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Liu L, Wang H, Guo Y, Yan Q, Chen J. Human-induced homogenization of microbial taxa and function in a subtropical river and its impacts on community stability. WATER RESEARCH 2024; 252:121198. [PMID: 38295455 DOI: 10.1016/j.watres.2024.121198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
Combination of taxa and function can provide a more comprehensive picture on human-induced microbial homogenization. Here, we obtained 2.58 billion high-throughput sequencing reads and 479 high-quality metagenome-assembled genomes (MAGs) of planktonic microbial communities in a subtropical river for 5 years. We found the microbial taxa homogenization and functional homogenization were uncoupled. Although human activities in downstream sites significantly decreased the taxonomic diversity of non-abundant ASV communities (16S rRNA gene amplicon sequence variants), they did not significantly decrease the taxonomic diversity of abundant ASV and total observed MAG communities. However, the total observed MAG communities in downstream sites tended to homogenize into some specific taxa which encode human-activity-related functional genes, such as nutrient cycles, greenhouse gas emission, antibiotic and arsenic resistance. Those specific MAGs with high taxonomic diversity caused the weak heterogenization of total observed MAG communities in downstream sites. Moreover, functional homogenization promoted the synchrony among downstream MAGs, and these MAGs constructed some specific network modules might to synergistically execute or resist the human-activity-related functions. High synchrony also led to the tandem effects among MAGs and thus decreased community stability. Overall, our findings revealed the links of microbial taxa, functions and stability under human activity impacts, and provided a strong evidence to encourage us re-thinking biotic homogenization based on microbial taxa and their functional attributes.
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Affiliation(s)
- Lemian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China.
| | - Hongwei Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China
| | - Yisong Guo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China
| | - Qi Yan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China
| | - Jianfeng Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China.
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2
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Lappan R, Thakar J, Molares Moncayo L, Besser A, Bradley JA, Goordial J, Trembath-Reichert E, Greening C. The atmosphere: a transport medium or an active microbial ecosystem? THE ISME JOURNAL 2024; 18:wrae092. [PMID: 38804464 PMCID: PMC11214262 DOI: 10.1093/ismejo/wrae092] [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: 03/14/2024] [Revised: 05/05/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.
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Affiliation(s)
- Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- School of Earth, Atmosphere & Environment, Monash University, Clayton, Victoria 3800, Australia
- Securing Antarctica’s Environmental Future, Monash University, Clayton, Victoria 3800, Australia
| | - Jordan Thakar
- School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Laura Molares Moncayo
- School of Geography, Queen Mary University of London, London E1 4NS, United Kingdom
- Natural History Museum, London SW7 5BD, United Kingdom
- Aix Marseille University, University of Toulon, CNRS, IRD, MIO, Marseille 13009, France
| | - Alexi Besser
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, United States
| | - James A Bradley
- Aix Marseille University, University of Toulon, CNRS, IRD, MIO, Marseille 13009, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Jacqueline Goordial
- School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | | | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Securing Antarctica’s Environmental Future, Monash University, Clayton, Victoria 3800, Australia
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3
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Liu L, Wang H, Luo Z, Chen J. Biogeographic patterns of micro-eukaryotic generalists and specialists and their effects on regional α-diversity at inter-oceanic scale. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106261. [PMID: 37981448 DOI: 10.1016/j.marenvres.2023.106261] [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: 11/24/2022] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023]
Abstract
Inter-oceanic scale studies allow us to understand the global spread of micro-organisms in marine ecosystems. In this study, micro-eukaryotic communities in marine surface sediment were collected from tropical to Arctic sites. We found that micro-eukaryotic generalists had much higher intraspecific variation than specialists which allow them to distribute more widely through higher spatiotemporal asynchrony and complementary niche preferences among conspecific taxa. Moreover, comparing to the host-associated protozoa and small metazoa, the algae and free-living protozoa with higher intraspecific variation allow them to have wider distribution ranges. Species abundance also played an important role in driving the distribution ranges of generalists and specialists. The generalists had important effects on regional α-diversity even at an inter-oceanic scale which led to the micro-eukaryotic species richness in polar sites to be mainly influenced by the regional generalists but not the local specialists. In particular, more than 97% of algal species in polar sites were shared with the tropical and subtropical sites (including toxic dinoflagellate). Overall, our study suggests that the effects of global change and human activities on the vulnerable high latitude habitats may lead to biotic homogenization for the whole microbial community (not only the dispersal of some harmful algae) through the potential long-distance spread of generalists.
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Affiliation(s)
- Lemian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China.
| | - Hongwei Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China
| | - Zhaohe Luo
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen 361005, China.
| | - Jianfeng Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China
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4
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Gao J, Geng H, Chai R, Wu T, Huang W, You Y, Zhan J. Fungal Community Composition and Its Relationship with Volatile Compounds during Spontaneous Fermentation of Cabernet Sauvignon from Two Chinese Wine-Growing Regions. Foods 2023; 13:106. [PMID: 38201134 PMCID: PMC10778937 DOI: 10.3390/foods13010106] [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: 11/29/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
The microbial community structure associated with wine in a wine-growing region is shaped by diverse ecological factors within that region, profoundly impacting the wine flavor. In wine fermentation, fungi contribute more sensory-active biochemical compounds than bacteria. In this study, we employed amplicon sequencing to measure samples from the spontaneous fermentation process of cabernet sauvignon wines from two wine-growing regions in China to study the diversity and structural evolution of fungi during spontaneous fermentation and analyze the correlation between fungi and volatile compounds. The results showed significant differences in fungal community structure and diversity in cabernet sauvignon musts from different geographical origins, and these differences affected the flavor quality of the wines. As alcoholic fermentation progressed, Saccharomyces became the dominant fungal genus and reshaped the fungal community structure, and the diversity of the fungal community decreased. However, the fungal communities of each wine-growing region remained distinct throughout the fermentation process. Furthermore, the correlation between the fungal community and volatile compounds indicated that wine is a product of fermentation involving multiple fungal genera, and the flavor is influenced by a variety of fungi. Our study enhances the comprehension of fungal communities in Chinese wine-growing regions, explaining the regulatory role of wine-related fungal microorganisms in wine flavor.
