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Seixas MH, Munroe JS, Eggleston EM. Bacterial diversity and geomicrobiology of Winter Wonderland ice cave, Utah, USA. Microbiologyopen 2024; 13:e1426. [PMID: 38995161 PMCID: PMC11241547 DOI: 10.1002/mbo3.1426] [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: 10/23/2023] [Revised: 06/19/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
The Winter Wonderland ice cave, located at an elevation of 3140 m above sea level in the Uinta Mountains of northern Utah, USA, maintains a constant sub-zero temperature. Seasonal snowmelt and rain enter the cave, freeze on the surface of the existing ice, and contribute to a 3-m-thick layered ice mass. This ice mass contains organic matter and cryogenic cave carbonates (CCCs) that date back centuries. In this study, samples of ice, liquid water, and exposed CCCs were collected to examine the bacterial communities within the cave and to determine if these communities vary spatially and between sample types. Flow cytometry showed that cell counts are an order of magnitude higher in liquid water samples than in ice. Epifluorescence microscopy and scanning electron microscopy imaging revealed potential coccoid and bacillus microbial morphologies in water samples and putative cells or calcite spherules in the CCCs. The diversity of bacteria associated with soil, identified through sequence-based analysis, supports the hypothesis that water enters the cave by filtering through soil and bedrock. A differential abundance of bacterial taxa was observed between sample types, with the greatest diversity found in CCCs. This supports a geomicrobiological framework where microbes aggregate in the water, sink into a concentrated layer, and precipitate out of the ice with the CCCs, thereby reducing the cell counts in the ice. These CCCs may provide essential nutrients for the bacteria or could themselves be products of biomineralization.
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Affiliation(s)
- Miranda Herschel Seixas
- Department of Earth and Climate SciencesMiddlebury CollegeMiddleburyVermontUSA
- Biology DepartmentMiddlebury CollegeMiddleburyVermontUSA
| | - Jeffrey S. Munroe
- Department of Earth and Climate SciencesMiddlebury CollegeMiddleburyVermontUSA
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2
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Jia P, Tian M, Zhang B, Wu X, He X, Zhang W. Habitat changes due to glacial freezing and melting reshape microbial networks. ENVIRONMENT INTERNATIONAL 2024; 189:108788. [PMID: 38838490 DOI: 10.1016/j.envint.2024.108788] [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: 03/03/2024] [Revised: 05/15/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
The phenomenon of glacial freezing and thawing involves microbial sequestration, release, and colonization, which has the potential to impact ecosystem functioning through changes in microbial diversity and interactions. In this study, we examined the structural features of microbial communities of the Dongkemadi glacier, including bacteria, fungi, and archaea, in four distinct glacial environments (snow, ice, meltwater, and frontier soil). The sequestration, release, and colonization of glacial microbes have been found to significantly impact the diversity and structure of glacial microbial communities, as well as the complexity of microbial networks. Specifically, the complexity of bacterial networks has been observed to increase in a sequential manner during these processes. Utilizing the Inter-Domain Ecological Network approach, researchers have further explored the cross-trophic interactions among bacteria, fungi, and archaea. The complexity of the bacteria-fungi-archaea network exhibited a sequential increase due to the processes of sequestration, release, and colonization of glacial microbes. The release and colonization of glacial microbes led to a shift in the role of archaea as key species within the network. Additionally, our findings suggest that the hierarchical interactions among various microorganisms contributed to the heightened complexity of the bacteria-fungi-archaea network. The primary constituents of the glacial microbial ecosystem are unclassified species associated with the Polaromonas. It is noteworthy that various key species in glacial ecosystems are influenced by the distinct environmental factors. Moreover, our findings suggest that key species are not significantly depleted in response to abrupt alterations in individual environmental factors, shedding light on the dynamics of microbial cross-trophic interactions within glacial ecosystems.
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Affiliation(s)
- Puchao Jia
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mao Tian
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Cryospheric Sciences and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Cryospheric Sciences and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiukun Wu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiaobo He
- Key Laboratory of Cryospheric Sciences and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Tanggula Mountain Cryosphere and Environment Observation and Research Station of Tibet Autonomous Region, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
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Buschi E, Dell’Anno A, Tangherlini M, Candela M, Rampelli S, Turroni S, Palladino G, Esposito E, Martire ML, Musco L, Stefanni S, Munari C, Fiori J, Danovaro R, Corinaldesi C. Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome. SCIENCE ADVANCES 2024; 10:eadk9117. [PMID: 38905343 PMCID: PMC11192080 DOI: 10.1126/sciadv.adk9117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.
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Affiliation(s)
- Emanuela Buschi
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luigi Musco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica “Anton Dohrn,” Villa Comunale, Napoli, Italy
| | - Cristina Munari
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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Wojczulanis-Jakubas K, Hoover B, Jakubas D, Fort J, Grémillet D, Gavrilo M, Zielińska S, Zagalska-Neubauer M. Diversity of major histocompatibility complex of II B gene and mate choice in a monogamous and long-lived seabird, the Little Auk (Alle alle). PLoS One 2024; 19:e0304275. [PMID: 38865310 PMCID: PMC11168636 DOI: 10.1371/journal.pone.0304275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024] Open
Abstract
The major histocompatibility complex (MHC) plays a key role in the adaptive immune system of vertebrates, and is known to influence mate choice in many species. In birds, the MHC has been extensively examined but mainly in galliforms and passerines while other taxa that represent specific ecological and evolutionary life-histories, like seabirds, are underexamined. Here, we characterized diversity of MHC Class II B exon 2 in a colonial pelagic seabird, the Little Auk (or Dovekie Alle alle). We further examined whether MHC variation could be maintained through balancing selection and disassortative mating. We found high polymorphism at the genotyped MHC fragment, characterizing 99 distinct alleles across 140 individuals from three populations. The alleles frequencies exhibited a similar skewed distribution in both sexes, with the four most commonly occurring alleles representing approximately 35% of allelic variation. The results of a Bayesian site-by-site selection analysis suggest evidence of balancing selection and no direct evidence for MHC-dependent disassortative mating preferences in the Little Auk. The latter result might be attributed to the high overall polymorphism of the examined fragment, which itself may be maintained by the large population size of the species.
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Affiliation(s)
| | - Brian Hoover
- Farallon Institute, Petaluma, California, United States of America
| | - Dariusz Jakubas
- Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Jérôme Fort
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS – La Rochelle University, 17000 La Rochelle, France
| | - David Grémillet
- Excellence Chair Nouvelle Aquitaine - CEBC UMR 7372 CNRS, La Rochelle Université, Villiers-en-Bois, France & FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, South Africa
| | | | - Sylwia Zielińska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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Sanyal A, Antony R, Samui G, Thamban M. Autotrophy to Heterotrophy: Shift in Bacterial Functions During the Melt Season in Antarctic Cryoconite Holes. J Microbiol 2024:10.1007/s12275-024-00140-1. [PMID: 38814540 DOI: 10.1007/s12275-024-00140-1] [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: 11/03/2023] [Revised: 03/27/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
Microbes residing in cryoconite holes (debris, water, and nutrient-rich ecosystems) on the glacier surface actively participate in carbon and nutrient cycling. Not much is known about how these communities and their functions change during the summer melt-season when intense ablation and runoff alter the influx and outflux of nutrients and microbes. Here, we use high-throughput-amplicon sequencing, predictive metabolic tools and Phenotype MicroArray techniques to track changes in bacterial communities and functions in cryoconite holes in a coastal Antarctic site and the surrounding fjord, during the summer season. The bacterial diversity in cryoconite hole meltwater was predominantly composed of heterotrophs (Proteobacteria) throughout the season. The associated functional potentials were related to heterotrophic-assimilatory and -dissimilatory pathways. Autotrophic Cyanobacterial lineages dominated the debris community at the beginning and end of summer, while heterotrophic Bacteroidota- and Proteobacteria-related phyla increased during the peak melt period. Predictive functional analyses based on taxonomy show a shift from predominantly phototrophy-related functions to heterotrophic assimilatory pathways as the melt-season progressed. This shift from autotrophic to heterotrophic communities within cryoconite holes can affect carbon drawdown and nutrient liberation from the glacier surface during the summer. In addition, the flushing out and export of cryoconite hole communities to the fjord could influence the biogeochemical dynamics of the fjord ecosystem.
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Affiliation(s)
- Aritri Sanyal
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India.
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Goa, 403206, India.
| | - Runa Antony
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India
- GFZ German Research Centre for Geosciences, 14473, Potsdam, Germany
| | - Gautami Samui
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Meloth Thamban
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India
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6
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Ali A, Vishnivetskaya TA, Chauhan A. Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches. Braz J Microbiol 2024:10.1007/s42770-024-01365-3. [PMID: 38758507 DOI: 10.1007/s42770-024-01365-3] [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: 03/09/2023] [Accepted: 04/08/2024] [Indexed: 05/18/2024] Open
Abstract
The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530 m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change.
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Affiliation(s)
- Ahmad Ali
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India
| | | | - Archana Chauhan
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India.
