtuthrix species causes us to pause and evaluate the future of cyanobacterial taxonomy. These same questions are faced by algal taxonomists studying other phyla, and the resolution may ultimately be similar.
Collapse
Affiliation(s)
- Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, University of South Bohemia, Branišovská 1760, Česke Budějovice, 370 05, Czech Republic
| | - Laura González-Resendiz
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana- Cuajimalpa, Av. Vasco de Quiroga 4871, Ciudad de México, C.P. 053000, Mexico
| | - Viviana Escobar-Sánchez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - Claudia Segal-Kischinevzky
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - José Martínez-Yerena
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - Joaquín Hernández-Sánchez
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - Gabriela Hernández-Pérez
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - Hilda León-Tejera
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| |
Collapse
|
7
|
Tan HT, Yusoff FM, Khaw YS, Ahmad SA, Shaharuddin NA. Uncovering Research Trends of Phycobiliproteins Using Bibliometric Approach. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112358. [PMID: 34834721 PMCID: PMC8622606 DOI: 10.3390/plants10112358] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Phycobiliproteins are gaining popularity as long-term, high-value natural products which can be alternatives to synthetic products. This study analyzed research trends of phycobiliproteins from 1909 to 2020 using a bibliometric approach based on the Scopus database. The current findings showed that phycobiliprotein is a burgeoning field in terms of publications outputs with "biochemistry, genetics, and molecular biology" as the most related and focused subject. The Journal of Applied Phycology was the most productive journal in publishing articles on phycobiliproteins. Although the United States of America (U.S.A.) contributed the most publications on phycobiliproteins, the Chinese Academy of Sciences (China) is the institution with the largest number of publications. The most productive author on phycobiliproteins was Glazer, Alexander N. (U.S.A.). The U.S.A. and Germany were at the forefront of international collaboration in this field. According to the keyword analysis, the most explored theme was the optimization of microalgae culture parameters and phycobiliproteins extraction methods. The bioactivity properties and extraction of phycobiliproteins were identified as future research priorities. Synechococcus and Arthrospira were the most cited genera. This study serves as an initial step in fortifying the phycobiliproteins market, which is expected to exponentially expand in the future. Moreover, further research and global collaboration are necessary to commercialize phycobiliproteins and increase the consumer acceptability of the pigments and their products.
Collapse
Affiliation(s)
- Hui Teng Tan
- Aquatic Animal Health and Therapeutics Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (H.T.T.); (Y.S.K.)
| | - Fatimah Md. Yusoff
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Port Dickson 71050, Negeri Sembilan, Malaysia
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Yam Sim Khaw
- Aquatic Animal Health and Therapeutics Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (H.T.T.); (Y.S.K.)
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (S.A.A.); (N.A.S.)
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (S.A.A.); (N.A.S.)
| |
Collapse
|
8
|
Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria. mBio 2021; 12:e0087321. [PMID: 34060332 PMCID: PMC8262939 DOI: 10.1128/mbio.00873-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The mechanisms driving cyanobacterial harmful algal blooms (HABs) like those caused by Microcystis aeruginosa remain elusive, but improved defense against viral predation has been implicated for success in eutrophic environments. Our genus-level analyses of 139,023 genomes revealed that HAB-forming cyanobacteria carry vastly more restriction modification systems per genome (RMPG) than nearly all other prokaryotic genera, suggesting that viral defense is a cornerstone of their ecological success. In contrast, picocyanobacteria that numerically dominate nutrient-poor systems have the fewest RMPG within the phylum Cyanobacteria. We used classic resource competition models to explore the hypothesis that nutrient enrichments drive ecological selection for high RMPG due to increased host-phage contact rate. These classic models, agnostic to the mechanism of defense, explain how nutrient loading can select for increased RMPG but, importantly, fail to explain the extreme accumulation of these defense systems. However, extreme accumulation of RMPG can be achieved in a novel “memory” model that accounts for a unique activity of restriction modification systems: the accidental methylation of viral DNA by the methyltransferase. The methylated virus “remembers” the RM defenses of its former host and can evade these defenses if they are present in the next host. This viral memory leads to continual RM system devaluation; RMs accumulate extensively because the benefit of each addition is diminished. Our modeling leads to the hypothesis that nutrient loading and virion methylation drive the extreme accumulation of RMPG in HAB-forming cyanobacteria. Finally, our models suggest that hosts with different RMPG values can coexist when hosts have unique sets of RM systems.