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Affiliation(s)
| | | | | | | | | | | | - Jicheng Zhan
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Tsinghua East Road 17, Haidian District, Beijing 100083, China; (J.G.); (H.G.); (R.C.); (T.W.); (W.H.); (Y.Y.)
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5
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Zhao RZ, Zhang WJ, Zhang W, Zhao ZF, Qiu XC. A Preliminary Study of Bacterioplankton Community Structure in the Taiyangshan Wetland in Ningxia and Its Driving Factors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12224. [PMID: 36231526 PMCID: PMC9565018 DOI: 10.3390/ijerph191912224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The Taiyangshan Wetland, a valuable wetland resource in the arid zone of central Ningxia, is critical for flood storage and drought resistance, climate regulation, and biodiversity protection. Nevertheless, the community structure and diversity of bacterioplankton in the Taiyangshan Wetland remains unclear. High-throughput sequencing was used to analyze the differences in bacterioplankton structure and major determinants in the Taiyangshan Wetland from April to October 2020. The composition and diversity of the bacterioplankton community varied significantly in different sampling periods but showed negligible differences across lake regions. Meanwhile, the relative abundances of bacterioplankton Bacteroidetes, Actinobacteria, Firmicutes, Chloroflexi, Tenericutes, Epsilonbacteraeota, and Patescibacteria were significantly different in different sampling periods, while the relative abundances of Cyanobacteria in different lake regions were quite different. Network analysis revealed that the topological attributes of co-occurrence pattern networks of bacterioplankton were high, and bacterioplankton community compositions were complicated in the month of July. A mantel test revealed that the bacterioplankton community in the entire wetland was affected by water temperature, electrical conductivity, dissolved oxygen, salinity, total nitrogen, ammonia nitrogen, chemical oxygen demand, fluoride, and sulfate. The bacterioplankton community structure was affected by ten environmental parameters (e.g., water temperature, dissolved oxygen, salinity, and permanganate index) in April, while the bacterioplankton community was only related to 1~2 environmental parameters in July and October. The bacterioplankton community structure in Lake Region IV was related to seven environmental parameters, including dissolved oxygen, pH, total nitrogen, and chemical oxygen demand, whereas the bacterioplankton community structures in the other three lake regions were related to two environmental parameters. This study facilitates the understanding of the bacterioplankton community in wetlands in arid areas and provides references to the evaluation of aquatic ecological management of the Taiyangshan Wetland.
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Affiliation(s)
- Rui-Zhi Zhao
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Wei-Jiang Zhang
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Wen Zhang
- Ningxia Supervision Institute for Veterinary Drugs and Animal Feedstuffs, Yinchuan 750004, China
| | - Zeng-Feng Zhao
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Xiao-Cong Qiu
- School of Life Science, Ningxia University, Yinchuan 750021, China
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6
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Alsante AN, Thornton DCO, Brooks SD. Ocean Aerobiology. Front Microbiol 2021; 12:764178. [PMID: 34777320 PMCID: PMC8586456 DOI: 10.3389/fmicb.2021.764178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022] Open
Abstract
Ocean aerobiology is defined here as the study of biological particles of marine origin, including living organisms, present in the atmosphere and their role in ecological, biogeochemical, and climate processes. Hundreds of trillions of microorganisms are exchanged between ocean and atmosphere daily. Within a few days, tropospheric transport potentially disperses microorganisms over continents and between oceans. There is a need to better identify and quantify marine aerobiota, characterize the time spans and distances of marine microorganisms’ atmospheric transport, and determine whether microorganisms acclimate to atmospheric conditions and remain viable, or even grow. Exploring the atmosphere as a microbial habitat is fundamental for understanding the consequences of dispersal and will expand our knowledge of biodiversity, biogeography, and ecosystem connectivity across different marine environments. Marine organic matter is chemically transformed in the atmosphere, including remineralization back to CO2. The magnitude of these transformations is insignificant in the context of the annual marine carbon cycle, but may be a significant sink for marine recalcitrant organic matter over long (∼104 years) timescales. In addition, organic matter in sea spray aerosol plays a significant role in the Earth’s radiative budget by scattering solar radiation, and indirectly by affecting cloud properties. Marine organic matter is generally a poor source of cloud condensation nuclei (CCN), but a significant source of ice nucleating particles (INPs), affecting the formation of mixed-phase and ice clouds. This review will show that marine biogenic aerosol plays an impactful, but poorly constrained, role in marine ecosystems, biogeochemical processes, and the Earth’s climate system. Further work is needed to characterize the connectivity and feedbacks between the atmosphere and ocean ecosystems in order to integrate this complexity into Earth System models, facilitating future climate and biogeochemical predictions.
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Affiliation(s)
- Alyssa N Alsante
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Daniel C O Thornton
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Sarah D Brooks
- Department of Atmospheric Sciences, Texas A&M University, College Station, TX, United States
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7
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Rubin S, Parr T, Da Costa L, Friston K. Future climates: Markov blankets and active inference in the biosphere. J R Soc Interface 2020; 17:20200503. [PMID: 33234063 PMCID: PMC7729048 DOI: 10.1098/rsif.2020.0503] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 02/01/2023] Open
Abstract
We formalize the Gaia hypothesis about the Earth climate system using advances in theoretical biology based on the minimization of variational free energy. This amounts to the claim that non-equilibrium steady-state dynamics-that underwrite our climate-depend on the Earth system possessing a Markov blanket. Our formalization rests on how the metabolic rates of the biosphere (understood as Markov blanket's internal states) change with respect to solar radiation at the Earth's surface (i.e. external states), through the changes in greenhouse and albedo effects (i.e. active states) and ocean-driven global temperature changes (i.e. sensory states). Describing the interaction between the metabolic rates and solar radiation as climatic states-in a Markov blanket-amounts to describing the dynamics of the internal states as actively inferring external states. This underwrites climatic non-equilibrium steady-state through free energy minimization and thus a form of planetary autopoiesis.
