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Mulay SA, Hahn CR, Klingeman DM, Elshahed MS, Youssef NH, Podar M. Metagenomic sequencing of a Patescibacteria-containing enrichment from Zodletone spring in Oklahoma, USA. Microbiol Resour Announc 2024; 13:e0011424. [PMID: 38497626 PMCID: PMC11008151 DOI: 10.1128/mra.00114-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024] Open
Abstract
An enrichment of sulfidic sediments from Zodletone spring was sequenced as a metagenome. Draft genomes representing Cloacimonadota, Deltabacterota, Firmicutes, and Patescibacteria were binned and annotated and will aid functional genomics and cultivation efforts.
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Affiliation(s)
- Sayali A. Mulay
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | - C. Ryan Hahn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mircea Podar
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Pratt CJ, Meili CH, Jones AL, Jackson DK, England EE, Wang Y, Hartson S, Rogers J, Elshahed MS, Youssef NH. Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution. Nat Commun 2024; 15:2714. [PMID: 38548766 PMCID: PMC10978972 DOI: 10.1038/s41467-024-47047-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.
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Affiliation(s)
- Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Casey H Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Adrienne L Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Darian K Jackson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Emma E England
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Yan Wang
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Steve Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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Meili CH, TagElDein MA, Jones AL, Moon CD, Andrews C, Kirk MR, Janssen PH, J. Yeoman C, Grace S, Borgogna JLC, Foote AP, Nagy YI, Kashef MT, Yassin AS, Elshahed MS, Youssef NH. Diversity and community structure of anaerobic gut fungi in the rumen of wild and domesticated herbivores. Appl Environ Microbiol 2024; 90:e0149223. [PMID: 38299813 PMCID: PMC10880628 DOI: 10.1128/aem.01492-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF mycobiome was highly diverse, with 81 out of 88 currently recognized AGF genera or candidate genera identified. However, only six genera (Neocallimastix, Orpinomyces, Caecomyces, Cyllamyces, NY9, and Piromyces) were present at >4% relative abundance. AGF diversity was higher in members of the families Antilocapridae and Cervidae compared to Bovidae. Community structure analysis identified a pattern of phylosymbiosis, where host family (10% of total variance) and species (13.5%) partially explained the rumen mycobiome composition. As well, diet composition (9%-19%), domestication (11.14%), and biogeography (14.1%) also partially explained AGF community structure; although sampling limitation, geographic range restrictions, and direct association between different factors hindered accurate elucidation of the relative contribution of each factor. Pairwise comparison of rumen and fecal samples obtained from the same subject (n = 13) demonstrated greater diversity and inter-sample variability in rumen versus fecal samples. The genera Neocallimastix and Orpinomyces were present in higher abundance in rumen samples, while Cyllamyces and Caecomyces were enriched in fecal samples. Comparative analysis of global rumen and feces data sets revealed a similar pattern. Our results provide a global view of AGF community in the rumen and identify patterns of AGF variability between rumen and feces in herbivores Gastrointestinal (GI) tract.IMPORTANCERuminants are highly successful and economically important mammalian suborder. Ruminants are herbivores that digest plant material with the aid of microorganisms residing in their GI tract. In ruminants, the rumen compartment represents the most important location where microbially mediated plant digestion occurs, and is known to house a bewildering array of microbial diversity. An important component of the rumen microbiome is the anaerobic gut fungi (AGF), members of the phylum Neocallimastigomycota. So far, studies examining AGF diversity have mostly employed fecal samples, and little is currently known regarding the identity of AGF residing in the rumen compartment, factors that impact the observed patterns of diversity and community structure of AGF in the rumen, and how AGF communities in the rumen compare to AGF communities in feces. Here, we examined the rumen AGF diversity using an amplicon-based survey targeting a wide range of wild and domesticated ruminants (n = 206, 15 different animal species) obtained from 15 different countries. Our results demonstrate that while highly diverse, no new AGF genera were identified in the rumen mycobiome samples examined. Our analysis also indicate that animal host phylogeny, diet, biogeography, and domestication status could play a role in shaping AGF community structure. Finally, we demonstrate that a greater level of diversity and higher inter-sample variability was observed in rumen compared to fecal samples, with two genera (Neocallimastix and Orpinomyces) present in higher abundance in rumen samples, and two others (Cyllamyces and Caecomyces) enriched in fecal samples. Our results provide a global view of the identity, diversity, and community structure of AGF in ruminants, elucidate factors impacting diversity and community structure of the rumen mycobiome, and identify patterns of AGF community variability between the rumen and feces in the herbivorous GI tract.
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Affiliation(s)
- Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Moustafa A. TagElDein
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Adrienne L. Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Christina D. Moon
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Catherine Andrews
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Michelle R. Kirk
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H. Janssen
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carl J. Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, USA
| | - Savannah Grace
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, USA
| | | | - Andrew P. Foote
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Yosra I. Nagy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mona T. Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Aymen S. Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Jones AL, Pratt CJ, Meili CH, Soo RM, Hugenholtz P, Elshahed MS, Youssef NH. Anaerobic gut fungal communities in marsupial hosts. mBio 2024; 15:e0337023. [PMID: 38259066 PMCID: PMC10865811 DOI: 10.1128/mbio.03370-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The anaerobic gut fungi (AGF) inhabit the alimentary tracts of herbivores. In contrast to placental mammals, information regarding the identity, diversity, and community structure of AGF in marsupials is extremely sparse. Here, we characterized AGF communities in 61 fecal samples from 10 marsupial species belonging to four families in the order Diprotodontia: Vombatidae (wombats), Phascolarctidae (koalas), Phalangeridae (possums), and Macropodidae (kangaroos, wallabies, and pademelons). An amplicon-based diversity survey using the D2 region of the large ribosomal subunit as a phylogenetic marker indicated that marsupial AGF communities were dominated by eight genera commonly encountered in placental herbivores (Neocallimastix, Caecomyces, Cyllamyces, Anaeromyces, Orpinomyces, Piromyces, Pecoramyces, and Khoyollomyces). Community structure analysis revealed a high level of stochasticity, and ordination approaches did not reveal a significant role for the animal host, gut type, dietary preferences, or lifestyle in structuring marsupial AGF communities. Marsupial foregut and hindgut communities displayed diversity and community structure patterns comparable to AGF communities typically encountered in placental foregut hosts while exhibiting a higher level of diversity and a distinct community structure compared to placental hindgut communities. Quantification of AGF load using quantitative PCR indicated a significantly smaller load in marsupial hosts compared to their placental counterparts. Isolation efforts were only successful from a single red kangaroo fecal sample and yielded a Khoyollomyces ramosus isolate closely related to strains previously isolated from placental hosts. Our results suggest that AGF communities in marsupials are in low abundance and show little signs of selection based on ecological and evolutionary factors.IMPORTANCEThe AGF are integral part of the microbiome of herbivores. They play a crucial role in breaking down plant biomass in hindgut and foregut fermenters. The majority of research has been conducted on the AGF community in placental mammalian hosts. However, it is important to note that many marsupial mammals are also herbivores and employ a hindgut or foregut fermentation strategy for breaking down plant biomass. So far, very little is known regarding the AGF diversity and community structure in marsupial mammals. To fill this knowledge gap, we conducted an amplicon-based diversity survey targeting AGF in 61 fecal samples from 10 marsupial species. We hypothesize that, given the distinct evolutionary history and alimentary tract architecture, novel and unique AGF communities would be encountered in marsupials. Our results indicate that marsupial AGF communities are highly stochastic, present in relatively low loads, and display community structure patterns comparable to AGF communities typically encountered in placental foregut hosts. Our results indicate that marsupial hosts harbor AGF communities; however, in contrast to the strong pattern of phylosymbiosis typically observed between AGF and placental herbivores, the identity and gut architecture appear to play a minor role in structuring AGF communities in marsupials.
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Affiliation(s)
- Adrienne L. Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Carrie J. Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Rochelle M. Soo
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Pratt CJ, Meili CH, Youssef NH, Hoback WW. Culture-independent analyses of carrion beetle (Coleoptera: Silphidae) secretion bacterial communities. Microbiol Spectr 2023; 11:e0169423. [PMID: 37874151 PMCID: PMC10714842 DOI: 10.1128/spectrum.01694-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 08/14/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE The manuscript explores the secretion bacterial community of carrion and burying beetles of the central plains of North America. A core secretion microbiome of 11 genera is identified. The host subfamily, secretion type, and collection locality significantly affects the secretion microbiome. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials.
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Affiliation(s)
- Carrie J. Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - W. Wyatt Hoback
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, USA
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Jones AL, Clayborn J, Pribil E, Foote AP, Montogomery D, Elshahed MS, Youssef NH. Temporal progression of anaerobic fungal communities in dairy calves from birth to maturity. Environ Microbiol 2023; 25:2088-2101. [PMID: 37305988 DOI: 10.1111/1462-2920.16443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023]
Abstract
Establishment of microbial communities in neonatal calves is vital for their growth and overall health. While this process has received considerable attention for bacteria, our knowledge on temporal progression of anaerobic gut fungi (AGF) in calves is lacking. Here, we examined AGF communities in faecal samples from six dairy cattle collected at 24 different time points during the pre-weaning (days 1-48), weaning (days 48-60), and post-weaning (days 60-360) phases. Quantitative polymerase chain reaction indicated that AGF colonisation occurs within 24 h after birth, with loads slowly increasing during pre-weaning and weaning, then drastically increasing post-weaning. Culture-independent amplicon surveys identified higher alpha diversity during pre-weaning/weaning, compared to post-weaning. AGF community structure underwent a drastic shift post-weaning, from a community enriched in genera commonly encountered in hindgut fermenters to one enriched in genera commonly encountered in adult ruminants. Comparison of AGF community between calves day 1 post-birth and their mothers suggest a major role for maternal transmission, with additional input from cohabitating subjects. This distinct pattern of AGF progression could best be understood in-light of their narrower niche preferences, metabolic specialisation, and physiological optima compared to bacteria, hence eliciting a unique response to changes in feeding pattern and associated structural GIT development during maturation.
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Affiliation(s)
- Adrienne L Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Jordan Clayborn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Elizabeth Pribil
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Andrew P Foote
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dagan Montogomery
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Meili CH, Jones AL, Arreola AX, Habel J, Pratt CJ, Hanafy RA, Wang Y, Yassin AS, TagElDein MA, Moon CD, Janssen PH, Shrestha M, Rajbhandari P, Nagler M, Vinzelj JM, Podmirseg SM, Stajich JE, Goetsch AL, Hayes J, Young D, Fliegerova K, Grilli DJ, Vodička R, Moniello G, Mattiello S, Kashef MT, Nagy YI, Edwards JA, Dagar SS, Foote AP, Youssef NH, Elshahed MS. Patterns and determinants of the global herbivorous mycobiome. Nat Commun 2023; 14:3798. [PMID: 37365172 PMCID: PMC10293281 DOI: 10.1038/s41467-023-39508-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.