Collapse
|
9
|
Labban A, Palacio AS, García FC, Hadaidi G, Ansari MI, López-Urrutia Á, Alonso-Sáez L, Hong PY, Morán XAG. Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain. Front Microbiol 2021; 12:612732. [PMID: 34040590 PMCID: PMC8141594 DOI: 10.3389/fmicb.2021.612732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24-34°C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94-1.38 d-1, was very similar (0.34 ± 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38-24.4 d-1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.
Collapse
Affiliation(s)
- Abbrar Labban
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Antonio S. Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Francisca C. García
- Environment and Sustainability Institute, University of Exeter, Penryn, United Kingdom
| | - Ghaida Hadaidi
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohd I. Ansari
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Gijón, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Gijón, Spain
| |
Collapse
|
10
|
Filling the Gaps in the Cyanobacterial Tree of Life-Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014. Genes (Basel) 2021; 12:genes12030389. [PMID: 33803228 PMCID: PMC8001431 DOI: 10.3390/genes12030389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022] Open
Abstract
Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.
Collapse
|
11
|
Fucich D, Xu Y, Sosa A, Jia Y, Zhang R, Jiao N, Chen F. Complete Genome Sequences of Chesapeake Bay Synechococcus Strains CBW1002 and CBW1006 Isolated in Winter. Genome Biol Evol 2021; 13:6126404. [PMID: 33528491 DOI: 10.1093/gbe/evab009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2021] [Indexed: 12/27/2022] Open
Abstract
Synechococcus are picocyanobacteria with a cosmopolitan distribution. They are capable of surviving in a wide variety of environmental conditions. Synechococcus have been isolated from the Chesapeake Bay during winter months, and they show an impressive tolerance to cold temperatures. Cold-adapted Synechococcus are unique and diverse, as they have complex phylogenetic lineages closely related to subalpine cluster II, Bornholm Sea cluster, CB7 cluster, and some novel lineages which are independent from summer estuarine strains in subcluster 5.2. CBW1002 and CBW1006 are the first complete genomes to represent Bornholm Sea cluster Synechococcus strains. They have some of the largest genomes among the Synechococcus (3.8 Mb) and share many unique and cryptic homologs which could give insight into their ability to tolerate such cold and dynamic conditions in the Chesapeake Bay estuary.
Collapse
Affiliation(s)
- Daniel Fucich
- The Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Ana Sosa
- The Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Yufeng Jia
- The Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Feng Chen
- The Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| |
Collapse
|
12
|
Tschoeke D, Salazar VW, Vidal L, Campeão M, Swings J, Thompson F, Thompson C. Unlocking the Genomic Taxonomy of the Prochlorococcus Collective. MICROBIAL ECOLOGY 2020; 80:546-558. [PMID: 32468160 DOI: 10.1007/s00248-020-01526-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.
Collapse
Affiliation(s)
- Diogo Tschoeke
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Vinicius W Salazar
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Livia Vidal
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Mariana Campeão
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Jean Swings
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
- Laboratory of Microbiology, Ghent University, Gent, Belgium
| | - Fabiano Thompson
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Cristiane Thompson
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil.