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Affiliation(s)
- Sergio Rubin
- Georges Lemaître Centre for Earth and Climate Research, Earth and Life Institute, Université catholique de Louvain, Louvain, Belgium
| | - Thomas Parr
- The Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, UK
| | - Lancelot Da Costa
- The Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, UK
- Department of Mathematics, Imperial College London, London, UK
| | - Karl Friston
- The Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, UK
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8
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Liu D, Zhang P, Chen D, Howell K. From the Vineyard to the Winery: How Microbial Ecology Drives Regional Distinctiveness of Wine. Front Microbiol 2019; 10:2679. [PMID: 31824462 PMCID: PMC6880775 DOI: 10.3389/fmicb.2019.02679] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/05/2019] [Indexed: 11/13/2022] Open
Abstract
Wine production is a complex process from the vineyard to the winery. On this journey, microbes play a decisive role. From the environment where the vines grow, encompassing soil, topography, weather and climate through to management practices in vineyards, the microbes present can potentially change the composition of wine. Introduction of grapes into the winery and the start of winemaking processes modify microbial communities further. Recent advances in next-generation sequencing (NGS) technology have progressed our understanding of microbial communities associated with grapes and fermentations. We now have a finer appreciation of microbial diversity across wine producing regions to begin to understand how diversity can contribute to wine quality and style characteristics. In this review, we highlight literature surrounding wine-related microorganisms and how these affect factors interact with and shape microbial communities and contribute to wine quality. By discussing the geography, climate and soil of environments and viticulture and winemaking practices, we claim microbial biogeography as a new perspective to impact wine quality and regionality. Depending on geospatial scales, habitats, and taxa, the microbial community respond to local conditions. We discuss the effect of a changing climate on local conditions and how this may alter microbial diversity and thus wine style. With increasing understanding of microbial diversity and their effects on wine fermentation, wine production can be optimised with enhancing the expression of regional characteristics by understanding and managing the microbes present.
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Affiliation(s)
| | | | | | - Kate Howell
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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9
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Rivas JA, Schröder T, Gill TE, Wallace RL, Walsh EJ. Anemochory of diapausing stages of microinvertebrates in North American drylands. FRESHWATER BIOLOGY 2019; 64:1303-1314. [PMID: 31787787 PMCID: PMC6884325 DOI: 10.1111/fwb.13306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 03/14/2019] [Indexed: 06/10/2023]
Abstract
1. Dry, ephemeral, desert wetlands are major sources of windblown sediment, as well as repositories for diapausing stages (propagules) of aquatic invertebrates. Zooplankton propagules are of the same size range as sand and dust grains. They can be deflated and transported in windstorm events. This study provides the evidence that dust storms aid in dispersal of microinvertebrate propagules via anemochory (aeolian transport). 2. We monitored 91 windstorms at six sites in the southwestern U.S. over a 17-year period. The primary study site was located in El Paso, Texas in the northern Chihuahuan Desert. Additional samples were collected from the Southern High Plains region. Dust carried by these events was collected and rehydrated to hatch viable propagules transported with it. 3. Using samples collected over a six-year period, 21 m above the ground which included 59 storm events, we tested the hypothesis that transport of propagules is correlated with storm intensity by monitoring meteorological conditions such as storm duration, wind direction, wind speed, and PM10 (fine dust concentration). An air quality monitoring site located adjacent to the dust samplers provided quantitative hourly measurements. 4. Rehydration results from all events showed that ciliates were found in 92% of the samples, rotifers in 81%, branchiopods in 29%, ostracods in 4%, nematodes in 13%, gastrotrichs in 16%, and tardigrades in 3%. Overall, four bdelloid and 11 monogonont rotifer species were identified from rehydrated windblown dust samples. 5. PCA results indicated gastrotrichs, branchiopods, nematodes, tardigrades, and monogonont rotifer occurrence positively correlated with PM10 and dust event duration. Bdelloid rotifers were correlated with amount of sediment deposited. NMDS showed a significant relationship between PM10 and occurrence of some taxa. Zero-inflated, general linear models with mixed-effects indicated significant relationships with bdelloid and nematode transport and PM10. 6. Thus, windstorms with high particulate matter concentration and long duration are more likely to transport microinvertebrate diapausing stages in drylands.
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Affiliation(s)
- J A Rivas
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, TX, USA 79968,
| | - T Schröder
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, TX, USA 79968,
| | - T E Gill
- Department of Geological Sciences and Environmental Science and Engineering Program, University of Texas at El Paso, 500 West University Avenue, El Paso, TX, USA 79968,
| | - R L Wallace
- Department of Biology, Ripon College, 300 W. Seward St. Ripon, WI, USA 54971,
| | - E J Walsh
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, TX, USA 79968
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10
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The Relationship between Air-Mass Trajectories and the Abundance of Dust-Borne Prokaryotes at the SE Mediterranean Sea. ATMOSPHERE 2019. [DOI: 10.3390/atmos10050280] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Airborne prokaryotes are transported along with dust/aerosols, yet very little attention is given to their temporal variability above the oceans and the factors that govern their abundance. We analyzed the abundance of autotrophic (cyanobacteria) and heterotopic airborne microbes in 34 sampling events between 2015–2018 at a coastal site in the SE Mediterranean Sea. We show that airborne autotrophic (0.2–7.6 cells × 103 m−3) and heterotrophic (0.2–30.6 cells × 103 m−3) abundances were affected by the origin and air mass trajectory, and the concentration of dust/aerosols in the air, while seasonality was not coherent. The averaged ratio between heterotrophic and autotrophic prokaryotes in marine-dominated trajectories was ~1.7 ± 0.6, significantly lower than for terrestrial routes (6.8 ± 6.1). Airborne prokaryotic abundances were linearly and positively correlated to the concentrations of total aerosol, while negatively correlated with the aerosol’s anthropogenic fraction (using Pb/Al or Cu/Al ratios as proxies). While aerosols may play a major role in dispersing terrestrial and marine airborne microbes in the SE Mediterranean Sea, the mechanisms involved in the dispersal and diversity of airborne microorganisms remain to be studied and should include standardization in collection and analysis protocols.