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Affiliation(s)
- Casey H Meili
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Adrienne L Jones
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Alex X Arreola
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Jeffrey Habel
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Carrie J Pratt
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Radwa A Hanafy
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Yan Wang
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Moustafa A TagElDein
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Christina D Moon
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H Janssen
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Mitesh Shrestha
- Department of Applied Microbiology and Food Technology, Research Institute for Bioscience and Biotechnology (RIBB), Kathmandu, Nepal
| | - Prajwal Rajbhandari
- Department of Applied Microbiology and Food Technology, Research Institute for Bioscience and Biotechnology (RIBB), Kathmandu, Nepal
| | - Magdalena Nagler
- Universität Innsbruck, Faculty of Biology, Department of Microbiology, Innsbruck, Austria
| | - Julia M Vinzelj
- Universität Innsbruck, Faculty of Biology, Department of Microbiology, Innsbruck, Austria
| | - Sabine M Podmirseg
- Universität Innsbruck, Faculty of Biology, Department of Microbiology, Innsbruck, Austria
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
| | | | | | - Diana Young
- Bavarian State Research Center for Agriculture, Freising, Germany
| | - Katerina Fliegerova
- Institute of Animal Physiology and Genetics Czech Academy of Sciences, Prague, Czechia
| | - Diego Javier Grilli
- Área de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | | | - Giuseppe Moniello
- Department of Veterinary Medicine, University of Sassari, Sardinia, Italy
| | - Silvana Mattiello
- University of Milan, Dept. of Agricultural and Environmental Sciences, Milan, Italy
| | - Mona T Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Yosra I Nagy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | | | - Andrew P Foote
- Oklahoma State University, Department of Animal and Food Sciences, Stillwater, OK, USA
| | - Noha H Youssef
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA.
| | - Mostafa S Elshahed
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA.
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8
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Pratt CJ, Chandler EE, Youssef NH, Elshahed MS. Testudinimyces gracilis gen. nov, sp. nov. and Astrotestudinimyces divisus gen. nov, sp. nov., two novel, deep-branching anaerobic gut fungal genera from tortoise faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37252853 DOI: 10.1099/ijsem.0.005921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
The anaerobic gut fungi (AGF, Neocallimastigomycota) represent a basal zoosporic phylum within the kingdom Fungi. Twenty genera are currently described, all of which were isolated from the digestive tracts of mammalian herbivores. Here, we report on the isolation and characterization of novel AGF taxa from faecal samples of tortoises. Twenty-nine fungal isolates were obtained from seven different tortoise species. Phylogenetic analysis using the D1/D2 region of the LSU rRNA gene, ribosomal internal transcribed spacer 1, and RNA polymerase II large subunit grouped all isolates into two distinct, deep-branching clades (clades T and B), with a high level of sequence divergence to their closest cultured relative (Khoyollomyces ramosus). Average amino acid identity values calculated using predicted peptides from the isolates' transcriptomes ranged between 60.80-66.21 % (clade T), and 61.24-64.83 % (clade B) when compared to all other AGF taxa; values that are significantly below recently recommended thresholds for genus (85%) and family (75%) delineation in the Neocallimastigomycota. Both clades displayed a broader temperature growth range (20-45 °C, optimal 30 °C for clade T, and 30-42 °C, optimal 39 °C for clade B) compared to all other AGF taxa. Microscopic analysis demonstrated that strains from both clades produced filamentous hyphae, polycentric rhizoidal growth patterns, and monoflagellated zoospores. Isolates in clade T were characterized by the production of unbranched, predominantly narrow hyphae, and small zoospores, while isolates in clade B were characterized by the production of multiple sporangiophores and sporangia originating from a single central swelling resulting in large multi-sporangiated structures. Based on the unique phylogenetic positions, AAI values, and phenotypic characteristics, we propose to accommodate these isolates into two novel genera (Testudinimyces and Astrotestudinimyces), and species (T. gracilis and A. divisus) within the order Neocallimastigales. The type species are strains T130AT (T. gracilis) and B1.1T (A. divisus).
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Affiliation(s)
- Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Emily E Chandler
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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9
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Mulay SA, Alexander WG, Hahn CR, Klingeman DM, Elshahed MS, Youssef NH, Podar M. Complete Genome Sequence of Desulfomicrobium sp. Strain ZS1 from Zodletone Spring in Oklahoma, USA. Microbiol Resour Announc 2023; 12:e0014523. [PMID: 37052391 DOI: 10.1128/mra.00145-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Desulfomicrobium sp. strain ZS1 is an obligate anaerobic, sulfate-reducing member of the Desulfobacterota from Zodletone Spring, an anoxic sulfide-rich spring in southwestern Oklahoma. Its complete genome was sequenced using a combination of Illumina and Oxford Nanopore platforms and encodes 3,364 proteins and 81 RNAs on a single chromosome.
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Affiliation(s)
- Sayali A Mulay
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | - William G Alexander
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - C Ryan Hahn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mircea Podar
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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10
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Hanafy RA, Wang Y, Stajich JE, Pratt CJ, Youssef NH, Elshahed MS. Phylogenomic analysis of the Neocallimastigomycota: proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae. Int J Syst Evol Microbiol 2023; 73. [PMID: 36827202 DOI: 10.1099/ijsem.0.005735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The anaerobic gut fungi (AGF) represent a coherent phylogenetic clade within the Mycota. Twenty genera have been described so far. Currently, the phylogenetic and evolutionary relationships between AGF genera remain poorly understood. Here, we utilized 52 transcriptomic datasets from 14 genera to resolve AGF inter-genus relationships using phylogenomics, and to provide a quantitative estimate (amino acid identity, AAI) for intermediate rank assignments. We identify four distinct supra-genus clades, encompassing all genera producing polyflagellated zoospores, bulbous rhizoids, the broadly circumscribed genus Piromyces, and the Anaeromyces and affiliated genera. We also identify the genus Khoyollomyces as the earliest evolving AGF genus. Concordance between phylogenomic outputs and RPB1 and D1/D2 LSU, but not RPB2, MCM7, EF1α or ITS1, phylogenies was observed. We combine phylogenomic analysis and AAI outputs with informative phenotypic traits to propose accommodating 14/20 AGF genera into four families: Caecomycetaceae fam. nov. (encompassing the genera Caecomyces and Cyllamyces), Piromycetaceae fam. nov. (encompassing the genus Piromyces), emend the description of the family Neocallimastigaceae to encompass the genera Neocallimastix, Orpinomyces, Pecoramyces, Feramyces, Ghazallomyces, Aestipascuomyces and Paucimyces, as well as the family Anaeromycetaceae to include the genera Oontomyces, Liebetanzomyces and Capellomyces in addition to Anaeromyces. We refrain from proposing families for the deeply branching genus Khoyollomyces and for genera with uncertain position (Buwchfawromyces, Joblinomyces, Tahromyces, Agriosomyces and Aklioshbomyces) pending availability of additional isolates and sequence data; and these genera are designated as 'genera incertae sedis' in the order Neocallimastigales. Our results establish an evolutionary-grounded Linnaean taxonomic framework for the AGF, provide quantitative estimates for rank assignments, and demonstrate the utility of RPB1 as an additional informative marker in Neocallimastigomycota taxonomy.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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11
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Young D, Joshi A, Huang L, Munk B, Wurzbacher C, Youssef NH, Elshahed MS, Moon CD, Ochsenreither K, Griffith GW, Callaghan TM, Sczyrba A, Lebuhn M, Flad V. Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages. Microorganisms 2022; 10:1749. [PMID: 36144352 PMCID: PMC9504928 DOI: 10.3390/microorganisms10091749] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara).
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Affiliation(s)
- Diana Young
- Micro and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
| | - Akshay Joshi
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, ZHAW, 8820 Wadenswil, Switzerland
- Department of Microbiology, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Liren Huang
- Center for Biotechnology (CeBiTec), University of Bielefeld, 33615 Bielefeld, Germany
| | - Bernhard Munk
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics (OSU), Oklahoma State University, Stillwater, OK 74074, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics (OSU), Oklahoma State University, Stillwater, OK 74074, USA
| | - Christina D. Moon
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Katrin Ochsenreither
- Process Engineering in Life Sciences 2: Technical Biology (KIT), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Gareth W. Griffith
- Department of Life Sciences (DoLS), Aberystwyth University, Aberystwyth SY23 3DD, Wales, UK
| | | | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), University of Bielefeld, 33615 Bielefeld, Germany
| | - Michael Lebuhn
- Micro and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
| | - Veronika Flad
- Micro and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
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12
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Duncan KT, Elshahed MS, Sundstrom KD, Little SE, Youssef NH. Influence of tick sex and geographic region on the microbiome of Dermacentor variabilis collected from dogs and cats across the United States. Ticks Tick Borne Dis 2022; 13:102002. [PMID: 35810549 DOI: 10.1016/j.ttbdis.2022.102002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/28/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022]
Abstract
As tick-borne diseases continue to increase across North America, current research strives to understand how the tick microbiome may affect pathogen acquisition, maintenance, and transmission. Prior high throughput amplicon-based microbial diversity surveys of the widespread tick Dermacentor variabilis have suggested that life stage, sex, and geographic region may influence the composition of the tick microbiome. Here, adult D. variabilis ticks (n = 145) were collected from dogs and cats from 32 states with specimens originating from all four regions of the United States (West, Midwest, South, and Northeast), and the tick microbiome was examined via V4-16S rRNA gene amplification and Illumina sequencing. A total of 481,246 bacterial sequences were obtained (median 2924 per sample, range 399-11,990). Fifty genera represented the majority (>80%) of the sequences detected, with the genera Allofrancisella and Francisella being the most abundant. Further, 97%, 23%, and 5.5% of the ticks contained sequences belonging to Francisella spp., Rickettsia spp., and Coxiella spp., respectively. No Ehrlichia spp. or Anaplasma spp. were identified. Co-occurrence analysis, by way of correlation coefficients, between the top 50 most abundant genera demonstrated five strong positive and no strong negative correlation relationships. Geographic region had a consistent effect on species richness with ticks from the Northeast having a significantly greater level of richness. Alpha diversity patterns were dependent on tick sex, with males exhibiting higher levels of diversity, and geographical region, with higher level of diversity observed in ticks obtained from the Northeast, but not on tick host. Community structure, or beta diversity, of tick microbiome was impacted by tick sex and geographic location, with microbiomes of ticks from the western US exhibiting a distinct community structure when compared to those from the other three regions (Northeast, South, and Midwest). In total, LEfSe (Linear discriminant analysis Effect Size) identified 18 specific genera driving these observed patterns of diversity and community structure. Collectively, these findings highlight the differences in bacterial diversity of D. variabilis across the US and supports the interpretation that tick sex and geographic region affects microbiome composition across a broad sampling distribution.
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Affiliation(s)
- Kathryn T Duncan
- Department of Pathobiology, College of Veterinary Medicine, Oklahoma State University, Room 250 McElroy Hall, Stillwater, OK 74078, USA.
