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Uko MP, Umana SI, Iwatt IJ, Udoekong NS, Mgbechidinma CL, Adie FU, Akan OD. Microbial ice-binding structures: A review of their applications. Int J Biol Macromol 2024; 275:133670. [PMID: 38971293 DOI: 10.1016/j.ijbiomac.2024.133670] [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: 03/12/2024] [Revised: 06/02/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
Microorganisms' ice-binding structures (IBS) are macromolecules with potential commercial value in agriculture, food technology, material technology, cryobiology, and medicine. Microbial ice-structuring or microbial ice-binding particles, with their multi-applications, are simple to use, effective in low amounts, non-toxic, and environmentally friendly. Due to their source and composition diversities, microbial ice-binding structures are gaining attention because they are useable in various conditions. Some microorganisms also produce structures with dual ice-nucleating and anti-freezing properties. Structures that promote ice formation (ice nucleating particles- INPs) act as ice nuclei, lowering the energy barrier between supercooled liquid and ice, causing ice crystals to form. In contrast, anti-freeze particles (AFPs) prevent ice formation and recrystallization through several mechanisms, including disturbing the formation of string hydrogen bonds amongst water molecules, melting already formed ice crystals, and preventing crystal formation by binding to specific sites. Knowledge of the type and function of microbial ice-binding structures lends fundamental insight for possible scaling the production of cheap, functional, and advanced microbial structure-inspired mimics and by-products. This review focuses on microbial ice-binding structures and their potential uses in the food, medicinal, environmental, and agricultural sectors.
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Affiliation(s)
- Mfoniso Peter Uko
- Faculty of Biological Science, Akwa-Ibom State University, Akwa-Ibom State, Uyo 1167, Nigeria
| | - Senyene Idorenyin Umana
- Faculty of Biological Science, Akwa-Ibom State University, Akwa-Ibom State, Uyo 1167, Nigeria; Department of Microbiology, Faculty of Michael Okpara of Agriculture, Umudike, Nigeria
| | - Ifiok Joseph Iwatt
- Center for Wetlands and Wastes Management Studies, Faculty of Agriculture, University of Uyo, Uyo, Nigeria
| | | | - Chiamaka Linda Mgbechidinma
- School of Life Sciences, Centre for Cell and Development Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Microbiology, University of Ibadan, Ibadan 200243, Nigeria
| | - Francisca Upekiema Adie
- Department of Microbiology, Faculty of Biological Sciences, Cross River State University of Technology, Calabar, Nigeria
| | - Otobong Donald Akan
- Faculty of Biological Science, Akwa-Ibom State University, Akwa-Ibom State, Uyo 1167, Nigeria; College of Food Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, China.
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Wu P, Hu D, Guo J, Li J, Zhong Q, Cheng D. Unraveling the spatial-temporal distribution patterns of soil abundant and rare bacterial communities in China's subtropical mountain forest. Front Microbiol 2024; 15:1323887. [PMID: 38410396 PMCID: PMC10895375 DOI: 10.3389/fmicb.2024.1323887] [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: 10/18/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction The pivotal roles of both abundant and rare bacteria in ecosystem function are widely acknowledged. Despite this, the diversity elevational patterns of these two bacterial taxa in different seasons and influencing factors remains underexplored, especially in the case of rare bacteria. Methods Here, a metabarcoding approach was employed to investigate elevational patterns of these two bacterial communities in different seasons and tested the roles of soil physico-chemical properties in structuring these abundant and rare bacterial community. Results and discussion Our findings revealed that variation in elevation and season exerted notably effects on the rare bacterial diversity. Despite the reactions of abundant and rare communities to the elevational gradient exhibited similarities during both summer and winter, distinct elevational patterns were observed in their respective diversity. Specifically, abundant bacterial diversity exhibited a roughly U-shaped pattern along the elevation gradient, while rare bacterial diversity increased with the elevational gradient. Soil moisture and N:P were the dominant factor leading to the pronounced divergence in elevational distributions in summer. Soil temperature and pH were the key factors in winter. The network analysis revealed the bacteria are better able to adapt to environmental fluctuations during the summer season. Additionally, compared to abundant bacteria, the taxonomy of rare bacteria displayed a higher degree of complexity. Our discovery contributes to advancing our comprehension of intricate dynamic diversity patterns in abundant and rare bacteria in the context of environmental gradients and seasonal fluctuations.
