114 results on '"microbial dispersal"'
Search Results
2. Wallace’s line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria
- Author
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Benjamin J. Wainwright, Josh Leon, Ernie Vilela, K. J. E. Hickman, Jensen Caldwell, Behlee Aimone, Porter Bischoff, Marissa Ohran, Magnolia W. Morelli, Irma S. Arlyza, Onny N. Marwayana, and Geoffrey Zahn
- Subjects
Marine biogeography ,Metabarcoding ,Microbial dispersal ,Microbiome ,Seagrass ,Wallace’s line ,Environmental sciences ,GE1-350 ,Microbiology ,QR1-502 - Abstract
Abstract Background The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace’s line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line. Results We found significant differences in microbial community structure on either side of this boundary (R 2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P
- Published
- 2024
- Full Text
- View/download PDF
3. Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria.
- Author
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Wainwright, Benjamin J., Leon, Josh, Vilela, Ernie, Hickman, K. J. E., Caldwell, Jensen, Aimone, Behlee, Bischoff, Porter, Ohran, Marissa, Morelli, Magnolia W., Arlyza, Irma S., Marwayana, Onny N., and Zahn, Geoffrey
- Subjects
- *
POTENTIAL barrier , *MARINE bacteria , *BIOGEOGRAPHY , *MICROBIAL communities , *MICROORGANISMS , *MARINE plants , *BACTERIA - Abstract
Background: The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line. Results: We found significant differences in microbial community structure on either side of this boundary (R2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community. Conclusion: Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
4. Disentangling the mechanisms underlying phylosymbiosis in mammals.
- Author
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Mallott, Elizabeth K.
- Subjects
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GUT microbiome , *MICROBIAL communities , *HOST specificity (Biology) , *MAMMALS , *PHENOTYPES - Abstract
Mammalian gut microbial communities are frequently found to be host‐specific—microbial community compositions are more similar within than between host species—and some individual microbial taxa consistently associate with a single or small set of host species. The ecoevolutionary dynamics that result in this pattern of phylosymbiosis or host specificity have been proposed, but robust tests of the mechanisms driving these relationships are lacking. In this issue of Molecular Ecology, Mazel et al. (2023) combine large amplicon sequencing data sets with bacterial phenotypic traits to test whether microbial dispersal patterns contribute to the host specificity of the gut microbiome. They find that both transmission mode and oxygen tolerance are predictive of how specialized a microbe is. Horizontally transmitted, oxygen‐tolerant microbes are more likely to be generalists, and vertically transmitted anaerobes are more likely to be limited to a few host species. This creative use of publicly available data provides a roadmap for testing hypotheses about the mechanisms underlying phylosymbiosis. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
5. Testing the contribution of dispersal to microbial succession following a wildfire
- Author
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Kristin M. Barbour, Claudia Weihe, Kendra E. Walters, and Jennifer B. H. Martiny
- Subjects
microbial dispersal ,wildfire ,succession ,Microbiology ,QR1-502 - Abstract
ABSTRACT Given increased wildfire activity, there is growing interest in understanding the drivers of microbial succession after fire. Dispersal may be especially important to post-fire succession as biotic communities can be more susceptible to invasion following a disturbance. Here, we experimentally manipulated dispersal into disturbed leaf litter communities collected following a wildfire and tracked bacterial and fungal dispersal assemblages over time. We show that the identity and source of microbes immigrating into the soil surface post-fire change across time with seasonal shifts and the reemergence of aboveground vegetation. Further, dispersal significantly contributed to the reassembly of leaf litter microbial communities after the fire, producing an increasingly distinct assembly trajectory. The effect of dispersal on α-diversity and β-diversity was ecosystem dependent but, unexpectedly, influenced bacterial and fungal communities in a similar manner within ecosystems. Collectively, these results demonstrate that dispersal explicitly alters the course of microbial community succession following a wildfire and may impact bacteria and fungi in parallel ways, despite differing in traits expected to alter dispersal patterns. IMPORTANCE Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.
