scholarly journals Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities

mBio ◽  
2021 ◽  
Vol 12 (3) ◽  
Author(s):  
Chelsea L. Murphy ◽  
Andriy Sheremet ◽  
Peter F. Dunfield ◽  
John R. Spear ◽  
Ramunas Stepanauskas ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Genomic Analysis ◽  
Freshwater Ecosystems ◽  
Marine Sponges ◽  
Comparative Genomic ◽  
Specific Substrate ◽  
Biosynthetic Pathways ◽  
Wide Range ◽  
Globally Distributed ◽  
Alkane Hydroxylases

ABSTRACT The recent leveraging of genome-resolved metagenomics has generated an enormous number of genomes from novel uncultured microbial lineages yet left many clades undescribed. Here, we present a global analysis of genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, and chloromethanes as the substrates. Methylotrophy in Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e., the utilization of diverse sets of genes, pathways, and combinations to achieve a specific metabolic goal. The genomes also encoded multiple alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β- and γ-carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified, although absence of key genes and failure to identify a photosynthetic reaction center preclude proposing phototrophic capacities. Analysis of 16S rRNA databases showed the preferences of Binatota to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges, supporting their potential role in mitigating methanol and methane emissions, breakdown of alkanes, and their association with sponges. Our results expand the lists of methylotrophic, aerobic alkane-degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion. IMPORTANCE A wide range of microbial lineages remain uncultured, yet little is known regarding their metabolic capacities, physiological preferences, and ecological roles in various ecosystems. We conducted a thorough comparative genomic analysis of 108 genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. We present evidence that members of the order Binatota specialize in methylotrophy and identify an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C1) compounds in Binatota genomes. The occurrence of multiple alkane hydroxylases and monooxygenases in these genomes was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids production. We also report on the presence of incomplete chlorophyll biosynthetic pathways in all genomes and propose several evolutionary-grounded scenarios that could explain such a pattern. Assessment of the ecological distribution patterns of the Binatota indicates preference of its members to terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.

scholarly journals Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

2020 ◽  
Author(s):  
Chelsea Murphy ◽  
Peter Dunfield ◽  
Andriy Sheremet ◽  
John Spear ◽  
Ramunas Stepanauskas ◽  
...  
Keyword(s):  
Global Analysis ◽  
Photosynthetic Reaction Center ◽  
Freshwater Ecosystems ◽  
Specific Substrate ◽  
Alkane Degradation ◽  
Microbial Genomes ◽  
Metabolic Versatility ◽  
Wide Range ◽  
Globally Distributed ◽  
Alkane Hydroxylases

Abstract The recent leveraging of genome-resolved metagenomics has opened a treasure trove of genomes from novel uncultured microbial lineages, yet left many clades undescribed. We here present a global analysis of genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in the Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, chloromethanes, and potentially methane as substrates. Methylotrophy in the Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e. the utilization of diverse sets of genes, pathways and combinations to achieve a specific metabolic goal. The genomes also encoded an arsenal of alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β and γ carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified; although absence of key genes and failure to identify a photosynthetic reaction center precludes proposing phototrophic capacities. Analysis of 16S rRNA databases showed Binatota’s preferences to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges supporting their suggested potential role in mitigating methanol and methane emissions, alkanes degradation, and nutritional symbiosis with sponges. Our results expand the lists of methylotrophic, aerobic alkane degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways and gene shrapnel in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.

scholarly journals Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

2020 ◽  
Author(s):  
Chelsea L. Murphy ◽  
Peter F. Dunfield ◽  
Andriy Sheremet ◽  
John R. Spear ◽  
Ramunas Stepanauskas ◽  
...  
Keyword(s):  
Global Analysis ◽  
Photosynthetic Reaction Center ◽  
Freshwater Ecosystems ◽  
Specific Substrate ◽  
Alkane Degradation ◽  
Microbial Genomes ◽  
Metabolic Versatility ◽  
Wide Range ◽  
Globally Distributed ◽  
Alkane Hydroxylases