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Affiliation(s)
- Panpan Wu
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Dandan Hu
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Jiaheng Guo
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Jinlong Li
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Quanlin Zhong
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Dongliang Cheng
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fuzhou, China
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Cao X, Liu H, Liu Y, Jing J, Wen L, Xu Z, Liu X, Liu D, Zhuo Y, Wang L. N 2O emission associated with shifts of bacterial communities in riparian wetland during the spring thawing periods. Ecol Evol 2023; 13:e9888. [PMID: 36911318 PMCID: PMC9994613 DOI: 10.1002/ece3.9888] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 03/14/2023] Open
Abstract
Soil freeze-thaw processes lead to high nitrous oxide (N2O) emissions and exacerbate the greenhouse effect. The wetlands of the Inner Mongolia Plateau are in the pronounced seasonal freeze-thaw zone, but the effect of spring thaw on N2O emissions and related microbial mechanisms is still unclear. We investigated the effects of different periods (freeze, freeze-thaw, and thaw) on soil bacterial community diversity and composition and greenhouse gas emissions during the spring freeze-thaw in the XiLin River riparian wetlands in China by amplicon sequencing and static dark box methods. The results showed that the freeze-thaw periods predominantly impact on the diversity and composition of the bacterial communities. The phyla composition of the soil bacteria communities of the three periods is similar in level, with Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria dominating the microbial communities. The alpha-diversity of bacterial communities in different periods varies that the freezing period is higher than that of the freeze-thaw period (p < .05). Soil total carbon, soil water content, and microbial biomass carbon were the primary factors regulating the abundance and compositions of the bacterial communities during spring thawing periods. Based on functional predictions, the relative abundance of nitrification and denitrification genes was higher in the freezing period than in the thawing period, while the abundance was lowest in the freeze-thawing period. The correlation results found that N2O emissions were significantly correlated with amoA and amoB in nitrification genes, indicating that nitrification may be the main process of N2O production during spring thaw. This study reveals potential microbial mechanisms of N2O emission during spring thaw and provides data support and theoretical basis for further insight into the mechanism of N2O emission during spring thaw.
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Affiliation(s)
- Xiaoai Cao
- College of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Huamin Liu
- College of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
- Yinshanbeilu Grassland Eco‐hydrology National Observation and Research StationChina Institute of Water Resources and Hydropower ResearchBeijingChina
| | - Yang Liu
- Bayannur Sub‐station, Inner Mongolia Environmental Monitoring StationBayannurChina
| | - Jin Jing
- Bayannur Sub‐station, Inner Mongolia Environmental Monitoring StationBayannurChina
| | - Lu Wen
- College of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
- Collaborative Innovation Center for Grassland Ecological Security (Jointly Supported by the Ministry of Education of China and Inner Mongolia Autonomous Region)HohhotChina
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian PlateauHohhotChina
| | - Zhichao Xu
- College of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Xuhua Liu
- College of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Dongwei Liu
- College of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
- Collaborative Innovation Center for Grassland Ecological Security (Jointly Supported by the Ministry of Education of China and Inner Mongolia Autonomous Region)HohhotChina
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian PlateauHohhotChina
| | - Yi Zhuo
- College of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
- Collaborative Innovation Center for Grassland Ecological Security (Jointly Supported by the Ministry of Education of China and Inner Mongolia Autonomous Region)HohhotChina
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian PlateauHohhotChina
| | - Lixin Wang
- College of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
- Collaborative Innovation Center for Grassland Ecological Security (Jointly Supported by the Ministry of Education of China and Inner Mongolia Autonomous Region)HohhotChina