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11
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Pietsch RB, Grothe H, Hanlon R, Powers CW, Jung S, Ross SD, Schmale Iii DG. Wind-driven spume droplet production and the transport of Pseudomonas syringae from aquatic environments. PeerJ 2018; 6:e5663. [PMID: 30280035 PMCID: PMC6163035 DOI: 10.7717/peerj.5663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/28/2018] [Indexed: 12/04/2022] Open
Abstract
Natural aquatic environments such as oceans, lakes, and rivers are home to a tremendous diversity of microorganisms. Some may cross the air-water interface within droplets and become airborne, with the potential to impact the Earth’s radiation budget, precipitation processes, and spread of disease. Larger droplets are likely to return to the water or adjacent land, but smaller droplets may be suspended in the atmosphere for transport over long distances. Here, we report on a series of controlled laboratory experiments to quantify wind-driven droplet production from a freshwater source for low wind speeds. The rate of droplet production increased quadratically with wind speed above a critical value (10-m equivalent 5.7 m/s) where droplet production initiated. Droplet diameter and ejection speeds were fit by a gamma distribution. The droplet mass flux and momentum flux increased with wind speed. Two mechanisms of droplet production, bubble bursting and fragmentation, yielded different distributions for diameter, speed, and angle. At a wind speed of about 3.5 m/s, aqueous suspensions of the ice-nucleating bacterium Pseudomonas syringae were collected at rates of 283 cells m−2 s−1 at 5 cm above the water surface, and at 14 cells m−2 s−1 at 10 cm above the water surface. At a wind speed of about 4.0 m/s, aqueous suspensions of P. syringae were collected at rates of 509 cells m−2 s−1 at 5 cm above the water surface, and at 81 cells m−2 s−1 at 10 cm above the water surface. The potential for microbial flux into the atmosphere from aquatic environments was calculated using known concentrations of bacteria in natural freshwater systems. Up to 3.1 × 104 cells m−2 s−1 of water surface were estimated to leave the water in potentially suspended droplets (diameters <100 µm). Understanding the sources and mechanisms for bacteria to aerosolize from freshwater aquatic sources may aid in designing management strategies for pathogenic bacteria, and could shed light on how bacteria are involved in mesoscale atmospheric processes.
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Affiliation(s)
- Renee B Pietsch
- Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Hinrich Grothe
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Institute of Materials Chemistry (E165), TU Wien, Vienna, Austria
| | - Regina Hanlon
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Craig W Powers
- Civil and Environmental Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Sunghwan Jung
- Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Shane D Ross
- Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - David G Schmale Iii
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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12
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Giraldo Herrera CE. Shamanic Microscopy: Cellular Souls, Microbial Spirits. ANTHROPOLOGY OF CONSCIOUSNESS 2018. [DOI: 10.1111/anoc.12087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Smith GJ, Daniels V. Algal blooms of the 18th and 19th centuries. Toxicon 2018; 142:42-44. [DOI: 10.1016/j.toxicon.2017.12.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 12/17/2017] [Accepted: 12/21/2017] [Indexed: 11/28/2022]
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14
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The sensitivity and stability of bacterioplankton community structure to wind-wave turbulence in a large, shallow, eutrophic lake. Sci Rep 2017; 7:16850. [PMID: 29203907 PMCID: PMC5715125 DOI: 10.1038/s41598-017-17242-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/05/2017] [Indexed: 12/03/2022] Open
Abstract
Lakes are strongly influenced by wind-driven wave turbulence. The direct physical effects of turbulence on bacterioplankton community structure however, have not yet been addressed and remains poorly understood. To examine the stability of bacterioplankton communities under turbulent conditions, we simulated conditions in the field to evaluate the responses of the bacterioplankton community to physical forcing in Lake Taihu, using high-throughput sequencing and flow cytometry. A total of 4,520,231 high quality sequence reads and 74,842 OTUs were obtained in all samples with α-proteobacteria, γ-proteobacteria and Actinobacteria being the most dominant taxa. The diversity and structure of bacterioplankton communities varied during the experiment, but were highly similar based on the same time of sampling, suggesting that bacterioplankton communities are insensitive to wind wave turbulence in the lake. This stability could be associated with the traits associated with bacteria. In particular, turbulence favored the growth of bacterioplankton, which enhanced biogeochemical cycling of nutrients in the lake. This study provides a better understanding of bacterioplankton communities in lake ecosystems exposed to natural mixing/disturbances.
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15
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Hiraoka S, Miyahara M, Fujii K, Machiyama A, Iwasaki W. Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan. Front Microbiol 2017; 8:1506. [PMID: 28848519 PMCID: PMC5554504 DOI: 10.3389/fmicb.2017.01506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/27/2017] [Indexed: 01/01/2023] Open
Abstract
The presence of microbes in the atmosphere and their transport over long distances across the Earth's surface was recently shown. Precipitation is likely a major path by which aerial microbes fall to the ground surface, affecting its microbial ecosystems and introducing pathogenic microbes. Understanding microbial communities in precipitation is of multidisciplinary interest from the perspectives of microbial ecology and public health; however, community-wide and seasonal analyses have not been conducted. Here, we carried out 16S rRNA amplicon sequencing of 30 precipitation samples that were aseptically collected over 1 year in the Greater Tokyo Area, Japan. The precipitation microbial communities were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria and were overall consistent with those previously reported in atmospheric aerosols and cloud water. Seasonal variations in composition were observed; specifically, Proteobacteria abundance significantly decreased from summer to winter. Notably, estimated ordinary habitats of precipitation microbes were dominated by animal-associated, soil-related, and marine-related environments, and reasonably consistent with estimated air mass backward trajectories. To our knowledge, this is the first amplicon-sequencing study investigating precipitation microbial communities involving sampling over the duration of a year.