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7
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Singh P, Singh SM, Segawa T, Singh PK. Bacterial diversity and biopotentials of Hamtah glacier cryoconites, Himalaya. Front Microbiol 2024; 15:1362678. [PMID: 38751720 PMCID: PMC11094618 DOI: 10.3389/fmicb.2024.1362678] [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: 12/28/2023] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
Cryoconite is a granular structure present on the glaciers and ice sheets found in polar regions including the Himalayas. It is composed of organic and inorganic matter which absorb solar radiations and reduce ice surface albedo, therefore impacting the melting and retreat of glaciers. Though climate warming has a serious impact on Himalayan glaciers, the biodiversity of sub-glacier ecosystems is poorly understood. Moreover, cryoconite holes are unique habitats for psychrophile biodiversity hotspots in the NW Himalayas, but unfortunately, studies on the microbial diversity of such habitats remain elusive. Therefore, the current study was designed to explore the bacterial diversity of the Hamtah Glacier Himalaya using both culturable and non-culturable approaches. The culturable bacterial count ranged from 2.0 × 103 to 8.8 × 105 colony-forming units (CFUs)/g at the different locations of the glacier. A total of 88 bacterial isolates were isolated using the culturable approach. Based on the 16S ribosomal RNA gene (16S rRNA), the identified species belong to seven genera, namely, Cryobacterium, Duganella, Janthinobacterium, Pseudomonas, Peribacillus, Psychrobacter, and Sphingomonas. In the non-culturable approach, high-throughput sequencing of 16S rRNA genes (using MiSeq) showed unique bacterial community profiles and represented 440 genera belonging to 20 phyla, namely, Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Acidobacteria, Planctomycetes, Cyanobacteria, Verrucomicrobia, Spirochaetes, Elusimicrobia, Armatimonadetes, Gemmatimonadetes, Deinococcus-Thermus, Nitrospirae, Chlamydiae, Chlorobi, Deferribacteres, Fusobacteria, Lentisphaerae, and others. High relative abundances of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were observed in the samples. Phototrophic (Cyanobacteria and Chloroflexi) and nitrifier (Nitrospirae) in bacterial populations indicated sustenance of the micro-ecosystem in the oligotrophic glacier environment. The isolates varied in their phenotypic characteristics, enzyme activities, and antibiotic sensitivity. Furthermore, the fatty acid profiles of bacterial isolates indicate the predominance of branched fatty acids. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a major proportion of the total fatty acid composition. High cold-adapted enzyme activities such as lipase and cellulase expressed by Cryobacterium arcticum (KY783365) and protease and cellulase activities by Pseudomonas sp. strains (KY783373, KY783377-79, KY783382) provide evidence of the possible applications of these organisms. Additionally, antibiotic tests indicated that most isolates were sensitive to antibiotics. In conclusion, the present study contributed for the first time to bacterial diversity and biopotentials of cryoconites of Hamtah Glacier, Himalayas. Furthermore, the cold-adapted enzymes and polyunsaturated fatty acids (PUFAs) may provide an opportunity for biotechnology in the Himalayas. Inductively coupled plasma mass spectrometry (ICPMS) analyses showed the presence of several elements in cryoconites, providing a clue for the accelerating melting and retreating of the Hamtah glacier.
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Affiliation(s)
- Purnima Singh
- Indian Institute of Technology, Banaras Hindu University (IIT-BHU), Varanasi, India
| | | | - Takahiro Segawa
- National Institute of Polar Research, Tachikawa-shi, Tokyo, Japan
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College, Mizoram University (A Central University), Aizawl, India
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Deming JW. Exceeding expectations out in the cold with Colwellia. Nat Microbiol 2024; 9:1159-1160. [PMID: 38671271 DOI: 10.1038/s41564-024-01675-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Affiliation(s)
- Jody W Deming
- School of Oceanography, University of Washington, Seattle, WA, USA.
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9
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Serra Moncadas L, Hofer C, Bulzu PA, Pernthaler J, Andrei AS. Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis. Nat Commun 2024; 15:3421. [PMID: 38653968 PMCID: PMC11039613 DOI: 10.1038/s41467-024-47767-7] [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: 07/18/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.
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Affiliation(s)
- Lucas Serra Moncadas
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Cyrill Hofer
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Adrian-Stefan Andrei
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.
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10
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Lu Q, Liu Y, Zhao J, Yao M. Successive accumulation of biotic assemblages at a fine spatial scale along glacier-fed waters. iScience 2024; 27:109476. [PMID: 38617565 PMCID: PMC11015461 DOI: 10.1016/j.isci.2024.109476] [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: 10/10/2023] [Revised: 01/14/2024] [Accepted: 03/08/2024] [Indexed: 04/16/2024] Open
Abstract
Glacier-fed waters create strong environmental filtering for biota, whereby different organisms may assume distinct distribution patterns. By using environmental DNA-based metabarcoding, we investigated the multi-group biodiversity distribution patterns of the Parlung No. 4 Glacier, on the Tibetan Plateau. Altogether, 642 taxa were identified from the meltwater stream and the downstream Ranwu Lake, including 125 cyanobacteria, 316 diatom, 183 invertebrate, and 18 vertebrate taxa. As the distance increased from the glacier terminus, community complexity increased via sequential occurrences of cyanobacteria, diatoms, invertebrates, and vertebrates, as well as increasing taxa numbers. The stream and lake showed different community compositions and distinct taxa. Furthermore, the correlations with environmental factors and community assembly mechanisms showed group- and habitat-specific patterns. Our results reveal the rapid spatial succession and increasing community complexity along glacial flowpaths and highlight the varying adaptivity of different organisms, while also providing insight into the ecosystem responses to global change.
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Affiliation(s)
- Qi Lu
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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11
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Styczinski MJ, Cooper ZS, Glaser DM, Lehmer O, Mierzejewski V, Tarnas J. Chapter 7: Assessing Habitability Beyond Earth. ASTROBIOLOGY 2024; 24:S143-S163. [PMID: 38498826 DOI: 10.1089/ast.2021.0097] [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: 03/20/2024]
Abstract
All known life on Earth inhabits environments that maintain conditions between certain extremes of temperature, chemical composition, energy availability, and so on (Chapter 6). Life may have emerged in similar environments elsewhere in the Solar System and beyond. The ongoing search for life elsewhere mainly focuses on those environments most likely to support life, now or in the past-that is, potentially habitable environments. Discussion of habitability is necessarily based on what we know about life on Earth, as it is our only example. This chapter gives an overview of the known and presumed requirements for life on Earth and discusses how these requirements can be used to assess the potential habitability of planetary bodies across the Solar System and beyond. We first consider the chemical requirements of life and potential feedback effects that the presence of life can have on habitable conditions, and then the planetary, stellar, and temporal requirements for habitability. We then review the state of knowledge on the potential habitability of bodies across the Solar System and exoplanets, with a particular focus on Mars, Venus, Europa, and Enceladus. While reviewing the case for the potential habitability of each body, we summarize the most prominent and impactful studies that have informed the perspective on where habitable environments are likely to be found.
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Affiliation(s)
- M J Styczinski
- University of Washington, Seattle, Washington, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Z S Cooper
- University of Washington, Seattle, Washington, USA
| | - D M Glaser
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - O Lehmer
- NASA Ames Research Center, Moffett Field, California, USA
| | - V Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Arizona, USA
| | - J Tarnas
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Xing T, Liu K, Ji M, Chen Y, Liu Y. Bacterial diversity in a continuum from supraglacial habitats to a proglacial lake on the Tibetan Plateau. FEMS Microbiol Lett 2024; 371:fnae021. [PMID: 38521984 DOI: 10.1093/femsle/fnae021] [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: 08/23/2023] [Revised: 01/14/2024] [Accepted: 03/22/2024] [Indexed: 03/25/2024] Open
Abstract
Mountain glaciers are frequently assessed for their hydrological connectivity from glaciers to proglacial lakes. Ecological process on glacier surfaces and downstream ecosystems have often been investigated separately, but few studies have focused on the connectivity between the different glacial habitats. Therefore, it remains a limited understanding of bacterial community assembly across different habitats along the glacier hydrological continuum. In this study, we sampled along a glacial catchment from supraglacial snow, cryoconite holes, supraglacial runoff, ice-marginal moraine and proglacial lake on the Tibetan Plateau. The bacterial communities in these habitats were analyzed using high-throughput DNA sequencing of the 16S rRNA gene to determine the bacterial composition and assembly. Our results showed that each habitat hosted unique bacterial communities, with higher bacterial α-diversity in transitional habitats (e.g. runoff and ice-marginal moraine). Null model analysis indicated that deterministic processes predominantly shaped bacterial assembly in snow, cryoconite holes and lake, while stochastic process dominantly governed bacterial community in transitional habitats. Collectively, our findings suggest that local environment play a critical role in filtering bacterial community composition within glacier habitats. This study enhances our understanding of microbial assembly process in glacier environments and provides valuable insights into the factors governing bacterial community compositions across different habitats along the glacial hydrological continuum.
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Affiliation(s)
- Tingting Xing
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
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13
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Heinrichs ME, Piedade GJ, Popa O, Sommers P, Trubl G, Weissenbach J, Rahlff J. Breaking the Ice: A Review of Phages in Polar Ecosystems. Methods Mol Biol 2024; 2738:31-71. [PMID: 37966591 DOI: 10.1007/978-1-0716-3549-0_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] [Indexed: 11/16/2023]
Abstract
Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.
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Affiliation(s)
- Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Ovidiu Popa
- Institute of Quantitative and Theoretical Biology Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | | | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Julia Weissenbach
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Janina Rahlff
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
- Aero-Aquatic Virus Research Group, Friedrich Schiller University Jena, Jena, Germany.
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14
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Perez-Bou L, Muñoz-Palazon B, Gonzalez-Lopez J, Gonzalez-Martinez A, Correa-Galeote D. Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes. MICROBIAL ECOLOGY 2023; 87:14. [PMID: 38091083 DOI: 10.1007/s00248-023-02325-4] [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: 09/03/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023]
Abstract
Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.
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Affiliation(s)
- Lizandra Perez-Bou
- Department of Microbiology and Virology, Faculty of Biology, University of Havana, Havana, Cuba
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
| | - Barbara Muñoz-Palazon
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jesus Gonzalez-Lopez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Alejandro Gonzalez-Martinez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - David Correa-Galeote
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain.
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.
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15
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Vance SD, Craft KL, Shock E, Schmidt BE, Lunine J, Hand KP, McKinnon WB, Spiers EM, Chivers C, Lawrence JD, Wolfenbarger N, Leonard EJ, Robinson KJ, Styczinski MJ, Persaud DM, Steinbrügge G, Zolotov MY, Quick LC, Scully JEC, Becker TM, Howell SM, Clark RN, Dombard AJ, Glein CR, Mousis O, Sephton MA, Castillo-Rogez J, Nimmo F, McEwen AS, Gudipati MS, Jun I, Jia X, Postberg F, Soderlund KM, Elder CM. Investigating Europa's Habitability with the Europa Clipper. SPACE SCIENCE REVIEWS 2023; 219:81. [PMID: 38046182 PMCID: PMC10687213 DOI: 10.1007/s11214-023-01025-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/03/2023] [Indexed: 12/05/2023]
Abstract
The habitability of Europa is a property within a system, which is driven by a multitude of physical and chemical processes and is defined by many interdependent parameters, so that its full characterization requires collaborative investigation. To explore Europa as an integrated system to yield a complete picture of its habitability, the Europa Clipper mission has three primary science objectives: (1) characterize the ice shell and ocean including their heterogeneity, properties, and the nature of surface-ice-ocean exchange; (2) characterize Europa's composition including any non-ice materials on the surface and in the atmosphere, and any carbon-containing compounds; and (3) characterize Europa's geology including surface features and localities of high science interest. The mission will also address several cross-cutting science topics including the search for any current or recent activity in the form of thermal anomalies and plumes, performing geodetic and radiation measurements, and assessing high-resolution, co-located observations at select sites to provide reconnaissance for a potential future landed mission. Synthesizing the mission's science measurements, as well as incorporating remote observations by Earth-based observatories, the James Webb Space Telescope, and other space-based resources, to constrain Europa's habitability, is a complex task and is guided by the mission's Habitability Assessment Board (HAB).