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian PlateauHohhotChina
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Li X, Yan Y, Lu X, Fu L, Liu Y. Responses of soil bacterial communities to precipitation change in the semi-arid alpine grassland of Northern Tibet. FRONTIERS IN PLANT SCIENCE 2022; 13:1036369. [PMID: 36325540 PMCID: PMC9619073 DOI: 10.3389/fpls.2022.1036369] [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: 09/04/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
A change in precipitation can profoundly change the structure of soil microbial communities, especially in arid and semi-arid areas which are limited by moisture conditions. Therefore, it is crucial to explore how soil bacterial community composition and diversity will respond to variation in precipitation. Here we conducted a precipitation control experiment to simulate precipitation change by reducing and increasing rainfall by 25%, 50%, and 75% in the alpine grasslands of northern Tibet. The composition, diversity, and species interaction network of soil microbial community were studied by high-throughput sequencing, and the relationship between microbial community species and soil environmental factors was analyzed. Our results showed that Proteobacteria (45%-52%) and Actinobacteria (37%-45%) were the dominant bacteria in the soil. The alpha diversity index based on Shannon, Chao1, and Simpson indices revealed that precipitation change had no significant effect on richness and evenness of soil microbial communities. Non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) showed that a clear separation of soil microbial communities between D2(-50%),D3(-75%) and W2(+50%), W3(+75%) treatments. The microbial interaction network indicated that the water-increasing treatment group had closer connections, and Proteobacteria and Actinomycetes were the core species. Furthermore, there was a stronger positive correlation between species in the water-reducing treatment group, the contribution of Proteobacteria decreased significantly, the role of connecting hub decreased, and Actinomycetes became the most important core microbial species. In addition, soil water content (SWC) and available phosphorus (AP) were closely related to the variations in soil microbial compositions. The findings of this study provide a theoretical basis for the driving mechanism of global climate change on soil microbial community and grassland ecosystem in alpine grassland.
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Affiliation(s)
- Xueqin Li
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yan Yan
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Xuyang Lu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Lijiao Fu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yanling Liu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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Response of Carbon Emissions and the Bacterial Community to Freeze-Thaw Cycles in a Permafrost-Affected Forest-Wetland Ecotone in Northeast China. Microorganisms 2022; 10:microorganisms10101950. [PMID: 36296226 PMCID: PMC9609725 DOI: 10.3390/microorganisms10101950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
Climate warming can affect freeze–thaw cycle (FTCs) patterns in northern high-latitude regions and may affect permafrost carbon emissions. The response of carbon release and microbial communities to FTCs has not been well characterized. Here, we conducted laboratory incubation experiments to investigate the relationships among carbon emissions, bacterial community, and soil variables in a permafrost-affected forest–wetland ecotone in Northeast China. The emission rates of CO2 and CH4 increased during the FTCs. FTC amplitude, FTC frequency, and patch type had significant effects on carbon emissions. FTCs increased the contents of soil DOC, NH4+-N, and NO3−-N but reduced bacterial alpha diversity. CO2 emissions were mainly affected by bacterial alpha diversity and composition, and the inorganic nitrogen content was the important factor affecting CH4 emissions. Our findings indicated that FTCs could significantly regulate CO2 and CH4 emissions by reducing bacterial community diversity and increasing the concentration of available soil substrates. Our findings shed new light on the microorganism-substrate mechanisms regulating the response patterns of the soil carbon cycle to FTCs in permafrost regions.
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6
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Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals. CRYSTALS 2022. [DOI: 10.3390/cryst12030312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.