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Kellee D Sundstrom
- Department of Pathobiology, College of Veterinary Medicine, Oklahoma State University, Room 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Susan E Little
- Department of Pathobiology, College of Veterinary Medicine, Oklahoma State University, Room 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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13
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Hanafy RA, Dagar SS, Griffith GW, Pratt CJ, Youssef NH, Elshahed MS. Taxonomy of the anaerobic gut fungi ( Neocallimastigomycota): a review of classification criteria and description of current taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35776761 DOI: 10.1099/ijsem.0.005322] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Members of the anaerobic gut fungi (Neocallimastigomycota) reside in the rumen and alimentary tract of larger mammalian and some reptilian, marsupial and avian herbivores. The recent decade has witnessed a significant expansion in the number of described Neocallimastigomycota genera and species. However, the difficulties associated with the isolation and maintenance of Neocallimastigomycota strains has greatly complicated comparative studies to resolve inter- and intra-genus relationships. Here, we provide an updated outline of Neocallimastigomycota taxonomy. We critically evaluate various morphological, microscopic and phylogenetic traits previously and currently utilized in Neocallimastigomycota taxonomy, and provide an updated key for quick characterization of all genera. We then synthesize data from taxa description manuscripts, prior comparative efforts and molecular sequence data to present an updated list of Neocallimastigomycota genera and species, with an emphasis on resolving relationships and identifying synonymy between recent and historic strains. We supplement data from published manuscripts with information and illustrations from strains in the authors' collections. Twenty genera and 36 species are recognized, but the status of 10 species in the genera Caecomyces, Piromyces, Anaeromyces and Cyllamyces remains uncertain due to the unavailability of culture and conferre (cf.) strains, lack of sequence data, and/or inadequacy of available microscopic and phenotypic data. Six cases of synonymy are identified in the genera Neocallimastix and Caecomyces, and two names in the genus Piromyces are rejected based on apparent misclassification.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Sumit S Dagar
- Bioenergy Group, Agharkar Research Institute, Pune, India
| | - Gareth W Griffith
- Institute of Biological, Environmental, and Rural Sciences (IBERS) Aberystwyth University, Aberystwyth, Wales, UK
| | - Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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14
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Elshahed MS, Hanafy RA, Cheng Y, Dagar SS, Edwards JE, Flad V, Fliegerová KO, Griffith GW, Kittelmann S, Lebuhn M, O'Malley MA, Podmirseg SM, Solomon KV, Vinzelj J, Young D, Youssef NH. Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota). Int J Syst Evol Microbiol 2022; 72. [PMID: 35852502 DOI: 10.1099/ijsem.0.005449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Establishing a solid taxonomic framework is crucial for enabling discovery and documentation efforts. This ensures effective communication between scientists as well as reproducibility of results between laboratories, and facilitates the exchange and preservation of biological material. Such framework can only be achieved by establishing clear criteria for taxa characterization and rank assignment. Within the anaerobic fungi (phylum Neocallimastigomycota), the need for such criteria is especially vital. Difficulties associated with their isolation, maintenance and long-term storage often result in limited availability and loss of previously described taxa. To this end, we provide here a list of morphological, microscopic, phylogenetic and phenotypic criteria for assessment and documentation when characterizing newly obtained Neocallimastigomycota isolates. We also recommend a polyphasic rank-assignment scheme for novel genus-, species- and strain-level designations for newly obtained Neocallimastigomycota isolates.
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Affiliation(s)
- Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA, USA
| | - Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark DE, USA
| | - Yanfen Cheng
- College of Animal Science and Technology, Nanjing Agricultural University., Nanjing, Jiangsu, PR China
| | - Sumit S Dagar
- Bioenergy Group, Agharkar Research Institute, Pune, India
| | | | - Veronika Flad
- Bavarian State Research Center for Agriculture (LfL), Central Department for Quality Assurance and Analytics, 85354 Freising, Germany
| | | | - Gareth W Griffith
- Institute of Biological, Environmental, and Rural Sciences (IBERS) Aberystwyth University, Aberystwyth, Wales, UK
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Michael Lebuhn
- Bavarian State Research Center for Agriculture (LfL), Central Department for Quality Assurance and Analytics, 85354 Freising, Germany
| | - Michelle A O'Malley
- Department of Chemical Engineering, Center for Bioengineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Sabine Marie Podmirseg
- Department of Microbiology, University of Innsbruck, Technikerstraße, Innsbruck, Austria
| | - Kevin V Solomon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark DE, USA
| | - Julia Vinzelj
- Department of Microbiology, University of Innsbruck, Technikerstraße, Innsbruck, Austria
| | - Diana Young
- Bavarian State Research Center for Agriculture (LfL), Central Department for Quality Assurance and Analytics, 85354 Freising, Germany
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA, USA
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15
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Elkenawy NM, Youssef NH, Aziz RK, Amin MA, Yassin AS. Draft genome sequence of a prodigiosin-hyperproducing Serratia marcescens strain isolated from Cairo, Egypt. G3 (Bethesda) 2021; 11:6343459. [PMID: 34568929 PMCID: PMC8473970 DOI: 10.1093/g3journal/jkab284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022]
Abstract
Serratia marcescens is a Gram-negative bacterium with both environmental and host-associated strains. Pigmentation is reportedly inversely correlated with infection frequency, and prodigiosin is one of Serratia pigments that has medical and industrial applications. Here, we report the draft genome sequence of prodigiosin-hyperproducing Serratia marcescens strain N2, isolated from Cairo, Egypt. The sequence is assembled into 142 contigs, with a combined size of 5,570,793 bp. The assembled genome carries typical S. marcescens genes, with potential prodigiosin-biosynthesizing genes detected.
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Affiliation(s)
- Nora M Elkenawy
- Drug Radiation Research Department, National Center for Radiation Research &Technology, 11787 Cairo, Egypt
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-5061, USA
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt.,The Center for Genome and Microbiome Research, Cairo University, 11562 Cairo, Egypt.,Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt 57357, 11617 Cairo, Egypt
| | - Magdy A Amin
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-5061, USA.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt.,The Center for Genome and Microbiome Research, Cairo University, 11562 Cairo, Egypt
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16
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Yadav A, Borrelli JC, Elshahed MS, Youssef NH. Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats. Appl Environ Microbiol 2021; 87:e0094721. [PMID: 34160232 PMCID: PMC8357285 DOI: 10.1128/aem.00947-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/14/2021] [Indexed: 12/19/2022] Open
Abstract
Approaches for recovering and analyzing genomes belonging to novel, hitherto-unexplored bacterial lineages have provided invaluable insights into the metabolic capabilities and ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent and ecologically successful lineages on Earth, yet currently, multiple lineages within this phylum remain unexplored. Here, we utilize genomes recovered from Zodletone Spring, an anaerobic sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil and nonsoil habitats, to examine the metabolic capabilities and ecological role of members of family UBA6911 (group 18) Acidobacteria. The analyzed genomes clustered into five distinct genera, with genera Gp18_AA60 and QHZH01 recovered from soils, genus Ga0209509 from anaerobic digestors, and genera Ga0212092 and UBA6911 from freshwater habitats. All genomes analyzed suggested that members of Acidobacteria group 18 are metabolically versatile heterotrophs capable of utilizing a wide range of proteins, amino acids, and sugars as carbon sources, possess respiratory and fermentative capacities, and display few auxotrophies. Soil-dwelling genera were characterized by larger genome sizes, higher numbers of CRISPR loci, an expanded carbohydrate active enzyme (CAZyme) machinery enabling debranching of specific sugars from polymers, possession of a C1 (methanol and methylamine) degradation machinery, and a sole dependence on aerobic respiration. In contrast, nonsoil genomes encoded a more versatile respiratory capacity for oxygen, nitrite, sulfate, and trimethylamine N-oxide (TMAO) respiration, as well as the potential for utilizing the Wood-Ljungdahl (WL) pathway as an electron sink during heterotrophic growth. Our results not only expand our knowledge of the metabolism of a yet-uncultured bacterial lineage but also provide interesting clues on how terrestrialization and niche adaptation drive metabolic specialization within the Acidobacteria. IMPORTANCE Members of the Acidobacteria are important players in global biogeochemical cycles, especially in soils. A wide range of acidobacterial lineages remain currently unexplored. We present a detailed genomic characterization of genomes belonging to family UBA6911 (also known as group 18) within the phylum Acidobacteria. The genomes belong to different genera and were obtained from soil (genera Gp18_AA60 and QHZH01), freshwater habitats (genera Ga0212092 and UBA6911), and an anaerobic digestor (genus Ga0209509). While all members of the family shared common metabolic features, e.g., heterotrophic respiratory abilities, broad substrate utilization capacities, and few auxotrophies, distinct differences between soil and nonsoil genera were observed. Soil genera were characterized by expanded genomes, higher numbers of CRISPR loci, a larger carbohydrate active enzyme (CAZyme) repertoire enabling monomer extractions from polymer side chains, and methylotrophic (methanol and methylamine) degradation capacities. In contrast, nonsoil genera encoded more versatile respiratory capacities for utilizing nitrite, sulfate, TMAO, and the WL pathway, in addition to oxygen as electron acceptors. Our results not only broaden our understanding of the metabolic capacities within the Acidobacteria but also provide interesting clues on how terrestrialization shaped Acidobacteria evolution and niche adaptation.
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Affiliation(s)
- Archana Yadav
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Jenna C. Borrelli
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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17
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Hanafy RA, Youssef NH, Elshahed MS. Paucimyces polynucleatus gen. nov, sp. nov., a novel polycentric genus of anaerobic gut fungi from the faeces of a wild blackbuck antelope. Int J Syst Evol Microbiol 2021; 71. [PMID: 34161217 DOI: 10.1099/ijsem.0.004832] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The anaerobic gut fungi (AGF; phylum Neocallimastigomycota) reside in the alimentary tracts of herbivores. Multiple novel, yet-uncultured AGF taxa have recently been identified in culture-independent diversity surveys. Here, we report on the isolation and characterization of the first representative of the RH5 lineage from faecal samples of a wild blackbuck (Indian Antelope, Antilope cervicapra) from Sutton County, Texas, USA. The isolates displayed medium sized (2-4 mm) compact circular colonies on agar roll tubes and thin loose biofilm-like growth in liquid medium. Microscopic examination revealed monoflagellated zoospores and polycentric thalli with highly branched nucleated filamentous rhizomycelium, a growth pattern encountered in a minority of described AGF genera so far. The obtained isolates are characterized by formation of spherical vesicles at the hyphal tips from which multiple sporangia formed either directly on the spherical vesicles or at the end of sporangiophores. Phylogenetic analysis using the D1/D2 regions of the large ribosomal subunit (D1/D2 LSU) and the ribosomal internal transcribed spacer 1 (ITS1) revealed sequence similarities of 93.5 and 81.3%, respectively, to the closest cultured relatives (Orpinomyces joyonii strain D3A (D1/D2 LSU) and Joblinomyces apicalis strain GFH681 (ITS1). Substrate utilization experiments using the type strain (BB-3T) demonstrated growth capabilities on a wide range of mono-, oligo- and polysaccharides, including glucose, xylose, mannose, fructose, cellobiose, sucrose, maltose, trehalose, lactose, cellulose, xylan, starch and raffinose. We propose accommodating these novel isolates in a new genus and species, for which the name Paucimyces polynucleatus gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
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18
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Murphy CL, Biggerstaff J, Eichhorn A, Ewing E, Shahan R, Soriano D, Stewart S, VanMol K, Walker R, Walters P, Elshahed MS, Youssef NH. Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the phylum. Environ Microbiol 2021; 23:4326-4343. [PMID: 34056821 DOI: 10.1111/1462-2920.15614] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/01/2022]
Abstract
We report on the genomic characterization of three novel classes in the phylum Desulfobacterota. One class (proposed name Candidatus 'Anaeroferrophillalia') was characterized by heterotrophic growth capacity, either fermentatively or utilizing polysulfide, tetrathionate or thiosulfate as electron acceptors. In the absence of organic carbon sources, autotrophic growth via the Wood-Ljungdahl (WL) pathway and using hydrogen or Fe(II) as an electron donor is also inferred for members of the 'Anaeroferrophillalia'. The second class (proposed name Candidatus 'Anaeropigmentia') was characterized by its capacity for growth at low oxygen concentration, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoid (lycopene) production. The third class (proposed name Candidatus 'Zymogenia') was characterized by fermentative heterotrophic growth capacity, broad substrate range and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial, freshwater and marine environments over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus 'Zymogenia' for hypersaline environments such as hypersaline microbial mats and lagoons was observed.