| |
Collapse
|
13
|
Pajares S, Varona-Cordero F, Hernández-Becerril DU. Spatial Distribution Patterns of Bacterioplankton in the Oxygen Minimum Zone of the Tropical Mexican Pacific. MICROBIAL ECOLOGY 2020; 80:519-536. [PMID: 32415330 DOI: 10.1007/s00248-020-01508-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 03/23/2020] [Indexed: 05/16/2023]
Abstract
Microbial communities within oxygen minimum zones (OMZs) are crucial drivers of marine biogeochemical cycles; however, we still lack an understanding of how these communities are distributed across an OMZ. We explored vertical (from 5 to 500 m depth) and horizontal (coast to open ocean) distribution of bacterioplankton and its relationships with the main oceanographic conditions in three transects of the tropical Mexican Pacific OMZ. The distribution of the microbial diversity and the main clades changed along the transition from oxygen-rich surface water to the OMZ core, demonstrating the sensitivity of key bacterial groups to deoxygenation. The euphotic zone was dominated by Synechococcales, followed by Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales, whereas the OMZ core was dominated by SAR11, followed by SAR406, SAR324, SAR202, UBA10353 marine group, Thiomicrospirales and Nitrospinales. The marked environmental gradients along the water column also supported a high potential for niche partitioning among OMZ microorganisms. Additionally, in the OMZ core, bacterial assemblages from the same water mass were more similar to each other than those from another water mass. There were also important differences between coastal and open-ocean communities: Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales were more abundant in coastal areas, while Synechococcales, SAR406, SAR324, SAR202, UBA10353 marine group, and Thiomicrospirales were more abundant in the open ocean. Our results suggest a biogeographic structure of the bacterioplankton in this OMZ region, with limited community mixing across water masses, except in upwelling events, and little dispersion of the community by currents in the euphotic zone.
Collapse
Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Institute of Marine Sciences and Limnology, National Autonomous University of Mexico, Mexico City, Mexico.
| | - Francisco Varona-Cordero
- Unidad Académica de Ecología y Biodiversidad Acuática, Institute of Marine Sciences and Limnology, National Autonomous University of Mexico, Mexico City, Mexico
| | - David Uriel Hernández-Becerril
- Unidad Académica de Ecología y Biodiversidad Acuática, Institute of Marine Sciences and Limnology, National Autonomous University of Mexico, Mexico City, Mexico
| |
Collapse
|
14
|
Doré H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, Pitt FD, Ostrowski M, Six C, Brillet-Guéguen L, Hoebeke M, Bisch A, Le Corguillé G, Corre E, Labadie K, Aury JM, Wincker P, Choi DH, Noh JH, Eveillard D, Scanlan DJ, Partensky F, Garczarek L. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria. Front Microbiol 2020; 11:567431. [PMID: 33042072 PMCID: PMC7522525 DOI: 10.3389/fmicb.2020.567431] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
Abstract
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.
Collapse
Affiliation(s)
- Hugo Doré
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gregory K Farrant
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ulysse Guyet
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Julie Haguait
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Florian Humily
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Morgane Ratin
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Frances D Pitt
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Martin Ostrowski
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Christophe Six
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Loraine Brillet-Guéguen
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France.,Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Mark Hoebeke
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Antoine Bisch
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gildas Le Corguillé
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Erwan Corre
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Jean-Marc Aury
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Évry, France
| | - Dong Han Choi
- Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea.,Ocean Science and Technology School, Korea Maritime and Ocean University, Busan, South Korea
| | - Jae Hoon Noh
- Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea.,Department of Marine Biology, Korea University of Science and Technology, Daejeon, South Korea
| | - Damien Eveillard
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France.,Research Federation (FR2022) Tara Océans GO-SEE, Paris, France
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Frédéric Partensky
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France.,Research Federation (FR2022) Tara Océans GO-SEE, Paris, France
| |
Collapse
|
15
|
Salazar VW, Tschoeke DA, Swings J, Cosenza CA, Mattoso M, Thompson CC, Thompson FL. A new genomic taxonomy system for the Synechococcus collective. Environ Microbiol 2020; 22:4557-4570. [PMID: 32700350 DOI: 10.1111/1462-2920.15173] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022]
Abstract
Cyanobacteria of the genus Synechococcus are major contributors to global primary productivity and are found in a wide range of aquatic ecosystems. This Synechococcus collective (SC) is metabolically diverse, with some lineages thriving in polar and nutrient-rich locations and others in tropical or riverine waters. Although many studies have discussed the ecology and evolution of the SC, there is a paucity of knowledge on its taxonomic structure. Thus, we present a new taxonomic classification framework for the SC based on recent advances in microbial genomic taxonomy. Phylogenomic analyses of 1085 cyanobacterial genomes demonstrate that organisms classified as Synechococcus are polyphyletic at the order rank. The SC is classified into 15 genera, which are placed into five distinct orders within the phylum Cyanobacteria: (i) Synechococcales (Cyanobium, Inmanicoccus, Lacustricoccus gen. Nov., Parasynechococcus, Pseudosynechococcus, Regnicoccus, Synechospongium gen. nov., Synechococcus and Vulcanococcus); (ii) Cyanobacteriales (Limnothrix); (iii) Leptococcales (Brevicoccus and Leptococcus); (iv) Thermosynechococcales (Stenotopis and Thermosynechococcus) and (v) Neosynechococcales (Neosynechococcus). The newly proposed classification is consistent with habitat distribution patterns (seawater, freshwater, brackish and thermal environments) and reflects the ecological and evolutionary relationships of the SC.