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7
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Airborne Microorganisms in Antarctica: Transport, Survival and Establishment. SPRINGER POLAR SCIENCES 2019. [DOI: 10.1007/978-3-030-02786-5_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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8
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Christel S, Fridlund J, Watkin EL, Dopson M. Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile. Extremophiles 2016; 20:903-913. [PMID: 27783177 PMCID: PMC5085989 DOI: 10.1007/s00792-016-0882-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 10/10/2016] [Indexed: 11/17/2022]
Abstract
Acidithiobacillus ferrivorans is an acidophilic bacterium that represents a substantial proportion of the microbial community in a low temperature mining waste stream. Due to its ability to grow at temperatures below 15 °C, it has previously been classified as 'psychrotolerant'. Low temperature-adapted microorganisms have strategies to grow at cold temperatures such as the production of cold acclimation proteins, DEAD/DEAH box helicases, and compatible solutes plus increasing their cellular membrane fluidity. However, little is known about At. ferrivorans adaptation strategies employed during culture at its temperature extremes. In this study, we report the transcriptomic response of At. ferrivorans SS3 to culture at 8 °C compared to 20 °C. Analysis revealed 373 differentially expressed genes of which, the majority were of unknown function. Only few changes in transcript counts of genes previously described to be cold adaptation genes were detected. Instead, cells cultured at cold (8 °C) altered the expression of a wide range of genes ascribed to functions in transcription, translation, and energy production. It is, therefore, suggested that a temperature of 8 °C imposed little cold stress on At. ferrivorans, underlining its adaptation to growth in the cold as well as suggesting it should be classified as a 'eurypsychrophile'.
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Affiliation(s)
- Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Jimmy Fridlund
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Elizabeth L Watkin
- School of Biomedical Sciences, Curtin University, Perth, 6845, Australia
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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9
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Zhao Y, Wu F, Yang W, He W, Tan B, Xu Z. Bacterial community changes during fir needle litter decomposition in an alpine forest in eastern Tibetan Plateau. RUSS J ECOL+ 2016. [DOI: 10.1134/s1067413616020156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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10
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Foster A, Jones DL, Cooper EJ, Roberts P. Freeze-thaw cycles have minimal effect on the mineralisation of low molecular weight, dissolved organic carbon in Arctic soils. Polar Biol 2016; 39:2387-2401. [PMID: 32669755 PMCID: PMC7346978 DOI: 10.1007/s00300-016-1914-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 01/23/2016] [Accepted: 02/26/2016] [Indexed: 12/04/2022]
Abstract
Warmer winters in Arctic regions may melt insulating snow cover and subject soils to more freeze–thaw cycles. The effect of freeze–thaw cycles on the microbial use of low molecular weight, dissolved organic carbon (LMW-DOC) is poorly understood. In this study, soils from the Arctic heath tundra, Arctic meadow tundra and a temperate grassland were frozen to −7.5 °C and thawed once and three times. Subsequently, the mineralisation of 3 LMW-DOC substrates types (sugars, amino acids and peptides) was measured over an 8-day period and compared to controls which had not been frozen. This allowed the comparison of freeze–thaw effects between Arctic and temperate soil and between different substrates. The results showed that freeze–thaw cycles had no significant effect on C mineralisation in the Arctic tundra soils. In contrast, for the same intensity freeze–thaw cycles, a significant effect on C mineralisation was observed for all substrate types in the temperate soil although the response was substrate specific. Peptide and amino acid mineralisation were similarly affected by FT, whilst glucose had a different response. Further work is required to fully understand microbial use of LMW-DOC after freeze–thaw, yet these results suggest that relatively short freeze–thaw cycles have little effect on microbial use of LMW-DOC in Arctic tundra soils after thaw.