AbstractThe recent leveraging of genome-resolved metagenomics has opened a treasure trove of genomes from novel uncultured microbial lineages, yet left many clades undescribed. We here present a global analysis of genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in the Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, chloromethanes, and potentially methane as substrates. Methylotrophy in the Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e. the utilization of diverse sets of genes, pathways and combinations to achieve a specific metabolic goal. The genomes also encoded an arsenal of alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β and γ carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified; although absence of key genes and failure to identify a photosynthetic reaction center precludes proposing phototrophic capacities. Analysis of 16S rRNA databases showed Binatota’s preferences to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges supporting their suggested potential role in mitigating methanol and methane emissions, alkanes degradation, and nutritional symbiosis with sponges. Our results expand the lists of methylotrophic, aerobic alkane degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways and gene shrapnel in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.

scholarly journals Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 298
Author(s):  
Despoina Konstantinou ◽  
Rafael V. Popin ◽  
David P. Fewer ◽  
Kaarina Sivonen ◽  
Spyros Gkelis
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Genome Reduction ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Symbiotic Relationships ◽  
Genes Encoding

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.

scholarly journals Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

2022 ◽  
Vol 12 ◽  
Author(s):  
Eiseul Kim ◽  
Seung-Min Yang ◽  
Dayoung Kim ◽  
Hae-Yeong Kim
Keyword(s):  
Complete Genome ◽  
Functional Characterization ◽  
Genomic Analysis ◽  
Raw Milk ◽  
Phenotypic Characterization ◽  
Comparative Genomic ◽  
Probiotic Properties ◽  
Bacterial Strains ◽  
Physiological Control ◽  
Wide Range

Lacticaseibacillus casei, Lacticaseibacillus chiayiensis, and Lacticaseibacillus zeae are very closely related Lacticaseibacillus species. L. casei has long been proposed as a probiotic, whereas studies on functional characterization for L. chiayiensis and L. zeae are some compared to L. casei. In this study, L. casei FBL6, L. chiayiensis FBL7, and L. zeae FBL8 were isolated from raw milk, and their probiotic properties were investigated. Genomic analysis demonstrated the role of L. chiayiensis and L. zeae as probiotic candidates. The three strains were tolerant to acid and bile salt, with inhibitory action against pathogenic bacterial strains and capacity of antioxidants. Complete genome sequences of the three strains were analyzed to highlight the probiotic properties at the genetic level, which results in the discovery of genes corresponding to phenotypic characterization. Moreover, genes known to confer probiotic characteristics were identified, including genes related to biosynthesis, defense machinery, adhesion, and stress adaptation. The comparative genomic analysis with other available genomes revealed 256, 214, and 32 unique genes for FBL6, FBL7, and FBL8, respectively. These genomes contained individual genes encoding proteins that are putatively involved in carbohydrate transport and metabolism, prokaryotic immune system for antiviral defense, and physiological control processes. In particular, L. casei FBL6 had a bacteriocin gene cluster that was not present in other genomes of L. casei, resulting in this strain may exhibit a wide range of antimicrobial activity compared to other L. casei strains. Our data can help us understand the probiotic functionalities of the three strains and suggest that L. chiayiensis and L. zeae species, which are closely related to L. casei, can also be considered as novel potential probiotic candidate strains.

scholarly journals Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales

2020 ◽  
Author(s):  
Laura A. Zinke ◽  
Paul N. Evans ◽  
Alena L. Schroeder ◽  
Donovan H. Parks ◽  
Ruth K. Varner ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic ◽  
New Order ◽  
Hydrogen Metabolism ◽  
Metabolic Potential ◽  
Conventional View ◽  
Sedimentary Environments ◽  
History Of ◽  
Subarctic Lake ◽  
Globally Distributed

AbstractRecent discoveries of mcr and mcr-like complexes in genomes from diverse archaeal lineages suggest that methane (and more broadly alkane) metabolism is an ancient pathway with complicated evolutionary histories. The conventional view is that methanogenesis is an ancestral metabolism of the archaeal class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs), we show that these microorganisms do not encode the genes required for methanogenesis, which suggests that this metabolism may have been laterally acquired by an ancestor of the order Methanomassiliicoccales. These MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG (95% complete) that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, such as heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two of these lineages are globally widespread among anoxic, sedimentary environments, with the exception of Ca. Lunaplasma lacustris, which has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide new insights into the evolutionary history of methanogenesis within the Thermoplasmata.

