Horizontal Gene Transfer As an Indispensable Driver For
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Fungal Evolution: Major Ecological Adaptations and Evolutionary Transitions
Biol. Rev. (2019), pp. 000–000. 1 doi: 10.1111/brv.12510 Fungal evolution: major ecological adaptations and evolutionary transitions Miguel A. Naranjo-Ortiz1 and Toni Gabaldon´ 1,2,3∗ 1Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain 2 Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain 3ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain ABSTRACT Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). -
Anaerobic Fungi: Past, Present, and Future Edited By: Robert Czajkowski, Matthias Hess1*†#, Shyam S
fmicb-11-584893 October 15, 2020 Time: 17:12 # 1 REVIEW published: 21 October 2020 doi: 10.3389/fmicb.2020.584893 Anaerobic Fungi: Past, Present, and Future Edited by: Robert Czajkowski, Matthias Hess1*†#, Shyam S. Paul2#, Anil K. Puniya3#, Mark van der Giezen4#, University of Gdansk,´ Poland Claire Shaw1#, Joan E. Edwards5‡# and Katerinaˇ Fliegerová6†# Reviewed by: 1 Mostafa S. Elshahed, Systems Microbiology & Natural Product Discovery Laboratory, Department of Animal Science, University of California, 2 Oklahoma State University, Davis, Davis, CA, United States, Gut Microbiome Lab, ICAR-Directorate of Poultry Research, Indian Council of Agricultural 3 United States Research, Hyderabad, India, Anaerobic Microbiology Lab, ICAR-National Dairy Research Institute, Dairy Microbiology 4 Birbal Singh, Division, ICAR-National Dairy Research Institute, Karnal, India, Department of Chemistry, Bioscience and Environmental 5 Indian Veterinary Research Institute Engineering, University of Stavanger, Stavanger, Norway, Laboratory of Microbiology, Wageningen University & Research, 6 (IVRI), India Wageningen, Netherlands, Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Prague, Czechia *Correspondence: Matthias Hess [email protected] Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber †These authors have contributed degrading enzymes and invasive growth. Much has been learned about this unusual equally to this work fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he #ORCID: Matthias Hess characterized the first AF. Molecular approaches targeting specific phylogenetic marker orcid.org/0000-0003-0321-0380 genes have facilitated taxonomic classification of AF, which had been previously been Shyam S. Paul complicated by the complex life cycles and associated morphologies. -
Longitudinal Characterization of the Gut Bacterial and Fungal Communities in Yaks
Journal of Fungi Article Longitudinal Characterization of the Gut Bacterial and Fungal Communities in Yaks Yaping Wang 1,2,3, Yuhang Fu 3, Yuanyuan He 3, Muhammad Fakhar-e-Alam Kulyar 3 , Mudassar Iqbal 3,4, Kun Li 1,2,* and Jiaguo Liu 1,2,* 1 Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; [email protected] 2 MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China 3 College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; [email protected] (Y.F.); [email protected] (Y.H.); [email protected] (M.F.-e.-A.K.); [email protected] (M.I.) 4 Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan * Correspondence: [email protected] (K.L.); [email protected] (J.L.) Abstract: Development phases are important in maturing immune systems, intestinal functions, and metabolism for the construction, structure, and diversity of microbiome in the intestine during the entire life. Characterizing the gut microbiota colonization and succession based on age-dependent effects might be crucial if a microbiota-based therapeutic or disease prevention strategy is adopted. The purpose of this study was to reveal the dynamic distribution of intestinal bacterial and fungal communities across all development stages in yaks. Dynamic changes (a substantial difference) in the structure and composition ratio of the microbial community were observed in yaks that Citation: Wang, Y.; Fu, Y.; He, Y.; matched the natural aging process from juvenile to natural aging. -
Microbial Community Structure in Rice, Crops, and Pastures Rotation Systems with Different Intensification Levels in the Temperate Region of Uruguay