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Affiliation(s)
- Steven D. Vance
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Kathleen L. Craft
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD USA
| | - Everett Shock
- School of Earth & Space Exploration and School of Molecular Sciences, Arizona State University, Tempe, AZ USA
| | - Britney E. Schmidt
- Department of Astronomy and Department of Earth & Atmospheric Sciences, Cornell University, Ithaca, NY USA
| | - Jonathan Lunine
- Department of Astronomy and Department of Earth & Atmospheric Sciences, Cornell University, Ithaca, NY USA
| | - Kevin P. Hand
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - William B. McKinnon
- Department of Earth and Planetary Sciences and McDonnell Center for the Space Sciences, Washington University in St. Louis, Saint Louis, MO USA
| | - Elizabeth M. Spiers
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
| | - Chase Chivers
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
- Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Justin D. Lawrence
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
- Honeybee Robotics, Altadena, CA USA
| | - Natalie Wolfenbarger
- Institute for Geophysics, John A. and Katherine G. Jackson School of Geosciences, University of Texas at Austin, Austin, TX USA
| | - Erin J. Leonard
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | | | | | - Divya M. Persaud
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Gregor Steinbrügge
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Mikhail Y. Zolotov
- School of Earth & Space Exploration and School of Molecular Sciences, Arizona State University, Tempe, AZ USA
| | | | | | | | - Samuel M. Howell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | | | - Andrew J. Dombard
- Dept. of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, USA
| | | | - Olivier Mousis
- Aix Marseille Université, CNRS, LAM (Laboratoire d’Astrophysique de Marseille), Marseille, France
| | - Mark A. Sephton
- Impacts and Astromaterials Research Centre, Department of Earth Science and Engineering, Imperial College London, London, United Kingdom
| | | | - Francis Nimmo
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA USA
| | - Alfred S. McEwen
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ USA
| | - Murthy S. Gudipati
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Insoo Jun
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Xianzhe Jia
- Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, MI USA
| | - Frank Postberg
- Institut für Geologische Wissenschaften, Freie Universität Berlin, Berlin, Germany
| | - Krista M. Soderlund
- Institute for Geophysics, John A. and Katherine G. Jackson School of Geosciences, University of Texas at Austin, Austin, TX USA
| | - Catherine M. Elder
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
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16
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Song Y, Sun L, Song C, Li M, Liu Z, Zhu M, Chen S, Yuan J, Gao J, Wang X, Wang W. Responses of soil microbes and enzymes to long-term warming incubation in different depths of permafrost peatland soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165733. [PMID: 37490945 DOI: 10.1016/j.scitotenv.2023.165733] [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: 04/03/2023] [Revised: 07/06/2023] [Accepted: 07/21/2023] [Indexed: 07/27/2023]
Abstract
Soil microbes and enzymes mediate soil carbon-climate feedback, and their responses to increasing temperature partly affect soil carbon stability subjected to the effects of climate change. We performed a 50-month incubation experiment to determine the effect of long-term warming on soil microbes and enzymes involved in carbon cycling along permafrost peatland profile (0-150 cm) and investigated their response to water flooding in the active soil layer. Soil bacteria, fungi, and most enzymes were observed to be sensitive to changes in temperature and water in the permafrost peatland. Bacterial and fungal abundance decreased in the active layer soil but increased in the deepest permafrost layer under warming. The highest decrease in the ratio of soil bacteria to fungi was observed in the deepest permafrost layer under warming. These results indicated that long-term warming promotes recalcitrant carbon loss in permafrost because fungi are more efficient in decomposing high-molecular-weight compounds. Soil microbial catabolic activity measured using Biolog Ecoplates indicated a greater degree of average well color development at 15 °C than at 5 °C. The highest levels of microbial catabolic activity, functional diversity, and carbon substrate utilization were found in the permafrost boundary layer (60-80 cm). Soil polyphenol oxidase that degrades recalcitrant carbon was more sensitive to increases in temperature than β-glucosidase, N-acetyl-β-glucosaminidase, and acid phosphatase, which degrade labile carbon. Increasing temperature and water flooding exerted a synergistic effect on the bacterial and fungal abundance and β-glucosidase, acid phosphatase, and RubisCO activity in the topsoil. Structural equation modeling analysis indicated that soil enzyme activity significantly correlated with ratio of soil bacteria to fungi and microbial catabolic activity. Our results provide valuable insights into the linkage response of soil microorganisms, enzymes to climate change and their feedback to permafrost carbon loss.
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Affiliation(s)
- Yanyu Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Li Sun
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Mengting Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; College of Tourism and Geographical Science, Jilin Normal University, Siping 136000, China
| | - Zhendi Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy Sciences, Beijing 100049, China
| | - Mengyuan Zhu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy Sciences, Beijing 100049, China
| | - Shuang Chen
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jiabao Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy Sciences, Beijing 100049, China
| | - Jinli Gao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xianwei Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Wenjuan Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
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17
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Schuler CG, Winebrenner DP, Elam WT, Burnett J, Boles BW, Mikucki JA. Microbial Transport by a Descending Ice Melting Probe: Implications for Subglacial and Ocean World Exploration. ASTROBIOLOGY 2023; 23:1153-1164. [PMID: 37279037 DOI: 10.1089/ast.2021.0106] [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: 06/07/2023]
Abstract
Ocean Worlds beneath thick ice covers in our solar system, as well as subglacial lakes on Earth, may harbor biological systems. In both cases, thick ice covers (>100 s of meters) present significant barriers to access. Melt probes are emerging as tools for reaching and sampling these realms due to their small logistical footprint, ability to transport payloads, and ease of cleaning in the field. On Earth, glaciers are immured with various abundances of microorganisms and debris. The potential for bioloads to accumulate around and be dragged by a probe during descent has not previously been investigated. Due to the pristine nature of these environments, minimizing and understanding the risk of forward contamination and considering the potential of melt probes to act as instrument-induced special regions are essential. In this study, we examined the effect that two engineering descent strategies for melt probes have on the dragging of bioloads. We also tested the ability of a field cleaning protocol to rid a common contaminant, Bacillus. These tests were conducted in a synthetic ice block immured with bioloads using the Ice Diver melt probe. Our data suggest minimal dragging of bioloads by melt probes, but conclude that modifications for further minimization and use in special regions should be made.
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Affiliation(s)
- Caleb G Schuler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Dale P Winebrenner
- Applied Physics Laboratory, University of Washington, Seattle, Washington, USA
| | - W Timothy Elam
- Applied Physics Laboratory, University of Washington, Seattle, Washington, USA
| | - Justin Burnett
- Applied Physics Laboratory, University of Washington, Seattle, Washington, USA
| | - Bruce W Boles
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jill A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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18
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Zhang C, Ren Z. The role of subsurface ice in sustaining bacteria in continental and maritime glaciers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165324. [PMID: 37414181 DOI: 10.1016/j.scitotenv.2023.165324] [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: 04/07/2023] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023]
Abstract
In supraglacial environments, surface and subsurface ices are two distinct and connected microhabitats in terms of physicochemical and biological aspects. At the frontline of climate change, glaciers lose tremendous ice masses to downstream ecosystems, serving as crucial sources of both biotic and abiotic materials. In this study, we studied the disparities and relationships of microbial communities between surface and subsurface ices collected from a maritime and a continental glacier during summer. The results showed that surface ices had significantly higher nutrients and were more physiochemically different than subsurface ices. Despite lower nutrients, subsurface ices had higher alpha-diversity with more unique and enriched operational taxonomic units (OTUs) than surface ices, indicating the potential role of subsurface as a bacterial refuge. Sorensen dissimilarity between bacterial communities in surface ices and subsurface ices was mainly contributed by the turnover component, suggesting strong species replacement from surface to subsurface ices due to large environmental gradients. For different glaciers, the maritime glacier had significantly higher alpha-diversity than the continental glacier. The difference between surface and subsurface communities was more pronounced in the maritime glacier than in the continental glacier. The network analysis revealed that surface-enriched and subsurface-enriched OTUs formed independent modules, with surface-enriched OTUs having closer interconnections and greater importance in the network of the maritime glacier. This study highlights the important role of subsurface ice as a bacterial refuge and enriches our knowledge of microbial properties in glaciers.
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Affiliation(s)
- Cheng Zhang
- School of Engineering Technology, Beijing Normal University, Zhuhai, China; Instrumentation and Service Center for Science and Technology, Beijing Normal University, Zhuhai, China
| | - Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
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19
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Hattori S, Li Z, Yoshida N, Takeuchi N. Isotopic Evidence for Microbial Nitrogen Cycling in a Glacier Interior of High-Mountain Asia. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15026-15036. [PMID: 37747413 DOI: 10.1021/acs.est.3c04757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Glaciers are now acknowledged as an important biome globally, but biological processes in the interior of the glacier (englacial) are thought to be slow and to play only a minor role in biogeochemical cycles. In this study, we demonstrate extensive, microbially driven englacial nitrogen cycling in an Asian glacier using the stable isotopes (δ15N, δ18O, and Δ17O values) of nitrate. Apparent decreases in Δ17O values of nitrate in an 8 m shallow firn core from the accumulation area indicate that nitrifiers gradually replaced ∼80% of atmospheric nitrate with nitrate from microbial nitrification on a decadal scale. Nitrate concentrations did not increase with depth in this core, suggesting the presence of nitrate sinks by microbial assimilation and denitrification within the firn layers. The estimated englacial metabolic rate using isotopic mass balance was classified as growth metabolism, which is approximately 2 orders of magnitude more active than previously known cold-environment metabolisms. In a 56 m ice core from the interior of the ablation area, we found less nitrification but continued microbial nitrate consumption, implying that organic matter is microbially accumulated over centuries before appearing on the ablating surface. Such englacial microbial products may support supraglacial microbes, potentially promoting glacial darkening and melting. With predicted global warming and higher nitrogen loads, englacial nutrient cycling and its roles may become increasingly important in the future.