Collapse
Affiliation(s)
- Vinícius W Salazar
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Department of Systems and Computer Engineering, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo A Tschoeke
- Department of Biomedical Engineering, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Jean Swings
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - Carlos A Cosenza
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Marta Mattoso
- Department of Systems and Computer Engineering, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane C Thompson
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| |
Collapse
|
16
|
Fucich D, Chen F. Presence of toxin-antitoxin systems in picocyanobacteria and their ecological implications. ISME JOURNAL 2020; 14:2843-2850. [PMID: 32814864 DOI: 10.1038/s41396-020-00746-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 07/22/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022]
Abstract
Picocyanobacteria (mainly Synechococcus and Prochlorococcus) contribute significantly to ocean's primary production. Toxin-Antitoxin (TA) systems present in bacteria and archaea are known to regulate cell growth in response to environmental stresses. However, little is known about the presence of TA systems in picocyanobacteria. This study investigated complete genomes of Synechococcus and Prochlorococcus to understand the prevalence of TA systems in picocyanobacteria. Using the TAfinder software, Type II TA systems were predicted in 27 of 33 (81%) Synechococcus strains, but none of 38 Prochlorococcus strains contain TA genes. Synechococcus strains with larger genomes tend to contain more putative type II TA systems. The number of TA pairs varies from 0 to 42 in Synechococcus strains isolated from various environments. A linear correlation between the genome size and the number of putative TA systems in both coastal and freshwater Synechococcus was established. In general, open ocean Synechococcus contain no or few TA systems, while coastal and freshwater Synechococcus contain more TA systems. The type II TA systems inhibit microbial translation via ribonucleases and allow cells to enter the "dormant" stage in adverse environments. Inheritance of TA genes in freshwater and coastal Synechococcus could confer a recoverable persister mechanism important to survive in variable environments.
Collapse
Affiliation(s)
- Daniel Fucich
- The Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Feng Chen
- The Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA.
| |
Collapse
|
17
|
Tromas N, Taranu ZE, Castelli M, Pimentel JSM, Pereira DA, Marcoz R, Shapiro BJ, Giani A. The evolution of realized niches within freshwater
Synechococcus. Environ Microbiol 2020; 22:1238-1250. [DOI: 10.1111/1462-2920.14930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Nicolas Tromas
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - Zofia E. Taranu
- Environnement et Changement Climatique Canada 105 Rue McGill, Montréal QC H2Y 2E7 Canada
| | | | | | - Daniel A. Pereira
- Federal University of Minas Gerais Belo Horizonte Minas Gerais Brazil
| | - Romane Marcoz
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - B. Jesse Shapiro
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - Alessandra Giani
- Federal University of Minas Gerais Belo Horizonte Minas Gerais Brazil
| |
Collapse
|
18
|
Casamatta DA, Villanueva CD, Garvey AD, Stocks HS, Vaccarino M, Dvořák P, Hašler P, Johansen JR. Reptodigitus Chapmanii (Nostocales, Hapalosiphonaceae) Gen. Nov.: A Unique Nostocalean (Cyanobacteria) Genus Based on a Polyphasic Approach 1. JOURNAL OF PHYCOLOGY 2020; 56:425-436. [PMID: 31837017 DOI: 10.1111/jpy.12954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
The Nostocales is a monophyletic, heterocytous lineage of cyanobacteria capable of akinete production and division in multiple planes, depending upon family-level clade. While present in a variety of ecosystems, the diversity of the Nostocales has been poorly elucidated. Due to environmentally -induced phenotypic plasticity, morphology alone is often insufficient to determine the true phylogenetic placement of these taxa. In order to bridge this gap, taxonomists now employ the polyphasic approach, combining methods such as morphological analysis, phylogenetic analysis based on DNA sequence and genetic identity based on ribosomal genes, and secondary structure of the 16S-23S ITS and 16S rRNA gene sequences, as well as ecological characterization. Using this combined approach, a new genus and species (Reptodigitus chapmanii gen. et sp. nov.) isolated from the St. Johns River (Jacksonville, Florida, USA) within the Nostocales is herein described. Phylogenetic analyses place this taxon within the Hapalosiphonaceae, sister to the clade containing Fischerella, Hapalosiphon, and Westiellopsis. The 16S-23S ITS secondary folding structure analysis also supports the erection of this new genus.