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Affiliation(s)
- Chelsea L Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - James Biggerstaff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexis Eichhorn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Essences Ewing
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Ryan Shahan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Diana Soriano
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Sydney Stewart
- Department of Animal Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Kaitlynn VanMol
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Ross Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Payton Walters
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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19
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Murphy CL, Sheremet A, Dunfield PF, Spear JR, Stepanauskas R, Woyke T, Elshahed MS, Youssef NH. Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities. mBio 2021; 12:e00985-21. [PMID: 34006650 PMCID: PMC8262859 DOI: 10.1128/mbio.00985-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/18/2023] Open
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.
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Affiliation(s)
- Chelsea L Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Andriy Sheremet
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkley, California, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Stabel M, Hanafy RA, Schweitzer T, Greif M, Aliyu H, Flad V, Young D, Lebuhn M, Elshahed MS, Ochsenreither K, Youssef NH. Aestipascuomyces dupliciliberans gen. nov, sp. nov., the First Cultured Representative of the Uncultured SK4 Clade from Aoudad Sheep and Alpaca. Microorganisms 2020; 8:E1734. [PMID: 33167420 PMCID: PMC7694369 DOI: 10.3390/microorganisms8111734] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022] Open
Abstract
We report on the isolation of the previously-uncultured Neocallimastigomycota SK4 lineage, by two independent research groups, from a wild aoudad sheep rumen sample (Texas, USA) and an alpaca fecal sample (Baden-Württemberg, Germany). Isolates from both locations showed near-identical morphological and microscopic features, forming medium-sized (2-5 mm) white filamentous colonies with a white center of sporangia, on agar roll tubes and a heavy biofilm in liquid media. Microscopic analysis revealed monocentric thalli, and spherical polyflagellated zoospores with 7-20 flagella. Zoospore release occurred through an apical pore as well as by sporangial wall rupturing, a duality that is unique amongst described anaerobic gut fungal strains. Isolates were capable of growing on a wide range of mono-, oligo-, and polysaccharide substrates as the sole carbon source. Phylogenetic assessment based on the D1-D2 28S large rRNA gene subunit (D1-D2 LSU) and internal transcribed spacer-1 (ITS-1) regions demonstrated high sequence identity (minimum identity of 99.07% and 96.96%, respectively) between all isolates; but low sequence identity (92.4% and 86.7%, respectively) to their closest cultured relatives. D1-D2 LSU phylogenetic trees grouped the isolates as a new monophyletic clade within the Orpinomyces-Neocallimastix-Pecoramyces-Feramyces-Ghazallamyces supragenus group. D1-D2 LSU and ITS-1 sequences recovered from the obtained isolates were either identical or displayed extremely high sequence similarity to sequences recovered from the same aoudad sheep sample on which isolation was conducted, as well as several sequences recovered from domestic sheep and few other herbivores. Interestingly, members of the SK4 clade seem to be encountered preferably in animals grazing on summer pasture. We hence propose accommodating these novel isolates in a new genus, Aestipascuomyces (derived from the Latin word for "summer pasture"), and a new species, A. dupliciliberans. The type strain is Aestipascuomycesdupliciliberans strain R4.
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Affiliation(s)
- Marcus Stabel
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Radwa A. Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA; (R.A.H.); (M.S.E.)
| | - Tabea Schweitzer
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Meike Greif
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Habibu Aliyu
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Veronika Flad
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Lange Point 6, 85354 Freising, Germany; (V.F.); (D.Y.); (M.L.)
| | - Diana Young
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Lange Point 6, 85354 Freising, Germany; (V.F.); (D.Y.); (M.L.)
| | - Michael Lebuhn
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Lange Point 6, 85354 Freising, Germany; (V.F.); (D.Y.); (M.L.)
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA; (R.A.H.); (M.S.E.)
| | - Katrin Ochsenreither
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA; (R.A.H.); (M.S.E.)
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Hanafy RA, Johnson B, Youssef NH, Elshahed MS. Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi-year isolation. Environ Microbiol 2020; 22:3883-3908. [PMID: 32656919 DOI: 10.1111/1462-2920.15164] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/22/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
The anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tracts of herbivores where they play a central role in the breakdown of plant material. Here, we report on the development of the hypervariable domains D1/D2 of the large ribosomal subunit (D1/D2 LSU) as a barcoding marker for the AGF. We generated a reference D1/D2 LSU database for all cultured AGF genera, as well as the majority of candidate genera encountered in prior internal transcribed spacer 1 (ITS1)-based surveys. Subsequently, a D1/D2 LSU-based diversity survey using long read PacBio SMRT sequencing was conducted on faecal samples from 21 wild and domesticated herbivores. Twenty-eight genera and candidate genera were identified, including multiple novel lineages that were predominantly, but not exclusively, identified in wild herbivores. Association between certain AGF genera and animal lifestyles, or animal host family was observed. Finally, to address the current paucity of AGF isolates, concurrent isolation efforts utilizing multiple approaches to maximize recovery yielded 216 isolates belonging to 12 different genera, several of which have no prior cultured-representatives. Our results establish the utility of D1/D2 LSU and PacBio sequencing for AGF diversity surveys, the culturability of multiple AGF taxa, and demonstrate that wild herbivores represent a yet-untapped reservoir of AGF diversity.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Britny Johnson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Havryliuk O, Hovorukha V, Patrauchan M, Youssef NH, Tashyrev O. Draft whole genome sequence for four highly copper resistant soil isolates Pseudomonas lactis strain UKR1, Pseudomonas panacis strain UKR2, and Pseudomonas veronii strains UKR3 and UKR4. Curr Res Microb Sci 2020; 1:44-52. [PMID: 34841301 PMCID: PMC8610347 DOI: 10.1016/j.crmicr.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 01/22/2023] Open
Abstract
Four bacterial strains with record resistance to Cu(II) have been isolated. Genomic sequences are available for genome mining and studying the genetic determinants of bacterial resistance to Cu(II). Genomic sequences provide the foundation necessary for transcriptional and functional studies of genes encoding for Cu(II) resistance mechanisms in Pseudomonas spp. The data will be of interest for a broad community of biotechnologists and microbiologists and will aid in developing novel technologies for copper detoxification in contaminated soils and industrial wastewaters.
Environmental copper pollution causes major destruction to ecological systems, which require the development of environmentally friendly biotechnological, in particular, microbial methods for copper removal. These methods rely on the availability of microorganisms resistant to high levels of copper. Here we isolated four bacterial strains with record resistance to up to 1.0 M Cu(II). The strains were isolated from ecologically diverse soil samples, and their genomes were sequenced. A 16S rRNA sequence-based phylogenetic analysis identified that all four isolates belong to the genus Pseudomonas. Particularly, strains UKR1 and UKR2 isolated from Kyiv region in Ukraine were identified as P. lactis and P. panacis, respectively, and strains UKR3 and UKR4 isolated from Svalbard Island in the Arctic Ocean and Galindez Island in Antarctica, respectively, were identified as P. veronii. Initial in-silico screening for genes encoding copper resistance mechanisms showed that all four strains encode copper resistance proteins CopA, CopB, CopD, CopA3, CopZ, as well as two-component regulatory system CusRS, all known to be associated with metal resistance in Pseudomonas genus. Further detailed studies will aim to characterize the full genomic potential of the isolates to enable their application for copper bioremediation in contaminated soils and industrial wastewaters.
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Affiliation(s)
- Olesia Havryliuk
- Department of Extremophilic Microorganisms Biology, D. K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 154 Zabolotny St., Kyiv 03143, Ukraine
- Corresponding author.
| | - Vira Hovorukha
- Department of Extremophilic Microorganisms Biology, D. K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 154 Zabolotny St., Kyiv 03143, Ukraine
| | - Marianna Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 LSE, Stillwater, Oklahoma 74075, United States of America
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 LSE, Stillwater, Oklahoma 74075, United States of America
| | - Oleksandr Tashyrev
- Department of Extremophilic Microorganisms Biology, D. K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 154 Zabolotny St., Kyiv 03143, Ukraine
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23
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Hanafy RA, Lanjekar VB, Dhakephalkar PK, Callaghan TM, Dagar SS, Griffith GW, Elshahed MS, Youssef NH. Seven new Neocallimastigomycota genera from wild, zoo-housed, and domesticated herbivores greatly expand the taxonomic diversity of the phylum. Mycologia 2020; 112:1212-1239. [PMID: 32057282 DOI: 10.1080/00275514.2019.1696619] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We isolated and characterized 65 anaerobic gut fungal (AGF; Neocallimastigomycota) strains from fecal samples of five wild (W, axis deer, white-tailed deer, Boer goat, mouflon, and Nilgiri tahr), one zoo-housed (Z, zebra), and three domesticated (D, horse, sheep, and goat) herbivores in the US states of Texas (TX) and Oklahoma (OK), Wales (WA), and the Indian states of Kerala (KE) and Haryana (HA). Phylogenetic assessment using the D1-D2 regions of the large subunit (28S) rDNA and internal transcribed spacer 1 (ITS1) identified seven monophyletic clades that are distinct from all currently recognized AGF genera. All strains displayed monocentric thalli and produced exclusively or predominantly monoflagellate zoospores, with the exception of axis deer strains, which produced polyflagellate zoospores. Analysis of amplicon-based AGF diversity surveys indicated that zebra and horse strains are representatives of uncultured AL1 group, whereas domesticated goat and sheep strains are representatives of uncultured AL5 group, previously encountered in fecal and rumen samples of multiple herbivores. The other five lineages, all of which were isolated from wild herbivores, have not been previously encountered in such surveys. Our results significantly expand the genus-level diversity within the Neocallimastigomycota and strongly suggest that wild herbivores represent a yet-untapped reservoir of AGF diversity. We propose seven novel genera and eight novel Neocallimastigomycota species to comprise these strains, for which we propose the names Agriosomyces longus (mouflon and wild Boer goat), Aklioshbomyces papillarum (white-tailed deer), Capellomyces foraminis (wild Boar goat), and C. elongatus (domesticated goat), Ghazallomyces constrictus (axis deer), Joblinomyces apicalis (domesticated goat and sheep), Khoyollomyces ramosus (zebra-horse), and Tahromyces munnarensis (Nilgiri tahr).
