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Liew KJ, Shahar S, Shamsir MS, Shaharuddin NB, Liang CH, Chan KG, Pointing SB, Sani RK, Goh KM. Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation. ENVIRONMENTAL MICROBIOME 2024; 19:29. [PMID: 38706006 PMCID: PMC11071339 DOI: 10.1186/s40793-024-00572-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism. RESULTS Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures. CONCLUSIONS This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.
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Grants
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- 4J549 UTM QuickWin grant
- 4J549 UTM QuickWin grant
- T2EP30123-0028 Singapore Ministry of Education ARC Tier 2 fund
- 1736255, 1849206, and 1920954 National Science Foundation
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Affiliation(s)
- Kok Jun Liew
- Codon Genomics, 42300 Seri Kembangan, Selangor, Malaysia
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Nawal Binti Shaharuddin
- School of Professional and Continuing Education, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Chee Hung Liang
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Stephen Brian Pointing
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
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Paul R, Rogers TJ, Fullerton KM, Selci M, Cascone M, Stokes MH, Steen AD, de Moor JM, Chiodi A, Stefánsson A, Halldórsson SA, Ramirez CJ, Jessen GL, Barry PH, Cordone A, Giovannelli D, Lloyd KG. Complex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems. PLoS One 2023; 18:e0281277. [PMID: 37594978 PMCID: PMC10437873 DOI: 10.1371/journal.pone.0281277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/30/2023] [Indexed: 08/20/2023] Open
Abstract
Microbial communities in terrestrial geothermal systems often contain chemolithoautotrophs with well-characterized distributions and metabolic capabilities. However, the extent to which organic matter produced by these chemolithoautotrophs supports heterotrophs remains largely unknown. Here we compared the abundance and activity of peptidases and carbohydrate active enzymes (CAZymes) that are predicted to be extracellular identified in metagenomic assemblies from 63 springs in the Central American and the Andean convergent margin (Argentinian backarc of the Central Volcanic Zone), as well as the plume-influenced spreading center in Iceland. All assemblies contain two orders of magnitude more peptidases than CAZymes, suggesting that the microorganisms more often use proteins for their carbon and/or nitrogen acquisition instead of complex sugars. The CAZy families in highest abundance are GH23 and CBM50, and the most abundant peptidase families are M23 and C26, all four of which degrade peptidoglycan found in bacterial cells. This implies that the heterotrophic community relies on autochthonous dead cell biomass, rather than allochthonous plant matter, for organic material. Enzymes involved in the degradation of cyanobacterial- and algal-derived compounds are in lower abundance at every site, with volcanic sites having more enzymes degrading cyanobacterial compounds and non-volcanic sites having more enzymes degrading algal compounds. Activity assays showed that many of these enzyme classes are active in these samples. High temperature sites (> 80°C) had similar extracellular carbon-degrading enzymes regardless of their province, suggesting a less well-developed population of secondary consumers at these sites, possibly connected with the limited extent of the subsurface biosphere in these high temperature sites. We conclude that in < 80°C springs, chemolithoautotrophic production supports heterotrophs capable of degrading a wide range of organic compounds that do not vary by geological province, even though the taxonomic and respiratory repertoire of chemolithoautotrophs and heterotrophs differ greatly across these regions.