Collapse
Affiliation(s)
- Dale A Casamatta
- Department of Biology, University of North Florida, Jacksonville, Florida, 32224, USA
| | - Chelsea D Villanueva
- Department of Biology, University of North Florida, Jacksonville, Florida, 32224, USA
| | - Alyssa D Garvey
- Department of Biology, University of North Florida, Jacksonville, Florida, 32224, USA
| | - Holly S Stocks
- Department of Biology, University of North Florida, Jacksonville, Florida, 32224, USA
| | - Melissa Vaccarino
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc, CZ-783 71, Czech Republic
| | - Petr Hašler
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc, CZ-783 71, Czech Republic
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| |
Collapse
|
19
|
Burgsdorf I, Handley KM, Bar-Shalom R, Erwin PM, Steindler L. Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont. mSystems 2019; 4:e00057-19. [PMID: 31086829 PMCID: PMC6506613 DOI: 10.1128/msystems.00057-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/02/2019] [Indexed: 02/06/2023] Open
Abstract
"Candidatus Synechococcus feldmannii" is a facultative intracellular symbiont of the Atlanto-Mediterranean sponge Petrosia ficiformis. Genomic information of sponge-associated cyanobacteria derives thus far from the obligate and extracellular symbiont "Candidatus Synechococcus spongiarum." Here we utilized a differential methylation-based approach for bacterial DNA enrichment combined with metagenomics to obtain the first draft genomes of "Ca. Synechococcus feldmannii." By comparative genomics, we revealed that some genomic features (e.g., iron transport mediated by siderophores, eukaryotic-like proteins, and defense mechanisms, like CRISPR-Cas [clustered regularly interspaced short palindromic repeats-associated proteins]) are unique to both symbiont types and absent or rare in the genomes of taxonomically related free-living cyanobacteria. These genomic features likely enable life under the conditions found inside the sponge host. Interestingly, there are many genomic features that are shared by "Ca. Synechococcus feldmannii" and free-living cyanobacteria, while they are absent in the obligate symbiont "Ca. Synechococcus spongiarum." These include genes related to cell surface structures, genetic regulation, and responses to environmental stress, as well as the composition of photosynthetic genes and DNA metabolism. We speculate that the presence of these genes confers on "Ca. Synechococcus feldmannii" its facultative nature (i.e., the ability to respond to a less stable environment when free-living). Our comparative analysis revealed that distinct genomic features depend on the nature of the symbiotic interaction: facultative and intracellular versus obligate and extracellular. IMPORTANCE Given the evolutionary position of sponges as one of the earliest phyla to depart from the metazoan stem lineage, studies on their distinct and exceptionally diverse microbial communities should yield a better understanding of the origin of animal-bacterium interactions. While genomes of several extracellular sponge symbionts have been published, the intracellular symbionts have, so far, been elusive. Here we compare the genomes of two unicellular cyanobacterial sponge symbionts that share an ancestor but followed different evolutionary paths-one became intracellular and the other extracellular. Counterintuitively, the intracellular cyanobacteria are facultative, while the extracellular ones are obligate. By sequencing the genomes of the intracellular cyanobacteria and comparing them to the genomes of the extracellular symbionts and related free-living cyanobacteria, we show how three different cyanobacterial lifestyles are reflected by adaptive genomic features.