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, Oklahoma, 74074
| | | | | | - Tony M Callaghan
- Institute of Biological, Environmental, and Rural Sciences (IBERS), Aberystwyth University , Aberystwyth, Wales, UK
| | - Sumit S Dagar
- Bioenergy Group, Agharkar Research Institute, Pune, India
| | - Gareth W Griffith
- Institute of Biological, Environmental, and Rural Sciences (IBERS), Aberystwyth University , Aberystwyth, Wales, UK
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, Oklahoma, 74074
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, Oklahoma, 74074
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24
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Yadav A, Vilcáez J, Farag IF, Johnson B, Mueller K, Youssef NH, Elshahed MS. Candidatus Mcinerneyibacterium aminivorans gen. nov., sp. nov., the first representative of the candidate phylum Mcinerneyibacteriota phyl. nov. recovered from a high temperature, high salinity tertiary oil reservoir in north central Oklahoma, USA. Syst Appl Microbiol 2020; 43:126057. [PMID: 31987701 DOI: 10.1016/j.syapm.2020.126057] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/02/2020] [Accepted: 01/13/2020] [Indexed: 11/17/2022]
Abstract
We report on the characterization of a novel genomic assembly (ARYD3) recovered from formation water (17.6% salinity) and crude oil enrichment amended by isolated soy proteins (0.2%), and incubated for 100 days under anaerobic conditions at 50°C. Phylogenetic and phylogenomic analysis demonstrated that the ARYD3 is unaffiliated with all currently described bacterial phyla and candidate phyla, as evident by the low AAI (34.7%), shared gene content (19.4%), and 78.9% 16S rRNA gene sequence similarity to Halothiobacillus neapolitanus, its closest cultured relative. Genomic characterization predicts a slow-growing, non-spore forming, and non-motile Gram-negative rod. Adaptation to high salinity is potentially mediated by the production of the compatible solutes cyclic 2,3-diphosphoglycerate (cDPG), α-glucosylglycerate, as well as the uptake of glycine betaine. Metabolically, the genome encodes primarily aminolytic capabilities for a wide range of amino acids and peptides. Interestingly, evidence of propionate degradation to succinate via methyl-malonyl CoA was identified, suggesting possible capability for syntrophic propionate degradation. Analysis of ARYD3 global distribution patterns identified its occurrence in a very small fraction of Earth Microbiome Project datasets examined (318/27,068), where it consistently represented an extremely rare fraction (maximum 0.28%, average 0.004%) of the overall community. We propose the Candidatus name Mcinerneyibacterium aminivorans gen. nov, sp. nov. for ARYD3T, with the genome serving as the type material for the novel family Mcinerneyibacteriaceae fam. nov., order Mcinerneyibacteriales ord. nov., class Mcinerneyibacteria class nov., and phylum Mcinerneyibacteriota phyl. nov. The type material genome assembly is deposited in GenBank under accession number VSIX00000000.
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MESH Headings
- Bacterial Proteins/genetics
- Culture Media
- DNA, Bacterial/genetics
- Ecosystem
- Genome, Bacterial/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/isolation & purification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/metabolism
- Oil and Gas Fields/chemistry
- Oil and Gas Fields/microbiology
- Oklahoma
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Salinity
- Sequence Analysis, DNA
- Soybean Proteins/metabolism
- Temperature
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Affiliation(s)
- Archana Yadav
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Javier Vilcáez
- Boone Pickens School of Geology, Oklahoma State University, Stillwater, OK, United States
| | - Ibrahim F Farag
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Britny Johnson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Katherine Mueller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States.
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Murphy CL, Youssef NH, Hartson S, Elshahed MS. The extraradical proteins of Rhizophagus irregularis: A shotgun proteomics approach. Fungal Biol 2019; 124:91-101. [PMID: 32008757 DOI: 10.1016/j.funbio.2019.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/04/2019] [Accepted: 12/01/2019] [Indexed: 12/28/2022]
Abstract
Arbuscular Mycorrhizal fungi (AMF, Glomeromycota) form obligate symbiotic associations with the roots of most terrestrial plants. Our understanding of the molecular mechanisms enabling AMF propagation and AMF-host interaction is currently incomplete. Analysis of AMF proteomes could yield important insights and generate hypotheses on the nature and mechanism of AMF-plant symbiosis. Here, we examined the extraradical mycelium proteomic profile of the arbuscular mycorrhizal fungus Rhizophagus irregularis grown on Ri T-DNA transformed Chicory roots in a root organ culture setting. Our analysis detected 529 different peptides that mapped to 474 translated proteins in the R. irregularis genome. R. irregularis proteome was characterized by a high proportion of proteins (9.9 % of total, 21.4 % of proteins with functional prediction) mediating a wide range of signal transduction processes, e.g. Rho1 and Bmh2, Ca-signaling (calmodulin, and Ca channel protein), mTOR signaling (MAP3K7, and MAPKAP1), and phosphatidate signaling (phospholipase D1/2) proteins, as well as members of the Ras signaling pathway. In addition, the proteome contained an unusually large proportion (53.6 %) of hypothetical proteins, the majority of which (85.8 %) were Glomeromycota-specific. Forty-eight proteins were predicted to be surface/membrane associated, including multiple hypothetical proteins of yet-unrecognized functions. However, no evidence for the overproduction of specific proteins, previously implicated in promoting soil health and aggregation was obtained. Finally, the comparison of R. irregularis proteome to previously published AMF proteomes identified a core set of pathways and processes involved in AMF growth. We conclude that R. irregularis growth on chicory roots requires the activation of a wide range of signal transduction pathways, the secretion of multiple novel hitherto unrecognized Glomeromycota-specific proteins, and the expression of a wide array of surface-membrane associated proteins for cross kingdom cell-to-cell communications.
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Affiliation(s)
- Chelsea L Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Steve Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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Wang Y, Youssef NH, Couger MB, Hanafy RA, Elshahed MS, Stajich JE. Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes. mSystems 2019; 4:e00247-19. [PMID: 31455637 PMCID: PMC6712302 DOI: 10.1128/msystems.00247-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/01/2019] [Indexed: 01/01/2023] Open
Abstract
The anaerobic gut fungi (AGF), or Neocallimastigomycota, inhabit the rumen and alimentary tract of herbivorous mammals, where they play important roles in the degradation of plant fiber. Comparative genomic and phylogenomic analyses of the AGF have long been hampered by their fastidious growth condition, as well as their large (up to 200 Mb) and AT-biased (78 to 84%) genomes. We sequenced 21 AGF transcriptomes and combined them with 5 available AGF genome sequences to explore their evolutionary relationships, time their divergence, and characterize gene gain/loss patterns associated with their evolution. We estimate that the most recent common ancestor of the AGF diverged 66 (±10) million years ago, a time frame that coincides with the evolution of grasses (Poaceae), as well as the mammalian transition from insectivory to herbivory. The concordance of independent estimations suggests that AGF have been important in shaping the success of mammalian herbivory transition by improving the efficiency of energy acquisition from recalcitrant plant materials. Comparative genomics identified multiple lineage-specific genes in the AGF, two of which were acquired from rumen gut bacteria and animal hosts via horizontal gene transfer (HGT). A third AGF domain, plant-like polysaccharide lyase, represents a novel gene in fungi that potentially aids AGF to degrade pectin. Analysis of genomic and transcriptomic sequences confirmed both the presence and expression of these lineage-specific genes in nearly all AGF clades. These genetic elements may contribute to the exceptional abilities of AGF to degrade plant biomass and enable metabolism of the rumen microbes and animal hosts.IMPORTANCE Anaerobic fungi living in the rumen of herbivorous mammals possess an extraordinary ability to degrade plant biomass. We examined the origin and genomic composition of these poorly characterized anaerobic gut fungi using both transcriptome and genomic data. Phylogenomics and molecular dating analyses found remarkable concurrence of the divergence times of the rumen fungi, the forage grasses, and the dietary shift of ancestral mammals from primarily insectivory to herbivory. Comparative genomics identified unique machinery in these fungi to utilize plant polysaccharides. The rumen fungi were also identified with the ability to code for three protein domains with putative functions in plant pectin degradation and microbial defense, which were absent from all other fungal organisms (examined over 1,000 fungal genomes). Two of these domains were likely acquired from rumen gut bacteria and animal hosts separately via horizontal gene transfer. The third one is a plant-like polysaccharide lyase, representing a unique fungal enzyme with potential pectin breakdown abilities.
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Affiliation(s)
- Yan Wang
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Matthew Brian Couger
- High Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
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Youssef NH, Farag IF, Rudy S, Mulliner A, Walker K, Caldwell F, Miller M, Hoff W, Elshahed M. The Wood-Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1). Environ Microbiol Rep 2019; 11:538-547. [PMID: 30888727 DOI: 10.1111/1758-2229.12753] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
The Wood-Ljungdahl (WL) pathway is an important component of the metabolic machinery in multiple anaerobic prokaryotes, including numerous yet-uncultured bacterial phyla. The pathway can operate in the reductive and oxidative directions, enabling a wide range of metabolic processes. Here, we present a detailed analysis of 14 newly acquired, previously analysed, and publicly available genomic assemblies belonging to the candidate phylum Bipolaricaulota (candidate division OP1, and candidatus Acetothermia), where the occurrence of WL pathway appears to be universal. In silico analysis of predicted metabolic capabilities indicates that the pathway enables homoacetogenic fermentation of sugars and amino acids in all three Bipolaricaulota orders (RBG-16-55-9, UBA7950 and Bipolaricaulales). In addition, members of RBG-16-55-9 appear to possess the additional capacity for syntrophic acetate oxidation using the WL pathway; as well as for respiratory growth using oxygen or nitrate. Anabolically, all UBA7950, and the majority of the Bipolaricaulales genomes possess the capacity for autotrophic growth using the WL pathway. Our results highlight the WL-enabled metabolic versatility in the Bipolaricaulota, emphasize the need for examining the WL pathway in context of the overall metabolic circuitry in uncultured taxa, and demonstrate the value of comparative genomic analysis for providing a detailed overview of metabolic potential in a target microbial lineage and its potential functional niche in an ecosystem.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Ibrahim F Farag
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Sydney Rudy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Ace Mulliner
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Kara Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Ford Caldwell
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Malik Miller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Wouter Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Mostafa Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
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Hanafy RA, Elshahed MS, Youssef NH. Feramyces austinii, gen. nov., sp. nov., an anaerobic gut fungus from rumen and fecal samples of wild Barbary sheep and fallow deer. Mycologia 2018; 110:513-525. [DOI: 10.1080/00275514.2018.1466610] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Radwa A. Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74074
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74074
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74074
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Hanafy RA, Johnson B, Elshahed MS, Youssef NH. Anaeromyces contortus, sp. nov., a new anaerobic gut fungal species (Neocallimastigomycota) isolated from the feces of cow and goat. Mycologia 2018; 110:502-512. [DOI: 10.1080/00275514.2018.1465773] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Radwa A. Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74074
| | - Britny Johnson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74074
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74074
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74074
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Calkins SS, Elledge NC, Mueller KE, Marek SM, Couger MB, Elshahed MS, Youssef NH. Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. PeerJ 2018; 6:e4276. [PMID: 29404209 PMCID: PMC5796279 DOI: 10.7717/peerj.4276] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/29/2017] [Indexed: 12/25/2022] Open
Abstract
Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.
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Affiliation(s)
- Shelby S Calkins
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Nicole C Elledge
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Current affiliation: University of Texas A&M Corpus Christi, Department of Life Sciences, Marine Biology Program, USA
| | - Katherine E Mueller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Stephen M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- High Performance Computing Center, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Morrison JM, Baker KD, Zamor RM, Nikolai S, Elshahed MS, Youssef NH. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). PLoS One 2017; 12:e0177488. [PMID: 28493994 PMCID: PMC5426677 DOI: 10.1371/journal.pone.0177488] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 12/14/2022] Open
Abstract
Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column. Here, we conducted a spatiotemporal survey of the particle-associated and free-living microbial communities in a warm monomictic freshwater reservoir (Grand Lake O’ the Cherokees) in northeastern Oklahoma, USA. Pre-stratification samples (March) harbored a homogeneous community throughout the oxygenated water column dominated by typical oligotrophic aquatic lineages (acl clade within Actinobacteria, and Flavobacterium within the Bacteroidetes). The onset of phototrophic blooming in June induced the progression of this baseline community into two distinct trajectories. Within the oxic epilimnion, samples were characterized by the propagation of phototrophic (Prochlorococcus), and heterotrophic (Planctomycetes, Verrucomicrobia, and Beta-Proteobacteria) lineages. Within the oxygen-deficient thermocline and hypolimnion, the sedimentation of surface biomass induced the development of a highly diverse community, with the enrichment of Chloroflexi, “Latescibacteria”, Armatimonadetes, and Delta-Proteobacteria in the particle-associated fraction, and Gemmatimonadetes and “Omnitrophica” in the free-living fraction. Our work documents the development of multiple spatially and temporally distinct niches during lake stratification, and supports the enrichment of multiple yet-uncultured and poorly characterized lineages in the lake’s deeper oxygen-deficient layers, an ecologically relevant microbial niche that is often overlooked in lakes diversity surveys.