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Affiliation(s)
- Shohei Hattori
- International Center for Isotope Effects Research (ICIER), Nanjing University, Nanjing 210023, China
- Frontiers Science Center for Critical Earth Material Cycling, State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Zhongqin Li
- State Key Laboratory of Cryospheric Sciences/Tien Shan Glaciological Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Naohiro Yoshida
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8502, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8551, Japan
- National Institute of Information and Communications Technology, Tokyo 184-8795, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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20
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Bendia AG, Moreira JCF, Ferreira JCN, Romano RG, Ferreira IGC, Franco DC, Evangelista H, Montone RC, Pellizari VH. Insights into Antarctic microbiomes: diversity patterns for terrestrial and marine habitats. AN ACAD BRAS CIENC 2023; 95:e20211442. [PMID: 37820122 DOI: 10.1590/0001-3765202320211442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/27/2022] [Indexed: 10/13/2023] Open
Abstract
Microorganisms in Antarctica are recognized for having crucial roles in ecosystems functioning and biogeochemical cycles. To explore the diversity and composition of microbial communities through different terrestrial and marine Antarctic habitats, we analyze 16S rRNA sequence datasets from fumarole and marine sediments, soil, snow and seawater environments. We obtained measures of alpha- and beta-diversities, as well as we have identified the core microbiome and the indicator microbial taxa of a particular habitat. Our results showed a unique microbial community structure according to each habitat, including specific taxa composing each microbiome. Marine sediments harbored the highest microbial diversity among the analyzed habitats. In the fumarole sediments, the core microbiome was composed mainly of thermophiles and hyperthermophilic Archaea, while in the majority of soil samples Archaea was absent. In the seawater samples, the core microbiome was mainly composed by cultured and uncultured orders usually identified on Antarctic pelagic ecosystems. Snow samples exhibited common taxa previously described for habitats of the Antarctic Peninsula, which suggests long-distance dispersal processes occurring from the Peninsula to the Continent. This study contributes as a baseline for further efforts on evaluating the microbial responses to environmental conditions and future changes.
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Affiliation(s)
- Amanda G Bendia
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Julio Cezar F Moreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Juliana C N Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Renato G Romano
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Ivan G C Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Diego C Franco
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Heitor Evangelista
- Universidade do Estado do Rio de Janeiro (UERJ), Instituto de Biologia Roberto Alcantara Gomes, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - Rosalinda C Montone
- Universidade de São Paulo (USP), Departamento de Oceanografia Física, Química e Geológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Vivian Helena Pellizari
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
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21
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Girard C, Vincent WF, Culley AI. Arctic bacterial diversity and connectivity in the coastal margin of the Last Ice Area. ISME COMMUNICATIONS 2023; 3:105. [PMID: 37752298 PMCID: PMC10522646 DOI: 10.1038/s43705-023-00313-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023]
Abstract
Arctic climate change is leading to sea-ice attrition in the Last Ice Area along the northern coast of Canada and Greenland, but less attention has been given to the associated land-based ecosystems. Here we evaluated bacterial community structure in a hydrologically coupled cryo-ecosystem in the region: Thores Glacier, proglacial Thores Lake, and its outlet to the sea. Deep amplicon sequencing revealed that Polaromonas was ubiquitous, but differed genetically among diverse niches. Surface glacier-ice was dominated by Cyanobacteria, while the perennially ice-capped, well-mixed water column of Thores Lake had a unique assemblage of Chloroflexi, Actinobacteriota, and Planctomycetota. Species richness increased downstream, but glacier microbes were little detected in the lake, suggesting strong taxonomic sorting. Ongoing climate change and the retreat of Thores Glacier would lead to complete drainage and loss of the lake microbial ecosystem, indicating the extreme vulnerability of diverse cryohabitats and unique microbiomes in the Last Ice coastal margin.
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Affiliation(s)
- Catherine Girard
- Département de biochimie, de microbiologie et de bio-informatique & Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada.
- Centre d'études nordiques (CEN), Québec, QC, Canada.
- Groupe de recherche interuniversitaire en limnologie et en écologie aquatique (GRIL), Montréal, QC, Canada.
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Chicoutimi, QC, Canada.
| | - Warwick F Vincent
- Centre d'études nordiques (CEN), Québec, QC, Canada
- Département de biologie & Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
| | - Alexander I Culley
- Département de biochimie, de microbiologie et de bio-informatique & Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
- Centre d'études nordiques (CEN), Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA
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22
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Son Y, Min J, Shin Y, Park W. Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress. Sci Rep 2023; 13:14970. [PMID: 37697016 PMCID: PMC10495460 DOI: 10.1038/s41598-023-42179-x] [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: 05/18/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Both culture-independent and culture-dependent analyses using Nanopore-based 16S rRNA sequencing showed that short-term exposure of Antarctic soils to low temperature increased biomass with lower bacterial diversity and maintained high numbers of the phylum Proteobacteria, Firmicute, and Actinobacteria including Pseudarthrobacter species. The psychrophilic Pseudarthrobacter psychrotolerans YJ56 had superior growth at 13 °C, but could not grow at 30 °C, compared to other bacteria isolated from the same Antarctic soil. Unlike a single rod-shaped cell at 13 °C, strain YJ56 at 25 °C was morphologically shifted into a filamentous bacterium with several branches. Comparative genomics of strain YJ56 with other genera in the phylum Actinobacteria indicate remarkable copy numbers of rimJ genes that are possibly involved in dual functions, acetylation of ribosomal proteins, and stabilization of ribosomes by direct binding. Our proteomic data suggested that Actinobacteria cells experienced physiological stresses at 25 °C, showing the upregulation of chaperone proteins, GroEL and catalase, KatE. Level of proteins involved in the assembly of 50S ribosomal proteins and L29 in 50S ribosomal proteins increased at 13 °C, which suggested distinct roles of many ribosomal proteins under different conditions. Taken together, our data highlights the cellular filamentation and protein homeostasis of a psychrophilic YJ56 strain in coping with high-temperature stress.
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Affiliation(s)
- Yongjun Son
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Yoonjae Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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23
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Magnuson E, Altshuler I, Freyria NJ, Leveille RJ, Whyte LG. Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring. MICROBIOME 2023; 11:203. [PMID: 37697305 PMCID: PMC10494364 DOI: 10.1186/s40168-023-01628-5] [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: 04/12/2023] [Accepted: 07/19/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (~ 7 °C), hypersaline (7-8% salinity), anoxic (~ 0.04 ppm O2), and highly reducing (~ - 430 mV) brines rich in sulfate (2.2 g.L-1) and sulfide (9.5 ppm), making Gypsum Hill an analog to putative sulfate-rich briny habitats on extraterrestrial bodies such as Mars. RESULTS Genome-resolved metagenomics and metatranscriptomics were utilized to describe an active microbial community containing novel metagenome-assembled genomes and dominated by sulfur-cycling Desulfobacterota and Gammaproteobacteria. Sulfate reduction was dominated by hydrogen-oxidizing chemolithoautotrophic Desulfovibrionaceae sp. and was identified in phyla not typically associated with sulfate reduction in novel lineages of Spirochaetota and Bacteroidota. Highly abundant and active sulfur-reducing Desulfuromusa sp. highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. Despite low oxygen availability, sulfide oxidation was primarily attributed to aerobic chemolithoautotrophic Halothiobacillaceae. Low abundance and transcription of photoautotrophs indicated sulfur-based chemolithoautotrophy drives primary productivity even during periods of constant illumination. CONCLUSIONS We identified a rare surficial chemolithoautotrophic, sulfur-cycling microbial community active in a unique anoxic, cold, hypersaline Arctic spring. We detected Mars-relevant metabolisms including hydrogenotrophic sulfate reduction, sulfur reduction, and sulfide oxidation, which indicate the potential for microbial life in analogous S-rich brines on past and present Mars. Video Abstract.
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Affiliation(s)
- Elisse Magnuson
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC Canada
| | - Ianina Altshuler
- MACE Laboratory, ALPOLE, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nastasia J. Freyria
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC Canada
| | - Richard J. Leveille
- Department of Earth and Planetary Sciences, McGill University, Montreal, QC Canada
- Geosciences Department, John Abbott College, Ste-Anne-de-Bellevue, QC Canada
| | - Lyle G. Whyte
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC Canada
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24
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Chen L, Hong T, Wu Z, Song W, Chen SX, Liu Y, Shen L. Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments. BMC Genomics 2023; 24:508. [PMID: 37653415 PMCID: PMC10468875 DOI: 10.1186/s12864-023-09597-7] [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: 03/20/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Cold-adapted archaea have diverse ecological roles in a wide range of low-temperature environments. Improving our knowledge of the genomic features that enable psychrophiles to grow in cold environments helps us to understand their adaptive responses. However, samples from typical cold regions such as the remote Arctic and Antarctic are rare, and the limited number of high-quality genomes available leaves us with little data on genomic traits that are statistically associated with cold environmental conditions. RESULTS In this study, we examined the haloarchaeal genus Halorubrum and defined a new clade that represents six isolates from polar and deep earth environments ('PD group' hereafter). The genomic G + C content and amino acid composition of this group distinguishes it from other Halorubrum and the trends are consistent with the established genomic optimization of psychrophiles. The cold adaptation of the PD group was further supported by observations of increased flexibility of proteins encoded across the genome and the findings of a growth test. CONCLUSIONS The PD group Halorubrum exhibited denser genome packing, which confers higher metabolic potential with constant genome size, relative to the reference group, resulting in significant differences in carbon, nitrogen and sulfur metabolic patterns. The most marked feature was the enrichment of genes involved in sulfur cycling, especially the production of sulfite from organic sulfur-containing compounds. Our study provides an updated view of the genomic traits and metabolic potential of Halorubrum and expands the range of sources of cold-adapted haloarchaea.
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Affiliation(s)
- Liangzhong Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, and Auhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, Anhui Normal University, Wuhu, 241000, China
| | - Tao Hong
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Zirui Wu
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Weizhi Song
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Shaoxing X Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- State Key Laboratory of Tibetan Plateau Earth System Science, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100085, Beijing, China
| | - Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China.
- State Key Laboratory of Tibetan Plateau Earth System Science, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100085, Beijing, China.