Supplementary Material Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay Sebastián Martínez Table S1. Relative abundance of the 20 most abundant bacterial taxa of classified sequences. Relative Taxa Phylum abundance 4,90 _Bacillus Firmicutes 3,21 _Bacillus aryabhattai Firmicutes 2,76 _uncultured Prosthecobacter sp. Verrucomicrobia 2,75 _uncultured Conexibacteraceae bacterium Actinobacteria 2,64 _uncultured Conexibacter sp. Actinobacteria 2,14 _Nocardioides sp. Actinobacteria 2,13 _Acidothermus Actinobacteria 1,50 _Bradyrhizobium Proteobacteria 1,23 _Bacillus Firmicutes 1,10 _Pseudolabrys_uncultured bacterium Proteobacteria 1,03 _Bacillus Firmicutes 1,02 _Nocardioidaceae Actinobacteria 0,99 _Candidatus Solibacter Acidobacteria 0,97 _uncultured Sphingomonadaceae bacterium Proteobacteria 0,94 _Streptomyces Actinobacteria 0,91 _Terrabacter_uncultured bacterium Actinobacteria 0,81 _Mycobacterium Actinobacteria 0,81 _uncultured Rubrobacteria Actinobacteria 0,77 _Xanthobacteraceae_uncultured forest soil bacterium Proteobacteria 0,76 _Streptomyces Actinobacteria Table S2. Relative abundance of the 20 most abundant fungal taxa of classified sequences. Relative Taxa Orden abundance. 20,99 _Fusarium oxysporum Ascomycota 11,97 _Aspergillaceae Ascomycota 11,14 _Chaetomium globosum Ascomycota 10,03 _Fungi 5,40 _Cucurbitariaceae; uncultured fungus Ascomycota 5,29 _Talaromyces purpureogenus Ascomycota 3,87 _Neophaeosphaeria; uncultured fungus Ascomycota -
Diversity and Roles of Mycorrhizal Fungi in the Bee Orchid Ophrys Apifera
Diversity and Roles of Mycorrhizal Fungi in the Bee Orchid Ophrys apifera By Wazeera Rashid Abdullah April 2018 A Thesis submitted to the University of Liverpool in fulfilment of the requirement for the degree of Doctor in Philosophy Table of Contents Page No. Acknowledgements ............................................................................................................. xiv Abbreviations ............................................................................ Error! Bookmark not defined. Abstract ................................................................................................................................... 2 1 Chapter one: Literature review: ........................................................................................ 3 1.1 Mycorrhiza: .................................................................................................................... 3 1.1.1Arbuscular mycorrhiza (AM) or Vesicular-arbuscular mycorrhiza (VAM): ........... 5 1.1.2 Ectomycorrhiza: ...................................................................................................... 5 1.1.3 Ectendomycorrhiza: ................................................................................................ 6 1.1.4 Ericoid mycorrhiza, Arbutoid mycorrhiza, and Monotropoid mycorrhiza: ............ 6 1.1.5 Orchid mycorrhiza: ................................................................................................. 7 1.1.5.1 Orchid mycorrhizal interaction: ...................................................................... -
Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau
animals Article Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau Wei Guo 1, Weiwei Wang 1, Sisi Bi 2, Ruijun Long 2, Farman Ullah 3, Muhammad Shafiq 4 , Mi Zhou 5,* and Ying Zhang 6,* 1 State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; [email protected] (W.G.); [email protected] (W.W.) 2 School of Life Sciences, Lanzhou University, Lanzhou 730020, China; [email protected] (S.B.); [email protected] (R.L.) 3 Department of Animal Breeding and Genetics, Lasbela University of Agriculture Water and Marine Sciences, Uthal 90150, Pakistan; [email protected] 4 College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; drshafi[email protected] 5 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada 6 School of Public Health, Lanzhou University, Lanzhou 730020, China * Correspondence: [email protected] (M.Z.); [email protected] (Y.Z.) Received: 30 November 2019; Accepted: 14 January 2020; Published: 16 January 2020 Simple Summary: Anaerobic rumen fungi play a vital role in fiber degradation. The objective of this study was to compare the anaerobic rumen fungal communities of full grazing ruminants in the Qinghai-Tibetan Plateau. Our results showed that the anaerobic rumen fungal community was affected by host species and the dynamic associations of them were host specific. This is the first study exploring the anaerobic rumen fungi in the full-grazing ruminants, which could lay a solid foundation to really identify fiber degradation fungal taxa using culture-dependent techniques in the future. -
Dynamics and Stabilization of the Rumen Microbiome in Yearling
www.nature.com/scientificreports OPEN Dynamics and stabilization of the rumen microbiome in yearling Tibetan sheep Lei Wang1,2,4, Ke Zhang3,4, Chenguang Zhang3, Yuzhe Feng1, Xiaowei Zhang1, Xiaolong Wang 3 & Guofang Wu1,2* The productivity of ruminants depends largely on rumen microbiota. However, there are few studies on the age-related succession of rumen microbial communities in grazing lambs. Here, we conducted 16 s rRNA gene sequencing for bacterial identifcation on rumen fuid samples from 27 Tibetan lambs at nine developmental stages (days (D) 0, 2, 7, 14, 28, 42, 56, 70, and 360, n = 3). We observed that Bacteroidetes and Proteobacteria populations were signifcantly changed during the growing lambs’ frst year of life. Bacteroidetes