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Affiliation(s)
- Raegan Paul
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Timothy J. Rogers
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Kate M. Fullerton
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Matteo Selci
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Martina Cascone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Murray H. Stokes
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Andrew D. Steen
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - J. Maarten de Moor
- Observatorio Volcanológico y Sismológico de Costa Rica (OVSICORI) Universidad Nacional, Heredia, Costa Rica
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM, United States of America
| | - Agostina Chiodi
- Instituto de Bio y Geociencias del NOA (IBIGEO, UNSa-CONICET), Salta, Argentina
| | - Andri Stefánsson
- NordVulk, Institute of Earth Sciences, University of Iceland, Reykjavík, Iceland
| | | | | | - Gerdhard L. Jessen
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
- Center for Oceanographic Research COPAS COASTAL, Universidad de Concepción, Concepción, Chile
| | - Peter H. Barry
- Marine Chemistry & Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
| | - Angelina Cordone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples “Federico II”, Naples, Italy
- Marine Chemistry & Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
- National Research Council–Institute of Marine Biological Resources and Biotechnologies—CNR-IRBIM, Ancona, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States of America
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Karen G. Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
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Bing RG, Willard DJ, Crosby JR, Adams MWW, Kelly RM. Whither the genus Caldicellulosiruptor and the order Thermoanaerobacterales: phylogeny, taxonomy, ecology, and phenotype. Front Microbiol 2023; 14:1212538. [PMID: 37601363 PMCID: PMC10434631 DOI: 10.3389/fmicb.2023.1212538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
The order Thermoanaerobacterales currently consists of fermentative anaerobic bacteria, including the genus Caldicellulosiruptor. Caldicellulosiruptor are represented by thirteen species; all, but one, have closed genome sequences. Interest in these extreme thermophiles has been motivated not only by their high optimal growth temperatures (≥70°C), but also by their ability to hydrolyze polysaccharides including, for some species, both xylan and microcrystalline cellulose. Caldicellulosiruptor species have been isolated from geographically diverse thermal terrestrial environments located in New Zealand, China, Russia, Iceland and North America. Evidence of their presence in other terrestrial locations is apparent from metagenomic signatures, including volcanic ash in permafrost. Here, phylogeny and taxonomy of the genus Caldicellulosiruptor was re-examined in light of new genome sequences. Based on genome analysis of 15 strains, a new order, Caldicellulosiruptorales, is proposed containing the family Caldicellulosiruptoraceae, consisting of two genera, Caldicellulosiruptor and Anaerocellum. Furthermore, the order Thermoanaerobacterales also was re-assessed, using 91 genome-sequenced strains, and should now include the family Thermoanaerobacteraceae containing the genera Thermoanaerobacter, Thermoanaerobacterium, Caldanaerobacter, the family Caldanaerobiaceae containing the genus Caldanaerobius, and the family Calorimonaceae containing the genus Calorimonas. A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. Comparative genomics of carbohydrate-active enzyme inventories suggested differentiating phenotypic features, even among strains of the same species, reflecting available nutrients and ecological roles in their native biotopes.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
| | - Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
| | - James R. Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
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4
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Zhang HS, Feng QD, Zhang DY, Zhu GL, Yang L. Bacterial community structure in geothermal springs on the northern edge of Qinghai-Tibet plateau. Front Microbiol 2023; 13:994179. [PMID: 37180363 PMCID: PMC10172933 DOI: 10.3389/fmicb.2022.994179] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/13/2022] [Indexed: 03/19/2023] Open
Abstract
Introduction:In order to reveal the composition of the subsurface hydrothermal bacterial community in the zones of magmatic tectonics and their response to heat storage environments.Methods:In this study, we performed hydrochemical analysis and regional sequencing of the 16S rRNA microbial V4-V5 region in 7 Pleistocene and Lower Neogene hot water samples from the Gonghe basin.Results:Two geothermal hot spring reservoirs in the study area were found to be alkaline reducing environments with a mean temperature of 24.83°C and 69.28°C, respectively, and the major type of hydrochemistry was SO4-Cl·Na. The composition and structure of microorganisms in both types of geologic thermal storage were primarily controlled by temperature, reducing environment intensity, and hydrogeochemical processes. Only 195 ASVs were shared across different temperature environments, and the dominant bacterial genera in recent samples from temperate hot springs were Thermus and Hydrogenobacter, with both genera being typical of thermophiles. The correlation analysis showed that the overall level of relative abundance of the subsurface hot spring relied on a high temperature and a slightly alkaline reducing environment. Nearly all of the top 4 species in the abundance level (53.99% of total abundance) were positively correlated with temperature and pH, whereas they were negatively correlated with ORP (oxidation–reduction potential), nitrate, and bromine ions.Discussion:In general, the composition of bacteria in the groundwater in the study area was sensitive to the response of the thermal storage environment and also showed a relationship with geochemical processes, such as gypsum dissolution, mineral oxidation, etc.