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25
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Roberts JH, McKinnon WB, Elder CM, Tobie G, Biersteker JB, Young D, Park RS, Steinbrügge G, Nimmo F, Howell SM, Castillo-Rogez JC, Cable ML, Abrahams JN, Bland MT, Chivers C, Cochrane CJ, Dombard AJ, Ernst C, Genova A, Gerekos C, Glein C, Harris CD, Hay HCFC, Hayne PO, Hedman M, Hussmann H, Jia X, Khurana K, Kiefer WS, Kirk R, Kivelson M, Lawrence J, Leonard EJ, Lunine JI, Mazarico E, McCord TB, McEwen A, Paty C, Quick LC, Raymond CA, Retherford KD, Roth L, Rymer A, Saur J, Scanlan K, Schroeder DM, Senske DA, Shao W, Soderlund K, Spiers E, Styczinski MJ, Tortora P, Vance SD, Villarreal MN, Weiss BP, Westlake JH, Withers P, Wolfenbarger N, Buratti B, Korth H, Pappalardo RT. Exploring the Interior of Europa with the Europa Clipper. SPACE SCIENCE REVIEWS 2023; 219:46. [PMID: 37636325 PMCID: PMC10457249 DOI: 10.1007/s11214-023-00990-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 07/20/2023] [Indexed: 08/29/2023]
Abstract
The Galileo mission to Jupiter revealed that Europa is an ocean world. The Galileo magnetometer experiment in particular provided strong evidence for a salty subsurface ocean beneath the ice shell, likely in contact with the rocky core. Within the ice shell and ocean, a number of tectonic and geodynamic processes may operate today or have operated at some point in the past, including solid ice convection, diapirism, subsumption, and interstitial lake formation. The science objectives of the Europa Clipper mission include the characterization of Europa's interior; confirmation of the presence of a subsurface ocean; identification of constraints on the depth to this ocean, and on its salinity and thickness; and determination of processes of material exchange between the surface, ice shell, and ocean. Three broad categories of investigation are planned to interrogate different aspects of the subsurface structure and properties of the ice shell and ocean: magnetic induction, subsurface radar sounding, and tidal deformation. These investigations are supplemented by several auxiliary measurements. Alone, each of these investigations will reveal unique information. Together, the synergy between these investigations will expose the secrets of the Europan interior in unprecedented detail, an essential step in evaluating the habitability of this ocean world.
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Affiliation(s)
| | | | - Catherine M Elder
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | | | | | - Ryan S Park
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Gregor Steinbrügge
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Francis Nimmo
- University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Samuel M Howell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Morgan L Cable
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | | | | | - Corey J Cochrane
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Carolyn Ernst
- Johns Hopkins Applied Physics Laboratory, Laurel, MD, USA
| | | | | | | | | | - Hamish C F C Hay
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Paul O Hayne
- University of Colorado Boulder, Boulder, CO, USA
| | | | - Hauke Hussmann
- German Aerospace Center Institute of Planetary Research, Berlin, Germany
| | | | | | - Walter S Kiefer
- Lunar and Planetary Institute, University Space Research Association, Houston, TX, USA
| | | | | | | | - Erin J Leonard
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | | | | | | | | | | | - Carol A Raymond
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Kurt D Retherford
- Sapienza University of Rome, Rome, Italy
- University of Texas at San Antonio, San Antonio, TX, USA
| | - Lorenz Roth
- KTH Royal Institute of Technology, Stockholm, Sweden
| | - Abigail Rymer
- Johns Hopkins Applied Physics Laboratory, Laurel, MD, USA
| | | | | | | | - David A Senske
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Wencheng Shao
- University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Marshall J Styczinski
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
- University of Washington, Seattle, WA, USA
| | - Paolo Tortora
- Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Steven D Vance
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | | | | | | | | | - Bonnie Buratti
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Haje Korth
- Johns Hopkins Applied Physics Laboratory, Laurel, MD, USA
| | - Robert T Pappalardo
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
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26
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Zhong ZP, Vik D, Rapp JZ, Zablocki O, Maughan H, Temperton B, Deming JW, Sullivan MB. Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines. MICROBIOME 2023; 11:174. [PMID: 37550784 PMCID: PMC10405475 DOI: 10.1186/s40168-023-01619-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/12/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Climate change threatens Earth's ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. RESULTS We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred "active" vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. CONCLUSIONS Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth's destabilized and rapidly disappearing cryosphere. Video Abstract.
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Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Dean Vik
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Josephine Z Rapp
- Department of Biology, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, Devon, UK
| | - Jody W Deming
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, WA, USA.
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.
- Department of Microbiology, Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA.
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27
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Li X, Zhang M, Dang C, Wu Z, Xia Y. In situ Nanopore sequencing reveals metabolic characteristics of the Qilian glacier meltwater microbiome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:84805-84813. [PMID: 37341942 DOI: 10.1007/s11356-023-28250-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 06/10/2023] [Indexed: 06/22/2023]
Abstract
Nanopore metagenomic sequencing enables rapid annotating microbiological ecosystems, and the previous glacier-related sequencing applications (e.g., targeted ice sheets, ice lake, and cryoconite holes) inspire us to explore high-altitude glacier meltwater at Qilian Mountain, China (3000 to 4000 m above sea level, MASL). Our findings suggest that (1) despite only several hundred meters apart, the microbial communities and functionalities are quite different among vertical alpine distributions; (2) the high-altitude Qilian meltwater microbiome serve several main metabolic functions, including sulfur oxidation, selenite decomposing, photosynthesis, energy production, enzymic, and UV tolerant activities. Meanwhile, our Nanopore metagenomic results indicate that the microbial classifications and functionalities (e.g., chaperones, cold-shock, specific tRNA species, oxidative stress, and resistance to toxic compounds) of Qilian meltwater are highly consistent with the other glacial microbiome, emphasizing that only certain microbial species can survive in the cold environment and the molecular adaptions and lifestyles remain stable all over the world. Besides, we have shown Nanopore metagenomic sequencing can provide reliable prokaryotic classifications within or among studies, which therefore can encourage more applications in the field given faster turnaround time. However, we recommend accumulating at least 400 ng nucleic acids (after extraction) and maximizing Nanopore library preparation efficiency before on-site sequencing to obtain better resolutions.
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Affiliation(s)
- Xiang Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Miao Zhang
- School of Environment, Harbin Institute of Technology, Harbin, 150001, China
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ziqi Wu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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28
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Touchette D, Maggiori C, Altshuler I, Tettenborn A, Bourdages LJ, Magnuson E, Blenner-Hassett O, Raymond-Bouchard I, Ellery A, Whyte LG. Microbial Characterization of Arctic Glacial Ice Cores with a Semiautomated Life Detection System. ASTROBIOLOGY 2023; 23:756-768. [PMID: 37126945 DOI: 10.1089/ast.2022.0130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The search for extant microbial life will be a major focus of future astrobiology missions; however, no direct extant life detection instrumentation is included in current missions to Mars. In this study, we developed the semiautomated MicroLife detection platform that collects and processes environmental samples, detects biosignatures, and characterizes microbial activity. This platform is composed of a drill for sample collection, a redox dye colorimetric system for microbial metabolic activity detection and assessment (μMAMA [microfluidics Microbial Activity MicroAssay]), and a MinION sequencer for biosignature detection and characterization of microbial communities. The MicroLife platform was field-tested on White Glacier on Axel Heiberg Island in the Canadian high Arctic, with two extracted ice cores. The μMAMA successfully detected microbial metabolism from the ice cores within 1 day of incubation. The MinION sequencing of the ice cores and the positive μMAMA card identified a microbial community consistent with cold and oligotrophic environments. Furthermore, isolation and identification of microbial isolates from the μMAMA card corroborated the MinION sequencing. Together, these analyses support the MicroLife platform's efficacy in identifying microbes natively present in cryoenvironments and detecting their metabolic activity. Given our MicroLife platform's size and low energy requirements, it could be incorporated into a future landed platform or rovers for life detection.
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Affiliation(s)
- David Touchette
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
- Environmental Engineering Institute, River Ecosystems Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Catherine Maggiori
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- Environmental Engineering Institute, MACE Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alex Tettenborn
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, Canada
| | - Louis-Jacques Bourdages
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- Department of Mechanical Engineering, Faculty of Engineering, McGill University, Montréal, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
| | - Olivia Blenner-Hassett
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
| | - Alex Ellery
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
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29
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Shi Y, Yuan Y, Feng Y, Zhang Y, Fan Y. Bacterial Diversity Analysis and Screening for ACC Deaminase-Producing Strains in Moss-Covered Soil at Different Altitudes in Tianshan Mountains-A Case Study of Glacier No. 1. Microorganisms 2023; 11:1521. [PMID: 37375023 DOI: 10.3390/microorganisms11061521] [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: 05/09/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The elevation of the snowline of the No. 1 Glacier in the Tianshan Mountains is increasing due to global warming, which has created favorable conditions for moss invasion and offers an opportunity to investigate the synergistic effects of incipient succession by mosses, plants, and soils. In this study, the concept of altitude distance was used instead of succession time. To investigate the changes of bacterial-community diversity in moss-covered soils during glacial degeneration, the relationship between bacterial community structure and environmental factors was analyzed and valuable microorganisms in moss-covered soils were explored. To do so, the determination of soil physicochemical properties, high-throughput sequencing, the screening of ACC-deaminase-producing bacteria, and the determination of ACC-deaminase activity of strains were performed on five moss-covered soils at different elevations. The results showed that the soil total potassium content, soil available phosphorus content, soil available potassium content, and soil organic-matter content of the AY3550 sample belt were significantly different compared with those of other sample belts (p < 0.05). Secondly, there was a significant difference (p < 0.05) in the ACE index or Chao1 index between the moss-covered-soil AY3550 sample-belt and the AY3750 sample-belt bacterial communities as the succession progressed. The results of PCA analysis, RDA analysis, and cluster analysis at the genus level showed that the community structure of the AY3550 sample belt and the other four sample belts differed greatly and could be divided into two successional stages. The enzyme activities of the 33 ACC-deaminase-producing bacteria isolated and purified from moss-covered soil at different altitudes ranged from 0.067 to 4.7375 U/mg, with strains DY1-3, DY1-4, and EY2-5 having the highest enzyme activities. All three strains were identified as Pseudomonas by morphology, physiology, biochemistry, and molecular biology. This study provides a basis for the changes in moss-covered soil microhabitats during glacial degradation under the synergistic effects of moss, soil, and microbial communities, as well as a theoretical basis for the excavation of valuable microorganisms under glacial moss-covered soils.
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Affiliation(s)
- Yanlei Shi
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science & Technology, Xinjiang University, Urumqi 830046, China
| | - Ye Yuan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science & Technology, Xinjiang University, Urumqi 830046, China
| | - Yingying Feng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science & Technology, Xinjiang University, Urumqi 830046, China
| | - Yinghao Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science & Technology, Xinjiang University, Urumqi 830046, China
| | - Yonghong Fan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science & Technology, Xinjiang University, Urumqi 830046, China
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Wei J, Fontaine L, Valiente N, Dörsch P, Hessen DO, Eiler A. Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat. Nat Commun 2023; 14:3234. [PMID: 37270637 DOI: 10.1038/s41467-023-38806-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/15/2023] [Indexed: 06/05/2023] Open
Abstract
Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.
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Affiliation(s)
- Jing Wei
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Laurent Fontaine
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Nicolas Valiente
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
- Division of Terrestrial Ecosystem Research, Center of Microbiology and Environmental Systems Science, University of Vienna, 1030, Vienna, Austria
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Dag O Hessen
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Alexander Eiler
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway.