scholarly journals Comparative genomic analysis reveals a monophyletic cold adapted Arthrobacter cluster from polar and alpine regions

2019 ◽  
Author(s):  
Liang Shen ◽  
Yongqin Liu ◽  
Baiqing Xu ◽  
Ninglian Wang ◽  
Sten Anslan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Low Temperature ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Cold Adapted ◽  
Monophyletic Cluster ◽  
Alpine Regions ◽  
Wide Range

AbstractDecrease in the frequency of arginine and increase in lysine are the trends that have been identified in the genomes of cold adapted bacteria. However, some cold adapted taxa show only limited or no detectable changes in the frequencies of amino acid composition. Here, we examined Arthrobacter spp. genomes from a wide range of environments on whether the genomic adaptations can be conclusively identified across genomes of taxa from polar and alpine regions. Phylogenetic analysis with a concatenated alignment of 119 orthologous proteins revealed a monophyletic clustering of seven polar and alpine isolated strains. Significant changes in amino acid composition related to cold adaptation were exclusive to seven of the twenty-nine strains from polar and alpine regions. Analysis of significant indicator genes and cold shock genes also revealed that clear differences could only be detected in the same seven strains. These unique characteristics may result from a vast exchange of genome content at the node leading to the monophyletic cold adapted Arthrobacter cluster predicted by the birth-and-death model. We then experimentally validated that strains with significant changes in amino acid composition have a better capacity to grow at low temperature than the mesophilic strains.ImportanceAcquisition of novel traits through horizontal gene transfer at the early divergence of the monophyletic cluster may accelerate their adaptation to low temperature. Our study reached a clear relationship between adaptation to cold and genomic features and would advanced in understanding the ambiguous results produced by the previous studies on genomic adaption to cold temperature.

scholarly journals Genome-wide characterization, evolutionary analysis of WRKY genes in Cucurbitaceae species and assessment of its roles in resisting to powdery mildew disease

2018 ◽  
Author(s):  
Zigao Jiao ◽  
Jianlei Sun ◽  
Chongqi Wang ◽  
Yumei Dong ◽  
Shouhua Xiao ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Large Family ◽  
Comparative Genomic ◽  
Evolutionary Analysis ◽  
Multiple Sequence ◽  
Wide Range ◽  
Wrky Proteins

AbstractThe WRKY proteins constitute a large family of transcription factors that have been known to play a wide range of regulatory roles in multiple biological processes. Over the past few years, many reports have focused on analysis of evolution and biological function of WRKY genes at the whole genome level in different plant species. However, little information is known about WRKY genes in melon (Cucumis melo L.). In the present study, a total of 56 putative WRKY genes were identified in melon, which were randomly distributed on their respective chromosomes. A multiple sequence alignment and phylogenetic analysis using melon, cucumber and watermelon predicted WRKY domains indicated that melon WRKY proteins could be classified into three main groups (I-III). Our analysis indicated that no recent duplication events of WRKY genes were detected in melon, and strong purifying selection was observed among the 85 orthologous pairs of Cucurbitaceae species. Expression profiles of CmWRKY derived from RNA-seq data and quantitative RT-PCR (qRT-PCR) analyses showed distinct expression patterns in various tissues, and the expression of 16 CmWRKY were altered following powdery mildew infection in melon. Besides, we also found that a total of 24 WRKY genes were co-expressed with 11 VQ family genes in melon. Our comparative genomic analysis provides a foundation for future functional dissection and understanding the evolution of WRKY genes in cucurbitaceae species, and will promote powdery mildew resistance study in melon.

scholarly journals Comparative Genomic Analysis of Bacillus thuringiensis Reveals Molecular Adaptations to Copper Tolerance

2018 ◽  
Author(s):  
Low Yi Yik ◽  
Grace Joy Wei Lie Chin ◽  
Collin Glen Joseph ◽  
Kenneth Francis Rodrigues
Keyword(s):  
Bacillus Thuringiensis ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Copper Resistance ◽  
Copper Tolerance ◽  
Contaminated Site ◽  
Comparative Genomic ◽  
Wide Range ◽  
Almost All