abundance increased from 18.9% on D0 to 53.9% on D360. On the other hand, Proteobacteria abundance decreased signifcantly from 40.8% on D0 to 5.9% on D360. Prevotella_1 established an absolute advantage in the rumen after 7 days of age. The co-occurrence network showed that the diferent microbial of the rumen presented a complex synergistic and cumbersome relationship. A phylogenetic tree was constructed, indicating that during the colonization process, may occur a phenomenon in which bacteria with close kinship are preferentially colonized. Overall, this study provides new insights into the colonization of bacterial communities in lambs that will beneft the development of management strategies to promote colonization of target communities to improve functional development. Rumen microbes are essential for ruminant health. Ruminants rely upon the action of microbial fermentation in the rumen to digest plant fbers and convert some nutrients that cannot be directly utilized into animal proteins for host utilization1. -
Comparative Genomic Analysis of the Neocallimastigomycota Cazyome
Chelsea Murphy Comparative Genomic Analysis of the Neocallimastigomycota CAZyome ABSTRACT: Members of the anaerobic fungi (Neocallimastigomycota) are known for their ability to degrade plant polysaccharides in the anoxic herbivorous gut. We aim to understand the evolutionary history, co-occurrence patterns and pangenomic diversity of the Carbohydrate Active Enzymes (CAZymes) repertoire in the Neocallimastigomycota. To this end, we sequenced the transcriptomes of fourteen different Neocallimastigomycota species. Those, along with four previously available transcriptomes, represent six different Neocallimastigomycota genera. From the transcriptomes, we extracted the protein families (pfam) domains encoding the glycoside hydrolases and polysaccharide lyases and analyzed the patterns of occurrence and phylogenetic diversity of these modules. The Neocallimastigomycota panCAZyome consisted of 128 families out of the 136 currently recognized, with the notable absence of the GH7 and GH61, both of which are ubiquitous in other fungal lineages. Interestingly, in spite of the large number of transcripts (465 to 1814) identified per transcriptome, it appears that all GH families consist of 1-5 distinct orthologues, suggesting massive gene duplication in the Neocallimastigomycota genomes. Further, within these orthologues, the majority appears to be obtained from bacterial donors by horizontal gene transfer, attesting to the importance of this process in conferring plant biomass degradation capacity and ecological fitness to this group of fungi. Most HGT events were observed in transcriptomes of all genera, suggesting the occurrence of this process prior to genus level diversification within this lineage. Major bacterial donors include lineages known to be prevalent in the herbivorous gut, e.g. Clostridiales, Chelsea Murphy Fibrobacteriales, and Ruminoccoccales, although additional events from lineages not associated with the herbivores guts were identified. -
UC Riverside UC Riverside Previously Published Works
UC Riverside UC Riverside Previously Published Works Title Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Permalink https://escholarship.org/uc/item/3fm155t1 Authors U'Ren, Jana M Miadlikowska, Jolanta Zimmerman, Naupaka B et al. Publication Date 2016-05-01 DOI 10.1016/j.ympev.2016.02.010 License https://creativecommons.org/licenses/by-nc-nd/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California *Graphical Abstract (for review) ! *Highlights (for review) • Endophytes illuminate Xylariaceae circumscription and phylogenetic structure. • Endophytes occur in lineages previously not known for endophytism. • Boreal and temperate lichens and non-flowering plants commonly host Xylariaceae. • Many have endophytic and saprotrophic life stages and are widespread generalists. *Manuscript Click here to view linked References 1 Contributions of North American endophytes to the phylogeny, 2 ecology, and taxonomy of Xylariaceae (Sordariomycetes, 3 Ascomycota) 4 5 6 Jana M. U’Ren a,* Jolanta Miadlikowska b, Naupaka B. Zimmerman a, François Lutzoni b, Jason 7 E. Stajichc, and A. Elizabeth Arnold a,d 8 9 10 a University of Arizona, School of Plant Sciences, 1140 E. South Campus Dr., Forbes 303, 11 Tucson, AZ 85721, USA 12 b Duke University, Department of Biology, Durham, NC 27708-0338, USA 13 c University of California-Riverside, Department of Plant Pathology and Microbiology and Institute 14 for Integrated Genome Biology, 900 University Ave., Riverside, CA 92521, USA 15 d University of Arizona, Department of Ecology and Evolutionary Biology, 1041 E. Lowell St., 16 BioSciences West 310, Tucson, AZ 85721, USA 17 18 19 20 21 22 23 24 * Corresponding author: University of Arizona, School of Plant Sciences, 1140 E. -