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Affiliation(s)
- Jessica M. Morrison
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Kristina D. Baker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Richard M. Zamor
- Grand River Dam Authority (GRDA), Vinita, OK, United States of America
| | - Steve Nikolai
- Grand River Dam Authority (GRDA), Vinita, OK, United States of America
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
- * E-mail:
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Hanafy RA, Elshahed MS, Liggenstoffer AS, Griffith GW, Youssef NH. Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. Mycologia 2017; 109:231-243. [PMID: 28494211 DOI: 10.1080/00275514.2017.1317190] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The anaerobic gut fungi (AGF) inhabit the rumen and alimentary tracts of multiple ruminant and nonruminant herbivores, belong to a distinct phylum-level lineage (Neocallimastigomycota), and play an important role in plant biomass degradation in many herbivores. As part of a wider effort to obtain AGF with high lignocellulolytic capacities, we isolated and characterized four different AGF strains from the feces of cattle and sheep. Microscopically, isolates produced monocentric thalli and monoflagellated zoospores. Phylogenetic analysis revealed that all isolates formed a monophyletic cluster with strong bootstrap support as a sister clade to the genus Orpinomyces and close to Neocallimastix, an unexpected result because these two genera of AGF form polyflagellated zoospores. Isolates displayed a smooth biofilm-like growth in liquid medium and formed small (0.5-1 mm) pinpoint circular colonies on agar roll tubes. Both endogenous and exogenous sporangia were observed with variable shapes and sizes. Zoospores were mainly spherical, with diameters ranging between 3.8 and 12.5 µm, and mostly a single flagellum. All strains exhibited similar substrate utilization patterns and comparable cellulolytic and xylanolytic activities. Similar ITS1 sequences falling within the same distinctive clade were found on GenBank, with all environmental samples obtained from diverse ruminant and pseudoruminant hosts from three continents, but not from any hindgut-fermenting hosts. Given the high level of sequence divergence between our strains and closest cultured representatives and their distinct microscopic/macroscopic features, we propose a new genus, Pecoramyces, from the name of the taxonomic infraorder Pecora ("horned ruminants" or "higher ruminants"; derived from the Latin word for horned livestock), and a new species, P. ruminantium (since occurrence seems to be specific to ruminant/pseudoruminant foregut, but not hindgut-fermenting mammals).
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Affiliation(s)
- Radwa A Hanafy
- a Department of Microbiology and Molecular Genetics , Oklahoma State University , 1110 S Innovation Way, Stillwater , Oklahoma 74074
| | - Mostafa S Elshahed
- a Department of Microbiology and Molecular Genetics , Oklahoma State University , 1110 S Innovation Way, Stillwater , Oklahoma 74074
| | - Audra S Liggenstoffer
- a Department of Microbiology and Molecular Genetics , Oklahoma State University , 1110 S Innovation Way, Stillwater , Oklahoma 74074
| | - Gareth W Griffith
- b Institute of Biological, Environmental, and Rural Sciences (IBERS) , Aberystwyth University , Aberystwyth , Wales , UK
| | - Noha H Youssef
- a Department of Microbiology and Molecular Genetics , Oklahoma State University , 1110 S Innovation Way, Stillwater , Oklahoma 74074
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Ranganathan A, Smith OP, Youssef NH, Struchtemeyer CG, Atiyeh HK, Elshahed MS. Utilizing Anaerobic Fungi for Two-stage Sugar Extraction and Biofuel Production from Lignocellulosic Biomass. Front Microbiol 2017; 8:635. [PMID: 28443088 PMCID: PMC5387070 DOI: 10.3389/fmicb.2017.00635] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/28/2017] [Indexed: 12/03/2022] Open
Abstract
Lignocellulosic biomass is a vast and underutilized resource for the production of sugars and biofuels. However, the structural complexity of lignocellulosic biomass and the need for multiple pretreatment and enzymatic steps for sugar release renders this process economically challenging. Here, we report a novel approach for direct, single container, exogenous enzyme-free conversion of lignocellulosic biomass to sugars and biofuels using the anaerobic fungal isolate strain C1A. This approach utilizes simple physiological manipulations for timely inhibition and uncoupling of saccharolytic and fermentative capabilities of strain C1A, leading to the accumulation of sugar monomers (glucose and xylose) in the culture medium. The produced sugars, in addition to fungal hyphal lysate, are subsequently converted by Escherichia coli strain K011 to ethanol. Using this approach, we successfully recovered 17.0% (w/w) of alkali-pretreated corn stover (20.0% of its glucan and xylan content) as sugar monomers in the culture media. More importantly, 14.1% of pretreated corn stover (17.1% of glucan and xylan content) was recovered as ethanol at a final concentration of 28.16 mM after the addition of the ethanologenic strain K011. The high ethanol yield obtained is due to its accumulation as a minor fermentation end product by strain C1A during its initial growth phase, the complete conversion of sugars to ethanol by strain K011, and the possible conversion of unspecified substrates in the hyphal lysate of strain C1A to ethanol by strain K011. This study presents a novel, versatile, and exogenous enzyme-free strategy that utilizes a relatively unexplored group of organisms (anaerobic fungi) for direct biofuel production from lignocellulosic biomass.
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Affiliation(s)
- Abhaya Ranganathan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, StillwaterOK, USA
| | - Olivia P Smith
- Department of Microbiology and Molecular Genetics, Oklahoma State University, StillwaterOK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, StillwaterOK, USA
| | | | - Hasan K Atiyeh
- Department of Biosystems and Agricultural Engineering, Oklahoma State University, StillwaterOK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, StillwaterOK, USA
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Morrison JM, Murphy CL, Baker K, Zamor RM, Nikolai SJ, Wilder S, Elshahed MS, Youssef NH. Microbial communities mediating algal detritus turnover under anaerobic conditions. PeerJ 2017; 5:e2803. [PMID: 28097050 PMCID: PMC5228501 DOI: 10.7717/peerj.2803] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/18/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored. RESULTS Here, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake (Grand Lake O' the Cherokees, OK; GL) as inoculum sources. Within all enrichments, the majority of algal biomass was metabolized within 13-16 weeks, and the process was accompanied by an increase in cell numbers and a decrease in community diversity. Community surveys based on the V4 region of the 16S rRNA gene identified different lineages belonging to the phyla Bacteroidetes, Proteobacteria (alpha, delta, gamma, and epsilon classes), Spirochaetes, and Firmicutes that were selectively abundant under various substrate and inoculum conditions. Within all kelp enrichments, the microbial communities structures at the conclusion of the experiment were highly similar regardless of the enrichment source, and were dominated by the genus Clostridium, or family Veillonellaceae within the Firmicutes. In all other enrichments the final microbial community was dependent on the inoculum source, rather than the type of algae utilized as substrate. Lineages enriched included the uncultured groups VadinBC27 and WCHB1-69 within the Bacteroidetes, genus Spirochaeta and the uncultured group SHA-4 within Spirochaetes, Ruminococcaceae, Lachnospiraceae, Yongiibacter, Geosporobacter, and Acidaminobacter within the Firmicutes, and genera Kluyvera, Pantoea, Edwardsiella and Aeromonas, and Buttiauxella within the Gamma-Proteobaceteria order Enterobacteriales. CONCLUSIONS Our results represent the first systematic survey of microbial communities mediating turnover of algal biomass under anaerobic conditions, and highlights the diversity of lineages putatively involved in the degradation process.
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Affiliation(s)
- Jessica M. Morrison
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Chelsea L. Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Kristina Baker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | | | - Shawn Wilder
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Calkins S, Youssef NH. Insights into the Utility of the Focal Adhesion Scaffolding Proteins in the Anaerobic Fungus Orpinomyces sp. C1A. PLoS One 2016; 11:e0163553. [PMID: 27685796 PMCID: PMC5042518 DOI: 10.1371/journal.pone.0163553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/11/2016] [Indexed: 12/30/2022] Open
Abstract
Focal adhesions (FAs) are large eukaryotic multiprotein complexes that are present in all metazoan cells and function as stable sites of tight adhesion between the extracellular matrix (ECM) and the cell's cytoskeleton. FAs consist of anchor membrane protein (integrins), scaffolding proteins (e.g. α-actinin, talin, paxillin, and vinculin), signaling proteins of the IPP complex (e.g. integrin-linked kinase, α-parvin, and PINCH), and signaling kinases (e.g. focal adhesion kinase (FAK) and Src kinase). While genes encoding complete focal adhesion machineries are present in genomes of all multicellular Metazoa; incomplete machineries were identified in the genomes of multiple non-metazoan unicellular Holozoa, basal fungal lineages, and amoebozoan representatives. Since a complete FA machinery is required for functioning, the putative role, if any, of these incomplete FA machineries is currently unclear. We sought to examine the expression patterns of FA-associated genes in the anaerobic basal fungal isolate Orpinomyces sp. strain C1A under different growth conditions and at different developmental stages. Strain C1A lacks clear homologues of integrin, and the two signaling kinases FAK and Src, but encodes for all scaffolding proteins, and the IPP complex proteins. We developed a protocol for synchronizing growth of C1A cultures, allowing for the collection and mRNA extraction from flagellated spores, encysted germinating spores, active zoosporangia, and late inactive sporangia of strain C1A. We demonstrate that the genes encoding the FA scaffolding proteins α-actinin, talin, paxillin, and vinculin are indeed transcribed under all growth conditions, and at all developmental stages of growth. Further, analysis of the observed transcriptional patterns suggests the putative involvement of these components in alternative non-adhesion-specific functions, such as hyphal tip growth during germination and flagellar assembly during zoosporogenesis. Based on these results, we propose putative alternative functions for such proteins in the anaerobic gut fungi. Our results highlight the presumed diverse functionalities of FA scaffolding proteins in basal fungi.
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Affiliation(s)
- Shelby Calkins
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, United States of America
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Morrison JM, Elshahed MS, Youssef NH. Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass. Sci Rep 2016; 6:29217. [PMID: 27381262 PMCID: PMC4933900 DOI: 10.1038/srep29217] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/13/2016] [Indexed: 02/08/2023] Open
Abstract
The anaerobic fungus Orpinomyces strain C1A is capable of growth on various types of lignocellulosic substrates, and harbors an impressive reservoir of carbohydrate active enzymes (CAZymes). Using a minimum enzyme cocktail strategy, we constituted a four-component lignocellulolytic cocktail derived from highly transcribed C1A, and evaluated its efficacy against pretreated corn stover and switchgrass. Hydrolysis yields ranged between 65–77.4%, depending on the lignocellulosic substrate and pretreatment applied. Addition of a highly expressed anaerobic fungal swollenin improved hydrolysis yields by up to 7%. Compared to the commercial cocktail CTec2, these anaerobic fungal cocktails provided comparable or slightly lower hydrolysis yields. Further, the differences in efficacy between commercial and anaerobic cocktails were often only realized after extended (168 hr) incubations. Under certain conditions, the hydrolysis yields of the anaerobic fungal cocktail was slightly superior to that realized by CTec2. We attribute the observed high hydrolysis yields to the high specific activity and affinity of the individual enzymes of the cocktail, as well as the high level of synergy and multi-functionality observed in multiple components. Collectively, this effort provides a novel platform for constructing highly effective enzymes for biofuel production and represents the first lignocellulolytic enzyme cocktail created from anaerobic fungal enzymes.
