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Angius F, Cremers G, Frank J, Witkowski C, Pol A, van Alen TA, Jetten MSM, Op den Camp HJM, Berben T. Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles. Antonie Van Leeuwenhoek 2024; 117:94. [PMID: 38954064 PMCID: PMC11219375 DOI: 10.1007/s10482-024-01995-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide. Hydrogen, methane, and carbon monoxide are minor components of these emissions which together can feed large quantities of bacteria and archaea that do contribute to the removal of these notorious greenhouse gases. Here we analyzed the metagenome of samples taken from the Levante bay on Vulcano Island, Italy. Using a gene-centric approach, the hydrothermal vent community appeared to be dominated by Proteobacteria, and Sulfurimonas was the most abundant genus. Metabolic reconstructions highlight a prominent role of formaldehyde oxidation and the reverse TCA cycle in carbon fixation. [NiFe]-hydrogenases seemed to constitute the preferred strategy to oxidize H2, indicating that besides H2S, H2 could be an essential electron donor in this system. Moreover, the sulfur cycle analysis showed a high abundance and diversity of sulfate reduction genes underpinning the H2S production. This study covers the diversity and metabolic potential of the microbial soil community in Levante bay and adds to our understanding of the biogeochemistry of volcanic ecosystems.
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Affiliation(s)
- Federica Angius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jeroen Frank
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Caitlyn Witkowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
- School of Earth Sciences, Wills Memorial Building, University of Bristol, Queens Road, Clifton, BS8 1RJ, UK
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Theo A van Alen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Kumari S, Choudhary G, Anu K, Devi S. Metagenomics insight into Puga geothermal geyser located in Himalayan Geothermal Belt (Trans-Himalayan Plateau) Ladakh, India. Braz J Microbiol 2024:10.1007/s42770-024-01408-9. [PMID: 38874746 DOI: 10.1007/s42770-024-01408-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/25/2024] [Indexed: 06/15/2024] Open
Abstract
Puga geothermal geyser and surrounding area, located in the Himalayan Geothermal Belt of the Trans-Himalayan Plateau in Ladakh, India, are very geographically isolated and considered pristine and free of anthropogenic activities. In this study, we have conducted the first metagenomic investigation of the microbes in and around the geyser. The whole genome sequencing analysis showed the presence of a total of 44.8%, 39.7% and 41.4% bacterial phyla in the PugW, PugS, and PugSo samples respectively, 8.6% of archaeal phyla (in all the samples), unclassified (derived from other sequences, PugW: 27.6%, PugS: 27.6%, and PugSo: 15.5%) and unclassified (derived from bacteria, PugW: 12%, PugS: 13.8%, and PugSo: 13.8%). The majority of archaeal sequences were linked to Euryarchaeota (2.84%) while the majority of the bacterial communities that predominated in most geothermal locations were linked to Pseudomonadota (67.14%) and Bacteroidota (12.52%). The abundant bacterial strains at the species level included Dechloromonas aromatica, Acinetobacter baumannii, and Arcobacter butzleri, in all the samples while the most abundant archaeal species were Methanosaeta thermophile, Methanoregula boonei, and Methanosarcina berkeri. Further, this geothermal geyser metagenome has a large number of unique sequences linked to unidentified and unclassified lineages, suggesting a potential source for novel species of microbes and their products. The present study which only examined one of the many geothermal geysers and springs in the Puga geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the geothermal springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Puga geothermal area, which serve as a repository for unidentified microbial lineages.
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Affiliation(s)
- Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Asif A, Chen JS, Hsu GJ, Hussain B, Nagarajan V, Koner S, Huang SW, Hsu BM. Influence of Geothermal Fumaroles in Driving the Microbial Community Dynamics and Functions of Adjacent Ecosystems. J Basic Microbiol 2024:e2400157. [PMID: 38859671 DOI: 10.1002/jobm.202400157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/07/2024] [Accepted: 05/19/2024] [Indexed: 06/12/2024]
Abstract
Growing evidence suggests that the hydrochemical properties of geothermal fumaroles may play a crucial role in shaping the diversity and functions of microbial communities in various environments. In the present study, the impact of geothermal furaneols on the microbial communities and their metabolic functions across the rock-soil-plant continuum was explored considering varying distances from the fumarole source. The results revealed that bacterial phylum Proteobacteria was predominant in all sample types, except in the 10 m rock sample, irrespective of the sampling distance. Archaeal phyla, such as Euryarchaeota and Crenarchaeota, were more prevalent in rock and soil samples, whereas bacterial phyla were more prevalent in plant samples. Thermoacidophilic archaeons, including Picrophilus, Ferroplasma, and Thermogymnomonas were dominant in rocks and soil samples of 1 and 5 m distances; acidophilic mesophiles, including Ferrimicrobium and Granulicella were abundant in the rhizoplane samples, whereas rhizosphere-associated microbes including Pseudomonas, Pedobacter, Rhizobium, and Novosphingobium were found dominant in the rhizosphere samples. The functional analysis highlighted the higher expression of sulfur oxidative pathways in the rock and soil samples; dark iron oxidation and nitrate/nitrogen respiratory functions in the rhizosphere samples. The findings underscore microbial adaptations across the rock-soil-plant continuum, emphasizing the intricate relationship between geothermal fumaroles and microbial communities in adjacent ecosystems. These insights offer a crucial understanding of the evolution of microbial life and highlight their pivotal roles in shaping ecosystem dynamics and functions.
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Affiliation(s)
- Aslia Asif
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
- Doctoral Program in Science, Technology, Environment and Mathematics (STEM), National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Gwo-Jong Hsu
- Division of Infectious Disease, Department of Internal Medicine, Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Shih-Wei Huang
- Center for Environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung, Taiwan
- Super Micro Research and Technology Center, Cheng Shiu University, Kaohsiung, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
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Choudhary G, Kumari S, Anu K, Devi S. Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach. Braz J Microbiol 2024; 55:1465-1476. [PMID: 38662153 PMCID: PMC11153388 DOI: 10.1007/s42770-024-01346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Due to their distinctive physicochemical characteristics, hot springs are extremely important. The whole genome metagenomic sequencing technology can be utilized to analyze the diverse microbial community that thrives in this habitat due to the particular selection pressure that prevails there. The current investigation emphasizes on culture-independent metagenomic study of the Panamik hot spring and its nearby areas from Ladakh, India. Based on different diversity indices, sequence analysis of the soil reservoir showed higher species richness and diversity in comparison to water and sediment samples. The mineral content and various physicochemical pameters like temperature, pH had an impact on the composition of the microbial community of the geothermal springs. The phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacter, Firmicutes, and Verrucomicrobia in bacterial domain dominate the thermos-alkaline spring at Panamik in different concentrations. Economically significant microbes from the genera Actinobacter, Thermosynechoccus, Candidatus Solibacter, Chthoniobacter, Synechoccus, Pseudomonas and Sphingomonas, were prevalent in hot spring. In the archaeal domain, the most dominant phylum and genera were Euryarchaeota and Thermococcus in all the samples. Further, the most abundant species were Methanosarcina barkeri, Nitrospumilus maritimus and Methanosarcina acetivorans. The present study which only examined one of the several thermal springs present in the Himalayan geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the hot springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Panamik hot spring, which serve as a repository for unidentified microbial lineages.
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Affiliation(s)
- Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Anu K, Kumari S, Choudhary G, Devi S. Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India. Braz J Microbiol 2024; 55:1545-1555. [PMID: 38421596 PMCID: PMC11153464 DOI: 10.1007/s42770-024-01284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
In light of their unique and challenging environment, the high-altitude Chumathang geothermal springs in Ladakh, India, are undeniably intriguing for microbiological study. The purpose of this study was to employ a culture-independent sequencing approach to give a comprehensive characterization of the unknown bacterial and archaeal community structure, composition and networks in water and soil from the Chumathang geothermal spring. A total of 50%, and 42.86% bacterial phyla were found in the water, and soil samples respectively and this analysis also showed a total of 9.62% and 7.94% of archaeal phyla in both the samples, respectively. Further, the presence of unclassified (derived from other sequences, water: 17.31%, and soil: 19.05%) and unclassified (derived from bacteria, water: 13.46%, and soil: 12.70%) were also observed in the current metagenomics investigation. Firmicutes and Proteobacteria were the most abundant bacterial phyla in water, whereas Proteobacteria and Bacteroidetes were the most abundant bacterial phyla in geothermal soil. Crenarchaeota and Euryarchaeota dominated archeal communities in soil and water, respectively. This metagenomic study gave a detailed insight into the microbial diversity found in Chumathang geothermal spring and surrounding area, located in Ladakh, India. Surprisingly, this finding indicated the existence of geographically distinct microbial communities that were suited to various geothermal water habitats along the Himalayan Geothermal Belt. Future studies must take into account the metabolic pathways of these microbial communities that exist in these extreme environments. This will allow us to obtain a better knowledge of the microbial metabolisms that are common at these geothermal locations, which have a lot of potential for biotechnological applications. They will also enable us to establish links between the microbial community composition and the physicochemical environment of geothermal water and area.