ABSTRACTBacillus thuringiensis is a type of Gram positive and rod shaped bacterium that is found in a wide range of habitats. Despite the intensive studies conducted on this bacterium, most of the information available are related to its pathogenic characteristics, with only a limited number of publications mentioning its ability to survive in extreme environments. Recently, a B. thuringiensis MCMY1 strain was successfully isolated from a copper contaminated site in Mamut Copper Mine, Sabah. This study aimed to conduct a comparative genomic analysis by using the genome sequence of MCMY1 strain published in GenBank (PRJNA374601) as a target genome for comparison with other available B. thuringiensis genomes at the GenBank. Whole genome alignment, Fragment all-against-all comparison analysis, phylogenetic reconstruction and specific copper genes comparison were applied to all forty-five B. thuringiensis genomes to reveal the molecular adaptation to copper tolerance. The comparative results indicated that B. thuringiensis MCMY1 strain is closely related to strain Bt407 and strain IS5056. This strain harbors almost all available copper genes annotated from the forty-five B. thuringiensis genomes, except for the gene for Magnesium and cobalt efflux protein (CorC) which plays an indirect role in reducing the oxidative stress that caused by copper and other metal ions. Furthermore, the findings also showed that the Copper resistance gene family, CopABCDZ and its repressor (CsoR) are conserved in almost all sequenced genomes but the presence of the genes for Cytoplasmic copper homeostasis protein (CutC) and CorC across the sample genomes are highly inconsonant. The variation of these genes across the B. thuringiensis genomes suggests that each strain may have adapted to their specific ecological niche. However, further investigations will be need to support this preliminary hypothesis.

scholarly journals Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Nikolaos Strepis ◽  
Henry D. Naranjo ◽  
Jan Meier-Kolthoff ◽  
Markus Göker ◽  
Nicole Shapiro ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Genomic Analysis ◽  
Single Species ◽  
The Other ◽  
Physiological Traits ◽  
Comparative Genomic ◽  
C Protein ◽  
Wide Range ◽  
Genes Encoding ◽  
Type Strains

Abstract Background The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. Results In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. Conclusions Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.

scholarly journals Nucleotide Sequence and Evolution of the Five-Plasmid Complement of the Phytopathogen Pseudomonas syringae pv. maculicola ES4326

2004 ◽  
Vol 186 (15) ◽  
pp. 5101-5115 ◽  
Author(s):  
John Stavrinides ◽  
David S. Guttman
Keyword(s):  
Nucleotide Sequence ◽  
Pseudomonas Syringae ◽  
Genomic Analysis ◽  
Type Iv Secretion ◽  
Comparative Genomic ◽  
Human Pathogens ◽  
Plasmid Evolution ◽  
Type Iv ◽  
Wide Range ◽  
Genomic Analyses

ABSTRACT Plasmids are transmissible, extrachromosomal genetic elements that are often responsible for environmental or host-specific adaptations. In order to identify the forces driving the evolution of these important molecules, we determined the complete nucleotide sequence of the five-plasmid complement of the radish and Arabidopsis pathogen Pseudomonas syringae pv. maculicola ES4326 and conducted an intraspecific comparative genomic analysis. To date, this is the most complex fully sequenced plasmid complement of any gram-negative bacterium. The plasmid complement comprises two pPT23A-like replicons, pPMA4326A (46,697 bp) and pPMA4326B (40,110 bp); a pPS10-like replicon, pPMA4326C (8,244 bp); and two atypical, replicase-deficient replicons, pPMA4326D (4,833 bp) and pPMA4326E (4,217 bp). A complete type IV secretion system is found on pPMA4326A, while the type III secreted effector hopPmaA is present on pPMA4326B. The region around hopPmaA includes a shorter hopPmaA homolog, insertion sequence (IS) elements, and a three-element cassette composed of a resolvase, an integrase, and an exeA gene that is also present in several human pathogens. We have also identified a novel genetic element (E622) that is present on all but the smallest plasmid (pPMA4326E) that has features of an IS element but lacks an identifiable transposase. This element is associated with virulence-related genes found in a wide range of P. syringae strains. Comparative genomic analyses of these and other P. syringae plasmids suggest a role for recombination and integrative elements in driving plasmid evolution.

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