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Varliero G, Lebre PH, Frey B, Fountain AG, Anesio AM, Cowan DA. Glacial Water: A Dynamic Microbial Medium. Microorganisms 2023; 11:1153. [PMID: 37317127 DOI: 10.3390/microorganisms11051153] [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: 03/22/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial communities and nutrient dynamics in glaciers and ice sheets continuously change as the hydrological conditions within and on the ice change. Glaciers and ice sheets can be considered bioreactors as microbiomes transform nutrients that enter these icy systems and alter the meltwater chemistry. Global warming is increasing meltwater discharge, affecting nutrient and cell export, and altering proglacial systems. In this review, we integrate the current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics to highlight their interdependence and variability on daily and seasonal time scales, as well as their impact on proglacial environments.
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Affiliation(s)
- Gilda Varliero
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Andrew G Fountain
- Departments of Geology and Geography, Portland State University, Portland, OR 97212, USA
| | - Alexandre M Anesio
- Department of Environmental Science, iClimate, Aarhus University, DK-4000 Roskilde, Denmark
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
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Pittino F, Zawierucha K, Poniecka E, Buda J, Rosatelli A, Zordan S, Azzoni RS, Diolaiuti G, Ambrosini R, Franzetti A. Functional and Taxonomic Diversity of Anaerobes in Supraglacial Microbial Communities. Microbiol Spectr 2023; 11:e0100422. [PMID: 36939373 PMCID: PMC10100660 DOI: 10.1128/spectrum.01004-22] [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: 03/20/2022] [Accepted: 02/16/2023] [Indexed: 03/21/2023] Open
Abstract
Cryoconite holes are small ponds present on the surface of most glaciers filled with meltwater and sediment at the bottom. Although they are characterized by extreme conditions, they host bacterial communities with high taxonomic and functional biodiversity. Despite that evidence for a potential niche for anaerobic microorganisms and anaerobic processes has recently emerged, the composition of the microbial communities of the cryoconite reported so far has not shown the relevant presence of anaerobic taxa. We hypothesize that this is due to the lower growth yield of anaerobes compared to aerobic microorganisms. In this work, we aim at evaluating whether the anaerobic bacterial community represents a relevant fraction of the biodiversity of the cryoconite and at describing its structure and functions. We collected sediment samples from cryoconite holes on the Forni Glacier (Italy) and sequenced both 16S rRNA amplicon genes and 16S rRNA amplicon transcripts at different times of the day along a clear summer day. Results showed that a relevant fraction of taxa has been detected only by 16S rRNA transcripts and was undetectable in 16S rRNA gene amplicons. Furthermore, in the transcript approach, anaerobic taxa were overrepresented compared with DNA sequencing. The metatranscriptomics approach was used also to investigate the expression of the main metabolic functions. Results showed the occurrence of syntrophic and commensalism relationships among fermentative bacteria, hydrogenothrophs, and consumers of fermentation end products, which have never been reported so far in cryoconite. IMPORTANCE Recent evidence disclosed the presence of a potential niche for anaerobic microorganisms and anaerobic processes in supraglacial sediments (cryoconite), but a detailed description of the structure and functions of the anaerobic population is still lacking. This work used rRNA and mRNA sequencing and demonstrated that anaerobes are very active in these environments and represent a relevant albeit neglected part of the ecosystem functions in these environments.
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Affiliation(s)
- Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Ewa Poniecka
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Buda
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Asia Rosatelli
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
| | - Simone Zordan
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
| | - Roberto S. Azzoni
- Department of Earth Science “Ardito Desio,” University of Milan, Milano, Italy
| | - Guglielmina Diolaiuti
- Department of Environmental Science and Policy (ESP), University of Milan, Milano, Italy
| | - Roberto Ambrosini
- Department of Environmental Science and Policy (ESP), University of Milan, Milano, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
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Pittino F, Ambrosini R, Seeger M, Azzoni RS, Diolaiuti G, Alviz Gazitua P, Franzetti A. Geographical variability of bacterial communities of cryoconite holes of Andean glaciers. Sci Rep 2023; 13:2633. [PMID: 36788266 PMCID: PMC9929092 DOI: 10.1038/s41598-022-24373-5] [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: 04/20/2022] [Accepted: 11/14/2022] [Indexed: 02/16/2023] Open
Abstract
Cryoconite holes, ponds full of melting water with sediment on the bottom, are hotspots of biodiversity on glacier surfaces and host dynamic micro-ecosystems. They have been extensively investigated in different areas of the world (e.g., the Arctic, Antarctic, Alps, and Himalaya), but so far no study has described the bacterial communities of the glaciers in the Andes, the world's longest mountain range. In this study, we describe the bacterial communities of three small (< 2 km2) high-elevation (< 4200 m a.s.l.) glaciers of the Central Andes (Iver, East Iver and Morado glaciers) and two large (> 85 km2) glaciers of the Patagonian Andes (Exploradores and Perito Moreno glaciers) whose ablation tongues reach low altitude (< 300 m a.s.l.). Results show that the bacterial communities were generally similar to those observed in the cryoconite holes of other continents, but with few cyanobacteria (0.5% of sequences). The most abundant orders were Betaproteobacteriales, Cytophagales, Chitinophagales, Acetobacterales, Frankiales, Armatimonadales, Sphingobacteriales, Rhizobiales, Bacteroidales, Sphingomonadales, and Micrococcales. The bacterial communities differed between glaciers and both water pH and O2 concentration appeared to influence the bacterial community composition. This work thus provides the first description of the bacterial communities in cryoconite holes of South American glaciers.
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Affiliation(s)
- F. Pittino
- grid.7563.70000 0001 2174 1754Department of Earth and Environmental Sciences (DISAT), Università degli Studi di Milano-Bicocca, Milan, Italy ,grid.419754.a0000 0001 2259 5533WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - R. Ambrosini
- grid.4708.b0000 0004 1757 2822Laboratory of Glacier Ecology, Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - M. Seeger
- grid.12148.3e0000 0001 1958 645XMolecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Valparaiso, Chile
| | - R. S. Azzoni
- grid.4708.b0000 0004 1757 2822Laboratory of Glacier Ecology, Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Earth Science “Ardito Desio”, Università degli Studi di Milano, Milan, Italy
| | - G. Diolaiuti
- grid.4708.b0000 0004 1757 2822Laboratory of Glacier Ecology, Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - P. Alviz Gazitua
- grid.442234.70000 0001 2295 9069Departamento de Ciencias Biológicas, Universidad de los Lagos, Osorno, Chile
| | - A. Franzetti
- grid.7563.70000 0001 2174 1754Department of Earth and Environmental Sciences (DISAT), Università degli Studi di Milano-Bicocca, Milan, Italy
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Nawaz S, Rafiq M, Pepper IL, Betancourt WQ, Shah AA, Hasan F. Prevalence and abundance of antibiotic-resistant genes in culturable bacteria inhabiting a non-polar passu glacier, karakorum mountains range, Pakistan. World J Microbiol Biotechnol 2023; 39:94. [PMID: 36754876 DOI: 10.1007/s11274-023-03532-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023]
Abstract
Natural pristine environments including cold habitats are thought to be the potent reservoirs of antibiotic-resistant genes and have been recurrently reported in polar glaciers' native bacteria, nevertheless, their abundance among the non-polar glaciers' inhabitant bacteria is mostly uncharted. Herein we evaluated antibiotic resistance profile, abundance of antibiotic-resistant genes plus class 1, 2, and 3 integron integrases in 65 culturable bacterial isolates retrieved from a non-polar glacier. The 16S rRNA gene sequencing analysis identified predominantly Gram-negative 43 (66.15%) and Gram-positive 22 (33.84%) isolates. Among the Gram-negative bacteria, Gammaproteobacteria were dominant (62.79%), followed by Betaproteobacteria (18.60%) and Alphaproteobacteria (9.30%), whereas Phyla Actinobacteria (50%) and Firmicutes (40.90%) were predominant among Gram-positive. The Kirby Bauer disc diffusion method evaluated significant antibiotic resistance among the isolates. PCR amplification revealed phylum Proteobacteria predominantly carrying 21 disparate antibiotic-resistant genes like; blaAmpC 6 (100%), blaVIM-1, blaSHV and blaDHA 5 (100%) each, blaOXA-1 1 (100%), blaCMY-4 4 (100%), followed by Actinobacteria 14, Firmicutes 13 and Bacteroidetes 11. Tested isolates were negative for blaKPC, qnrA, vanA, ermA, ermB, intl2, and intl3. Predominant Gram-negative isolates had higher MAR index values, compared to Gram-positive. Alignment of protein homology sequences of antibiotic-resistant genes with references revealed amino acid variations in blaNDM-1, blaOXA-1, blaSHV, mecA, aac(6)-Ib3, tetA, tetB, sul2, qnrB, gyrA, and intI1. Promising antibiotic-resistant bacteria, harbored with numerous antibiotic-resistant genes and class 1 integron integrase with some amino acid variations detected, accentuating the mandatory focus to evaluate the intricate transcriptome analysis of glaciated bacteria conferring antibiotic resistance.
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Affiliation(s)
- Sabir Nawaz
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Rafiq
- Department of Microbiology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan.
| | - Ian L Pepper
- Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W. Calle Agua Nueva, 85745, Tucson, AZ, USA
| | - Walter Q Betancourt
- Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W. Calle Agua Nueva, 85745, Tucson, AZ, USA
| | - Aamer Ali Shah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
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Ruiz-Blas F, Muñoz-Hisado V, Garcia-Lopez E, Moreno A, Bartolomé M, Leunda M, Martinez-Alonso E, Alcázar A, Cid C. The hidden microbial ecosystem in the perennial ice from a Pyrenean ice cave. Front Microbiol 2023; 14:1110091. [PMID: 36778858 PMCID: PMC9909108 DOI: 10.3389/fmicb.2023.1110091] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
Over the last years, perennial ice deposits located within caves have awakened interest as places to study microbial communities since they represent unique cryospheric archives of climate change. Since the beginning of the twentieth century, the temperature has gradually increased, and it is estimated that by the end of this century the increase in average temperature could be around 4.0°C. In this context of global warming the ice deposits of the Pyrenean caves are undergoing a significant regression. Among this type of caves, that on the Cotiella Massif in the Southern Pyrenees is one of the southernmost studied in Europe. These types of caves house microbial communities which have so far been barely explored, and therefore their study is necessary. In this work, the microbial communities of the Pyrenean ice cave A294 were identified using metabarcoding techniques. In addition, research work was carried out to analyze how the age and composition of the ice affect the composition of the bacterial and microeukaryotic populations. Finally, the in vivo effect of climate change on the cellular machinery that allow microorganisms to live with increasing temperatures has been studied using proteomic techniques.