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Affiliation(s)
- A Foster
- School of the Environment, Natural Resources and Geography, Bangor University, Bangor, UK
| | - D L Jones
- School of the Environment, Natural Resources and Geography, Bangor University, Bangor, UK
| | - E J Cooper
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - P Roberts
- School of the Environment, Natural Resources and Geography, Bangor University, Bangor, UK
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Zhao Y, Wu F, Yang W, Tan B, He W. Variations in bacterial communities during foliar litter decomposition in the winter and growing seasons in an alpine forest of the eastern Tibetan Plateau. Can J Microbiol 2015; 62:35-48. [PMID: 26606037 DOI: 10.1139/cjm-2015-0448] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bacterial communities are the primary engineers during litter decomposition and related material cycling, and they can be strongly controlled by seasonal changes in temperature and other environmental factors. However, limited information is available on changes in the bacterial community from winter to the growing season as litter decomposition proceeds in cold climates. Here, we investigated the abundance and structure of bacterial communities using real-time quantitative PCR and denaturing gradient gel electrophoresis (DGGE) during a 2-year field study of the decomposition of litter of 4 species in the winter and growing seasons of an alpine forest of the eastern Tibetan Plateau. The abundance of the bacterial 16S rRNA gene was relatively high during decomposition of cypress and birch litter in the first winter, but for the other litters 16S rRNA abundance during both winters was significantly lower than during the following growing season. A large number of bands were observed on the DGGE gels, and their intensities and number from the winter samples were lower than those from the growing season during the 2-year decomposition experiment. Eighty-nine sequences from the bands of bacteria that had been cut from the DGGE gels were affiliated with 10 distinct classes of bacteria and an unknown group. A redundancy analysis indicated that the moisture, mass loss, and elemental content (e.g., C, N, and P) of the litter significantly affected the bacterial communities. Collectively, the results suggest that uneven seasonal changes in climate regulate bacterial communities and other decomposers, thus affecting their contribution to litter decomposition processes in the alpine forest.
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Affiliation(s)
- Yeyi Zhao
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China.,Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China
| | - Fuzhong Wu
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China.,Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China
| | - Wanqin Yang
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China.,Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China
| | - Bo Tan
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China.,Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China
| | - Wei He
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China.,Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology and Forest, Sichuan Agricultural University, Chengdu 611130, People's Republic of China. Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, Chengdu 611130, People's Republic of China
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12
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Lorv JSH, Rose DR, Glick BR. Bacterial ice crystal controlling proteins. SCIENTIFICA 2014; 2014:976895. [PMID: 24579057 PMCID: PMC3918373 DOI: 10.1155/2014/976895] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 12/15/2013] [Indexed: 05/31/2023]
Abstract
Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions.
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Affiliation(s)
- Janet S. H. Lorv
- Department of Biology, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - David R. Rose
- Department of Biology, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada N2L 3G1
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The effect of freeze-thaw conditions on arctic soil bacterial communities. BIOLOGY 2013; 2:356-77. [PMID: 24832666 PMCID: PMC4009868 DOI: 10.3390/biology2010356] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/31/2013] [Accepted: 02/17/2013] [Indexed: 11/20/2022]
Abstract
Climate change is already altering the landscape at high latitudes. Permafrost is thawing, the growing season is starting earlier, and, as a result, certain regions in the Arctic may be subjected to an increased incidence of freeze-thaw events. The potential release of carbon and nutrients from soil microbial cells that have been lysed by freeze-thaw transitions could have significant impacts on the overall carbon balance of arctic ecosystems, and therefore on atmospheric CO2 concentrations. However, the impact of repeated freezing and thawing with the consequent growth and recrystallization of ice on microbial communities is still not well understood. Soil samples from three distinct sites, representing Canadian geographical low arctic, mid-arctic and high arctic soils were collected from Daring Lake, Alexandra Fjord and Cambridge Bay sampling sites, respectively. Laboratory-based experiments subjected the soils to multiple freeze-thaw cycles for 14 days based on field observations (0 °C to −10 °C for 12 h and −10 °C to 0 °C for 12 h) and the impact on the communities was assessed by phospholipid fatty acid (PLFA) methyl ester analysis and 16S ribosomal RNA gene sequencing. Both data sets indicated differences in composition and relative abundance between the three sites, as expected. However, there was also a strong variation within the two high latitude sites in the effects of the freeze-thaw treatment on individual PLFA and 16S-based phylotypes. These site-based heterogeneities suggest that the impact of climate change on soil microbial communities may not be predictable a priori; minor differential susceptibilities to freeze-thaw stress could lead to a “butterfly effect” as described by chaos theory, resulting in subsequent substantive differences in microbial assemblages. This perspectives article suggests that this is an unwelcome finding since it will make future predictions for the impact of on-going climate change on soil microbial communities in arctic regions all but impossible.