Collapse
Affiliation(s)
- Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Patrick M. Erwin
- Department of Biology and Marine Biology, Centre for Marine Science, University of North Carolina—Wilmington, Wilmington, North Carolina, USA
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| |
Collapse
|
20
|
Gan HM, Lee MVL, Savka MA. Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4. PeerJ 2019; 7:e6366. [PMID: 30775173 PMCID: PMC6369824 DOI: 10.7717/peerj.6366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/20/2018] [Indexed: 12/21/2022] Open
Abstract
The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
Collapse
Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Melvin V L Lee
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Michael A Savka
- College of Science, The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| |
Collapse
|
21
|
Sánchez-Baracaldo P, Bianchini G, Di Cesare A, Callieri C, Chrismas NAM. Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes ( mpeBA and cpeBA). Front Microbiol 2019; 10:45. [PMID: 30761097 PMCID: PMC6363710 DOI: 10.3389/fmicb.2019.00045] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/11/2019] [Indexed: 11/13/2022] Open
Abstract
Marine picocyanobacteria, Prochlorococcus and Synechococcus, substantially contribute to marine primary production and have been the subject of extensive ecological and genomic studies. Little is known about their close relatives from freshwater and non-marine environments. Phylogenomic analyses (using 136 proteins) provide strong support for the monophyly of a clade of non-marine picocyanobacteria consisting of Cyanobium, Synechococcus and marine Sub-cluster 5.2; this clade itself is sister to marine Synechococcus and Prochlorococcus. The most basal lineage within the Syn/Pro clade, Sub-Cluster 5.3, includes marine and freshwater strains. Relaxed molecular clock (SSU, LSU) analyses show that while ancestors of the Syn/Pro clade date as far back as the end of the Pre-Cambrian, modern crown groups evolved during the Carboniferous and Triassic. Comparative genomic analyses reveal novel gene cluster arrangements involved in phycobilisome (PBS) metabolism in freshwater strains. Whilst PBS genes in marine Synechococcus are mostly found in one type of phycoerythrin (PE) rich gene cluster (Type III), strains from non-marine habitats, so far, appear to be more diverse both in terms of pigment content and gene arrangement, likely reflecting a wider range of habitats. Our phylogenetic analyses show that the PE genes (mpeBA) evolved via a duplication of the cpeBA genes in an ancestor of the marine and non-marine picocyanobacteria and of the symbiotic strains Synechococcus spongiarum. A 'primitive' Type III-like ancestor containing cpeBA and mpeBA had thus evolved prior to the divergence of the Syn/Pro clade and S. spongiarum. During the diversification of Synechococcus lineages, losses of mpeBA genes may explain the emergence of pigment cluster Types I, II, IIB, and III in both marine and non-marine habitats, with few lateral gene transfer events in specific taxa.
Collapse
Affiliation(s)
| | - Giorgio Bianchini
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Andrea Di Cesare
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
- Department of Earth, Environment and Life Sciences, University of Genoa, Genoa, Italy
| | - Cristiana Callieri
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
| | - Nathan A. M. Chrismas
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
- The Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| |
Collapse
|
22
|
Affe HMDJ, Rigonato J, Nunes JMDC, Menezes M. Metagenomic Analysis of Cyanobacteria in an Oligotrophic Tropical Estuary, South Atlantic. Front Microbiol 2018; 9:1393. [PMID: 29997603 PMCID: PMC6029486 DOI: 10.3389/fmicb.2018.01393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 06/07/2018] [Indexed: 11/20/2022] Open
Abstract
This study assessed the species composition, distribution, and functional profiles of cyanobacteria in Camamu Bay, a tropical oligotrophic estuarine system on the northeast coast of Brazil, using shotgun metagenomic sequencing. Surface-water samples were evaluated in two different rainfall periods (rainy and dry seasons), at nine stations in the three hydrodynamic regions of the bay. At a fixed sampling station, on each season, samples were taken over a tidal cycle at 3-h intervals over 12 h. A total of 219 cyanobacterial taxa were identified, demonstrating a diverse community of freshwater, euryhaline, and marine cyanobacteria. The genera of greater relative abundance, Synechococcus and Prochlorococcus, corresponded to the picoplankton fraction. Although Camamu Bay has conspicuous marine characteristics, the contribution of freshwater during the rainy season caused variation in cyanobacteria community, with an increase in species richness. Due the high prevalence of Synechococcus (90% of the sequences), the functional analysis revealed only minor differences in gene content between the dry and rainy seasons. In both rainy and dry seasons, an increase in Prochlorococcus relative abundance occurred during high tide, demonstrating the tidal influence in the bay. The environmental characteristics of the bay provide niche conditions for a wide variety of cyanobacteria, including freshwater, euryhaline, and marine strains.