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Affiliation(s)
- Fátima Ruiz-Blas
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | | | | | - Ana Moreno
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología - CSIC, Zaragoza, Spain
| | - Miguel Bartolomé
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología - CSIC, Zaragoza, Spain
- Institut für Geologie und Mineralogie, Universität zu Köln, Köln, Germany
| | - Maria Leunda
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
- Swiss Federal Research Institute for Forest, Snow and Landscape Research WSL, Zurich, Switzerland
- Department of Plant Biology and Ecology, University of the Basque Country, Leioa, Spain
| | - Emma Martinez-Alonso
- Department of Investigation, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | - Alberto Alcázar
- Department of Investigation, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
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Cultivable bacteria in the supraglacial lake formed after a glacial lake outburst flood in northern Pakistan. Int Microbiol 2022; 26:309-325. [PMID: 36484912 DOI: 10.1007/s10123-022-00306-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Recently, a supraglacial lake formed as a result of a glacial lake outburst flood (GLOF) in the Dook Pal Glacier. Lake debris and meltwater samples were collected from the supraglacial lake to determine bacterial diversity. Geochemical analyses of samples showed free amino acids (FAAs), anions, cations, and heavy metals. Comparable viable bacterial counts were observed in meltwater and debris samples. Using R2A media, a total of 52 bacterial isolates were identified: 40 from debris and 12 from meltwater. The relative abundance of Gram-positive (80.8%) bacteria was greater than Gram-negative (19.2%). Molecular identification of these isolates revealed that meltwater was dominated by Firmicutes (41.6%) and Proteobacteria (41.6%), while lake debris was dominated by Firmicutes (65.0%). The isolates belonged to 14 genera with the greatest relative abundance in Bacillus. Tolerance level of isolates to salts was high. Most of the Gram-positive bacteria were eurypsychrophiles, while most of the Gram-negative bacteria were stenopsychrophiles. Gram-negative bacteria displayed a higher minimum inhibitory concentration of selected heavy metals and antibiotics than Gram-positive. This first-ever study of culturable bacteria from a freshly formed supraglacial lake improves our understanding of the bacterial diversity and antibiotic resistance released from the glaciers as a result of GLOF.
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Matinja AI, Kamarudin NHA, Leow ATC, Oslan SN, Ali MSM. Cold-Active Lipases and Esterases: A Review on Recombinant Overexpression and Other Essential Issues. Int J Mol Sci 2022; 23:ijms232315394. [PMID: 36499718 PMCID: PMC9740821 DOI: 10.3390/ijms232315394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Cold environments characterised by diverse temperatures close to or below the water freezing point dominate about 80% of the Earth's biosphere. One of the survival strategies adopted by microorganisms living in cold environments is their expression of cold-active enzymes that enable them to perform an efficient metabolic flux at low temperatures necessary to thrive and reproduce under those constraints. Cold-active enzymes are ideal biocatalysts that can reduce the need for heating procedures and improve industrial processes' quality, sustainability, and cost-effectiveness. Despite their wide applications, their industrial usage is still limited, and the major contributing factor is the lack of complete understanding of their structure and cold adaptation mechanisms. The current review looked at the recombinant overexpression, purification, and recent mechanism of cold adaptation, various approaches for purification, and three-dimensional (3D) crystal structure elucidation of cold-active lipases and esterase.
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Affiliation(s)
- Adamu Idris Matinja
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Biochemistry, Faculty of Science, Bauchi State University, Gadau 751105, Nigeria
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence:
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Liu Y, Xu Y, Cui X, Zhang B, Wang X, Qin X, Wang J, Li Y, Zhang W, Liu G, Chen T, Zhang G. Temporary Survival Increasing the Diversity of Culturable Heterotrophic Bacteria in the Newly Exposed Moraine at a Glacier Snout. BIOLOGY 2022; 11:biology11111555. [PMID: 36358257 PMCID: PMC9687651 DOI: 10.3390/biology11111555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/11/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
Abstract
Laohugou Glacier No. 12 is located on the northern slope of the western Qilian Mountains with a temperate continental wet climate and an extremely cold winter. Bacteria in a newly exposed moraine have to cope with various pressures owing to deglaciation at the glacier snout. However, limited information is available regarding the high diversity and temporary survival of culturable heterotrophic bacteria under various environmental stresses. To examine the tolerance of extremophiles against varying environmental conditions in a newly exposed moraine, we simulated environmental stress in bacterial cultures. The results showed that the isolated strains belonged to actinobacteria, Proteobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes. Actinobacteria was the most abundant phylum, followed by Proteobacteria, at both high and low temperatures. Pseudarthrobacter was the most abundant genus, accounting for 14.2% of the total isolates. Although several microorganisms grew at 10 °C, the proportion of microorganisms that grew at 25 °C was substantially higher. In particular, 50% of all bacterial isolates grew only at a high temperature (HT), whereas 21.4% of the isolates grew at a low temperature (LT), and 38.6% of the isolates grew at both HT and LT. In addition, many radiation-resistant extremophiles were identified, which adapted to both cold and oxidative conditions. The nearest neighbors of approximately >90% of bacteria belonged to a nonglacial environment, such as oil-contaminated soil, rocks, and black sand, instead of glacial niches. This study provides insights into the ecological traits, stress responses, and temporary survival of culturable heterotrophic bacteria in a newly exposed moraine with variable environmental conditions and the relationship of these communities with the non-glacial environment. This study may help to understand the evolution, competition, and selective growth of bacteria in the transition regions between glaciers and retreats in the context of glacier melting and retreat owing to global warming.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xinyue Wang
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiang Qin
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yanzhao Li
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
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Tian C, Lv Y, Yang Z, Zhang R, Zhu Z, Ma H, Li J, Zhang Y. Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02116-3. [PMID: 36239777 DOI: 10.1007/s00248-022-02116-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.
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Affiliation(s)
- Chen Tian
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yongxin Lv
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhifeng Yang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Ruifeng Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Zhuoyi Zhu
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Hongmei Ma
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Jing Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yu Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China.
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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Dang Z, Luo Z, Wang S, Liao Y, Jiang Z, Zhu X, Ji G. Using hierarchical stable isotope to reveal microbial food web structure and trophic transfer efficiency differences during lake melt season. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156893. [PMID: 35753488 DOI: 10.1016/j.scitotenv.2022.156893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/31/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
The microbial food web (MFW) is a material and energy source in lake water ecosystems. Although it is crucial to determine its structure and function for water ecological health, MFW changes during lake melt period have not been well studied. In this study, the MFW was divided into three categories by analyzing its structure and trophic transfer efficiency using hierarchical C/N stable isotopes and eDNA sequencing techniques, including the detrital food web (DFC, 15 %), classical grazing food web (CFC, 60 %), and mixed trophic food web (MFC, 25 %). The trophic structure and type of MFW in ice-melting lakes are always in the process of succession and adaptation, which is in a relatively low trophic transfer efficiency stage under stable conditions (i.e. CFC), whereas the input of exogenous debris and organic pollutants may lead to an increase in MFW trophic transfer efficiency (i.e. MFC, DFC). The trophic transfer efficiency from the previous trophic level to protozoa and micrometazoa was 16.32 % and 20.77 % in DFC and 10.20 % and 29.43 % in MFC, respectively. Both are obviously higher than those of the CFC (11.69 % and 9.45 %, respectively). In terms of trophic structure, the community interaction and trophic cascade effect of DFC and MFC were enhanced but easily changed with environmental factors. In contrast, the core species and cascading effects of the CFC were clearer, and the MFW structure was relatively stable. Overall, this study reveals that the explosive increase in MFW trophic transfer efficiency induced by exogenous input during the lake melt period may subsequently lead to the destabilization of the microbial community structure and cause potential ecological risks. These are manifested in the absence of ecological trophic processes, the decrease in trophic structure complexity and stability, and the weakening of microecology self-adaptive regulation ability.
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Affiliation(s)
- Zhengzhu Dang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Zhongxin Luo
- China Institute of Water Resources and Hydropower Research, Beijing 100038, China; National Research Center for Sustainable Hydropower Development, Beijing 100038, China
| | - Shuo Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Yinhao Liao
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Zhuo Jiang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Xianfang Zhu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
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41
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Thiele S, Storesund JE, Fernández-Méndez M, Assmy P, Øvreås L. A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice. Microorganisms 2022; 10:1618. [PMID: 36014036 PMCID: PMC9414599 DOI: 10.3390/microorganisms10081618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
The Arctic is warming 2-3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.
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Affiliation(s)
- Stefan Thiele
- Department of Biological Science, University of Bergen, Thormøhlensgate 53 A/B, 5020 Bergen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | | | - Mar Fernández-Méndez
- Norwegian Polar Institute, Fram Centre, Hjalmar Johansens Gate 14, 9296 Tromsø, Norway
- Biological Oceanography, GEOMAR Helmholtz Centre of Ocean Research, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, Hjalmar Johansens Gate 14, 9296 Tromsø, Norway
| | - Lise Øvreås
- Department of Biological Science, University of Bergen, Thormøhlensgate 53 A/B, 5020 Bergen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
- Department of Arctic Biology, University Center in Svalbard, UNIS, 9171 Longyearbyen, Norway
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42
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Brandani J, Peter H, Busi SB, Kohler TJ, Fodelianakis S, Ezzat L, Michoud G, Bourquin M, Pramateftaki P, Roncoroni M, Lane SN, Battin TJ. Spatial patterns of benthic biofilm diversity among streams draining proglacial floodplains. Front Microbiol 2022; 13:948165. [PMID: 36003939 PMCID: PMC9393633 DOI: 10.3389/fmicb.2022.948165] [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: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Glacier shrinkage opens new proglacial terrain with pronounced environmental gradients along longitudinal and lateral chronosequences. Despite the environmental harshness of the streams that drain glacier forelands, their benthic biofilms can harbor astonishing biodiversity spanning all domains of life. Here, we studied the spatial dynamics of prokaryotic and eukaryotic photoautotroph diversity within braided glacier-fed streams and tributaries draining lateral terraces predominantly fed by groundwater and snowmelt across three proglacial floodplains in the Swiss Alps. Along the lateral chronosequence, we found that benthic biofilms in tributaries develop higher biomass than those in glacier-fed streams, and that their respective diversity and community composition differed markedly. We also found spatial turnover of bacterial communities in the glacier-fed streams along the longitudinal chronosequence. These patterns along the two chronosequences seem unexpected given the close spatial proximity and connectivity of the various streams, suggesting environmental filtering as an underlying mechanism. Furthermore, our results suggest that photoautotrophic communities shape bacterial communities across the various streams, which is understandable given that algae are the major source of organic matter in proglacial streams. Overall, our findings shed new light on benthic biofilms in proglacial streams now changing at rapid pace owing to climate-induced glacier shrinkage.