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Affiliation(s)
- Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Kurokawa M, Higashi K, Yoshida K, Sato T, Maruyama S, Mori H, Kurokawa K. Metagenomic Thermometer. DNA Res 2023; 30:dsad024. [PMID: 37940329 PMCID: PMC10660216 DOI: 10.1093/dnares/dsad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/06/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
Various microorganisms exist in environments, and each of them has its optimal growth temperature (OGT). The relationship between genomic information and OGT of each species has long been studied, and one such study revealed that OGT of prokaryotes can be accurately predicted based on the fraction of seven amino acids (IVYWREL) among all encoded amino-acid sequences in its genome. Extending this discovery, we developed a 'Metagenomic Thermometer' as a means of predicting environmental temperature based on metagenomic sequences. Temperature prediction of diverse environments using publicly available metagenomic data revealed that the Metagenomic Thermometer can predict environmental temperatures with small temperature changes and little influx of microorganisms from other environments. The accuracy of the Metagenomic Thermometer was also confirmed by a demonstration experiment using an artificial hot water canal. The Metagenomic Thermometer was also applied to human gut metagenomic samples, yielding a reasonably accurate value for human body temperature. The result further suggests that deep body temperature determines the dominant lineage of the gut community. Metagenomic Thermometer provides a new insight into temperature-driven community assembly based on amino-acid composition rather than microbial taxa.
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Affiliation(s)
- Masaomi Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Higashi
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Keisuke Yoshida
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Tomohiko Sato
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Shigenori Maruyama
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroshi Mori
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Genome Diversity Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Ken Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
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Nosalova L, Mekadim C, Mrazek J, Pristas P. Thiothrix and Sulfurovum genera dominate bacterial mats in Slovak cold sulfur springs. ENVIRONMENTAL MICROBIOME 2023; 18:72. [PMID: 37730677 PMCID: PMC10512639 DOI: 10.1186/s40793-023-00527-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
Microbiota of sulfur-rich environments has been extensively studied due to the biotechnological potential of sulfur bacteria, or as a model of ancient life. Cold terrestrial sulfur springs are less studied compared to sulfur-oxidizing microbiota of hydrothermal vents, volcanic environments, or soda lakes. Despite that, several studies suggested that sulfur springs harbor diverse microbial communities because of the unique geochemical conditions of upwelling waters. In this study, the microbiota of five terrestrial sulfur springs was examined using a 16 S rRNA gene sequencing. The clear dominance of the Proteobacteria and Campylobacterota phyla of cold sulfur springs microbiota was observed. Contrary to that, the microbiota of the hot sulfur spring was dominated by the Aquificota and Firmicutes phylum respectively. Sulfur-oxidizing genera constituted a dominant part of the microbial populations with the Thiothrix and Sulfurovum genera identified as the core microbiota of cold sulfur terrestrial springs in Slovakia. Additionally, the study emphasizes that sulfur springs in Slovakia support unique, poorly characterized bacterial communities of sulfur-oxidizing bacteria.
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Affiliation(s)
- Lea Nosalova
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, Kosice, 041 54, Slovakia
| | - Chahrazed Mekadim
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Videnska, Prague, 1083, 14220, Czech Republic
| | - Jakub Mrazek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Videnska, Prague, 1083, 14220, Czech Republic
| | - Peter Pristas
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, Kosice, 041 54, Slovakia.
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, Soltesovej 4-6, Kosice, 040 01, Slovakia.
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Chen JS, Hussain B, Tsai HC, Nagarajan V, Koner S, Hsu BM. Analysis and interpretation of hot springs water, biofilms, and sediment bacterial community profiling and their metabolic potential in the area of Taiwan geothermal ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159115. [PMID: 36181827 DOI: 10.1016/j.scitotenv.2022.159115] [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: 07/26/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Microorganisms developed a mechanism that copes with heat, acidity, and high dissolved metal concentrations that likely first evolved. The geothermal fluids emerging in the geothermal springs of Taiwan, located at a subduction zone, are still under signs of progress in the characterization of the various microbial taxonomic changes over time. However, no systematic studies have been performed to compare water, biofilms, and sediment bacterial communities and the primary driving force of dissolved and mineral substrates capable of supporting microbial metabolism. In this study, 16S rRNA gene sequencing was employed for bacterial community exploration, and their potential metabolic pathways involved from water, biofilms, and sediment samples, collected from the geothermal valley (Ti-re-ku). Metagenomic data revealed that the water samples had higher bacterial diversity and richness than biofilms and sediment samples. At the genus level, Alicyclobacillus, Thiomonas, Acidocella, Metallibacterium, Picrophilus, and Legionella were significantly abundant in the water samples. The biofilms were rich in Aciditerrimonas, Bacillus, Acidithiobacillus, and Lysinibacillus, whereas the sediment samples were abundant in Sulfobacillus. The PICRUSt2-predicted functional results revealed that heavy metal-related functions such as heavy-metal exporter system, cobalt‑zinc‑cadmium resistance, arsenical pump, high-affinity nickel-transport, and copper resistance metabolisms were significant in the water samples. Moreover, sulfur-related pathways such as thiosulfate oxidation, dissimilatory sulfate reduction, and assimilatory sulfate reduction were important in water samples, followed by biofilms and sediment. Therefore, our findings highlighted the comparative taxonomic diversity and functional composition contributions to geothermal fluid, with implications for understanding the evolution and ecological niche dimension of microbes which are the key to geothermal ecosystem function.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung City 824, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien 970, Taiwan; Department of Psychiatry, Tzu-Chi General Hospital, Hualien 970, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chiayi County 621, Taiwan.
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Liu Z, Yang F, Chen Y. Interspecific and intraspecific Taylor's laws for frog skin microbes. Comput Struct Biotechnol J 2022; 21:251-259. [PMID: 36544471 PMCID: PMC9755231 DOI: 10.1016/j.csbj.2022.11.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Amphibians are known to have an abundance of microorganisms colonizing their skin, and these symbionts often protect the host from disease. There are now many comprehensive studies on amphibian skin microbes, but the interspecific and intraspecific abundance distributions (or abundance heterogeneity) of amphibian skin microbes remain unclear. Furthermore, we have a very limited understanding of how the abundance and heterogeneity of microbial communities relate to the body size (or more specifically, skin surface area) of amphibian hosts. In this study, we evaluated the interspecific and intraspecific abundance distribution patterns of amphibian skin microbes and evaluated whether the symbiotic skin microbes of different anuran species share a fundamental heterogeneity scaling parameter. If scaling invariance exists, we hypothesize that a fundamental heterogeneity scaling value also exists. A total of 358 specimens of 10 amphibian host species were collected, and we used Type-I and III Taylor's power law expansions (TPLE) to assess amphibian skin microbial heterogeneity at the community and mixed-species population levels, respectively. The obtained results showed that, at the community scale, a high aggregation of the microbial abundance distribution on the skin barely changed with host size. In a mixed-species population (i.e., a community context), the abundance distribution pattern of mixed microbial species populations also does not change with host size and always remains highly aggregated. These findings suggest that while amphibian skin microbiomes located in different hosts may have different environmental conditions, they share a fundamental heterogeneity scaling parameter, and thus, scale invariance exists. Finally, we found that microhabitat area provided by the host skin is vital to the stability of the symbiotic microbial community.
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Affiliation(s)
- Zhidong Liu
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Yang
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youhua Chen
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China,Corresponding author.
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Neira G, Vergara E, Holmes DS. Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments. Front Microbiol 2022; 13:900531. [PMID: 36212841 PMCID: PMC9543262 DOI: 10.3389/fmicb.2022.900531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2–3) and moderately thermophilic conditions (50–60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including “first line of defense” mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the “second line of defense” where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.
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Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes
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11
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Mitrović M, Kostešić E, Marković T, Selak L, Hausmann B, Pjevac P, Orlić S. Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia. Syst Appl Microbiol 2022; 45:126359. [PMID: 36150364 DOI: 10.1016/j.syapm.2022.126359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/28/2022] [Accepted: 09/07/2022] [Indexed: 10/31/2022]
Abstract
In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by Hydrogenophilus, Sulfuricurvum, Sulfurovum, Thiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.
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Affiliation(s)
- Maja Mitrović
- Ruđer Bošković Institute, Division of Materials Chemistry, Laboratory for Precipitation Processes, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Ema Kostešić
- Ruđer Bošković Institute, Division of Materials Chemistry, Laboratory for Precipitation Processes, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Tamara Marković
- Croatian Geological Survey, Milan Sachs 2 Street, 10 000 Zagreb, Croatia
| | - Lorena Selak
- Ruđer Bošković Institute, Division of Materials Chemistry, Laboratory for Precipitation Processes, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; University of Vienna, Department of Microbiology and Ecosystem Science, Divison of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Sandi Orlić
- Ruđer Bošković Institute, Division of Materials Chemistry, Laboratory for Precipitation Processes, Bijenička cesta 54, 10 000 Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia.