- Published
- 2023
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6. Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing.
- Author
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Griggs, Reid G, Steenwerth, Kerri L, Mills, David A, Cantu, Dario, and Bokulich, Nicholas A
- Subjects
biogeography ,metagenomics ,microbial dispersal ,microbial ecology ,microbiome ,terroir ,viticulture ,Environmental Science and Management ,Soil Sciences ,Microbiology - Abstract
Microbiomes are integral to viticulture and winemaking - collectively termed winegrowing - where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.
- Published
- 2021
7. Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion
- Author
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Goss-Souza, Dennis, Mendes, Lucas William, Rodrigues, Jorge Luiz Mazza, and Tsai, Siu Mui
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Life on Land ,Agriculture ,Bacteria ,Biodiversity ,Forests ,Microbiota ,Phylogeny ,Rhizosphere ,Soil Microbiology ,Soybeans ,Trees ,Metagenomics ,Microbial dispersal ,Neutral theory ,Selection ,Soybean rhizosphere ,Soil Sciences ,Ecology ,Microbiology - Abstract
Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.
- Published
- 2020
8. Ecological corridors homogenize plant root endospheric mycobiota.
- Author
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Hu, Jie, Vandenkoornhuyse, Philippe, Khalfallah, Fadwa, Causse‐Védrines, Romain, and Mony, Cendrine
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CORRIDORS (Ecology) , *PLANT roots , *FUNGI , *FRAGMENTED landscapes , *COEXISTENCE of species , *MICROBIAL diversity - Abstract
Summary: Ecological corridors promote species coexistence in fragmented habitats where dispersal limits species fluxes. The corridor concept was developed and investigated with macroorganisms in mind, while microorganisms, the invisible majority of biodiversity, were disregarded.We analyzed the effect of corridors on the dynamics of endospheric fungal assemblages associated with plant roots at the scale of 1 m over 2 years (i.e. at five time points) by combining an experimental corridor‐mesocosm with high‐throughput amplicon sequencing.We showed that plant root endospheric mycobiota were sensitive to corridor effects when the corridors were set up at a small spatial scale. The endospheric mycobiota of connected plants had higher species richness, lower beta‐diversity, and more deterministic assembly than the mycobiota of isolated plants. These effects became more pronounced with the development of host plants.Biotic corridors composed of host plants may thus play a key role in the spatial dynamics of microbial communities and may influence microbial diversity and related ecological functions. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
9. Testing the passive sampling hypothesis: The role of dispersal in shaping microbial species-area relationship
- Author
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Wei Deng, Guo-Bin Yu, Xiao-Yan Yang, and Wen Xiao
- Subjects
biodiversity patterns ,rare species ,species replacement ,microbial dispersal ,passive sampling hypothesis ,Microbiology ,QR1-502 - Abstract
Dispersal is one of the key processes determining biodiversity. The passive sampling hypothesis, which emphasizes dispersal processes, suggests that larger habitats receive more species from the species pool as the main mechanism leading to more species in larger habitats than in smaller habitats (i.e., species-area relationships). However, the specific mechanisms by which dispersion shapes biodiversity still need to be discovered due to the difficulties of quantifying dispersal and the influence of multiple factors. Solving the above problem with a designed experiment is necessary to test the passive sampling hypothesis. This study designed a passive sampling experiment using sterile filter paper to quantify the microbial diffusion process, excluding the effects of pure sampling effects, habitat heterogeneity, and extinction processes. The results of high-throughput sequencing showed that a larger filter paper could receive more colonists, and the passive sampling hypothesis of SAR was confirmed. Dispersal shaped SAR by increasing species richness, especially rare species, and increasing the species replacement rate between habitats. These two processes are the mechanisms by which dispersal shapes biodiversity patterns. Compared with the results of this study, the commonly used mathematical model of passive sampling was able to predict the richness of non-rare species accurately but underestimated the richness of rare species. Underestimating rare species by mathematical models of passive sampling is more severe in small habitats. These findings provide new insights into the study of dispersal processes and the mechanism of species-area relationships.