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5
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Goh KM, Donati ER, Sani RK, Chan KG. Editorial: Genetics, Genomics and -omics of Thermophiles, Volume II. Front Microbiol 2022; 13:879450. [PMID: 35432290 PMCID: PMC9008572 DOI: 10.3389/fmicb.2022.879450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/14/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Kian Mau Goh
- Department of Biosciences, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
- *Correspondence: Kian Mau Goh
| | - Edgardo Rubén Donati
- Facultad de Ciencias Exactas, Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (CCT La Plata-CONICET, UNLP), La Plata, Argentina
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, China
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6
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Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures. Sci Rep 2022; 12:2850. [PMID: 35181739 PMCID: PMC8857248 DOI: 10.1038/s41598-022-06943-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbohydrate degrading enzymes (CAZymes) that have a high potential for future applications. Green microbial mat, predominantly photosynthetic bacteria, was attached to submerged or floating leaves litter. At the spring head, the sediment mixture consisted of plant debris, predominantly brownish-reddish gelatinous microbial mat, pale tan biofilm, and grey-white filament biofilm. The population in the spring head had a higher percentage of archaea and hyperthermophiles than the green mat. Concurrently, we cataloged nearly 10,000 sequences of CAZymes in both green and brown biofilms using the shotgun metagenomic sequencing approach. These sequences include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α-l-arabinofuranosidase, and other CAZymes. In conclusion, this work elucidated that SKY is a unique hot spring due to its rich lignocellulosic material, often absent in other hot springs. The data collected from this study serves as a repository of new thermostable macromolecules, in particular families of glycoside hydrolases.
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7
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Centeno-Leija S, Espinosa-Barrera L, Velazquez-Cruz B, Cárdenas-Conejo Y, Virgen-Ortíz R, Valencia-Cruz G, Saenz RA, Marín-Tovar Y, Gómez-Manzo S, Hernández-Ochoa B, Rocha-Ramirez LM, Zataraín-Palacios R, Osuna-Castro JA, López-Munguía A, Serrano-Posada H. Mining for novel cyclomaltodextrin glucanotransferases unravels the carbohydrate metabolism pathway via cyclodextrins in Thermoanaerobacterales. Sci Rep 2022; 12:730. [PMID: 35031648 PMCID: PMC8760340 DOI: 10.1038/s41598-021-04569-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/20/2021] [Indexed: 11/21/2022] Open
Abstract
Carbohydrate metabolism via cyclodextrins (CM-CD) is an uncommon starch-converting pathway that thoroughly depends on extracellular cyclomaltodextrin glucanotransferases (CGTases) to transform the surrounding starch substrate to α-(1,4)-linked oligosaccharides and cyclodextrins (CDs). The CM-CD pathway has emerged as a convenient microbial adaptation to thrive under extreme temperatures, as CDs are functional amphipathic toroids with higher heat-resistant values than linear dextrins. Nevertheless, although the CM-CD pathway has been described in a few mesophilic bacteria and archaea, it remains obscure in extremely thermophilic prokaryotes (Topt ≥ 70 °C). Here, a new monophyletic group of CGTases with an exceptional three-domain ABC architecture was detected by (meta)genome mining of extremely thermophilic Thermoanaerobacterales living in a wide variety of hot starch-poor environments on Earth. Functional studies of a representative member, CldA, showed a maximum activity in a thermoacidophilic range (pH 4.0 and 80 °C) with remarkable product diversification that yielded a mixture of α:β:γ-CDs (34:62:4) from soluble starch, as well as G3-G7 linear dextrins and fermentable sugars as the primary products. Together, comparative genomics and predictive functional analysis, combined with data of the functionally characterized key proteins of the gene clusters encoding CGTases, revealed the CM-CD pathway in Thermoanaerobacterales and showed that it is involved in the synthesis, transportation, degradation, and metabolic assimilation of CDs.
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Affiliation(s)
- Sara Centeno-Leija
- Consejo Nacional de Ciencia y Tecnología, Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico.
| | - Laura Espinosa-Barrera
- Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico
| | - Beatriz Velazquez-Cruz
- Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico
| | - Yair Cárdenas-Conejo
- Consejo Nacional de Ciencia y Tecnología, Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico
| | - Raúl Virgen-Ortíz
- Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico
| | - Georgina Valencia-Cruz
- Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Avenida 25 de julio 965, Colonia Villa de San Sebastián, 28045, Colima, Colima, Mexico
| | - Roberto A Saenz
- Facultad de Ciencias, Universidad de Colima, Bernal Díaz del Castillo 340, 28045, Colima, Colima, Mexico
| | - Yerli Marín-Tovar
- Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Mexico
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530, Mexico City, Mexico
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica y Biología Celular, Hospital Infantil de México Federico Gómez, Secretaría de Salud, 06720, Mexico City, Mexico
| | - Luz María Rocha-Ramirez
- Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Dr. Márquez No. 162, Colonia Doctores, 06720, Delegación Cuauhtémoc, Mexico
| | - Rocío Zataraín-Palacios
- Escuela de Medicina General, Universidad José Martí, Bosques del Decán 351, 28089, Colima, Colima, México
| | - Juan A Osuna-Castro
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad de Colima, Autopista Colima-Manzanillo, 28100, Tecomán, Colima, Mexico
| | - Agustín López-Munguía
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Hugo Serrano-Posada
- Consejo Nacional de Ciencia y Tecnología, Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico.
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Popova LI, Bahl H, Egorova MA, Leont’eva MR, Netrusov AI, Tsavkelova EA. Isolation of Cellulose-Degrading Thermoanaerobacterium Strains from Thermophilic Methanogenic Microbial Communities. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721020090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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9
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Cullings K, Stott MB, Marinkovich N, DeSimone J, Bhardwaj S. Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert. Microbiologyopen 2020; 9:e1062. [PMID: 32478485 PMCID: PMC7424252 DOI: 10.1002/mbo3.1062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.
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Affiliation(s)
- Ken Cullings
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Julia DeSimone
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Shilpa Bhardwaj
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
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10
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Blumer-Schuette SE. Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology. Microorganisms 2020; 8:E385. [PMID: 32164310 PMCID: PMC7142884 DOI: 10.3390/microorganisms8030385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 11/16/2022] Open
Abstract
Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.
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Lee LL, Crosby JR, Rubinstein GM, Laemthong T, Bing RG, Straub CT, Adams MW, Kelly RM. The biology and biotechnology of the genus Caldicellulosiruptor: recent developments in ‘Caldi World’. Extremophiles 2019; 24:1-15. [DOI: 10.1007/s00792-019-01116-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/09/2019] [Indexed: 12/01/2022]
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12
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Suleiman M, Klippel B, Busch P, Schäfers C, Moccand C, Bel-Rhlid R, Palzer S, Antranikian G. Enrichment of anaerobic heterotrophic thermophiles from four Azorean hot springs revealed different community composition and genera abundances using recalcitrant substrates. Extremophiles 2019; 23:277-281. [PMID: 30741334 DOI: 10.1007/s00792-019-01079-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/03/2019] [Indexed: 11/26/2022]
Abstract
DGGE analysis combined with a metagenomic approach was used to get insights into heterotrophic anoxic enrichment cultures of four hot springs of Vale das Furnas, Portugal, using the recalcitrant substrate spent coffee ground (SCG). Parallel enrichment cultures were performed using the major components of spent coffee ground, namely arabinogalactan, galactomannan, cellulose, and proteins. DGGE revealed that heterotrophic thermophilic bacteria are highly abundant in the hydrothermal springs and significant differences in community composition depending on the substrate were observed. DNA, isolated from enrichment cultures of different locations that were grown on the same substrate were pooled, and the respective metagenomes were analyzed. Results indicated that cultures grown on recalcitrant substrate SCG consists of a totally different thermophilic community, dominated by Dictyoglomus. Enrichments with galactomannan and arabinogalactan were dominated by Thermodesulfovibrio, while cultures with casein and cellulose were dominated by Thermus. This study indicates the high potential of thermophilic bacteria degrading recalcitrant substrate such as SCG and furthermore how the accessibility to complex polymers shapes the bacterial community.
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Affiliation(s)
- Marcel Suleiman
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Barbara Klippel
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Philip Busch
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Christian Schäfers
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | | | | | | | - Garabed Antranikian
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany.
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13
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Lee LL, Blumer-Schuette SE, Izquierdo JA, Zurawski JV, Loder AJ, Conway JM, Elkins JG, Podar M, Clum A, Jones PC, Piatek MJ, Weighill DA, Jacobson DA, Adams MWW, Kelly RM. Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses. Appl Environ Microbiol 2018; 84:e02694-17. [PMID: 29475869 PMCID: PMC5930323 DOI: 10.1128/aem.02694-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/16/2018] [Indexed: 11/20/2022] Open
Abstract
Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. strain Rt8.B8 (renamed here Caldicellulosiruptor morganii), Thermoanaerobacter cellulolyticus strain NA10 (renamed here Caldicellulosiruptor naganoensis), and Caldicellulosiruptor sp. strain Wai35.B1 (renamed here Caldicellulosiruptor danielii), degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than Caldicellulosiruptor bescii in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that of Caldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter, Fervidobacterium, Caloramator, and Clostridium). One enrichment, containing 89.8% Caldicellulosiruptor and 9.7% Caloramator, had a capacity for switchgrass solubilization comparable to that of C. bescii These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes.IMPORTANCE The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.