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12
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Simona C, Venturi S, Tassi F, Simona R, Cabassi J, Capecchiacci F, Bicocchi G, Vaselli O, Morrison HG, Sogin ML, Fazi S. Geochemical and microbiological profiles in hydrothermal extreme acidic environments (Pisciarelli Spring, Campi Flegrei, Italy). FEMS Microbiol Ecol 2022; 98:6650346. [PMID: 35883234 DOI: 10.1093/femsec/fiac088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/16/2022] [Accepted: 07/22/2022] [Indexed: 11/14/2022] Open
Abstract
Although terrestrial hydrothermal systems are considered among the most fascinating environments, how their unique and extreme conditions can affect microorganisms selection and the role in biogeochemical cycles has not yet been well elucidated. A combined geochemical and microbiological exploration in waters and sediments from ten sampling points along a sharp temperature gradient (15-90 °C) within an extremely acidic hydrothermal system (Pisciarelli Spring, Campi Flegrei area, southern Italy) displayed how hydrothermal fluids influence the microbial dynamics. This area was characterized by high levels of reduced gaseous species (e.g. H2S, H2, CH4, CO), and very low pH values (<2.3). Thermodynamic calculations revealed a high microbial catabolic potential in oxidation/reduction reactions of N-, S-, and Fe-bearing species. Overall, an increase of the archaeal/bacterial abundance ratio was observed by decreasing temperature and pH values. In particular, Archaea and Bacteria were present in almost equal cell abundance (up to 1.1 × 109 and 9.3 × 108 cell/g, respectively) in the <70 °C sampling points (average pH = 2.09); on the contrary, highest temperature waters (85-90 °C; average pH = 2.26) were characterized by low abundance of archaeal cells. The high-throughput sequencing of 16S rRNA gene indicated strong differences in archaeal and bacterial communities' composition along temperature gradient. However, the microbiome in this extreme environment was mainly constituted by chemoautotrophic microorganisms that were likely involved in N-, S-, and Fe-bearing species transformations (e.g. Acidianus infernus, Ferroplasma acidarmanus, Acidithiobacillus, Sulfobacillus, Thaumarchaeota), in agreement with thermodynamic calculations.
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Affiliation(s)
- Crognale Simona
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 - CP10, 00015 Monterotondo, Rome (Italy)
| | - Stefania Venturi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | - Franco Tassi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | - Rossetti Simona
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 - CP10, 00015 Monterotondo, Rome (Italy)
| | - Jacopo Cabassi
- IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | - Francesco Capecchiacci
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy).,Istituto Nazionale di Geofisica e Vulcanologia (INGV), Sezione di Napoli, Osservatorio Vesuviano, Via Diocleziano 328, 80125 Napoli, Italy
| | - Gabriele Bicocchi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy)
| | - Orlando Vaselli
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | | | | | - Stefano Fazi
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 - CP10, 00015 Monterotondo, Rome (Italy)
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13
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Chen JS, Tsai HC, Hsu YL, Nagarajan V, Su HY, Hussain B, Hsu BM. Comprehensive assessment of bacterial communities and their functional profiles in the Huang Gang Creek in the Tatun Volcano Group basin, Taiwan using 16S rRNA amplicon sequencing. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113375. [PMID: 35278991 DOI: 10.1016/j.ecoenv.2022.113375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
The microbial characteristics of water bodies located in the outflow of hot springs may affect the water quality parameters of the associated river ecosystem. Using 16S rRNA amplicon sequencing, we investigated the bacterial diversity and functional profiles of the Huang Gang (HG) Creek, located in the trace metal-rich, acid-sulfate thermal springs zone of the Tatun Volcano Group (TVG). Biofilms and water samples were collected from the upstream, midstream, and geothermal valleys and downstream of the creek. The results showed that the biofilm and water samples had distinct bacterial diversity and abundance profiles. Acidophilic sulfur-oxidizing bacteria were found to be more abundant in water samples, whereas aquatic photosynthetic bacterial communities were dominant in biofilms. The water samples were contaminated with Legionella and Chlamydiae, which could contaminate the nearby river and cause clinical infections in humans. The upstream samples were highly unique and displayed higher diversity than the other sites. Moderate thermo-acidophiles were dominant in the upstream and midstream regions, whereas the geothermal valley and downstream samples were abundant in thermo-acidophiles. In addition, functional profiling revealed higher expression of sulfur, arsenic, and iron-related functions in water and lead-related functions in the biofilms of the creek. As described in previous studies, the hydrochemical properties of the HG Creek were influenced by the TVG hot springs. Our findings indicated that the hydrochemical properties of the HG Creek were highly correlated with the bacterial diversity and functional potential of running water as compared to biofilms.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Yu-Ling Hsu
- Department of Nuclear Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Hung-Yuan Su
- Department of Emergency Medicine, E-Da Hospital and I-Shou University, Kaohsiung, Taiwan; School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan.
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14
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Fang S, Yan J. Analysis of prokaryotic microbial diversity in hot spring water from Bantang (China) using the targeted amplicon analysis. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2049899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Shu Fang
- School of Chemistry and Material Engineering, Chaohu University, Chaohu, Anhui, People’s Republic of China
| | - Juan Yan
- School of Chemistry and Material Engineering, Chaohu University, Chaohu, Anhui, People’s Republic of China
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15
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Nagarajan V, Tsai HC, Chen JS, Hussain B, Fan CW, Asif A, Hsu BM. The Evaluation of Bacterial Abundance and Functional Potentials in the Three Major Watersheds, Located in the Hot Spring Zone of the Tatun Volcano Group Basin, Taiwan. Microorganisms 2022; 10:microorganisms10030500. [PMID: 35336075 PMCID: PMC8949176 DOI: 10.3390/microorganisms10030500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
The Tatun Volcanic Group (TVG), located in northern Taiwan, is characterized by acidic hot springs where the outflow of the hot springs may affect the properties of the associated lotic water bodies. We investigated the bacterial diversity and functional profiles of the Peihuang (PHC), HuangGang (HGC), and Nanhuang Creeks (NHC) located in the TVG basin using 16S rRNA gene sequencing coupled with statistical analyses. Water samples were collected from various streams of the creeks for two months of the year. The NHC showed the highest diversity, richness, and a unique number of phyla, which was followed by the HGC. A reduced number of phyla and a lower diversity was noticed in the PHC. The NHC was found to be abundant in the genera Armatimonas, Prosthecobacter, Pirellula, and Bdellovibrio, whereas the HGC was rich in Thiomonas, Acidiphilium, Prevotella, Acidocella, Acidithiobacillus, and Metallibacterium. The PHC was abundant in Thiomonsa, Legionella, Acidocella, and Sulfuriferula. The samples did not show any strong seasonal variations with the bacterial diversity and abundance; however, the relative abundance of each sampling site varied within the sampling months. The iron transport protein- and the sulfur metabolism-related pathways were predicted to be the key functions in all the creeks, whereas the heavy metal-related functions, such as the cobalt/nickel transport protein and the cobalt–zinc–cadmium efflux system were found to be abundant in the HGC and PHC, respectively. The abundance of Bdellovibrio in the NHC, Diplorickettsia in the HGC, and Legionella in the PHC samples indicated a higher anthropogenic impact over the creek water quality. This study provides the data to understand the distinct bacterial community structure, as well as the functional potentials of the three major watersheds, and helps the knowledge of the impact of the physicochemical properties of the TVG hot springs upon the watersheds.
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Affiliation(s)
- Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien 970, Taiwan;
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien 970, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung 824, Taiwan;
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 621, Taiwan
| | - Cheng-Wei Fan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
| | - Aslia Asif
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Doctoral Program in Science, Technology, Environment and Mathematics (STEM), National Chung Cheng University, Chiayi 621, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Correspondence: ; Tel.: +886-52-720-411 (ext. 66218)
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16
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Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV. Diversity of Thermophilic Prokaryotes Inhabiting Russian Natural Hot Springs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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17
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LIU J, LI Q, TAN R. An exploratory to analysis the effects of the dirrerent roles of mathca on lipid metabolism and intestinal flora regulation between normal and diabetic mice fed a high-fat diet. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.25022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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LIU J, LV YJ, PAN JX, JIANG YL, ZHU YJ, ZHANG SK. Effects of tea polyphenols and EGCG on glucose metabolism and intestinal flora in diabetic mice fed a cornstarch-based functional diet. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.50821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jun LIU
- Hangzhou Tea Research Institute, China
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19
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Functional and Taxonomic Effects of Organic Amendments on the Restoration of Semiarid Quarry Soils. mSystems 2021; 6:e0075221. [PMID: 34812648 PMCID: PMC8609970 DOI: 10.1128/msystems.00752-21] [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] [Indexed: 11/20/2022] Open
Abstract
The application of organic amendments to mining soils has been shown to be a successful method of restoration, improving key physicochemical soil properties. However, there is a lack of a clear understanding of the soil bacterial community taxonomic and functional changes that are brought about by these treatments. We present further metagenomic sequencing (MGS) profiling of the effects of different restoration treatments applied to degraded, arid quarry soils in southern Spain which had previously been profiled only with 16S rRNA gene (16S) and physicochemical analyses. Both taxonomic and functional MGS profiles showed clear separation of organic treatment amendments from control samples, and although taxonomic differences were quite clear, functional redundancy was higher than expected and the majority of the latter signal came from the aggregation of minor (<0.1%) community differences. Significant taxonomic differences were seen with the presumably less-biased MGS-for example, the phylum Actinobacteria and the two genera Chloracidobacterium (Acidobacteria) and Paenibacillus (Firmicutes) were determined to be major players by the MGS and this was consistent with their potential functional roles. The former phylum was much less present, and the latter two genera were either minor components or not detected in the 16S data. Mapping of reads to MetaCyc/BioCyc categories showed overall slightly higher biosynthesis and degradation capabilities in all treatments versus control soils, with sewage amendments showing highest values and vegetable-based amendments being at intermediate levels, matching higher nutrient levels, respiration rates, enzyme activities, and bacterial biomass previously observed in the treated soils. IMPORTANCE The restoration of soils impacted by human activities poses specific challenges regarding the reestablishment of functional microbial communities which will further support the reintroduction of plant species. Organic fertilizers, originating from either treated sewage or vegetable wastes, have shown promise in restoration experiments; however, we still do not have a clear understanding of the functional and taxonomic changes that occur during these treatments. We used metagenomics to profile restoration treatments applied to degraded, arid quarry soils in southern Spain. We found that the assortments of individual functions and taxa within each soil could clearly identify treatments, while at the same time they demonstrated high functional redundancy. Functions grouped into higher pathways tended to match physicochemical measurements made on the same soils. In contrast, significant taxonomic differences were seen when the treatments were previously studied with a single marker gene, highlighting the advantage of metagenomic analysis for complex soil communities.