Collapse
Affiliation(s)
- Helen M de Jesus Affe
- Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Janaina Rigonato
- Centro de Energia Nuclear e Agricultura, Universidade de São Paulo, Piracicaba, Brazil.,CEA, Centre de Sequençage Genoscope, Institut de Biologie François Jacob, Evry, France
| | - José M de Castro Nunes
- Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Mariângela Menezes
- Laboratório de Ficologia, Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
23
|
Coutinho FH, Gregoracci GB, Walter JM, Thompson CC, Thompson FL. Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses. Trends Microbiol 2018; 26:955-965. [PMID: 29937307 DOI: 10.1016/j.tim.2018.05.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 01/31/2023]
Abstract
Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus-host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.
Collapse
Affiliation(s)
- Felipe Hernandes Coutinho
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Evolutionary Genomics Group, Departamento de Produccíon Vegetal y Microbiología, Universidad Miguel Hernández (UMH), Alicante, Spain
| | | | - Juline Marta Walter
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Carneiro Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Federal Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| |
Collapse
|
24
|
Mogany T, Swalaha FM, Allam M, Mtshali PS, Ismail A, Kumari S, Bux F. Phenotypic and genotypic characterisation of an unique indigenous hypersaline unicellular cyanobacterium, Euhalothece sp.nov. Microbiol Res 2018; 211:47-56. [PMID: 29705205 DOI: 10.1016/j.micres.2018.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 02/16/2018] [Accepted: 04/02/2018] [Indexed: 11/28/2022]
Abstract
A novel halotolerant species of cyanobacterium of the order Chroococcales was isolated from hypersaline estuary in Kwa-Zulu Natal, South Africa. A comprehensive polyphasic approach viz., cell morphology, pigment composition and complete genome sequence analysis was conducted to elucidate the taxonomic position of the isolated strain. The blue-green oval to rod-shaped cells were 14-18 μm in size, and contained a high amount of phycocyanin pigments. The strain was moderate thermotolerant/alkalitolerant halophile with the optimum conditions for growth at 35 °C, pH 8.5 and 120 g/l of NaCl. Based on 16S rRNA gene sequence phylogeny, the strain was related to members of the 'Euhalothece' subcluster (99%). The whole genome sequence was determined, and the annotated genes showed a 90% sequence similarity to the gas-vacuolate, spindle-shaped Dactylococcopsis salina PCC 8305. The size of the genome was determined to be 5,113,178 bp and contained 4332 protein-coding genes and 69 RNA genes with a G + C content of 46.7%. Genes encoding osmoregulation, oxidative stress, heat shock, persister cells, and UV-absorbing secondary metabolites, among others, were identified. Based on the phylogenetic analysis of the 16S rRNA gene sequences, physiological data, pigment compositions and genomic data, the strain is considered to represent a novel species of Euhalothece.
Collapse
Affiliation(s)
- Trisha Mogany
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, South Africa
| | - Feroz M Swalaha
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4001, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, 2192, Johannesburg, South Africa
| | - Phillip Senzo Mtshali
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, 2192, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, 2192, Johannesburg, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, South Africa.
| |
Collapse
|
25
|
Moldovan MA, Gelfand MS. Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. Front Microbiol 2018; 9:428. [PMID: 29593678 PMCID: PMC5857598 DOI: 10.3389/fmicb.2018.00428] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/23/2018] [Indexed: 11/13/2022] Open
Abstract
The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature. However, it has revealed that abundant marine cyanobacteria Prochlorococcus marinus should be divided into two species. As a control we have confirmed the paraphyletic origin of Yersinia pseudotuberculosis (with embedded, monophyletic Y. pestis) and Burkholderia pseudomallei (with B. mallei). We also demonstrate that by our definition and in accordance with recent studies Escherichia coli and Shigella spp. are one species.