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- 2023
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10. Ecological Processes and Human Behavior Provide a Framework for Studying the Skin Microbial Metacommunity.
- Author
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Manus, Melissa B.
- Subjects
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HUMAN behavior , *MICROBIAL communities , *GUT microbiome , *COMMUNITIES , *MICROBIAL ecology , *DISPERSAL (Ecology) , *SKIN , *HUMAN-animal relationships - Abstract
Metacommunity theory dictates that a microbial community is supported both by local ecological processes and the dispersal of microbes between neighboring communities. Studies that apply this perspective to human-associated microbial communities are thus far limited to the gut microbiome. Yet, the skin serves as the primary barrier between the body and the external environment, suggesting frequent opportunities for microbial dispersal to the variable microbial communities that are housed across skin sites. This paper applies metacommunity theory to understand the dispersal of microbes to the skin from the physical and social environment, as well as between different skin sites on an individual's body. This includes highlighting the role of human behavior in driving microbial dispersal, as well as shaping physiological properties of skin that underscore local microbial community dynamics. By leveraging data from research on the skin microbiomes of amphibians and other animals, this paper provides recommendations for future research on the skin microbial metacommunity, including generating testable predictions about the ecological underpinnings of the skin microbiome. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
11. Microbial ecology of the atmosphere.
- Author
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Šantl-Temkiv, Tina, Amato, Pierre, Casamayor, Emilio O, Lee, Patrick K H, and Pointing, Stephen B
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MICROBIAL ecology , *ICE nuclei , *MARINE habitats , *MICROBIAL cells , *PARTICULATE matter , *ATMOSPHERE , *HYDROLOGIC cycle - Abstract
The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
12. Vertical stratification of the air microbiome in the lower troposphere.
- Author
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Drautz-Moses, Daniela I., Luhung, Irvan, Gusareva, Elena S., Kee, Carmon, Gaultier, Nicolas E., Premkrishnan, Balakrishnan N. V., Choou Fook Lee, See Ting Leong, Changsook Park, Zhei Hwee Yap, Heinle, Cassie E., Lau, Kenny J. X., Purbojati, Rikky W., Lim, Serene B. Y., Yee Hui Lim, Kutmutia, Shruti Ketan, Ngu War Aung, Oliveira, Elaine L., Soo Guek Ng, and Dacanay, Justine
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ATMOSPHERIC turbulence , *ATMOSPHERIC temperature , *TROPOSPHERE , *METEOROLOGICAL research , *WIND measurement , *AIRCRAFT cabins - Abstract
The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
13. Bowel Movement: Integrating Host Mobility and Microbial Transmission Across Host Taxa.
- Author
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Weinhold, Arne
- Subjects
GUT microbiome ,ANIMAL mechanics ,FOOD chains ,CONTRAST effect ,SOCIAL groups ,DISPERSAL (Ecology) ,HABITATS - Abstract
The gut microbiota of animals displays a high degree of plasticity with respect to environmental or dietary adaptations and is shaped by factors like social interactions, diet diversity or the local environment. But the contribution of these drivers varies across host taxa and our ability to explain microbiome variability within wild populations remains limited. Terrestrial animals have divergent mobility ranges and can either crawl, walk or fly, from a couple of centimeters toward thousands of kilometers. Animal movement has been little regarded in host microbiota frameworks, though it can directly influence major drivers of the host microbiota: (1) Aggregation movement can enhance social transmissions, (2) foraging movement can extend range of diet diversity, and (3) dispersal movement determines the local environment of a host. Here, I would like to outline how movement behaviors of different host taxa matter for microbial acquisition across mammals, birds as well as insects. Host movement can have contrasting effects and either reduce or enlarge spatial scale. Increased dispersal movement could dissolve local effects of sampling location, while aggregation could enhance inter-host transmissions and uniformity among social groups. Host movement can also extend the boundaries of microbial dispersal limitations and connect habitat patches across plant-pollinator networks, while the microbiota of wild populations could converge toward a uniform pattern when mobility is interrupted in captivity or laboratory settings. Hence, the implementation of host movement would be a valuable addition to the metacommunity concept, to comprehend microbial dispersal within and across trophic levels. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
14. Particle foraging strategies promote microbial diversity in marine environments
- Author
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Ali Ebrahimi, Akshit Goyal, and Otto X Cordero
- Subjects
marine ecology ,microbial dispersal ,optimal foraging ,biodiversity ,metacommunities ,phage–bacteria interactions ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Microbial foraging in patchy environments, where resources are fragmented into particles or pockets embedded in a large matrix, plays a key role in natural environments. In the oceans and freshwater systems, particle-associated bacteria can interact with particle surfaces in different ways: some colonize only during short transients, while others form long-lived, stable colonies. We do not yet understand the ecological mechanisms by which both short- and long-term colonizers can coexist. Here, we address this problem with a mathematical model that explains how marine populations with different detachment rates from particles can stably coexist. In our model, populations grow only while on particles, but also face the increased risk of mortality by predation and sinking. Key to coexistence is the idea that detachment from particles modulates both net growth and mortality, but in opposite directions, creating a trade-off between them. While slow-detaching populations show the highest growth return (i.e., produce more net offspring), they are more susceptible to suffer higher rates of mortality than fast-detaching populations. Surprisingly, fluctuating environments, manifesting as blooms of particles (favoring growth) and predators (favoring mortality) significantly expand the likelihood that populations with different detachment rates can coexist. Our study shows how the spatial ecology of microbes in the ocean can lead to a predictable diversification of foraging strategies and the coexistence of multiple taxa on a single growth-limiting resource.
- Published
- 2022
- Full Text
- View/download PDF
15. Bowel Movement: Integrating Host Mobility and Microbial Transmission Across Host Taxa
- Author
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Arne Weinhold
- Subjects
gut microbiota ,movement ecology ,microbial dispersal ,host movement ,migration ,environmental acquisition ,Microbiology ,QR1-502 - Abstract
The gut microbiota of animals displays a high degree of plasticity with respect to environmental or dietary adaptations and is shaped by factors like social interactions, diet diversity or the local environment. But the contribution of these drivers varies across host taxa and our ability to explain microbiome variability within wild populations remains limited. Terrestrial animals have divergent mobility ranges and can either crawl, walk or fly, from a couple of centimeters toward thousands of kilometers. Animal movement has been little regarded in host microbiota frameworks, though it can directly influence major drivers of the host microbiota: (1) Aggregation movement can enhance social transmissions, (2) foraging movement can extend range of diet diversity, and (3) dispersal movement determines the local environment of a host. Here, I would like to outline how movement behaviors of different host taxa matter for microbial acquisition across mammals, birds as well as insects. Host movement can have contrasting effects and either reduce or enlarge spatial scale. Increased dispersal movement could dissolve local effects of sampling location, while aggregation could enhance inter-host transmissions and uniformity among social groups. Host movement can also extend the boundaries of microbial dispersal limitations and connect habitat patches across plant-pollinator networks, while the microbiota of wild populations could converge toward a uniform pattern when mobility is interrupted in captivity or laboratory settings. Hence, the implementation of host movement would be a valuable addition to the metacommunity concept, to comprehend microbial dispersal within and across trophic levels.
- Published
- 2022
- Full Text
- View/download PDF
16. Continental-scale distributions of dust-associated bacteria and fungi
- Author
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Barberán, Albert, Ladau, Joshua, Leff, Jonathan W, Pollard, Katherine S, Menninger, Holly L, Dunn, Robert R, and Fierer, Noah
- Subjects
Microbiology ,Biological Sciences ,Earth Sciences ,Rural Health ,2.2 Factors relating to the physical environment ,Aetiology ,Aerosols ,Air Microbiology ,Allergens ,Animals ,Atmosphere ,Bacteria ,Biodiversity ,Cities ,Dust ,Environmental Monitoring ,Feces ,Fungi ,Geography ,Humans ,Multivariate Analysis ,Oceans and Seas ,Seasons ,Skin ,Soil Microbiology ,United States ,Water Microbiology ,Wind ,aerobiology ,microbial ecology ,microbial dispersal ,urbanization ,allergens - Abstract
It has been known for centuries that microorganisms are ubiquitous in the atmosphere, where they are capable of long-distance dispersal. Likewise, it is well-established that these airborne bacteria and fungi can have myriad effects on human health, as well as the health of plants and livestock. However, we have a limited understanding of how these airborne communities vary across different geographic regions or the factors that structure the geographic patterns of near-surface microbes across large spatial scales. We collected dust samples from the external surfaces of ∼1,200 households located across the United States to understand the continental-scale distributions of bacteria and fungi in the near-surface atmosphere. The microbial communities were highly variable in composition across the United States, but the geographic patterns could be explained by climatic and soil variables, with coastal regions of the United States sharing similar airborne microbial communities. Although people living in more urbanized areas were not found to be exposed to distinct outdoor air microbial communities compared with those living in more rural areas, our results do suggest that urbanization leads to homogenization of the airborne microbiota, with more urban communities exhibiting less continental-scale geographic variability than more rural areas. These results provide our first insight into the continental-scale distributions of airborne microbes, which is information that could be used to identify likely associations between microbial exposures in outdoor air and incidences of disease in crops, livestock, and humans.
- Published
- 2015
17. The aerobiome uncovered: Multi-marker metabarcoding reveals potential drivers of turn-over in the full microbial community in the air
- Author
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G. Arjen de Groot, Stefan Geisen, E.R. Jasper Wubs, Liz Meulenbroek, Ivo Laros, L. Basten Snoek, Dennis R. Lammertsma, Lars H. Hansen, and Pieter A. Slim
- Subjects
Aerobiome monitoring ,Microbiome ,Microbial dispersal ,Potential pathogens ,Early-warning system ,Meteorology ,Environmental sciences ,GE1-350 - Abstract
Air is a major conduit for the dispersal of organisms at the local and the global scale. Most research has focused on the dispersal of plants, vertebrates and human disease agents. However, the air represents a key dispersal medium also for bacteria, fungi and protists. Many of those represent potential pathogens of animals and plants and have until now gone largely unrecorded. Here we studied the turnover in composition of the entire aerobiome, the collective diversity of airborne microorganisms. For that we performed daily analyses of all prokaryotes and eukaryotes (including plants) using multi-marker high-throughput sequencing for a total of three weeks. We linked the resulting communities to local weather conditions, to assess determinants of aerobiome composition and distribution. We observed hundreds of microbial taxa, mostly belonging to spore-forming organisms including fungi, but also protists. Additionally, we detected many potential human- and plant-pathogens. Community composition fluctuated on a daily basis and was linked to concurrent weather conditions, particularly air pressure and temperature. Using network analyses, we identified taxonomically diverse groups of organisms with correlated temporal dynamics. In part, this was due to co-variation with environmental conditions, while we could also detect specific host-parasite interactions. This study provides the first full inventory of the aerobiome and identifies putative drivers of its dynamics in terms of taxon composition. This knowledge can help develop early warning systems against pathogens and improve our understanding of microbial dispersal.
- Published
- 2021
- Full Text
- View/download PDF
18. Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing
- Author
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Reid G. Griggs, Kerri L. Steenwerth, David A. Mills, Dario Cantu, and Nicholas A. Bokulich
- Subjects
viticulture ,terroir ,microbial ecology ,microbiome ,metagenomics ,microbial dispersal ,Microbiology ,QR1-502 - Abstract
Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.
- Published
- 2021
- Full Text
- View/download PDF
19. Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing.
- Author
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Griggs, