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Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses. Proc Natl Acad Sci U S A 2022; 119:2115449119. [PMID: 35022241 PMCID: PMC8784108 DOI: 10.1073/pnas.2115449119] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 11/18/2022] Open
Abstract
Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum "Candidatus Micrarchaeota" (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera-Metallosphaera, Acidianus, and Saccharolobus-originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions.
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Complete Genome Sequence of a Novel Sulfolobales Archaeon Strain, HS-7, Isolated from the Unzen Hot Spring in Japan. Microbiol Resour Announc 2021; 10:e0058221. [PMID: 34553995 PMCID: PMC8459659 DOI: 10.1128/mra.00582-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The order Sulfolobales includes thermoacidophilic archaea that thrive in acidic geothermal environments. A novel Sulfolobales archaeon strain, HS-7, which may represent a novel genus, was isolated from an acidic hot spring in Japan. We report the 2.15-Mb complete genome sequence of strain HS-7.
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Yasir M, Qureshi AK, Azhar EI. 16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients. PeerJ 2021; 9:e10995. [PMID: 33859871 PMCID: PMC8020870 DOI: 10.7717/peerj.10995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/02/2021] [Indexed: 12/05/2022] Open
Abstract
Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from the non-enriched Tatta Pani hot spring sediment samples, and 33 distinct bacterial phyla and 890 genera from the enriched sediment samples. Unique phyla specimens from the enriched samples included Candidatus Cloacimonetes, Caldiserica, and Korarchaeota archaea. The enriched samples yielded specific microbiota including 805 bacteria and 42 archaea operational taxonomic units with 97% similarity, though decreased thermophilic microbiota were observed in the enriched samples. Microbial diversity increased as temperature decreased. Candidate novel species were isolated from the culture-dependent screening, along with several genera that were not found in the 16S amplicon sequencing data. Overall, the enriched sediments showed high microbial diversity but with adverse changes in the composition of relatively dominant bacteria. Metagenomic analyses are needed to study the diversity, phylogeny, and functional investigation of hot spring microbiota.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arooj K Qureshi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Xu R, Li B, Xiao E, Young LY, Sun X, Kong T, Dong Y, Wang Q, Yang Z, Chen L, Sun W. Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114226. [PMID: 32113110 DOI: 10.1016/j.envpol.2020.114226] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/23/2020] [Accepted: 02/16/2020] [Indexed: 05/09/2023]
Abstract
Acid mine drainage (AMD) is harmful to the environment and human health. Microorganisms-mineral interactions are responsible for AMD generation but can also remediate AMD contamination. Understanding the microbial response to AMD irrigation will reveal microbial survival strategies and provide approaches for AMD remediation. A terrace with sharp geochemical gradients caused by AMD flooding were selected to study the microbial response to changes in environmental parameters related to AMD contamination. AMD intrusion reduced soil microbial community diversity and further changed phylogenetic clustering patterns along the terrace gradient. We observed several genera seldom reported in AMD-related environments (i.e., Corynebacterium, Ochrobactrum, Natronomonas), suggesting flexible survival strategies such as nitrogen fixation, despite the poor nutritional environment. A co-occurrence network of heavily-contaminated fields was densely connected. The phyla Proteobacteria, Acidobacteria, Chloroflexi, and Euryarchaeota were all highly interconnected members, which may affect the formation of AMD. Detailed microbial response to different soil characterizations were highlighted by random forest model. Results revealed the top three parameters influencing the microbial diversity and interactions were pH, Fe(III), and sulfate. Various acidophilic Fe- and S-metabolizing bacteria were enriched in the lower fields, which were heavily contaminated by AMD, and more neutrophiles prevailed in the less-contaminated upper fields. Many indicator species in the lower fields were identified, including Desulfosporosinus, Thermogymnomonas, Corynebacterium, Shewanella, Acidiphilium, Ochrobactrum, Leptospirillum, and Allobaculum, representing acid-tolerant bacteria community in relevant environment. The detection of one known sulfate-reducing bacteria (i.e., Desulfosporosinus) suggested that biotic sulfate reduction may occur in acidic samples, which offers multiple advantages to AMD contamination treatment. Collectively, results suggested that the geochemical gradients substantially altered the soil microbiota and enriched the relevant microorganisms adapted to the different conditions. These findings provide mechanistic insights into the effects of contamination on the soil microbiota and establish a basis for in situ AMD bioremediation strategies.
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Affiliation(s)
- Rui Xu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Enzong Xiao
- Innovation Center and Key Laboratory of Waters Safety & Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Lily Y Young
- Department of Environmental Sciences, Rutgers University, New Brunswick, 08540, USA
| | - Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Tianle Kong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, China
| | - Qi Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China
| | - Lei Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China.