Collapse
Affiliation(s)
- Mikhail A. Moldovan
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (RAS), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail S. Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (RAS), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
| |
Collapse
|
26
|
Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model. ISME JOURNAL 2018; 12:1180-1187. [PMID: 29330536 DOI: 10.1038/s41396-017-0023-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 11/14/2017] [Accepted: 11/21/2017] [Indexed: 01/13/2023]
Abstract
An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model. The model simulates 2 × 108 cells, which allows random genetic drift to act in a realistic manner. Each cell has a whole genome subject to base-substitution mutation and recombination, which affect the carbon and nitrogen requirements of DNA and protein pools. Nonsynonymous changes can be functionally deleterious. Together, these factors affect the growth and fitness. Simulations show that experimentally determined mutation bias toward GC is not sufficient to build the GC-rich genome of DSS-3. While nitrogen availability has been repeatedly hypothesized to drive the evolution of GC content in marine bacterioplankton, our model instead predicts that DSS-3 and its ancestors have been evolving in environments primarily limited by carbon.
Collapse
|
27
|
Kim Y, Jeon J, Kwak MS, Kim GH, Koh I, Rho M. Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons. PLoS One 2018; 13:e0190266. [PMID: 29293601 PMCID: PMC5749766 DOI: 10.1371/journal.pone.0190266] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/11/2017] [Indexed: 12/27/2022] Open
Abstract
Synechococcus is an important photosynthetic picoplankton in the temperate to tropical oceans. As a photosynthetic bacterium, Synechococcus has an efficient mechanism to adapt to the changes in salinity and light intensity. The analysis of the distributions and functions of such microorganisms in the ever changing river mouth environment, where freshwater and seawater mix, should help better understand their roles in the ecosystem. Toward this objective, we have collected and sequenced the ocean microbiome in the river mouth of Kwangyang Bay, Korea, as a function of salinity and temperature. In conjunction with comparative genomics approaches using the sequenced genomes of a wide phylogeny of Synechococcus, the ocean microbiome was analyzed in terms of their composition and clade-specific functions. The results showed significant differences in the compositions of Synechococcus sampled in different seasons. The photosynthetic functions in such enhanced Synechococcus strains were also observed in the microbiomes in summer, which is significantly different from those in other seasons.
Collapse
Affiliation(s)
- Yihwan Kim
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea
| | - Jehyun Jeon
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea
| | - Min Seok Kwak
- Department of Biology, Kongju National University, Kongju, Korea
| | - Gwang Hoon Kim
- Department of Biology, Kongju National University, Kongju, Korea
| | - InSong Koh
- Department of Biomedical Informatics, Hanyang University, Seoul, Korea
| | - Mina Rho
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea
- Department of Biomedical Informatics, Hanyang University, Seoul, Korea
- * E-mail:
| |
Collapse
|
28
|
Walter JM, Coutinho FH, Dutilh BE, Swings J, Thompson FL, Thompson CC. Ecogenomics and Taxonomy of Cyanobacteria Phylum. Front Microbiol 2017; 8:2132. [PMID: 29184540 PMCID: PMC5694629 DOI: 10.3389/fmicb.2017.02132] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/18/2017] [Indexed: 01/15/2023] Open
Abstract
Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.
Collapse
Affiliation(s)
- Juline M Walter
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Felipe H Coutinho
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Bas E Dutilh
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Jean Swings
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Center of Technology - CT2, SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane C Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
29
|
|
30
|
Coutinho FH, Dutilh BE, Thompson CC, Thompson FL. Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features. Arch Microbiol 2016; 198:973-986. [PMID: 27339259 DOI: 10.1007/s00203-016-1256-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/23/2016] [Accepted: 06/07/2016] [Indexed: 01/24/2023]
Abstract
Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.
Collapse
Affiliation(s)
- F H Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - B E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - C C Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - F L Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- COPPE, SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- CCS, IB, BIOMAR, Laboratório de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho. S/N, BLOCO A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, 21941-599, Brazil.
| |
Collapse
|