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Affiliation(s)
- Laura L Lee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Sara E Blumer-Schuette
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Javier A Izquierdo
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Jeffrey V Zurawski
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Andrew J Loder
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alicia Clum
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Piet C Jones
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Marek J Piatek
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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14
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Lee LS, Goh KM, Chan CS, Annie Tan GY, Yin WF, Chong CS, Chan KG. Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring. Microbiologyopen 2018; 7:e00615. [PMID: 29602271 PMCID: PMC6291792 DOI: 10.1002/mbo3.615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/29/2018] [Accepted: 02/12/2018] [Indexed: 11/12/2022] Open
Abstract
The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y-shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y-shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.
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Affiliation(s)
- Li Sin Lee
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Geok Yuan Annie Tan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Chun Shiong Chong
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia.,Jiangsu University, Zhenjiang, China
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Shrestha S, Fonoll X, Khanal SK, Raskin L. Biological strategies for enhanced hydrolysis of lignocellulosic biomass during anaerobic digestion: Current status and future perspectives. BIORESOURCE TECHNOLOGY 2017; 245:1245-1257. [PMID: 28941664 DOI: 10.1016/j.biortech.2017.08.089] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 05/23/2023]
Abstract
Lignocellulosic biomass is the most abundant renewable bioresource on earth. In lignocellulosic biomass, the cellulose and hemicellulose are bound with lignin and other molecules to form a complex structure not easily accessible to microbial degradation. Anaerobic digestion (AD) of lignocellulosic biomass with a focus on improving hydrolysis, the rate limiting step in AD of lignocellulosic feedstocks, has received considerable attention. This review highlights challenges with AD of lignocellulosic biomass, factors contributing to its recalcitrance, and natural microbial ecosystems, such as the gastrointestinal tracts of herbivorous animals, capable of performing hydrolysis efficiently. Biological strategies that have been evaluated to enhance hydrolysis of lignocellulosic biomass include biological pretreatment, co-digestion, and inoculum selection. Strategies to further improve these approaches along with future research directions are outlined with a focus on linking studies of microbial communities involved in hydrolysis of lignocellulosics to process engineering.
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Affiliation(s)
- Shilva Shrestha
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA; Department of Molecular Biosciences and Bioengineering (MBBE), University of Hawai'i at Mānoa, 1955 East-West Road, Agricultural Science Building 218, Honolulu, HI 96822, USA
| | - Xavier Fonoll
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering (MBBE), University of Hawai'i at Mānoa, 1955 East-West Road, Agricultural Science Building 218, Honolulu, HI 96822, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA.
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Moon JW, Phelps TJ, Fitzgerald Jr CL, Lind RF, Elkins JG, Jang GG, Joshi PC, Kidder M, Armstrong BL, Watkins TR, Ivanov IN, Graham DE. Manufacturing demonstration of microbially mediated zinc sulfide nanoparticles in pilot-plant scale reactors. Appl Microbiol Biotechnol 2016; 100:7921-31. [DOI: 10.1007/s00253-016-7556-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/06/2016] [Accepted: 04/14/2016] [Indexed: 10/21/2022]
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17
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Brumm PJ, Land ML, Mead DA. Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 2015; 10:73. [PMID: 26442136 PMCID: PMC4593210 DOI: 10.1186/s40793-015-0031-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 06/29/2015] [Indexed: 11/29/2022] Open
Abstract
Geobacillus thermoglucosidasius C56-YS93 was one of several thermophilic organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. Comparison of 16 S rRNA sequences confirmed the classification of the strain as a G. thermoglucosidasius species. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2011 (CP002835). The genome of G. thermoglucosidasius C56-YS93 consists of one circular chromosome of 3,893,306 bp and two circular plasmids of 80,849 and 19,638 bp and an average G + C content of 43.93 %. G. thermoglucosidasius C56-YS93 possesses a xylan degradation cluster not found in the other G. thermoglucosidasius sequenced strains. This cluster appears to be related to the xylan degradation cluster found in G. stearothermophilus. G. thermoglucosidasius C56-YS93 possesses two plasmids not found in the other two strains. One plasmid contains a novel gene cluster coding for proteins involved in proline degradation and metabolism, the other contains a collection of mostly hypothetical proteins.
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Affiliation(s)
- Phillip J Brumm
- Lucigen Corporation, Middleton, WI USA ; Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI USA
| | | | - David A Mead
- Lucigen Corporation, Middleton, WI USA ; Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI USA
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