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Affiliation(s)
- Jessica M Morrison
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Dalvi S, Youssef NH, Fathepure BZ. Microbial community structure analysis of a benzoate-degrading halophilic archaeal enrichment. Extremophiles 2016; 20:311-21. [PMID: 26995683 DOI: 10.1007/s00792-016-0823-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/01/2016] [Indexed: 02/01/2023]
Abstract
A benzoate-degrading archaeal enrichment was developed using sediment samples from Rozel Point at Great Salt Lake, UT. The enrichment degraded benzoate as the sole carbon source at salinity ranging from 2.0 to 5.0 M NaCl with highest rate of degradation observed at 4.0 M. The enrichment was also tested for its ability to grow on other aromatic compounds such as 4-hydroxybenzoic acid (4-HBA), gentisic acid, protocatechuic acid (PCA), catechol, benzene and toluene as the sole sources of carbon and energy. Of these, the culture only utilized 4-HBA as the carbon source. To determine the initial steps in benzoate degradation pathway, a survey of ring-oxidizing and ring-cleaving genes was performed using degenerate PCR primers. Results showed the presence of 4-hydroxybenzoate 3-monooxygenase (4-HBMO) and protocatechuate 3, 4-dioxygenase (3,4-PCA) genes suggesting that the archaeal enrichment might degrade benzoate to 4-HBA that is further converted to PCA by 4-HBMO and, thus, formed PCA would undergo ring-cleavage by 3,4-PCA to form intermediates that enter the Krebs cycle. Small subunit rRNA gene-based diversity survey revealed that the enrichment consisted entirely of class Halobacteria members belonging to the genera Halopenitus, Halosarcina, Natronomonas, Halosimplex, Halorubrum, Salinarchaeum and Haloterrigena. Of these, Halopenitus was the dominant group accounting for almost 91 % of the total sequences suggesting their potential role in degrading oxygenated aromatic compounds at extreme salinity.
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Affiliation(s)
- Sonal Dalvi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Babu Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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Coveley S, Elshahed MS, Youssef NH. Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA). PeerJ 2015; 3:e1182. [PMID: 26312178 PMCID: PMC4548494 DOI: 10.7717/peerj.1182] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/23/2015] [Indexed: 01/09/2023] Open
Abstract
Within highly diverse ecosystems, the majority of bacterial taxa are present in low abundance as members of the rare biosphere. The rationale for the occurrence and maintenance of the rare biosphere, and the putative ecological role(s) and dynamics of its members within a specific ecosystem is currently debated. We hypothesized that in highly diverse ecosystems, a fraction of the rare biosphere acts as a backup system that readily responds to environmental disturbances. We tested this hypothesis by subjecting sediments from Zodletone spring, a sulfide- and sulfur-rich spring in Southwestern OK, to incremental levels of salinity (1, 2, 3, 4, and 10% NaCl), or temperature (28°, 30°, 32°, and 70 °C), and traced the trajectories of rare members of the community in response to these manipulations using 16S rRNA gene analysis. Our results indicate that multiple rare bacterial taxa are promoted from rare to abundant members of the community following such manipulations and that, in general, the magnitude of such recruitment is directly proportional to the severity of the applied manipulation. Rare members that are phylogenetically distinct from abundant taxa in the original sample (unique rare biosphere) played a more important role in the microbial community response to environmental disturbances, compared to rare members that are phylogenetically similar to abundant taxa in the original sample (non-unique rare biosphere). The results emphasize the dynamic nature of the rare biosphere, and highlight its complexity and non-monolithic nature.
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Affiliation(s)
- Suzanne Coveley
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, OK , USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, OK , USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater, OK , USA
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Couger MB, Youssef NH, Struchtemeyer CG, Liggenstoffer AS, Elshahed MS. Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A. Biotechnol Biofuels 2015; 8:208. [PMID: 26649073 PMCID: PMC4672494 DOI: 10.1186/s13068-015-0390-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/16/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Anaerobic fungi reside in the rumen and alimentary tract of herbivores where they play an important role in the digestion of ingested plant biomass. The anaerobic fungal isolate Orpinomyces sp. strain C1A is an efficient biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple types of lignocellulosic biomass. To understand the mechanistic and regulatory basis of biomass deconstruction in anaerobic fungi, we analyzed the transcriptomic profiles of C1A when grown on four different types of lignocellulosic biomass (alfalfa, energy cane, corn stover, and sorghum) versus a soluble sugar monomer (glucose). RESULTS A total of 468.2 million reads (70.2 Gb) were generated and assembled into 27,506 distinct transcripts. CAZyme transcripts identified included 385, 246, and 44 transcripts belonging to 44, 13, and 8 different glycoside hydrolases (GH), carbohydrate esterases, and polysaccharide lyases families, respectively. Examination of CAZyme transcriptional patterns indicates that strain C1A constitutively transcribes a high baseline level of CAZyme transcripts on glucose. Although growth on lignocellulosic biomass substrates was associated with a significant increase in transcriptional levels in few GH families, including the highly transcribed GH1 β-glucosidase, GH6 cellobiohydrolase, and GH9 endoglucanase, the transcriptional levels of the majority of CAZyme families and transcripts were not significantly altered in glucose-grown versus lignocellulosic biomass-grown cultures. Further, strain C1A co-transcribes multiple functionally redundant enzymes for cellulose and hemicellulose saccharification that are mechanistically and structurally distinct. Analysis of fungal dockerin domain-containing transcripts strongly suggests that anaerobic fungal cellulosomes represent distinct catalytic units capable of independently attacking and converting intact plant fibers to sugar monomers. CONCLUSIONS Collectively, these results demonstrate that strain C1A achieves fast, effective biomass degradation by the simultaneous employment of a wide array of constitutively-transcribed cellulosome-bound and free enzymes with considerable functional overlap. We argue that the utilization of this indiscriminate strategy could be justified by the evolutionary history of anaerobic fungi, as well as their functional role within their natural habitat in the herbivorous gut.
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Affiliation(s)
- M. B. Couger
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK USA
| | - Noha H. Youssef
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK USA
| | - Christopher G. Struchtemeyer
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK USA
- />Department of Biology and Health Sciences, McNeese State University, Lake Charles, LA USA
| | - Audra S. Liggenstoffer
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK USA
| | - Mostafa S. Elshahed
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK USA
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Youssef NH, Couger MB, McCully AL, Criado AEG, Elshahed MS. Assessing the global phylum level diversity within the bacterial domain: A review. J Adv Res 2014; 6:269-82. [PMID: 26257925 PMCID: PMC4522544 DOI: 10.1016/j.jare.2014.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022] Open
Abstract
Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexandra L McCully
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Liggenstoffer AS, Youssef NH, Wilkins MR, Elshahed MS. Evaluating the utility of hydrothermolysis pretreatment approaches in enhancing lignocellulosic biomass degradation by the anaerobic fungus Orpinomyces sp. strain C1A. J Microbiol Methods 2014; 104:43-8. [DOI: 10.1016/j.mimet.2014.06.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/12/2014] [Accepted: 06/13/2014] [Indexed: 11/30/2022]
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Youssef NH, Rinke C, Stepanauskas R, Farag I, Woyke T, Elshahed MS. Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'. ISME J 2014; 9:447-60. [PMID: 25083931 DOI: 10.1038/ismej.2014.141] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/22/2014] [Accepted: 07/01/2014] [Indexed: 11/09/2022]
Abstract
The archaeal phylum 'Diapherotrites' was recently proposed based on phylogenomic analysis of genomes recovered from an underground water seep in an abandoned gold mine (Homestake mine in Lead, SD, USA). Here we present a detailed analysis of the metabolic capabilities and genomic features of three single amplified genomes (SAGs) belonging to the 'Diapherotrites'. The most complete of the SAGs, Candidatus 'Iainarchaeum andersonii' (Cand. IA), had a small genome (∼1.24 Mb), short average gene length (822 bp), one ribosomal RNA operon, high coding density (∼90.4%), high percentage of overlapping genes (27.6%) and low incidence of gene duplication (2.16%). Cand. IA genome possesses limited catabolic capacities that, nevertheless, could theoretically support a free-living lifestyle by channeling a narrow range of substrates such as ribose, polyhydroxybutyrate and several amino acids to acetyl-coenzyme A. On the other hand, Cand. IA possesses relatively well-developed anabolic capabilities, although it remains auxotrophic for several amino acids and cofactors. Phylogenetic analysis suggests that the majority of Cand. IA anabolic genes were acquired from bacterial donors via horizontal gene transfer. We thus propose that members of the 'Diapherotrites' have evolved from an obligate symbiotic ancestor by acquiring anabolic genes from bacteria that enabled independent biosynthesis of biological molecules previously acquired from symbiotic hosts. 'Diapherotrites' 16S rRNA genes exhibit multiple mismatches with the majority of archaeal 16S rRNA primers, a fact that could be responsible for their observed rarity in amplicon-generated data sets. The limited substrate range, complex growth requirements and slow growth rate predicted could be responsible for its refraction to isolation.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | | | - Ibrahim Farag
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Youssef NH, Savage-Ashlock KN, McCully AL, Luedtke B, Shaw EI, Hoff WD, Elshahed MS. Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales. ISME J 2013; 8:636-649. [PMID: 24048226 DOI: 10.1038/ismej.2013.165] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 11/09/2022]
Abstract
We investigated the mechanisms of osmoadaptation in the order Halobacteriales, with special emphasis on Haladaptatus paucihalophilus, known for its ability to survive in low salinities. H. paucihalophilus genome contained genes for trehalose synthesis (trehalose-6-phosphate synthase/trehalose-6-phosphatase (OtsAB pathway) and trehalose glycosyl-transferring synthase pathway), as well as for glycine betaine uptake (BCCT family of secondary transporters and QAT family of ABC transporters). H. paucihalophilus cells synthesized and accumulated ∼1.97-3.72 μmol per mg protein of trehalose in a defined medium, with its levels decreasing with increasing salinities. When exogenously supplied, glycine betaine accumulated intracellularly with its levels increasing at higher salinities. RT-PCR analysis strongly suggested that H. paucihalophilus utilizes the OtsAB pathway for trehalose synthesis. Out of 83 Halobacteriales genomes publicly available, genes encoding the OtsAB pathway and glycine betaine BCCT family transporters were identified in 38 and 60 genomes, respectively. Trehalose (or its sulfonated derivative) production and glycine betaine uptake, or lack thereof, were experimentally verified in 17 different Halobacteriales species. Phylogenetic analysis suggested that trehalose synthesis is an ancestral trait within the Halobacteriales, with its absence in specific lineages reflecting the occurrence of gene loss events during Halobacteriales evolution. Analysis of multiple culture-independent survey data sets demonstrated the preference of trehalose-producing genera to saline and low salinity habitats, and the dominance of genera lacking trehalose production capabilities in permanently hypersaline habitats. This study demonstrates that, contrary to current assumptions, compatible solutes production and uptake represent a common mechanism of osmoadaptation within the Halobacteriales.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Kristen N Savage-Ashlock
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,3Present address: Department of Biology, Georgia State University, Atlanta, Georgia
| | - Alexandra L McCully
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,4Present address: Department of Biology, Indiana University, Bloomington IN
| | - Brandon Luedtke
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,5Present address: US Department of Agriculture, Agricultural Research Service, Roman L. Hruska Meat Animal Research Center, Clay Center, NE 68933-0166
| | - Edward I Shaw
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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Youssef NH, Wofford N, McInerney MJ. Importance of the long-chain fatty acid beta-hydroxylating cytochrome P450 enzyme YbdT for lipopeptide biosynthesis in Bacillus subtilis strain OKB105. Int J Mol Sci 2011; 12:1767-86. [PMID: 21673922 PMCID: PMC3111633 DOI: 10.3390/ijms12031767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 02/08/2011] [Accepted: 03/03/2011] [Indexed: 11/25/2022] Open
Abstract
Bacillus species produce extracellular, surface-active lipopeptides such as surfactin that have wide applications in industry and medicine. The steps involved in the synthesis of 3-hydroxyacyl-coenzyme A (CoA) substrates needed for surfactin biosynthesis are not understood. Cell-free extracts of Bacillus subtilis strain OKB105 synthesized lipopeptide biosurfactants in presence of l-amino acids, myristic acid, coenzyme A, ATP, and H2O2, which suggested that 3-hydroxylation occurs prior to CoA ligation of the long chain fatty acids (LCFAs). We hypothesized that YbdT, a cytochrome P450 enzyme known to beta-hydroxylate LCFAs, functions to form 3-hydroxy fatty acids for lipopeptide biosynthesis. An in-frame mutation of ybdT was constructed and the resulting mutant strain (NHY1) produced predominantly non-hydroxylated lipopeptide with diminished biosurfactant and beta-hemolytic activities. Mass spectrometry showed that 95.6% of the fatty acids in the NHY1 biosurfactant were non-hydroxylated compared to only ∼61% in the OKB105 biosurfactant. Cell-free extracts of the NHY1 synthesized surfactin containing 3-hydroxymyristic acid from 3-hydroxymyristoyl-CoA at a specific activity similar to that of the wild type (17 ± 2 versus 17.4 ± 6 ng biosurfactant min−1·ng·protein−1, respectively). These results showed that the mutation did not affect any function needed to synthesize surfactin once the 3-hydroxyacyl-CoA substrate was formed and that YbdT functions to supply 3-hydroxy fatty acid for surfactin biosynthesis. The fact that YbdT is a peroxidase could explain why biosurfactant production is rarely observed in anaerobically grown Bacillus species. Manipulation of LCFA specificity of YbdT could provide a new route to produce biosurfactants with activities tailored to specific functions.
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Affiliation(s)
- Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-405-744-3193; Fax: +1-405-744-1112
| | - Neil Wofford
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 74078, USA; E-Mails: (N.W.); (M.J.M.)
| | - Michael J. McInerney
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 74078, USA; E-Mails: (N.W.); (M.J.M.)
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Youssef NH, Couger MB, Elshahed MS. Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone Spring, OK, USA): the role of the rare biosphere. PLoS One 2010; 5:e12414. [PMID: 20865128 PMCID: PMC2932559 DOI: 10.1371/journal.pone.0012414] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 07/09/2010] [Indexed: 12/18/2022] Open
Abstract
Background The adaptation of pyrosequencing technologies for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems. Methodology/Principal Findings We examined the patterns of fine scale Beta diversity in four adjacent sediment samples (1mm apart) from the source of an anaerobic sulfide and sulfur rich spring (Zodletone spring) in southwestern Oklahoma, USA. Using pyrosequencing, a total of 292,130 16S rRNA gene sequences were obtained. The beta diversity patterns within the four datasets were examined using various qualitative and quantitative similarity indices. Low levels of Beta diversity (high similarity indices) were observed between the four samples at the phylum-level. However, at a putative species (OTU0.03) level, higher levels of beta diversity (lower similarity indices) were observed. Further examination of beta diversity patterns within dominant and rare members of the community indicated that at the putative species level, beta diversity is much higher within rare members of the community. Finally, sub-classification of rare members of Zodletone spring community based on patterns of novelty and uniqueness, and further examination of fine scale beta diversity of each of these subgroups indicated that members of the community that are unique, but non novel showed the highest beta diversity within these subgroups of the rare biosphere. Conclusions/Significance The results demonstrate the occurrence of high inter-sample diversity within seemingly identical samples from a complex habitat. We reason that such unexpected diversity should be taken into consideration when exploring gamma diversity of various ecosystems, as well as planning for sequencing-intensive metagenomic surveys of highly complex ecosystems.
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Affiliation(s)
- Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - M. B. Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * E-mail:
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Liggenstoffer AS, Youssef NH, Couger MB, Elshahed MS. Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J 2010; 4:1225-35. [PMID: 20410935 DOI: 10.1038/ismej.2010.49] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phylogenetic diversity and community structure of members of the gut anaerobic fungi (AF) (phylum Neocallimastigomycota) were investigated in 30 different herbivore species that belong to 10 different mammalian and reptilian families using the internal transcribed spacer region-1 (ITS-1) ribosomal RNA (rRNA) region as a phylogenetic marker. A total of 267 287 sequences representing all known anaerobic fungal genera were obtained in this study. Sequences affiliated with the genus Piromyces were the most abundant, being encountered in 28 different samples, and representing 36% of the sequences obtained. On the other hand, sequences affiliated with the genera Cyllamyces and Orpinomyces were the least abundant, being encountered in 2, and 8 samples, and representing 0.7%, and 1.1% of the total sequences obtained, respectively. Further, 38.3% of the sequences obtained did not cluster with previously identified genera and formed eight phylogenetically distinct novel anaerobic fungal lineages. Some of these novel lineages were widely distributed (for example NG1 and NG3), whereas others were animal specific, being encountered in only one or two animals (for example NG4, NG6, NG7, and NG8). The impact of various physiological and environmental factors on the diversity and community structure of AF was examined. The results suggest that animal host phylogeny exerts the most significant role on shaping anaerobic fungal diversity and community composition. These results greatly expand the documented global phylogenetic diversity of members of this poorly studied group of fungi that has an important function in initiating plant fiber degradation during fermentative digestion in ruminant and non-ruminant herbivores.
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Affiliation(s)
- Audra S Liggenstoffer
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Youssef NH, Elshahed MS. Species richness in soil bacterial communities: a proposed approach to overcome sample size bias. J Microbiol Methods 2008; 75:86-91. [PMID: 18585806 DOI: 10.1016/j.mimet.2008.05.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 05/07/2008] [Accepted: 05/07/2008] [Indexed: 11/17/2022]
Abstract
Estimates of species richness based on 16S rRNA gene clone libraries are increasingly utilized to gauge the level of bacterial diversity within various ecosystems. However, previous studies have indicated that regardless of the utilized approach, species richness estimates obtained are dependent on the size of the analyzed clone libraries. We here propose an approach to overcome sample size bias in species richness estimates in complex microbial communities. Parametric (Maximum likelihood-based and rarefaction curve-based) and non-parametric approaches were used to estimate species richness in a library of 13,001 near full-length 16S rRNA clones derived from soil, as well as in multiple subsets of the original library. Species richness estimates obtained increased with the increase in library size. To obtain a sample size-unbiased estimate of species richness, we calculated the theoretical clone library sizes required to encounter the estimated species richness at various clone library sizes, used curve fitting to determine the theoretical clone library size required to encounter the "true" species richness, and subsequently determined the corresponding sample size-unbiased species richness value. Using this approach, sample size-unbiased estimates of 17,230, 15,571, and 33,912 were obtained for the ML-based, rarefaction curve-based, and ACE-1 estimators, respectively, compared to bias-uncorrected values of 15,009, 11,913, and 20,909.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, United States
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Nguyen TT, Youssef NH, McInerney MJ, Sabatini DA. Rhamnolipid biosurfactant mixtures for environmental remediation. Water Res 2008; 42:1735-1743. [PMID: 18035390 DOI: 10.1016/j.watres.2007.10.038] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 10/18/2007] [Accepted: 10/23/2007] [Indexed: 05/25/2023]
Abstract
This study investigated the efficiency of rhamnolipid biosurfactant and synthetic surfactant mixtures for improving the interfacial activity of the surfactant system against several light non-aqueous-phase liquids (LNAPLs). Since the rhamnolipid biosurfactant proved to be relatively hydrophilic, we hypothesized that mixtures of rhamnolipid biosurfactants with more hydrophobic synthetic surfactants would produce lower interfacial tensions (IFTs) than an individual rhamnolipid biosurfactant. The minimum IFT observed for rhamnolipid alone and toluene (0.03mN/m) was one order of magnitude lower than for hexane, decane, and hexadecane, demonstrating the relatively hydrophilic nature of the rhamnolipid. The low IFTs even at the low surfactant concentration used suggest mobilization as the dominant oil-removal mechanism versus supersolubilization. The critical micelle concentration (CMC) and critical microemulsion concentration (CmicroC) of the rhamnolipid were found to be 0.001w/w% (0.019mM) and 0.01w/w% (0.19mM), respectively. Three alkyl propoxylated (PO) sulfate synthetic surfactants were individually mixed with the rhamnolipid. As the hydrophobicity of the surfactant mixture approached that of the hydrocarbon, IFT values decreased by one to two orders of magnitude below that achieved with individual surfactants. This work shows that the rhamnolipid has excellent phase behavior at low concentrations and can be used in surfactant mixtures to achieve the low IFT values needed for environmental remediation, enhanced oil recovery (EOR), and other applications.
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Affiliation(s)
- Thu T Nguyen
- Chemical, Biological and Materials Engineering, Norman, OK 73019, USA
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Elshahed MS, Youssef NH, Luo Q, Najar FZ, Roe BA, Sisk TM, Bühring SI, Hinrichs KU, Krumholz LR. Phylogenetic and metabolic diversity of Planctomycetes from anaerobic, sulfide- and sulfur-rich Zodletone Spring, Oklahoma. Appl Environ Microbiol 2007; 73:4707-16. [PMID: 17545322 PMCID: PMC1951033 DOI: 10.1128/aem.00591-07] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 05/27/2007] [Indexed: 11/20/2022] Open
Abstract
We investigated the phylogenetic diversity and metabolic capabilities of members of the phylum Planctomycetes in the anaerobic, sulfide-saturated sediments of a mesophilic spring (Zodletone Spring) in southwestern Oklahoma. Culture-independent analyses of 16S rRNA gene sequences generated using Planctomycetes-biased primer pairs suggested that an extremely diverse community of Planctomycetes is present at the spring. Although sequences that are phylogenetically affiliated with cultured heterotrophic Planctomycetes were identified, the majority of the sequences belonged to several globally distributed, as-yet-uncultured Planctomycetes lineages. Using complex organic media (aqueous extracts of the spring sediments and rumen fluid), we isolated two novel strains that belonged to the Pirellula-Rhodopirellula-Blastopirellula clade within the Planctomycetes. The two strains had identical 16S rRNA gene sequences, and their closest relatives were isolates from Kiel Fjord (Germany), Keauhou Beach (HI), a marine aquarium, and tissues of marine organisms (Aplysina sp. sponges and postlarvae of the giant tiger prawn Penaeus monodon). The closest recognized cultured relative of strain Zi62 was Blastopirellula marina (93.9% sequence similarity). Detailed characterization of strain Zi62 revealed its ability to reduce elemental sulfur to sulfide under anaerobic conditions, as well as its ability to produce acids from sugars; both characteristics may potentially allow strain Zi62 to survive and grow in the anaerobic, sulfide- and sulfur-rich environment at the spring source. Overall, this work indicates that anaerobic metabolic abilities are widely distributed among all major Planctomycetes lineages and suggests carbohydrate fermentation and sulfur reduction as possible mechanisms employed by heterotrophic Planctomycetes for growth and survival under anaerobic conditions.
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Affiliation(s)
- Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA.
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