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Wilson SL, Frazer C, Cumming BF, Nuin PAS, Walker VK. Cross-tolerance between osmotic and freeze-thaw stress in microbial assemblages from temperate lakes. FEMS Microbiol Ecol 2012; 82:405-15. [PMID: 22551442 DOI: 10.1111/j.1574-6941.2012.01404.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 04/21/2012] [Accepted: 04/25/2012] [Indexed: 12/01/2022] Open
Abstract
Osmotic stress can accompany increases in solute concentrations because of freezing or high-salt environments. Consequently, microorganisms from environments with a high-osmotic potential may exhibit cross-tolerance to freeze stress. To test this hypothesis, enrichments derived from the sediment and water of temperate lakes with a range of salt concentrations were subjected to multiple freeze-thaw cycles. Surviving isolates were identified and metagenomes were sampled prior to and following selection. Enrichments from alkali lakes were typically the most freeze-thaw resistant with only 100-fold losses in cell viability, and those from freshwater lakes were most susceptible, with cell numbers reduced at least 100,000-fold. Metagenomic analysis suggested that selection reduced assemblage diversity more in freshwater samples than in those from saline lakes. Survivors included known psychro-, halo- and alkali-tolerant bacteria. Characterization of freeze-thaw-resistant isolates from brine and alkali lakes showed that few isolates had ice-associating activities such as antifreeze or ice nucleation properties. However, all brine- and alkali-derived isolates had high intracellular levels of osmolytes and/or appeared more likely to form biofilms. Conversely, these phenotypes were infrequent amongst the freshwater-derived isolates. These observations are consistent with microbial cross-tolerance between osmotic and freeze-thaw stresses.
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Affiliation(s)
- Sandra L Wilson
- Department of Biology, Queen's University, Kingston, ON, Canada
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Wilson SL, Grogan P, Walker VK. Prospecting for ice association: characterization of freeze-thaw selected enrichment cultures from latitudinally distant soils. Can J Microbiol 2012; 58:402-12. [PMID: 22435705 DOI: 10.1139/w2012-010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Freeze-thaw stress has previously been shown to alter soil community structure and function. We sought to further investigate this stress on enriched microbial consortia with the aim of identifying microbes with ice-associating adaptations that facilitate survival. Enrichments were established to obtain culturable psychrotolerant microbes from soil samples from the latitudinal extremes of the Canadian Shield plateau. The resulting consortia were subjected to consecutive freeze-thaw cycles, and survivors were putatively identified by their 16S rRNA gene sequences. Even though the northerly site was exposed to longer, colder winters and large spring-time temperature fluctuations, the selective regime similarly affected both enriched consortia. Quantitative PCR and metagenomic sequencing were used to determine the frequency of a subset of the resistant microbes in the original enrichments. The metagenomes showed 22 initial genera, only 6 survived and these were not dominant prior to selection. When survivors were assayed for ice recrystallization inhibition and ice nucleation activities, over 60% had at least one of these properties. These phenotypes were not more prevalent in the northern enrichment, indicating that regarding these adaptations, the enrichment strategy yielded seemingly functionally similar consortia from each site.
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Affiliation(s)
- Sandra L Wilson
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
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