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Wang XW, Tan X, Dang CC, Lu Y, Xie GJ, Liu BF. Thermophilic microorganisms involved in the nitrogen cycle in thermal environments: Advances and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165259. [PMID: 37400035 DOI: 10.1016/j.scitotenv.2023.165259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
Thermophilic microorganisms mediated significant element cycles and material conversion in the early Earth as well as mediating current thermal environments. Over the past few years, versatile microbial communities that drive the nitrogen cycle have been identified in thermal environments. Understanding the microbial-mediated nitrogen cycling processes in these thermal environments has important implications for the cultivation and application of thermal environment microorganisms as well as for exploring the global nitrogen cycle. This work provides a comprehensive review of different thermophilic nitrogen-cycling microorganisms and processes, which are described in detail according to several categories, including nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and dissimilatory nitrate reduction to ammonium. In particular, we assess the environmental significance and potential applications of thermophilic nitrogen-cycling microorganisms, and highlight knowledge gaps and future research opportunities.
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Affiliation(s)
- Xiao-Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Sadeepa D, Sirisena K, Manage PM. Diversity of microbial communities in hot springs of Sri Lanka as revealed by 16S rRNA gene high-throughput sequencing analysis. Gene 2021; 812:146103. [PMID: 34896522 DOI: 10.1016/j.gene.2021.146103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 01/16/2023]
Abstract
Characterization of hot spring microbiota is useful as an initial platform for exploring industrially important microbes. The present study focused on characterization of microbiota in four hot springs in Sri Lanka: Maha Oya; Wahava; Madunagala; and Kivlegama using high throughput 16S amplicon sequencing. Temperatures of the selected springs were ranged from 33.7 °C to 52.4 °C, whereas pH ranged from 7.2 to 8.2. Bacteria were found to be the dominant microbial group (>99%) compared to Archaea which represented less than 1% of microbiota. Four hot springs comprised of unique microbial community structures. Proteobacteria, Firmicutes, Bacteroidetes, Cloroflexi, Deinococcus and Actenobacteria were the major bacterial phyla. Moderately thermophilic genera such as Thermodesulfobacteria and Deinococcus-Thermus were detected as major genera that could be used in industrial applications operating at temperatures around 50 °C and alkaline reaction conditions.
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Affiliation(s)
- Dilini Sadeepa
- Centre for Water Quality and Algae Research, Department of Zoology, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka; Faculty of Graduate Studies, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | - Kosala Sirisena
- Department of Environmental Technology, Faculty of Technology, University of Colombo, Sri Lanka
| | - Pathmalal M Manage
- Centre for Water Quality and Algae Research, Department of Zoology, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka; Faculty of Graduate Studies, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka.
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Thermoactinomycetes isolated from geothermal springs in Armenia capable of producing extracellular hydrolases. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42398-019-00066-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Rozanov AS, Bryanskaya AV, Ivanisenko TV, Malup TK, Peltek SE. Biodiversity of the microbial mat of the Garga hot spring. BMC Evol Biol 2017; 17:254. [PMID: 29297382 PMCID: PMC5751763 DOI: 10.1186/s12862-017-1106-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. RESULTS In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. CONCLUSIONS High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.
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Affiliation(s)
- Alexey Sergeevich Rozanov
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - Alla Victorovna Bryanskaya
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Timofey Vladimirovich Ivanisenko
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Tatyana Konstantinovna Malup
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey Evgenievich Peltek
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Chan CS, Chan KG, Ee R, Hong KW, Urbieta MS, Donati ER, Shamsir MS, Goh KM. Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs. Front Microbiol 2017; 8:1252. [PMID: 28729863 PMCID: PMC5498555 DOI: 10.3389/fmicb.2017.01252] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/21/2017] [Indexed: 11/13/2022] Open
Abstract
Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3–V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334–26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.
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Affiliation(s)
- Chia S Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi MalaysiaSkudai, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
| | - Kar-Wai Hong
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
| | - María S Urbieta
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La PlataLa Plata, Argentina
| | - Edgardo R Donati
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La PlataLa Plata, Argentina
| | - Mohd S Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi MalaysiaSkudai, Malaysia
| | - Kian M Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi MalaysiaSkudai, Malaysia
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Sakai HD, Kurosawa N. Exploration and isolation of novel thermophiles in frozen enrichment cultures derived from a terrestrial acidic hot spring. Extremophiles 2016; 20:207-14. [PMID: 26860120 DOI: 10.1007/s00792-016-0815-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/28/2016] [Indexed: 11/25/2022]
Abstract
An isolation strategy, exploring novel microorganisms in frozen enrichment cultures (ENFE), which uses a combination of enrichment culture and 16S rRNA gene clone analysis, was evaluated for isolating uncultured thermophiles from a terrestrial acidic hot spring. The procedure comprised (a) multiple enrichment cultures under various conditions, (b) cryostorage of all enrichments, (c) microbial community analyses of the enrichments using 16S rRNA gene sequences, and (d) purification of microorganisms from enrichments containing previously uncultured microorganisms. The enrichments were performed under a total of 36 conditions, and 16 of these enrichments yielded positive microbial growth with the detection of three previously uncultured archaea. Two of the three previously uncultured archaea, strains HS-1 and HS-3, were successfully isolated. Strain HS-1 and HS-3 represented a novel lineage of the order Sulfolobales and novel species of the genus Sulfolobus, respectively. Although innovative isolation methods play strategic roles in isolating previously uncultured microorganisms, the ENFE strategy showed potential for characterizing and isolating such microorganisms using conventional media and techniques.
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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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Hotta F, Eguchi H, Naito T, Mitamura Y, Kusujima K, Kuwahara T. Achromobacter buckle infection diagnosed by a 16S rDNA clone library analysis: a case report. BMC Ophthalmol 2014; 14:142. [PMID: 25421607 PMCID: PMC4255664 DOI: 10.1186/1471-2415-14-142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 11/18/2014] [Indexed: 11/15/2022] Open
Abstract
Background In clinical settings, bacterial infections are usually diagnosed by isolation
of colonies after laboratory cultivation followed by species identification with
biochemical tests. However, biochemical tests result in misidentification due to
similar phenotypes of closely related species. In such cases, 16S rDNA sequence
analysis is useful. Herein, we report the first case of an Achromobacter-associated buckle infection that was diagnosed by 16S
rDNA sequence analysis. This report highlights the significance of Achromobacter spp. in device-related ophthalmic
infections. Case presentation A 56-year-old woman, who had received buckling surgery using a silicone solid
tire for retinal detachment eighteen years prior to this study, presented purulent
eye discharge and conjunctival hyperemia in her right eye. Buckle infection was
suspected and the buckle material was removed. Isolates from cultures of
preoperative discharge and from deposits on the operatively removed buckle
material were initially identified as Alcaligenes and Corynebacterium
species. However, sequence analysis of a 16S rDNA clone library using the DNA
extracted from the deposits on the buckle material demonstrated that all of the
16S rDNA sequences most closely matched those of Achromobacter spp. We concluded that the initial misdiagnosis of
this case as an Alcaligenes buckle infection
was due to the unreliability of the biochemical test in discriminating Achromobacter and Alcaligenes species due to their close taxonomic positions and
similar phenotypes. Corynebacterium species
were found to be contaminants from the ocular surface. Conclusions Achromobacter spp. should be recognized as
causative agents for device-related ophthalmic infections. Molecular species
identification by 16S rDNA sequence analysis should be combined with conventional
cultivation techniques to investigate the significance of Achromobacter spp. in ophthalmic infections.
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Affiliation(s)
| | - Hiroshi Eguchi
- Department of Ophthalmology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan.
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