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Affiliation(s)
- Satoshi Hiraoka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoChiba, Japan
| | - Masaya Miyahara
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoChiba, Japan
| | - Kazushi Fujii
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoChiba, Japan
| | - Asako Machiyama
- Atmosphere and Ocean Research Institute, The University of TokyoChiba, Japan.,Department of Biological Sciences, Graduate School of Science, The University of TokyoTokyo, Japan
| | - Wataru Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoChiba, Japan.,Atmosphere and Ocean Research Institute, The University of TokyoChiba, Japan.,Department of Biological Sciences, Graduate School of Science, The University of TokyoTokyo, Japan
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Kawaguchi Y, Yokobori SI, Hashimoto H, Yano H, Tabata M, Kawai H, Yamagishi A. Investigation of the Interplanetary Transfer of Microbes in the Tanpopo Mission at the Exposed Facility of the International Space Station. ASTROBIOLOGY 2016; 16:363-76. [PMID: 27176813 DOI: 10.1089/ast.2015.1415] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
UNLABELLED The Tanpopo mission will address fundamental questions on the origin of terrestrial life. The main goal is to test the panspermia hypothesis. Panspermia is a long-standing hypothesis suggesting the interplanetary transport of microbes. Another goal is to test the possible origin of organic compounds carried from space by micrometeorites before the terrestrial origin of life. To investigate the panspermia hypothesis and the possible space origin of organic compounds, we performed space experiments at the Exposed Facility (EF) of the Japanese Experiment Module (JEM) of the International Space Station (ISS). The mission was named Tanpopo, which in Japanese means dandelion. We capture any orbiting microparticles, such as micrometeorites, space debris, and terrestrial particles carrying microbes as bioaerosols, by using blocks of silica aerogel. We also test the survival of microbial species and organic compounds in the space environment for up to 3 years. The goal of this review is to introduce an overview of the Tanpopo mission with particular emphasis on the investigation of the interplanetary transfer of microbes. The Exposed Experiment Handrail Attachment Mechanism with aluminum Capture Panels (CPs) and Exposure Panels (EPs) was exposed on the EF-JEM on May 26, 2015. The first CPs and EPs will be returned to the ground in mid-2016. Possible escape of terrestrial microbes from Earth to space will be evaluated by investigating the upper limit of terrestrial microbes by the capture experiment. Possible mechanisms for transfer of microbes over the stratosphere and an investigation of the effect of the microbial cell-aggregate size on survivability in space will also be discussed. KEY WORDS Panspermia-Astrobiology-Low-Earth orbit. Astrobiology 16, 363-376.
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Affiliation(s)
- Yuko Kawaguchi
- 1 Institute of Space and Astronautical Science , Japan Aerospace Exploration Agency (ISAS/JAXA), Sagamihara, Japan
- 2 School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Tokyo, Japan
| | - Shin-Ichi Yokobori
- 2 School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Tokyo, Japan
| | - Hirofumi Hashimoto
- 1 Institute of Space and Astronautical Science , Japan Aerospace Exploration Agency (ISAS/JAXA), Sagamihara, Japan
| | - Hajime Yano
- 1 Institute of Space and Astronautical Science , Japan Aerospace Exploration Agency (ISAS/JAXA), Sagamihara, Japan
| | - Makoto Tabata
- 3 Graduate School of Science, Chiba University , Chiba-shi, Japan
| | - Hideyuki Kawai
- 3 Graduate School of Science, Chiba University , Chiba-shi, Japan
| | - Akihiko Yamagishi
- 2 School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Tokyo, Japan
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17
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18
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Liu L, Yang J, Lv H, Yu X, Wilkinson DM, Yang J. Phytoplankton Communities Exhibit a Stronger Response to Environmental Changes than Bacterioplankton in Three Subtropical Reservoirs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:10850-10858. [PMID: 26287966 DOI: 10.1021/acs.est.5b02637] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The simultaneous analysis of multiple components of ecosystems is crucial for comprehensive studies of environmental changes in aquatic ecosystems, but such studies are rare. In this study, we analyzed simultaneously the bacterioplankton and phytoplankton communities in three Chinese subtropical reservoirs and compared the response of these two components to seasonal environmental changes. Time-lag analysis indicated that the temporal community dynamics of both bacterioplankton and phytoplankton showed significant directional changes, and variance partitioning suggested that the major reason was the gradual improvement of reservoir water quality from middle eutrophic to oligo-mesotrophic levels during the course of our study. In addition, we found a higher level of temporal stability or stochasticity in the bacterioplankton community than in the phytoplankton community. Potential explanations are that traits associated with bacteria, such as high abundance, widespread dispersal, potential for rapid growth rates, and rapid evolutionary adaptation, may underlie the different stability or stochasticity of bacterioplankton and phytoplankton communities to the environmental changes. In addition, the indirect response of bacterioplankton to nitrogen and phosphorus may result in the fact that environmental deterministic selection was stronger for the phytoplankton than for the bacterioplankton communities.
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Affiliation(s)
- Lemian Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, People's Republic of China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Hong Lv
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, People's Republic of China
| | - Xiaoqing Yu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, People's Republic of China
| | - David M Wilkinson
- School of Natural Science and Psychology, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, U.K
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, People's Republic of China
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Liu L, Yang J, Yu Z, Wilkinson DM. The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China. THE ISME JOURNAL 2015; 9:2068-77. [PMID: 25748371 PMCID: PMC4542038 DOI: 10.1038/ismej.2015.29] [Citation(s) in RCA: 305] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 01/11/2015] [Accepted: 01/30/2015] [Indexed: 11/09/2022]
Abstract
Bacteria play key roles in the ecology of both aquatic and terrestrial ecosystems; however, little is known about their diversity and biogeography, especially in the rare microbial biosphere of inland freshwater ecosystems. Here we investigated aspects of the community ecology and geographical distribution of abundant and rare bacterioplankton using high-throughput sequencing and examined the relative influence of local environmental variables and regional (spatial) factors on their geographical distribution patterns in 42 lakes and reservoirs across China. Our results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance-decay relationship. This suggests that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa. However, we identified some differences between the abundant and rare groups as both groups of bacteria showed a significant positive relationship between sites occupancy and abundance, but the abundant bacteria exhibited a weaker distance-decay relationship than the rare bacteria. Our results implied that rare subcommunities were mostly governed by local environmental variables, whereas the abundant subcommunities were mainly affected by regional factors. In addition, both local and regional variables that were significantly related to the spatial variation of abundant bacterial community composition were different to those of rare ones, suggesting that abundant and rare bacteria may have discrepant ecological niches and may play different roles in natural ecosystems.