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Affiliation(s)
- Jade Brandani
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Hannes Peter
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tyler J. Kohler
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stilianos Fodelianakis
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Leila Ezzat
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Grégoire Michoud
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Massimo Bourquin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Paraskevi Pramateftaki
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Roncoroni
- Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Lausanne, Switzerland
| | - Stuart N. Lane
- Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Lausanne, Switzerland
| | - Tom J. Battin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- *Correspondence: Tom J. Battin,
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43
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Abundance and activity of sympagic viruses near the Western Antarctic Peninsula. Polar Biol 2022. [DOI: 10.1007/s00300-022-03073-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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44
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Glaciers as microbial habitats: current knowledge and implication. J Microbiol 2022; 60:767-779. [DOI: 10.1007/s12275-022-2275-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 10/16/2022]
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45
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Jensen LZ, Glasius M, Gryning SE, Massling A, Finster K, Šantl-Temkiv T. Seasonal Variation of the Atmospheric Bacterial Community in the Greenlandic High Arctic Is Influenced by Weather Events and Local and Distant Sources. Front Microbiol 2022; 13:909980. [PMID: 35879956 PMCID: PMC9307761 DOI: 10.3389/fmicb.2022.909980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
The Arctic is a hot spot for climate change with potentially large consequences on a global scale. Aerosols, including bioaerosols, are important players in regulating the heat balance through direct interaction with sunlight and indirectly, through inducing cloud formation. Airborne bacteria are the major bioaerosols with some species producing the most potent ice nucleating compounds known, which are implicated in the formation of ice in clouds. Little is known about the numbers and dynamics of airborne bacteria in the Arctic and even less about their seasonal variability. We collected aerosol samples and wet deposition samples in spring 2015 and summer 2016, at the Villum Research Station in Northeast Greenland. We used amplicon sequencing and qPCR targeting the 16S rRNA genes to assess the quantities and composition of the DNA and cDNA-level bacterial community. We found a clear seasonal variation in the atmospheric bacterial community, which is likely due to variable sources and meteorology. In early spring, the atmospheric bacterial community was dominated by taxa originating from temperate and Subarctic regions and arriving at the sampling site through long-range transport. We observed an efficient washout of the aerosolized bacterial cells during a snowstorm, which was followed by very low concentrations of bacteria in the atmosphere during the consecutive 4 weeks. We suggest that this is because in late spring, the long-range transport ceased, and the local sources which comprised only of ice and snow surfaces were weak resulting in low bacterial concentrations. This was supported by observed changes in the chemical composition of aerosols. In summer, the air bacterial community was confined to local sources such as soil, plant material and melting sea-ice. Aerosolized and deposited Cyanobacteria in spring had a high activity potential, implying their activity in the atmosphere or in surface snow. Overall, we show how the composition of bacterial aerosols in the high Arctic varies on a seasonal scale, identify their potential sources, demonstrate how their community sizes varies in time, investigate their diversity and determine their activity potential during and post Arctic haze.
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Affiliation(s)
- Lasse Z. Jensen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
- iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, Roskilde, Denmark
| | | | - Sven-Erik Gryning
- DTU Wind and Energy Systems, Technical University of Denmark, Roskilde, Denmark
| | - Andreas Massling
- iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, Roskilde, Denmark
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Kai Finster
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
| | - Tina Šantl-Temkiv
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
- iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, Roskilde, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- *Correspondence: Tina Šantl-Temkiv,
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46
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Najar IN, Das S, Kumar S, Sharma P, Mondal K, Sherpa MT, Thakur N. Coexistence of Heavy Metal Tolerance and Antibiotic Resistance in Thermophilic Bacteria Belonging to Genus Geobacillus. Front Microbiol 2022; 13:914037. [PMID: 36110304 PMCID: PMC9469766 DOI: 10.3389/fmicb.2022.914037] [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: 04/06/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Hot springs are thought to be potential repositories for opportunistic infections, such as antibiotic-resistant strains. However, there is a scarcity of information on the mechanisms of antibiotic resistance gene (ARG) uptake, occurrence, and expression in thermophilic bacteria. Furthermore, because the genesis and proliferation of ARGs in environmental microorganisms are unknown, the research on antibiotic resistance profiles and probable mechanisms in thermophilic bacteria will become increasingly important. The goals of this study are to explore bacterial diversity, antibiotic and heavy metal resistance, and the prevalence and presence of ARG and metal resistance gene (MRG) in Geobacillus species. The 16S rRNA sequencing was used to determine the culturable bacterium diversity of 124 isolates. Standard Kirby Bauer Disc Diffusion and tube dilution procedures were used to determine antibiotic sensitivity and minimum inhibitory concentration (MIC). The tube dilution method was also used to check metal tolerance. To detect ARG and heavy MRG (HMRG), whole genome sequencing studies of the type species of the genus Geobacillus and five randomly selected Geobacillus species were performed. Graph Pad Prism and XLSTAT were used to perform statistical analyses such as ANOVA, EC50 analysis, and principal component analysis (PCA). The phylum Firmicutes and the genus Geobacillus dominated the culture-dependent bacterial diversity. Surprisingly, all thermophilic isolates, i.e., Geobacillus species, were sensitive to at least 10 different antibiotics, as evidenced by the lack of ARGs in whole genome sequencing analysis of numerous Geobacillus species. However, some of these isolates were resistant to at least five different heavy metals, and whole genome sequencing revealed the presence of MRGs in these thermophilic bacteria. The thermophilic genus Geobacillus is generally antibiotic sensitive, according to this study. In contrast, heavy metal is tolerated by them. As a result, it is possible that ARGs and MRGs do not coexist in these bacteria living in hot springs.
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Affiliation(s)
| | - Sayak Das
- Department of Microbiology, Sikkim University, Gangtok, India
| | - Santosh Kumar
- Department of Microbiology, Sikkim University, Gangtok, India
| | - Prayatna Sharma
- Department of Microbiology, Sikkim University, Gangtok, India
| | | | | | - Nagendra Thakur
- Department of Microbiology, Sikkim University, Gangtok, India
- *Correspondence: Nagendra Thakur
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Liu Y, Ji M, Yu T, Zaugg J, Anesio AM, Zhang Z, Hu S, Hugenholtz P, Liu K, Liu P, Chen Y, Luo Y, Yao T. A genome and gene catalog of glacier microbiomes. Nat Biotechnol 2022; 40:1341-1348. [PMID: 35760913 DOI: 10.1038/s41587-022-01367-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/19/2022] [Indexed: 12/31/2022]
Abstract
Glaciers represent a unique inventory of microbial genetic diversity and a record of evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is particularly vulnerable to global warming. By sequencing 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice and cryoconite habitats, we present a specialized glacier microbial genome and gene catalog to archive glacial genomic and functional diversity. This comprehensive Tibetan Glacier Genome and Gene (TG2G) catalog includes 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes, the utility of which is demonstrated by the exploration of secondary metabolite biosynthetic potentials, virulence factor identification and global glacier metagenome comparison. The TG2G catalog is a valuable resource that enables enhanced understanding of the structure and functions of Tibetan glacial microbiomes.
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Affiliation(s)
- Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China. .,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Tao Yu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Julian Zaugg
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St. Lucia, QLD, Australia
| | - Alexandre M Anesio
- Department of Environmental Science, iClimate, Aarhus University, Roskilde, Denmark
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St. Lucia, QLD, Australia
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Pengfei Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Luo
- University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Tandong Yao
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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48
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Archiving the genomic and genetic resources of glaciers. Nat Biotechnol 2022; 40:1330-1331. [PMID: 35760916 DOI: 10.1038/s41587-022-01378-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Temperature- and Nutrients-Induced Phenotypic Changes of Antarctic Green Snow Bacteria Probed by High-Throughput FTIR Spectroscopy. BIOLOGY 2022; 11:biology11060890. [PMID: 35741411 PMCID: PMC9220083 DOI: 10.3390/biology11060890] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/21/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary Green snow microorganisms play an important role in biogeochemical cycle and carbon sink processes and they can be a source of biotechnologically interesting cell factories. A wide temperature tolerance is a unique property of bacteria isolated from cold environments, which has received great attention in the last years. The present paper examines the growth and chemical profile flexibility for green snow bacteria exposed to different temperature and nutrient fluctuations. By applying high-throughput chemical phenotyping with FTIR spectroscopy we discovered chemical changes possessed by green snow bacteria when grown at high/low temperature and rich/minimal media. Abstract Temperature fluctuations and nutrient composition are the main parameters influencing green snow microbiome. In this study we investigated the influence of temperature and nutrient conditions on the growth and cellular chemical profile of bacteria isolated from green snow. Chemical profiling of the green snow bacteria was done by high-throughput FTIR spectroscopy combined with multivariate data analysis. We showed that temperature and nutrients fluctuations strongly affect growth ability and chemical profile of the green snow bacteria. The size of colonies for green snow bacteria grown at higher (25 °C) and lower (4 °C and 10 °C) than optimal temperature (18 °C) was smaller. All isolates grew on rich medium, and only 19 isolates were able to grow on synthetic minimal media. Lipid and mixed spectral regions showed to be phylogeny related. FTIR fingerprinting indicates that lipids are often affected by the temperature fluctuations. Growth on different media resulted in the change of the whole chemical profile, where lipids showed to be more affected than proteins and polysaccharides. Correlation analysis showed that nutrient composition is clearly strongly influencing chemical changes in the cells, followed by temperature.
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Cooper ZS, Rapp JZ, Shoemaker AMD, Anderson RE, Zhong ZP, Deming JW. Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics. Front Microbiol 2022; 13:879116. [PMID: 35733954 PMCID: PMC9207381 DOI: 10.3389/fmicb.2022.879116] [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: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter, particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.
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Affiliation(s)
- Zachary S. Cooper
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
- *Correspondence: Zachary S. Cooper, , orcid.org/0000-0001-6515-7971
| | - Josephine Z. Rapp
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
- Institute of Integrative Biology and Systems (IBIS), Université Laval, Québec, QC, Canada
| | - Anna M. D. Shoemaker
- Department of Earth Sciences, Montana State University, Bozeman, MT, United States
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, MN, United States
| | - Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W. Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
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