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Talamantes-Becerra B, Carling J, Kilian A, Georges A. Discovery of thermophilic Bacillales using reduced-representation genotyping for identification. BMC Microbiol 2020; 20:114. [PMID: 32404118 PMCID: PMC7222431 DOI: 10.1186/s12866-020-01800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Background This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across the bacterial genomes. Isolates were obtained from compost, hot water systems, and artesian bores of the Great Artesian Basin. Genomic DNA was double-digested with two combinations of restriction enzymes followed by PCR amplification, using a commercial provider of DArTseq™, Diversity Arrays Technology Pty Ltd. (Canberra, Australia). The resulting fragments which formed a reduced-representation of approximately 2.3% of the genome were sequenced. The sequence tags obtained were aligned against all available RefSeq bacterial genome assemblies by BLASTn to identify the nearest reference genome. Results Based on the preliminary identifications, a total of 99 bacterial isolates were identified to species level, from which 8 isolates were selected for whole-genome sequencing to assess the identification results. Novel species and strains were discovered within this set of isolates. The preliminary identifications obtained by reduced-representation genotyping, as well as identifications obtained by BLASTn alignment of the 16S rRNA gene sequence, were compared with those derived from the whole-genome sequence data, using the same RefSeq sequence database for the three methods. Identifications obtained with reduced-representation sequencing agreed with the identifications provided by whole-genome sequencing in 100% of cases. The identifications produced by BLASTn alignment of 16S rRNA gene sequence to the same database differed from those provided by whole-genome sequencing in 37.5% of cases, and produced ambiguous identifications in 50% of cases. Conclusions Previously, this method has been successfully demonstrated for use in bacterial identification for medical microbiology. This study demonstrates the first successful use of DArTseq™ for preliminary identification of thermophilic bacterial isolates, providing results in complete agreement with those obtained from whole-genome sequencing of the same isolates. The growing database of bacterial genome sequences provides an excellent resource for alignment of reduced-representation sequence data for identification purposes, and as the available sequenced genomes continue to grow, the technique will become more effective.
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Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute of Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
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Sakai HD, Kurosawa N. Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1 T, the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone, Japan. BMC Res Notes 2019; 12:444. [PMID: 31331368 PMCID: PMC6647314 DOI: 10.1186/s13104-019-4488-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/17/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Sulfodiicoccus acidiphilus HS-1T is the type species of the genus Sulfodiicoccus, a thermoacidophilic archaeon belonging to the order Sulfolobales (class Thermoprotei; phylum Crenarchaeota). While S. acidiphilus HS-1T shares many common physiological and phenotypic features with other Sulfolobales species, the similarities in their 16S rRNA gene sequences are less than 89%. In order to know the genomic features of S. acidiphilus HS-1T in the order Sulfolobales, we determined and characterized the genome of this strain. RESULTS The circular genome of S. acidiphilus HS-1T is comprised of 2353,189 bp with a G+C content of 51.15 mol%. A total of 2459 genes were predicted, including 2411 protein coding and 48 RNA genes. The notable genomic features of S. acidiphilus HS-1T in Sulfolobales species are the absence of genes for polB3 and the autotrophic carbon fixation pathway, and the distribution pattern of essential genes and sequences related to genomic replication initiation. These insights contribute to an understanding of archaeal genomic diversity and evolution.
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Affiliation(s)
- Hiroyuki D Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan.,Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, 102-8471, Japan
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan.
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Sakai HD, Kurosawa N. Saccharolobus caldissimus gen. nov., sp. nov., a facultatively anaerobic iron-reducing hyperthermophilic archaeon isolated from an acidic terrestrial hot spring, and reclassification of Sulfolobus solfataricus as Saccharolobus solfataricus comb. nov. and Sulfolobus shibatae as Saccharolobus shibatae comb. nov. Int J Syst Evol Microbiol 2018; 68:1271-1278. [PMID: 29485400 DOI: 10.1099/ijsem.0.002665] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel hyperthermophilic archaeon of strain HS-3T, belonging to the family Sulfolobaceae, was isolated from an acidic terrestrial hot spring in Hakone Ohwaku-dani, Japan. Based on 16S rRNA gene sequence analysis, the closest phylogenetic relatives of strain HS-3T were, first, Sulfolobus solfataricus (96.4 %) and, second, Sulfolobus shibatae (96.2 %), indicating that the strain belongs to the genus Sulfolobus. However, the sequence similarity to the type species of the genus Sulfolobus (Sulfolobus acidocaldarius) was remarkably low (91.8 %). In order to determine whether strain HS-3T belongs to the genus Sulfolobus, its morphological, biochemical and physiological characteristics were examined in parallel with those of S. solfataricus and S. shibatae. Although there were some differences in chemolithotrophic growth between strain HS-3T, S. solfataricus and S. shibatae, their temperature, pH and facultatively anaerobic characteristics of growth, and their utilization of various sugars were almost identical. In contrast, the utilization of various sugars by S. acidocaldarius was quite different from that of HS-3T, S. solfataricus and S. shibatae. Phylogenetic evidence based on the 16S and the 23S rRNA gene sequences also clearly distinguished the monophyletic clade composed of strain HS-3T, S. solfataricus, and S. shibatae from S. acidocaldarius. Based on these results, we propose a new genus and species, Saccharolobus caldissimus gen. nov., sp. nov., for strain HS-3T, as well as two reclassifications, Saccharolobus solfataricus comb. nov. and Saccharolobus shibatae comb. nov. The type strain of Saccharolobus caldissimus is HS-3T (=JCM 32116T and InaCC Ar80T). The type species of the genus is Saccharolobus solfataricus.
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Affiliation(s)
- Hiroyuki D Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
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Sakai HD, Kurosawa N. Sulfodiicoccus acidiphilus gen. nov., sp. nov., a sulfur-inhibited thermoacidophilic archaeon belonging to the order Sulfolobales isolated from a terrestrial acidic hot spring. Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001881] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hiroyuki D. Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
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Valdebenito-Rolack E, Ruiz-Tagle N, Abarzúa L, Aroca G, Urrutia H. Characterization of a hyperthermophilic sulphur-oxidizing biofilm produced by archaea isolated from a hot spring. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2016.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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