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Affiliation(s)
- Lemian Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
| | - Zheng Yu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
| | - David M Wilkinson
- School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
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20
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Measurement of ice nucleation-active bacteria on plants and in precipitation by quantitative PCR. Appl Environ Microbiol 2013; 80:1256-67. [PMID: 24317082 DOI: 10.1128/aem.02967-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Ice nucleation-active (INA) bacteria may function as high-temperature ice-nucleating particles (INP) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. We know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. To facilitate these investigations, we developed two quantitative PCR (qPCR) tests of the ina gene to directly count INA bacteria in environmental samples. Each of two primer pairs amplified most alleles of the ina gene and, taken together, they should amplify all known alleles. To aid primer design, we collected many new INA isolates. Alignment of their partial ina sequences revealed new and deeply branching clades, including sequences from Pseudomonas syringae pv. atropurpurea, Ps. viridiflava, Pantoea agglomerans, Xanthomonas campestris, and possibly Ps. putida, Ps. auricularis, and Ps. poae. qPCR of leaf washings recorded ∼10(8) ina genes g(-1) fresh weight of foliage on cereals and 10(5) to 10(7) g(-1) on broadleaf crops. Much lower populations were found on most naturally occurring vegetation. In fresh snow, ina genes from various INA bacteria were detected in about half the samples but at abundances that could have accounted for only a minor proportion of INP at -10°C (assuming one ina gene per INA bacterium). Despite this, an apparent biological source contributed an average of ∼85% of INP active at -10°C in snow samples. In contrast, a thunderstorm hail sample contained 0.3 INA bacteria per INP active at -10°C, suggesting a significant contribution to this sample.
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21
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Tsuji K. Kin selection, species richness and community. Biol Lett 2013; 9:20130491. [PMID: 24132096 PMCID: PMC3871341 DOI: 10.1098/rsbl.2013.0491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/05/2013] [Indexed: 11/12/2022] Open
Abstract
Can evolutionary and ecological dynamics operating at one level of the biological hierarchy affect the dynamics and structure at other levels? In social insects, strong hostility towards unrelated individuals can evolve as a kin-selected counter-adaptation to intraspecific social parasitism. This aggression in turn might cause intraspecific competition to predominate over interspecific competition, permitting coexistence with other social insect species. In other words, kin selection-a form of intra-population dynamics-might enhance the species richness of the community, a higher-level structure. The converse effect, from higher to lower levels, might also operate, whereby strong interspecific competition may limit the evolution of selfish individual traits. If the latter effect were to prove more important, it would challenge the common view that intra-population dynamics (via individual or gene selection) is the main driver of evolution.
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Affiliation(s)
- Kazuki Tsuji
- Faculty of Agriculture, University of the Ryukyus (The United Graduate School of Agricultural Sciences, Kagoshima University), Nishihara, Okinawa 9030213, Japan
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22
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Yang Y, Chan CY, Tao J, Lin M, Engling G, Zhang Z, Zhang T, Su L. Observation of elevated fungal tracers due to biomass burning in the Sichuan Basin at Chengdu City, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2012; 431:68-77. [PMID: 22664540 DOI: 10.1016/j.scitotenv.2012.05.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/31/2012] [Accepted: 05/10/2012] [Indexed: 05/22/2023]
Abstract
Fungal material (i.e., spores and fragments) is an important component of atmospheric aerosols. In order to examine the variability of fungal abundance in fine particles (PM(2.5)) during a biomass burning season, an intensive measurement campaign was conducted in the Sichuan Basin at Chengdu, a megacity in southwest China, in spring 2009. The aerosol samples were analyzed for carbonaceous species, including molecular tracers for biomass burning and fungal material, and water soluble ions. The results were interpreted with the help of principle component analysis, fire count maps, and the WRF model. Elevated concentrations of arabitol and mannitol were found with average concentrations of 21.5±16.6 ng m(-3) and 43.9±19.3 ng m(-3), respectively, which were unexpectedly higher than those measured in fine particles in any other study reported previously. Even higher concentrations were observed in cases with simultaneous enhancements in the biomass burning tracers levoglucosan and K(+). In the case of influence by pollution plumes from biomass burning regions, the fungal tracer concentrations reached maximum values of 79.6 ng m(-3) and 121.8 ng m(-3), coinciding with peak levels of levoglucosan and K(+). Statistically significant correlations were found between the simultaneously observed fungal tracers (arabitol and mannitol) and biomass burning tracers (levoglucosan and K(+)), suggesting that these species were emitted by co-located sources, and hence the elevated fungal tracers were likely associated with biomass burning activities.
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Affiliation(s)
- Yihong Yang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
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23
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Taylor NG, Verner-Jeffreys DW, Baker-Austin C. Aquatic systems: maintaining, mixing and mobilising antimicrobial resistance? Trends Ecol Evol 2011; 26:278-84. [DOI: 10.1016/j.tree.2011.03.004] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 02/26/2011] [Accepted: 03/05/2011] [Indexed: 01/17/2023]
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24
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Welsh D, Viaroli P, Hamilton W, Lenton T. Is DMSP synthesis in chlorophycean macro-algae linked to aerial dispersal? ETHOL ECOL EVOL 2010. [DOI: 10.1080/08927014.1999.9522827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- D.T. Welsh
- a Dipartimento di Scienze Ambientali , Università degli Studi di Parma , Viale delle Scienze, I-43100 , Parma , Italy
| | - P. Viaroli
- a Dipartimento di Scienze Ambientali , Università degli Studi di Parma , Viale delle Scienze, I-43100 , Parma , Italy
| | - W.D. Hamilton
- b Department of Zoology , University of Oxford , South Parks Road, Oxford , OX1 3PS , U.K
| | - T.M. Lenton
- c Institute of Terrestrial Ecology, Edinburgh Research Station, Bush Estate, Penicuick , Midlothian , EH26 0QB , Scotland
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25
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Pearce DA, Bridge PD, Hughes KA, Sattler B, Psenner R, Russell NJ. Microorganisms in the atmosphere over Antarctica. FEMS Microbiol Ecol 2009; 69:143-57. [PMID: 19527292 DOI: 10.1111/j.1574-6941.2009.00706.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Antarctic microbial biodiversity is the result of a balance between evolution, extinction and colonization, and so it is not possible to gain a full understanding of the microbial biodiversity of a location, its biogeography, stability or evolutionary relationships without some understanding of the input of new biodiversity from the aerial environment. In addition, it is important to know whether the microorganisms already present are transient or resident - this is particularly true for the Antarctic environment, as selective pressures for survival in the air are similar to those that make microorganisms suitable for Antarctic colonization. The source of potential airborne colonists is widespread, as they may originate from plant surfaces, animals, water surfaces or soils and even from bacteria replicating within the clouds. On a global scale, transport of air masses from the well-mixed boundary layer to high-altitude sites has frequently been observed, particularly in the warm season, and these air masses contain microorganisms. Indeed, it has become evident that much of the microbial life within remote environments is transported by air currents. In this review, we examine the behaviour of microorganisms in the Antarctic aerial environment and the extent to which these microorganisms might influence Antarctic microbial biodiversity.