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20
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Huang Y, Li XT, Jiang Z, Liang ZL, Wang P, Liu ZH, Li LZ, Yin HQ, Jia Y, Huang ZS, Liu SJ, Jiang CY. Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH <3). Front Microbiol 2021; 12:761579. [PMID: 34917049 PMCID: PMC8670003 DOI: 10.3389/fmicb.2021.761579] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022] Open
Abstract
The microbial community of acid mine drainage (AMD) fascinates researchers by their adaption and roles in shaping the environment. Molecular surveys have recently helped to enhance the understanding of the distribution, adaption strategy, and ecological function of microbial communities in extreme AMD environments. However, the interactions between the environment and microbial community of extremely acidic AMD (pH <3) from different mining areas kept unanswered questions. Here, we measured physicochemical parameters and profiled the microbial community of AMD collected from four mining areas with different mineral types to provide a better understanding of biogeochemical processes within the extremely acidic water environment. The prominent physicochemical differences across the four mining areas were in SO42−, metal ions, and temperature, and distinct microbial diversity and community assemblages were also discovered in these areas. Mg2+ and SO42− were the predominant factors determining the microbial structure and prevalence of dominant taxa in AMD. Leptospirillum, Ferroplasma, and Acidithiobacillus were abundant but showed different occurrence patterns in AMD from different mining areas. More diverse communities and functional redundancy were identified in AMD of polymetallic mining areas compared with AMD of copper mining areas. Functional prediction revealed iron, sulfur, nitrogen, and carbon metabolisms driven by microorganisms were significantly correlated with Mg2+ and SO42−, Ca2+, temperature, and Fe2+, which distinguish microbial communities of copper mine AMD from that of polymetallic mine AMD. In summary, microbial diversity, composition, and metabolic potential were mainly shaped by Mg2+ and SO42− concentrations of AMD, suggesting that the substrate concentrations may contribute to the distinct microbiological profiles of AMD from different mining areas. These findings highlight the microbial community structure in extremely acidic AMD forming by types of minerals and the interactions of physicochemical parameters and microbiology, providing more clues of the microbial ecological function and adaptation mechanisms in the extremely acidic environment.
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Affiliation(s)
- Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zong-Lin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Hua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liang-Zhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yan Jia
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Zhong-Sheng Huang
- Zijin Mining Group Company Limited, Fujian, China.,School of Metallurgy and Environment, Central South University, Changsha, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
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21
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Asamatsu K, Yoshitake K, Saito M, Prasitwuttisak W, Ishibashi JI, Tsutsumi A, Mustapha NA, Maeda T, Yanagawa K. A Novel Archaeal Lineage in Boiling Hot Springs around Oyasukyo Gorge (Akita, Japan). Microbes Environ 2021; 36. [PMID: 34819404 PMCID: PMC8674440 DOI: 10.1264/jsme2.me21048] [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] [Indexed: 11/12/2022] Open
Abstract
A novel deep-branching archaeal lineage was discovered at high-temperature hot springs around Oyasukyo Gorge in Akita Prefecture, Japan. Actively boiling hot spring water contained >1×104 microbes mL-1. The microbial community composition assessed by analyzing 16S rRNA gene amplicons revealed that the dominant bacterial phyla were Proteobacteria and Aquificae (>50% of the microbial composition) in samples collected in 2016 and 2019, respectively. Approximately 10% of the reads obtained in both years were not assigned to any taxonomy. The more detailed phylogenetic positions of the unassigned sequences identified using a clone library and phylogenetic tree showed that they formed a clade that was independent, distantly related to known phyla, and had low similarity (<82%) to all other sequences in available databases. The present results suggest that this novel archaeal phylum-level lineage thrives in boiling hot springs in Japan.
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Affiliation(s)
| | - Kai Yoshitake
- Faculty of Environmental Engineering, The University of Kitakyushu
| | - Makoto Saito
- Faculty of Environmental Engineering, The University of Kitakyushu
| | | | - Jun-Ichiro Ishibashi
- Department of Earth and Planetary Sciences, Faculty of Science, Kyushu University
| | - Akihi Tsutsumi
- Department of Earth and Planetary Sciences, Faculty of Science, Kyushu University
| | - Nurul Asyifah Mustapha
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
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22
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DeCastro ME, Escuder-Rodríguez JJ, Becerra M, Rodríguez-Belmonte E, González-Siso MI. Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide. Front Microbiol 2021; 12:769065. [PMID: 34899652 PMCID: PMC8661477 DOI: 10.3389/fmicb.2021.769065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 01/12/2023] Open
Abstract
With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.
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Affiliation(s)
| | | | | | | | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
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23
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Rozanov AS, Korzhuk AV, Shekhovtsov SV, Vasiliev GV, Peltek SE. Microorganisms of Two Thermal Pools on Kunashir Island, Russia. BIOLOGY 2021; 10:924. [PMID: 34571800 PMCID: PMC8468003 DOI: 10.3390/biology10090924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022]
Abstract
The Kuril Archipelago is a part of the Circum-Pacific Belt (Ring of Fire). These islands have numerous thermal springs. There are very few studies on these microbial communities, and none of them have been conducted by modern molecular biological methods. Here we performed the first metagenomic study on two thermophilic microbial communities of Kunashir Island. Faust Lake is hot (48 °C) and highly acidic (pH 2.0). We constructed 28 metagenome-assembled genomes as well as 17 16S ribosomal RNA sequences. We found that bottom sediments of Faust Lake are dominated by a single species of red algae belonging to the Cyanidiaceae family. Archaeans in Faust Lake are more diverse than bacteria but less abundant. The Tretyakovsky Thermal Spring is also hot (52 °C) but only weakly acidic (pH 6.0). It has much higher microbial diversity (233 metagenome-assembled genomes; 93 16S ribosomal RNAs) and is dominated by bacteria, with only several archaeans and one fungus. Despite their geographic proximity, these two thermal springs were found to not share any species. A comparison of these two lakes with other thermal springs of the Circum-Pacific Belt revealed that only a few members of the communities are shared among different locations.
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Affiliation(s)
- Aleksei S. Rozanov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Anton V. Korzhuk
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergei V. Shekhovtsov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Gennady V. Vasiliev
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Sergei E. Peltek
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
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24
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Zlatkov N, Nadeem A, Uhlin BE, Wai SN. Eco-evolutionary feedbacks mediated by bacterial membrane vesicles. FEMS Microbiol Rev 2021; 45:fuaa047. [PMID: 32926132 PMCID: PMC7968517 DOI: 10.1093/femsre/fuaa047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial membrane vesicles (BMVs) are spherical extracellular organelles whose cargo is enclosed by a biological membrane. The cargo can be delivered to distant parts of a given habitat in a protected and concentrated manner. This review presents current knowledge about BMVs in the context of bacterial eco-evolutionary dynamics among different environments and hosts. BMVs may play an important role in establishing and stabilizing bacterial communities in such environments; for example, bacterial populations may benefit from BMVs to delay the negative effect of certain evolutionary trade-offs that can result in deleterious phenotypes. BMVs can also perform ecosystem engineering by serving as detergents, mediators in biochemical cycles, components of different biofilms, substrates for cross-feeding, defense systems against different dangers and enzyme-delivery mechanisms that can change substrate availability. BMVs further contribute to bacteria as mediators in different interactions, with either other bacterial species or their hosts. In short, BMVs extend and deliver phenotypic traits that can have ecological and evolutionary value to both their producers and the ecosystem as a whole.
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Affiliation(s)
- Nikola Zlatkov
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Aftab Nadeem
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
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25
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DeCastro ME, Doane MP, Dinsdale EA, Rodríguez-Belmonte E, González-Siso MI. Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases. Sci Rep 2021; 11:101. [PMID: 33420292 PMCID: PMC7794327 DOI: 10.1038/s41598-020-80489-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/17/2020] [Indexed: 01/29/2023] Open
Abstract
In the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquificae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter, was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin-Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta-galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli. The pTsbg enzyme had activity towards o-Nitrophenyl-β-D-galactopyranoside (ONPG) and p-Nitrophenyl-β-D-fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This finding highlights the challenge of finding novel active enzymes based only on their sequence.
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Affiliation(s)
- María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| | - Michael P Doane
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- Syndey Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
| | - Elizabeth Ann Dinsdale
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- College of Science and Engineering, Flinders University, Sturt Rd, Bedford Park, SA, 5042, Australia
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain.
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26
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Hart C, Gorman-Lewis D. Energetics of Acidianus ambivalens growth in response to oxygen availability. GEOBIOLOGY 2021; 19:48-62. [PMID: 32902110 DOI: 10.1111/gbi.12413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/30/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
All life requires energy to drive metabolic reactions such as growth and cell maintenance; therefore, fluctuations in energy availability can alter microbial activity. There is a gap in our knowledge concerning how energy availability affects the growth of extreme chemolithoautotrophs. Toward this end, we investigated the growth of thermoacidophile Acidianus ambivalens during sulfur oxidation under aerobic to microaerophilic conditions. Calorimetry was used to measure enthalpy (ΔHinc ) of microbial activity, and chemical changes in growth media were measured to calculate Gibbs energy change (ΔGinc ) during incubation. In all experiments, Gibbs energy was primarily dissipated through the release of heat, which suggests enthalpy-driven growth. In microaerophilic conditions, growth was significantly more efficient in terms of biomass yield (defined as C-mol biomass per mole sulfur consumed) and resulted in lower ΔGinc and ΔHinc . ΔGinc in oxygen-limited (OL) and oxygen- and CO2 -limited (OCL) microaerophilic growth conditions resulted in averages of -1.44 × 103 kJ/C-mol and -7.56 × 102 kJ/C-mol, respectively, and average ΔHinc values of -1.11 × 105 kJ/C-mol and -4.43 × 104 kJ/C-mol, respectively. High-oxygen experiments resulted in lower biomass yield values, an increase in ΔGinc to -1.71 × 104 kJ/C-mol, and more exothermic ΔHinc values of -4.71 × 105 kJ/C-mol. The observed inefficiency in high-oxygen conditions may suggest larger maintenance energy demands due to oxidative stresses and a preference for growth in microaerophilic environments.
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Affiliation(s)
- Chloe Hart
- Department of Earth and Space Sciences, University of Washington, Seattle, WA, USA
| | - Drew Gorman-Lewis
- Department of Earth and Space Sciences, University of Washington, Seattle, WA, USA
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27
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Hot in Cold: Microbial Life in the Hottest Springs in Permafrost. Microorganisms 2020; 8:microorganisms8091308. [PMID: 32867302 PMCID: PMC7565842 DOI: 10.3390/microorganisms8091308] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
Chukotka is an arctic region located in the continuous permafrost zone, but thermal springs are abundant there. In this study, for the first time, the microbial communities of the Chukotka hot springs (CHS) biofilms and sediments with temperatures 54–94 °C were investigated and analyzed by NGS sequencing of 16S rRNA gene amplicons. In microbial mats (54–75 °C), phototrophic bacteria of genus Chloroflexus dominated (up to 89% of all prokaryotes), while Aquificae were the most numerous at higher temperatures in Fe-rich sediments and filamentous “streamers” (up to 92%). The electron donors typical for Aquificae, such as H2S and H2, are absent or present only in trace amounts, and the prevalence of Aquificae might be connected with their ability to oxidize the ferrous iron present in CHS sediments. Armatimonadetes, Proteobacteria, Deinococcus-Thermus, Dictyoglomi, and Thermotogae, as well as uncultured bacteria (candidate divisions Oct-Spa1-106, GAL15, and OPB56), were numerous, and Cyanobacteria were present in low numbers. Archaea (less than 8% of the total community of each tested spring) belonged to Bathyarchaeota, Aigarchaeota, and Thaumarchaeota. The geographical location and the predominantly autotrophic microbial community, built on mechanisms other than the sulfur cycle-based ones, make CHS a special and unique terrestrial geothermal ecosystem.
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28
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Aszalós JM, Szabó A, Felföldi T, Jurecska L, Nagy B, Borsodi AK. Effects of Active Volcanism on Bacterial Communities in the Highest-Altitude Crater Lake of Ojos del Salado (Dry Andes, Altiplano-Atacama Region). ASTROBIOLOGY 2020; 20:741-753. [PMID: 32525737 DOI: 10.1089/ast.2018.2011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Periglacial and volcanic environments are considered terrestrial analogs of Mars with regard to astrobiological characteristics due to their specific set of extreme features. Ojos del Salado, the highest volcano on Earth (6893 m a.s.l.), is surrounded by several craters, one of which harbors the highest known altitude lake (6480 m a.s.l.), which is influenced by a rare combination of extreme environmental factors, that is, low mean temperature, permafrost, fumarolic activity, acidity, and extreme low organic matter content. To assess the genetic diversity and ecological tolerance of bacteria, samples were taken in February 2016 from the sediments covered with acidic cold (pH 4.88, 3.8°C) and warm (pH 2.08, 40.8°C) water. As a control, a nonvolcanic high-altitude lake (at 5900 m a.s.l.) was also studied by both cultivation-based and next-generation DNA sequencing methods. Isolates from the crater lake showed tolerance toward acidic pH values, unlike isolates from the nonvolcanic lake. Illumina MiSeq sequencing of the 16S rRNA gene exposed simplified, although characteristically different, bacterial communities in the warm and cold water-saturated sediments. In the fumarolic creek sediments, acidophilic iron oxidizers (Ferrithrix, Gallionella) and iron reducers (Acidiphilium) were abundant, and bacteria involved in the sulfur oxidation (Hydrogenobaculum, Thiomonas) and reduction (Desulfosporosinus) were also detected. Therefore, we propose an integrated model that addresses the potential role of bacteria in the sulfur and iron geomicrobiological cycles.
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Affiliation(s)
| | - Attila Szabó
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Laura Jurecska
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Balázs Nagy
- Department of Physical Geography, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Andrea K Borsodi
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary
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29
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Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau. Sci Rep 2020; 10:5917. [PMID: 32246033 PMCID: PMC7125080 DOI: 10.1038/s41598-020-62797-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 03/17/2020] [Indexed: 11/30/2022] Open
Abstract
Little is known about life in the boron-rich hot springs of Trans-Himalayas. Here, we explore the geomicrobiology of a 4438-m-high spring which emanates ~70 °C-water from a boratic microbialite called Shivlinga. Due to low atmospheric pressure, the vent-water is close to boiling point so can entropically destabilize biomacromolecular systems. Starting from the vent, Shivlinga’s geomicrobiology was revealed along the thermal gradients of an outflow-channel and a progressively-drying mineral matrix that has no running water; ecosystem constraints were then considered in relation to those of entropically comparable environments. The spring-water chemistry and sinter mineralogy were dominated by borates, sodium, thiosulfate, sulfate, sulfite, sulfide, bicarbonate, and other macromolecule-stabilizing (kosmotropic) substances. Microbial diversity was high along both of the hydrothermal gradients. Bacteria, Eukarya and Archaea constituted >98%, ~1% and <1% of Shivlinga’s microbiome, respectively. Temperature constrained the biodiversity at ~50 °C and ~60 °C, but not below 46 °C. Along each thermal gradient, in the vent-to-apron trajectory, communities were dominated by Aquificae/Deinococcus-Thermus, then Chlorobi/Chloroflexi/Cyanobacteria, and finally Bacteroidetes/Proteobacteria/Firmicutes. Interestingly, sites of >45 °C were inhabited by phylogenetic relatives of taxa for which laboratory growth is not known at >45 °C. Shivlinga’s geomicrobiology highlights the possibility that the system’s kosmotrope-dominated chemistry mitigates against the biomacromolecule-disordering effects of its thermal water.
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30
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Giessen TW, Orlando BJ, Verdegaal AA, Chambers MG, Gardener J, Bell DC, Birrane G, Liao M, Silver PA. Large protein organelles form a new iron sequestration system with high storage capacity. eLife 2019; 8:46070. [PMID: 31282860 PMCID: PMC6668986 DOI: 10.7554/elife.46070] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/06/2019] [Indexed: 12/21/2022] Open
Abstract
Iron storage proteins are essential for cellular iron homeostasis and redox balance. Ferritin proteins are the major storage units for bioavailable forms of iron. Some organisms lack ferritins, and it is not known how they store iron. Encapsulins, a class of protein-based organelles, have recently been implicated in microbial iron and redox metabolism. Here, we report the structural and mechanistic characterization of a 42 nm two-component encapsulin-based iron storage compartment from Quasibacillus thermotolerans. Using cryo-electron microscopy and x-ray crystallography, we reveal the assembly principles of a thermostable T = 4 shell topology and its catalytic ferroxidase cargo and show interactions underlying cargo-shell co-assembly. This compartment has an exceptionally large iron storage capacity storing over 23,000 iron atoms. Our results reveal a new approach for survival in diverse habitats with limited or fluctuating iron availability via an iron storage system able to store 10 to 20 times more iron than ferritin. People often think of the cell as the basic unit of life. Despite this, individual cells are also subdivided into many compartments, called ‘organelles’ because they act like the internal organs of the cell. For example, organelles can break down nutrients, store information in the form of DNA, or help remove waste. Even bacterial cells, despite being smaller and simpler than most other cell types, contain organelle-like structures. These are tiny compartments, termed protein organelles, which are enclosed by ‘shells’ made from self-assembling proteins within the cell. Cells need iron to carry out the chemical reactions necessary for life. Iron is therefore an essential nutrient, but it can also be toxic if not stored properly inside the cell. Cells often solve this problem by locking iron away inside small, specialised protein cages called ferritins until it can be used. Most organisms, from humans to bacteria, have ferritins, but some do not, and the way these organisms store iron remains largely unknown. The bacterium Quasibacillus thermotolerans is an example of an organism that lacks ferritins. However, it does contain a recently discovered type of protein organelle, called an encapsulin. Giessen et al. wanted to find out more about the structure of this protein organelle, and to determine if it helped these bacteria store iron. Q. thermotolerans’ encapsulin turned out to be the largest of its kind discovered to date. Detailed imaging experiments, using a combination of electron microscopy and X-ray- based techniques, revealed that the protein shell of the encapsulin had an overall structure resembling chain mail and contained multiple pores. These pores were negatively charged, meaning that they could efficiently attract iron (which has a positive charge) and funnel it into the interior of the compartment. The compartment itself was able to store at least 20 times more iron than ferritins, making this encapsulin one of the most efficient methods of iron storage in any cell. These findings will help us better understand how bacteria that lack ferritins cope with the problem of iron storage. In the future, encapsulins could also be used as a target for new therapies to fight bacterial infections, or even as the building blocks for microscopic chemical reactors or ‘storage facilities’ in industrial applications.
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Affiliation(s)
- Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, United States
| | - Benjamin J Orlando
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Andrew A Verdegaal
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States
| | - Melissa G Chambers
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Jules Gardener
- Center for Nanoscale Systems, Harvard University, Cambridge, United States
| | - David C Bell
- Center for Nanoscale Systems, Harvard University, Cambridge, United States.,School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
| | - Gabriel Birrane
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, United States
| | - Maofu Liao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, United States
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31
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Thomas SC, Tamadonfar KO, Seymour CO, Lai D, Dodsworth JA, Murugapiran SK, Eloe-Fadrosh EA, Dijkstra P, Hedlund BP. Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures. Front Microbiol 2019; 10:1427. [PMID: 31333598 PMCID: PMC6624737 DOI: 10.3389/fmicb.2019.01427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/05/2019] [Indexed: 12/02/2022] Open
Abstract
Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60–95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across the temperature gradient and many individual metagenome-assembled genomes had complete pathways. In contrast, genes encoding cellulosomes and many genes involved in plant matter degradation and photosynthesis were absent at higher temperatures. In situ13C-CO2 production from labeled isotopomer pairs of glucose, pyruvate, and acetate suggested lower relative oxidative pentose phosphate pathway activity and/or fermentation at 60°C, and a stable or decreased maintenance energy demand at higher temperatures. Catabolism of 13C-labeled citrate, succinate, L-alanine, L-serine, and L-cysteine was observed at 85°C, demonstrating broad heterotrophic activity and confirming functioning of the TCA cycle. Together, these results suggest that temperature-driven losses in biodiversity and gene content in geothermal systems may not alter CCMP function or maintenance energy demands at a community level.
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Affiliation(s)
- Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Kevin O Tamadonfar
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | | | - Emiley A Eloe-Fadrosh
- Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA, United States
| | - Paul Dijkstra
- Department of Biological Sciences, Center of Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
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32
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Wei Z, Hao Z, Li X, Guan Z, Cai Y, Liao X. The effects of phytoremediation on soil bacterial communities in an abandoned mine site of rare earth elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:950-960. [PMID: 30921727 DOI: 10.1016/j.scitotenv.2019.03.118] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Overexploitation of rare earth elements (REEs) has caused serious desertification and environmental pollution. The ecological restoration of mining areas has attracted increasing attention in China. Soil microbiota is important for successful ecological remediation of abandoned mine land. In this study, soil samples were collected from a restored REE mine site, and the bacterial community composition and diversity were assessed by Illumina high-throughput sequencing targeting the V3-V4 region of the 16S rRNA gene. Microbiota significantly developed in the remediated land. A total of 663,781 effective 16S rRNA gene sequences were obtained, which were classified into 28 bacterial phyla and 3 archaeal phyla. The dominant phyla across all samples (>5% of total effective sequences) were Proteobacteria, Acidobacteria and Firmicutes. Bacterial diversity indices (OTU number, Shannon index and Chao1 index) of the restored soils were higher than those of the tailings and even surpassed those in the unmined site. Redundancy analysis indicated that soil nutrients (soil organic carbon, available phosphorus and total nitrogen) were the dominant factors, followed by soil pH, affecting bacterial community structure. In general, these results suggested that soil amendment and phytoremediation effectively improved the soil environment of the abandoned mine site, which also increased our understanding of the correlation between microbial variation and soil properties in restored REE mine soils.
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Affiliation(s)
- Zhiwen Wei
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou 221116, China
| | - Zhikui Hao
- Institute of Applied Biotechnology, Taizhou Vocational and Technical College, Taizhou 318000, China
| | - Xunhang Li
- The Bioscience and Engineering College, Jiangxi Agriculture University, Nanchang 330045, China
| | - Zhengbing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiangru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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Li L, Ma ZS. Comparative power law analysis for the spatial heterogeneity scaling of the hot-spring microbiomes. Mol Ecol 2019; 28:2932-2943. [PMID: 31066936 DOI: 10.1111/mec.15124] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/29/2019] [Accepted: 05/01/2019] [Indexed: 01/15/2023]
Abstract
Spatial heterogeneity is a fundamental property of any natural ecosystems, including hot spring and human microbiomes. Two important scales that spatial heterogeneity exhibits are population and community scales, and Taylor's power law (PL) and its extensions (PLEs) offer ideal quantitative models to assess population- and community-level heterogeneities. Here we analyse 165 hot spring microbiome samples at the global scale that cover a wide range of temperatures (7.5-99°C) and pH levels (3.3-9). We explore a question of fundamental importance for measuring the spatial heterogeneity of the hot-spring microbiome and further discuss their ecological implications: How do critical environmental factors such as temperature and pH influence the scaling of community spatial heterogeneity? We are particularly interested in the existence of a universal scaling model that is independent of environmental gradients. By applying PL and PLEs, we were able to obtain such scaling parameters of the hot spring at both community and population levels, which are temperature- and pH-invariant. These findings suggest that while the hot-spring microbiomes located at different regions may have different environmental conditions, they share a fundamental heterogeneity scaling parameter, analogically similar to the gravitational acceleration on Earth, which may vary slightly depending on altitude and latitude, but is invariant overall. In contrast, similar to the physics of the Moon and Earth, which have different gravitational accelerations, the hot spring and human microbiomes can have different scaling parameters as demonstrated in this study.
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Affiliation(s)
- Lianwei Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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34
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Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives. Mol Biotechnol 2019; 61:579-601. [DOI: 10.1007/s12033-019-00187-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Li Q, Becker T, Zhang R, Xiao T, Sand W. Investigation on adhesion of Sulfobacillus thermosulfidooxidans via atomic force microscopy equipped with mineral probes. Colloids Surf B Biointerfaces 2019; 173:639-646. [DOI: 10.1016/j.colsurfb.2018.10.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/08/2018] [Accepted: 10/17/2018] [Indexed: 11/30/2022]
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Nishiyama E, Higashi K, Mori H, Suda K, Nakamura H, Omori S, Maruyama S, Hongoh Y, Kurokawa K. The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan. Front Bioeng Biotechnol 2018; 6:202. [PMID: 30619848 PMCID: PMC6306410 DOI: 10.3389/fbioe.2018.00202] [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: 08/16/2018] [Accepted: 12/10/2018] [Indexed: 12/02/2022] Open
Abstract
Diverse microorganisms specifically inhabit extreme environments, such as hot springs and deep-sea hydrothermal vents. To test the hypothesis that the microbial community structure is predictable based on environmental factors characteristic of such extreme environments, we conducted correlation analyses of microbial taxa/functions and environmental factors using metagenomic and 61 types of physicochemical data of water samples from nine hot springs in the Kirishima area (Kyusyu, Japan), where hot springs with diverse chemical properties are distributed in a relatively narrow area. Our metagenomic analysis revealed that the samples can be classified into two major types dominated by either phylum Crenarchaeota or phylum Aquificae. The correlation analysis showed that Crenarchaeota dominated in nutrient-rich environments with high concentrations of ions and total carbons, whereas Aquificae dominated in nutrient-poor environments with low ion concentrations. These environmental factors were also important explanatory variables in the generalized linear models constructed to predict the abundances of Crenarchaeota or Aquificae. Functional enrichment analysis of genes also revealed that the separation of the two major types is primarily attributable to genes involved in autotrophic carbon fixation, sulfate metabolism and nitrate reduction. Our results suggested that Aquificae and Crenarchaeota play a vital role in the Kirishima hot spring water ecosystem through their metabolic pathways adapted to each environment. Our findings provide a basis to predict microbial community structures in hot springs from environmental parameters, and also provide clues for the exploration of biological resources in extreme environments.
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Affiliation(s)
- Eri Nishiyama
- Biotechnological Research Support Division, FASMAC Co. Ltd, Kanagawa, Japan.,Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Koichi Higashi
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Konomi Suda
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Hitomi Nakamura
- Department of Solid Earth Geochemistry, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Soichi Omori
- Faculty of Liberal Arts, The Open University of Japan, Chiba, Japan
| | - Shigenori Maruyama
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ken Kurokawa
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
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Stewart LC, Stucker VK, Stott MB, de Ronde CEJ. Marine-influenced microbial communities inhabit terrestrial hot springs on a remote island volcano. Extremophiles 2018; 22:687-698. [PMID: 29713821 DOI: 10.1007/s00792-018-1029-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/19/2018] [Indexed: 11/25/2022]
Abstract
Raoul Island is a subaerial island volcano approximately 1000 km northeast of New Zealand. Its caldera contains a circumneutral closed-basin volcanic lake and several associated pools, as well as intertidal coastal hot springs, all fed by a hydrothermal system sourced from both meteoric water and seawater. Here, we report on the geochemistry, prokaryotic community diversity, and cultivatable abundance of thermophilic microorganisms of four terrestrial features and one coastal feature on Raoul. Hydrothermal fluid contributions to the volcanic lake and pools make them brackish, and consequently support unusual microbial communities dominated by Planctomycetes, Chloroflexi, Alphaproteobacteria, and Thaumarchaeota, as well as up to 3% of the rare sister phylum to Cyanobacteria, Candidatus Melainabacteria. The dominant taxa are mesophilic to moderately thermophilic, phototrophic, and heterotrophic marine groups related to marine Planctomycetaceae. The coastal hot spring/shallow hydrothermal vent community is similar to other shallow systems in the Western Pacific Ocean, potentially due to proximity and similarities of geochemistry. Although rare in community sequence data, thermophilic methanogens, sulfur-reducers, and iron-reducers are present in culture-based assays.
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Affiliation(s)
- Lucy C Stewart
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand.
| | - Valerie K Stucker
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand
| | - Matthew B Stott
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand
- University of Canterbury, Christchurch, 8140, New Zealand
| | - Cornel E J de Ronde
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand
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Differences in Temperature and Water Chemistry Shape Distinct Diversity Patterns in Thermophilic Microbial Communities. Appl Environ Microbiol 2017; 83:AEM.01363-17. [PMID: 28821552 DOI: 10.1128/aem.01363-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/11/2017] [Indexed: 01/22/2023] Open
Abstract
This report describes the biodiversity and ecology of microbial mats developed in thermal gradients (20 to 65°C) in the surroundings of three drillings (Chiraleu [CH], Ciocaia [CI], and Mihai Bravu [MB]) tapping a hyperthermal aquifer in Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physicochemical factors were explored. Additionally, the cDNA data were used for in silico functionality predictions, bringing new insights into the functional potential and dynamics of these communities. The results showed that each hot spring determined the formation of distinct microbial communities. In the CH mats (40 to 53°C), the abundance of Cyanobacteria decreased with temperature, opposite to those of Chloroflexi and ProteobacteriaEctothiorhodospira, Oscillatoria, and methanogenic archaea dominated the CI communities (20 to 65°C), while the MB microbial mats (53 to 65°C) were mainly composed of Chloroflexi, Hydrogenophilus, Thermi, and Aquificae Alpha-diversity was negatively correlated with the increase in water temperature, while beta-diversity was shaped in each hot spring by the unique combination of physicochemical parameters, regardless of the type of nucleic acid analyzed (DNA versus cDNA). The rank correlation analysis revealed a unique model that associated environmental data with community composition, consisting in the combined effect of Na+, K+, HCO3-, and PO43- concentrations, together with temperature and electrical conductivity. These factors seem to determine the grouping of samples according to location, rather than with the similarities in thermal regimes, showing that other parameters beside temperature are significant drivers of biodiversity.IMPORTANCE Hot spring microbial mats represent a remarkable manifestation of life on Earth and have been intensively studied for decades. Moreover, as hot spring areas are isolated and have a limited exchange of organisms, nutrients, and energy with the surrounding environments, hot spring microbial communities can be used in model studies to elucidate the colonizing potential within extreme settings. Thus, they are of great importance in evolutionary biology, microbial ecology, and exobiology. In spite of all the efforts that have been made, the current understanding of the influence of temperature and water chemistry on the microbial community composition, diversity, and abundance in microbial mats is limited. In this study, the composition and diversity of microbial communities developed in thermal gradients in the vicinity of three hot springs from Romania were investigated, each having particular physicochemical characteristics. Our results expose new factors that could determine the formation of these ecosystems, expanding the current knowledge in this regard.
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Ghilamicael AM, Budambula NLM, Anami SE, Mehari T, Boga HI. Evaluation of prokaryotic diversity of five hot springs in Eritrea. BMC Microbiol 2017; 17:203. [PMID: 28938870 PMCID: PMC5610464 DOI: 10.1186/s12866-017-1113-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
Background Total community rDNA was used to determine the diversity of bacteria and archaea from water, wet sediment and microbial mats samples of hot springs in the Eastern lowlands of Eritrea. The temperatures of the springs range from 49.5 °C to 100 °C while pH levels varied from 6.97 to 7.54. Akwar and Maiwooi have high carbonate levels. The springs near the seashore, Garbanabra and Gelti, are more saline with higher levels of sodium and chlorides. Elegedi, situated in the Alid volcanic area, has the highest temperature, iron and sulfate concentrations. Results The five hot springs shared 901 of 4371 OTUs recovered while the three sample types (water, wet sediment and microbial mats) also shared 1429 OTUs. The Chao1 OTU estimate in water sample was significantly higher than the wet sediment and microbial mat samples. As indicated by NMDS, the community samples at genus level showed location specific clustering. Certain genera correlated with temperature, sodium, carbonate, iron, sulfate and ammonium levels in water. The abundant phyla included Proteobacteria (6.2–82.3%), Firmicutes (1.6–63.5%), Deinococcus-Thermus (0.0–19.2%), Planctomycetes (0.0–11.8%), Aquificae (0.0–9.9%), Chlorobi (0.0–22.3%) and Bacteroidetes (2.7–8.4%). Conclusion There were significant differences in microbial community structure within the five locations and sample types at OTU level. The occurence of Aquificae, Deinococcus-Thermus, some Cyanobacteria and Crenarchaeota were highly dependent on temperature. The Halobacterium, unclassified Thaumarchaeota, Actinobacteria and Cyanobacteria showed significant correlation with salinity occurring abundantly in Garbanabra and Gelti. Firmicutes and unclassified Rhodocylaceae were higher in the microbial mat samples, while Archaea were prominent in the wet sediment samples. Electronic supplementary material The online version of this article (10.1186/s12866-017-1113-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amanuel M Ghilamicael
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | | | - Sylvester E Anami
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | - Tadesse Mehari
- National Commission for Higher Education in Eritrea, Asmara, Eritrea
| | - Hamadi I Boga
- Taita Taveta University, P.O. Box 635-80300, Voi, Kenya.
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Prieto-Barajas CM, Alfaro-Cuevas R, Valencia-Cantero E, Santoyo G. Effect of seasonality and physicochemical parameters on bacterial communities in two hot spring microbial mats from Araró, Mexico. REV MEX BIODIVERS 2017. [DOI: 10.1016/j.rmb.2017.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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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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The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China. PLoS One 2017; 12:e0174411. [PMID: 28379996 PMCID: PMC5381875 DOI: 10.1371/journal.pone.0174411] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/08/2017] [Indexed: 11/19/2022] Open
Abstract
Soil bacteria are important drivers of biogeochemical cycles and participate in many nutrient transformations in the soil. Meanwhile, bacterial diversity and community composition are related to soil physic-chemical properties and vegetation factors. However, how the soil and vegetation factors affect the diversity and community composition of bacteria is poorly understood, especially for bacteria associated with evergreen and deciduous trees in subtropical forest ecosystems. In the present paper, the microbial communities of rhizospheric soils associated with different types of trees were analyzed by Illumina MiSeq sequencing the V3-V4 region of the 16S rRNA gene. A total of 121,219 effective 16S rRNA gene sequences were obtained, which were classified into 29 bacterial phyla and 2 archaeal phyla. The dominant phyla across all samples (>5% of good-quality sequences in each sample) were Proteobacteria, Acidobacteria, Firmicutes and Bacteroidetes. The bacterial community composition and diversity were largely affected by both soil pH and tree species. The soil pH was the key factor influencing bacterial diversity, with lower pH associated with less diverse communities. Meanwhile, the contents of NO3− were higher in evergreen tree soils than those associated with deciduous trees, while less NH4+ than those associated with deciduous trees, leading to a lower pH and indirectly influencing the diversity and composition of the bacteria. The co-occurrence patterns were assessed by network analysis. A total of 415 pairs of significant and robust correlations (co-occurrence and negative) were identified from 89 genera. Sixteen hubs of co-occurrence patterns, mainly under the phyla Acidobacteria, Proteobacteria, Firmicutes and Bacteroidetes, may play important roles in sustaining the stability of the rhizospheric microbial communities. In general, our results suggested that local environmental conditions and soil pH were important in shaping the bacterial community of the Taihu Lake zone in east China.
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DeCastro ME, Rodríguez-Belmonte E, González-Siso MI. Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes. Front Microbiol 2016; 7:1521. [PMID: 27729905 PMCID: PMC5037290 DOI: 10.3389/fmicb.2016.01521] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/12/2016] [Indexed: 11/24/2022] Open
Abstract
Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.
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Affiliation(s)
- María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
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Complete metagenome sequencing based bacterial diversity and functional insights from basaltic hot spring of Unkeshwar, Maharashtra, India. GENOMICS DATA 2015; 7:140-3. [PMID: 26981391 PMCID: PMC4778638 DOI: 10.1016/j.gdata.2015.12.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 12/30/2015] [Indexed: 11/25/2022]
Abstract
Unkeshwar hot springs are located at geographical South East Deccan Continental basalt of India. Here, we report the microbial community analysis of this hot spring using whole metagenome shotgun sequencing approach. The analysis revealed a total of 848,096 reads with 212.87 Mbps with 50.87% G + C content. Metagenomic sequences were deposited in SRA database with accession number (SUB1242219). Community analysis revealed 99.98% sequences belonging to bacteria and 0.01% to archaea and 0.01% to Viruses. The data obtained revealed 41 phyla including bacteria and Archaea and including 719 different species. In taxonomic analysis, the dominant phyla were found as, Actinobacteria (56%), Verrucomicrobia (24%), Bacteriodes (13%), Deinococcus-Thermus (3%) and firmicutes (2%) and Viruses (2%). Furthermore, functional annotation using pathway information revealed dynamic potential of hot spring community in terms of metabolism, environmental information processing, cellular processes and other important aspects. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of each contig sequence by assigning KEGG Orthology (KO) numbers revealed contig sequences that were assigned to metabolism, organismal system, Environmental Information Processing, cellular processes and human diseases with some unclassified sequences. The Unkeshwar hot springs offer rich phylogenetic diversity and metabolic potential for biotechnological applications.
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Lin KH, Liao BY, Chang HW, Huang SW, Chang TY, Yang CY, Wang YB, Lin YTK, Wu YW, Tang SL, Yu HT. Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. BMC Genomics 2015; 16:1029. [PMID: 26630941 PMCID: PMC4668684 DOI: 10.1186/s12864-015-2230-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. Results In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. Conclusions Our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2230-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kuei-Han Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Ben-Yang Liao
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China.
| | - Hao-Wei Chang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Molecular Microbiology and Microbial Pathogenesis Program, Division of Biology and Biomedical Science, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Shiao-Wei Huang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Ting-Yan Chang
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China.
| | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Yu-Bin Wang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Yu-Teh Kirk Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Hon-Tsen Yu
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Degree Program of Genome and Systems Biology, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan, Republic of China.
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Metagenomics: Retrospect and Prospects in High Throughput Age. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2015; 2015:121735. [PMID: 26664751 PMCID: PMC4664791 DOI: 10.1155/2015/121735] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/26/2015] [Indexed: 01/30/2023]
Abstract
In recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. In the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. A brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenomes of diverse habitats. The present review also highlights the paradigm shift of metagenomics from basic study of community composition to insight into the microbial community dynamics for harnessing the full potential of uncultured microbes with more emphasis on the implication of breakthrough developments, namely, Next Generation Sequencing, advanced bioinformatics tools, and systems biology.
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Badhai J, Ghosh TS, Das SK. Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India. Front Microbiol 2015; 6:1166. [PMID: 26579081 PMCID: PMC4620158 DOI: 10.3389/fmicb.2015.01166] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/08/2015] [Indexed: 12/31/2022] Open
Abstract
This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40–58°C; pH: 7.2–7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.
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Affiliation(s)
- Jhasketan Badhai
- Department of Biotechnology, Institute of Life Sciences Bhubaneswar, India
| | | | - Subrata K Das
- Department of Biotechnology, Institute of Life Sciences Bhubaneswar, India
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Estrella Alcamán M, Fernandez C, Delgado A, Bergman B, Díez B. The cyanobacterium Mastigocladus fulfills the nitrogen demand of a terrestrial hot spring microbial mat. THE ISME JOURNAL 2015; 9:2290-303. [PMID: 26230049 PMCID: PMC4579480 DOI: 10.1038/ismej.2015.63] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 11/09/2022]
Abstract
Cyanobacteria from Subsection V (Stigonematales) are important components of microbial mats in non-acidic terrestrial hot springs. Despite their diazotrophic nature (N2 fixers), their impact on the nitrogen cycle in such extreme ecosystems remains unknown. Here, we surveyed the identity and activity of diazotrophic cyanobacteria in the neutral hot spring of Porcelana (Northern Patagonia, Chile) during 2009 and 2011-2013. We used 16S rRNA and the nifH gene to analyze the distribution and diversity of diazotrophic cyanobacteria. Our results demonstrate the dominance of the heterocystous genus Mastigocladus (Stigonematales) along the entire temperature gradient of the hot spring (69-38 °C). In situ nitrogenase activity (acetylene reduction), nitrogen fixation rates (cellular uptake of (15)N2) and nifH transcription levels in the microbial mats showed that nitrogen fixation and nifH mRNA expression were light-dependent. Nitrogen fixation activities were detected at temperatures ranging from 58 °C to 46 °C, with maximum daily rates of 600 nmol C2H4 cm(-2) per day and 94.1 nmol N cm(-2) per day. These activity patterns strongly suggest a heterocystous cyanobacterial origin and reveal a correlation between nitrogenase activity and nifH gene expression during diurnal cycles in thermal microbial mats. N and C fixation in the mats contributed ~3 g N m(-2) per year and 27 g C m(-2) per year, suggesting that these vital demands are fully met by the diazotrophic and photoautotrophic capacities of the cyanobacteria in the Porcelana hot spring.
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Affiliation(s)
- María Estrella Alcamán
- Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Camila Fernandez
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Banyuls/mer, France
- CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Banyuls/mer, France
- Department of Oceanography, Interdisciplinary Center for Aquaculture Research (INCAR) and COPAS SURAUSTRAL Program, University of Concepción, Concepción, Chile
| | - Antonio Delgado
- Instituto Andaluz de Ciencias de la Tierra (CSIC-Univ. Granada), Armilla, Granada, Spain
| | - Birgitta Bergman
- Department of Ecology, Environment and Plant Sciences and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, Santiago, Chile
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Chernyh NA, Mardanov AV, Gumerov VM, Miroshnichenko ML, Lebedinsky AV, Merkel AY, Crowe D, Pimenov NV, Rusanov II, Ravin NV, Moran MA, Bonch-Osmolovskaya EA. Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka. Extremophiles 2015; 19:1157-71. [DOI: 10.1007/s00792-015-0787-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/30/2015] [Indexed: 11/29/2022]
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Hedlund BP, Murugapiran SK, Alba TW, Levy A, Dodsworth JA, Goertz GB, Ivanova N, Woyke T. Uncultivated thermophiles: current status and spotlight on 'Aigarchaeota'. Curr Opin Microbiol 2015; 25:136-45. [PMID: 26113243 DOI: 10.1016/j.mib.2015.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/03/2015] [Accepted: 06/03/2015] [Indexed: 01/28/2023]
Abstract
Meta-analysis of cultivation-independent sequence data shows that geothermal systems host an abundance of novel organisms, representing a vast unexplored phylogenetic and functional diversity among yet-uncultivated thermophiles. A number of thermophiles have recently been interrogated using metagenomic and/or single-cell genomic approaches, including members of taxonomic groups that inhabit both thermal and non-thermal environments, such as 'Acetothermia' (OP1) and 'Atribacteria' (OP9/JS1), as well as the exclusively thermophilic lineages 'Korarchaeota', 'Calescamantes' (EM19), 'Fervidibacteria' (OctSpA1-106), and 'Aigarchaeota' (HWCG-I). The 'Aigarchaeota', a sister lineage to the Thaumarchaeota, likely includes both hyperthermophiles and moderate thermophiles. They inhabit terrestrial, marine, and subsurface thermal environments and comprise at least nine genus-level lineages, several of which are globally distributed.
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Affiliation(s)
- Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
| | | | - Timothy W Alba
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Asaf Levy
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Gisele B Goertz
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
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