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Affiliation(s)
- David A Pearce
- British Antarctic Survey, Biological Sciences Division, Natural Environment Research Council, Cambridge, UK.
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26
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Abstract
The influence of body size on the energetic cost of movement is well studied in animals but has been rarely investigated in bacteria. Here, I calculate the cost of four chemotactic strategies for different-sized bacteria by adding the costs of their locomotion and reorientation. Size differences of 0.1 microm result in 100,000-fold changes in the energetic cost of chemotaxis. The exact cost for any given size is a nonlinear function of flagella length, the minimum speed necessary to detect and respond to a signal, and the gradient of the signal. These parameters are interlinked in such a way that body size and strategy are tightly coupled to particular environmental gradients, offering avenues for explaining and exploring diversity and competition. The analysis here has implications beyond bacteria. Power-law regression through the minimum costs of transport for different kinds of chemotaxis has the same slope as that for swimming animals, suggesting a universal allometric equation for all swimming organisms.
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Affiliation(s)
- James G Mitchell
- School of Biological Sciences, Flinders University, GPO 2100, Adelaide, South Australia 5001, Australia
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28
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Moletta M, Delgenes JP, Godon JJ. Differences in the aerosolization behavior of microorganisms as revealed through their transport by biogas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2007; 379:75-88. [PMID: 17445868 DOI: 10.1016/j.scitotenv.2007.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 02/12/2007] [Accepted: 02/19/2007] [Indexed: 05/15/2023]
Abstract
The aerosol microbial diversity of biogas was analyzed in order to examine the aerosolization behavior of microorganisms. Six biogas samples were analyzed: five from mesophilic and thermophilic anaerobic digestors treating different wastes, and one from landfill. Epifluorescent microscopic counts reveal that with 10(6) Prokarya m(-3), only one per one thousand billion were aerosolized from the digestor sludges to the biogas. SSU (Small Sub Unit) ribosomal fingerprinting (Single Strand Conformation Polymorphism) shows that microbial communities in the biogas were not just a rough copy of anaerobic digestor microbial communities and underlines that all microorganisms are not equally convoyed by biogas. To assess the difference occurring in aerosolization, 675 biogas-borne SSU ribosomal DNA were analyzed and compared to published anaerobic digestor microbial diversity. Results show that microorganisms belonging to Archaea, Deltaproteobacteria, Spirochaetes, Thermotogae, Chloroflexi phyla and sulfate-reducing groups were non-aerosolized whereas microorganisms belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, TM7 phyla as well as strictly aerobic and occasionally pathogenic species presented high levels of aerosolization. Finally, microorganisms belonging to Actinobacteria, Firmicutes and Bacteroidetes phyla represent passively-aerosolized microorganisms with similar frequencies in biogas-borne and anaerobic digestor microbial communities.
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Affiliation(s)
- Marina Moletta
- Laboratoire de Biotechnologie de l'Environnement, 11100 Narbonne, France.
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29
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Tanghe A, Van Dijck P, Thevelein JM. Why do microorganisms have aquaporins? Trends Microbiol 2006; 14:78-85. [PMID: 16406529 DOI: 10.1016/j.tim.2005.12.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 11/16/2005] [Accepted: 12/13/2005] [Indexed: 10/25/2022]
Abstract
Aquaporins are channel proteins that enhance the permeability of cell membranes for water. They have been found in Bacteria, Archaea and Eukaryotes. However, their absence in many microorganisms suggests that aquaporins do not fulfill a broad role such as turgor regulation or osmoadaptation but, instead, fulfill a role that enables microorganisms to have specific lifestyles. The recent discovery that aquaporins enhance cellular tolerance against rapid freezing suggests that they have ecological relevance. We have identified several examples of large-scale freeze-thawing of microbes in nature and we also draw attention to alternative lifestyle-related functions for aquaporins, which will be a focus of future research.
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Affiliation(s)
- An Tanghe
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Katholieke Universiteit Leuven and Flanders Interuniversity Institute for Biotechnology (VIB), Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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30
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Han X, Li Z, Hui C, Zhang F. Polymorphism maintenance in a spatially structured population: A two-locus genetic model of niche construction. Ecol Modell 2006. [DOI: 10.1016/j.ecolmodel.2005.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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32
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Abstract
We define the Gaia system of life and its environment on Earth, review the status of the Gaia theory, introduce potentially relevant concepts from complexity theory, then try to apply them to Gaia. We consider whether Gaia is a complex adaptive system (CAS) in terms of its behaviour and suggest that the system is self-organizing but does not reside in a critical state. Gaia has supported abundant life for most of the last 3.8 Gyr. Large perturbations have occasionally suppressed life but the system has always recovered without losing the capacity for large-scale free energy capture and recycling of essential elements. To illustrate how complexity theory can help us understand the emergence of planetary-scale order, we present a simple cellular automata (CA) model of the imaginary planet Daisyworld. This exhibits emergent self-regulation as a consequence of feedback coupling between life and its environment. Local spatial interaction, which was absent from the original model, can destabilize the system by generating bifurcation regimes. Variation and natural selection tend to remove this instability. With mutation in the model system, it exhibits self-organizing adaptive behaviour in its response to forcing. We close by suggesting how artificial life ('Alife') techniques may enable more comprehensive feasibility tests of Gaia.
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Affiliation(s)
- Timothy M Lenton
- Centre for Ecology and Hydrology, Edinburgh Research Station, Bush Estate, Penicuik, Midlothian EH26 0QB, UK.
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33
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Uromyces vankyorum sp. nov. and Uromyces atriplicis, putative vicariant rust species of Patagonian and Australian semi-desert biomes. Mycol Prog 2002. [DOI: 10.1007/s11557-006-0017-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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35
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36
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Simó R. Production of atmospheric sulfur by oceanic plankton: biogeochemical, ecological and evolutionary links. Trends Ecol Evol 2001; 16:287-294. [PMID: 11369106 DOI: 10.1016/s0169-5347(01)02152-8] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Biological production of the volatile compound dimethylsulfide in the ocean is the main natural source of tropospheric sulfur on a global scale, with important consequences for the radiative balance of the Earth. In the late 1980s, a Gaian feedback link between marine phytoplankton and climate through the release of atmospheric sulfur was hypothesized. However, the idea of microalgae producing a substance that could regulate climate has been criticized on the basis of its evolutionary feasibility. Recent advances have shown that volatile sulfur is a result of ecological interactions and transformation processes through planktonic food webs. It is, therefore, not only phytoplankton biomass, taxonomy or activity, but also food-web structure and dynamics that drive the oceanic production of atmospheric sulfur. Accordingly, the viewpoint on the ecological and evolutionary basis of this amazing marine biota-atmosphere link is changing.
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Abstract
Recent studies of microorganisms have revealed diverse complex social behaviors, including cooperation in foraging, building, reproducing, dispersing and communicating. These microorganisms should provide novel, tractable systems for the analysis of social evolution. The application of evolutionary and ecological theory to understanding their behavior will aid in developing better means to control the many pathogenic bacteria that use social interactions to affect humans.
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38
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McArthur JV, Tuckfield RC. Spatial patterns in antibiotic resistance among stream bacteria: effects of industrial pollution. Appl Environ Microbiol 2000; 66:3722-6. [PMID: 10966382 PMCID: PMC92212 DOI: 10.1128/aem.66.9.3722-3726.2000] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The spatial distribution of antibiotic resistance to streptomycin and kanamycin was examined in natural bacterial communities of two streams. The proportion of resistant bacteria was substantially higher (P < 0.05) in the midreaches of an industrially perturbed stream, but no such pattern was apparent in an undisturbed reference stream. The highest relative frequency of resistance was found at the confluence of a tributary draining a nuclear reactor and industrial complex. Antibiotic resistance increased with distance upstream from the confluence and was positively correlated (r(2) = 0. 54, P = 0.023) with mercury concentrations in the sediments. When the data for two years were compared, this pattern was stable for streptomycin resistance (paired t test, P < 0.05) but not for kanamycin resistance (P > 0.05). Our results imply that heavy metal pollution may contribute to increased antibiotic resistance through indirect selection.
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Affiliation(s)
- J V McArthur
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina 29801, USA.
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Welsh DT. Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate. FEMS Microbiol Rev 2000; 24:263-90. [PMID: 10841973 DOI: 10.1111/j.1574-6976.2000.tb00542.x] [Citation(s) in RCA: 273] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The osmoadaptation of most micro-organisms involves the accumulation of K(+) ions and one or more of a restricted range of low molecular mass organic solutes, collectively termed 'compatible solutes'. These solutes are accumulated to high intracellular concentrations, in order to balance the osmotic pressure of the growth medium and maintain cell turgor pressure, which provides the driving force for cell extension growth. In this review, I discuss the alternative roles which compatible solutes may also play as intracellular reserves of carbon, energy and nitrogen, and as more general stress metabolites involved in protection of cells against other environmental stresses including heat, desiccation and freezing. Thus, the evolutionary selection for the accumulation of a specific compatible solute may not depend solely upon its function during osmoadaptation, but also upon the secondary benefits its accumulation provides, such as increased tolerance of other environmental stresses prevalent in the organism's niche or even anti-herbivory or dispersal functions in the case of dimethylsulfoniopropionate (DMSP). In the second part of the review, I discuss the ecological consequences of the release of compatible solutes to the environment, where they can provide sources of compatible solutes, carbon, nitrogen and energy for other members of the micro-flora. Finally, at the global scale the metabolism of specific compatible solutes (betaines and DMSP) in brackish water, marine and hypersaline environments may influence global climate, due to the production of the trace gases, methane and dimethylsulfide (DMS) and in the case of DMS, also couple the marine and terrestrial sulfur cycles.
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Affiliation(s)
- D T Welsh
- Dipartimento di Scienze Ambientali, Universitá degli Studi di Parma, Viale delle Scienze, I-43100, Parma, Italy.
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Thornton DC. Phytoplankton mucilage production in coastal waters: a dispersal mechanism in a front dominated system? ETHOL ECOL EVOL 1999. [DOI: 10.1080/08927014.1999.9522835] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Banks D, Midtgård AK, Frengstad B, Krog JR, Strand T. The chemistry of Norwegian groundwaters: II. The chemistry of 72 groundwaters from Quaternary sedimentary aquifers. THE SCIENCE OF THE TOTAL ENVIRONMENT 1998; 222:93-105. [PMID: 9842754 DOI: 10.1016/s0048-9697(98)00292-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Seventy-two samples of groundwater derived from Norwegian Quaternary (largely glaciofluvial or glacial) aquifers were analysed for a wide range of major and minor hydrochemical parameters. The waters exhibit a relatively uncomplex evolution from Na-Cl dominated, immature waters (which reflect marine salts in precipitation) to Ca-HCO3 dominated waters via calcite dissolution. The median pH of these waters is 7.37, in contrast to similar waters from crystalline bedrock aquifers with a median pH of 8.07. The water samples provide little evidence of significant acidification or sulphatisation of groundwaters by 'acid rain'. In fact, a positive correlation emerges between non-marine sulphate and alkalinity/pH, suggesting dominantly lithological sources for non-marine sulphate. No groundwaters from Quaternary deposits exceed maximum recommended concentrations for Rn, F- and Na, while 10% fall outside the required pH range. This again contrasts with bedrock aquifers where 30% of waters are non-compliant with respect to one or more of these parameters.
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Affiliation(s)
- D Banks
- Norges geologiske undersøkelse, Trondheim, Norway
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Abstract
Evidence indicates that the Earth self-regulates at a state that is tolerated by life, but why should the organisms that leave the most descendants be the ones that contribute to regulating their planetary environment? The evolving Gaia theory focuses on the feedback mechanisms, stemming from naturally selected traits of organisms, that could generate such self-regulation.
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Affiliation(s)
- T M Lenton
- School of Environmental Sciences, University of East Anglia, Norwich, UK.
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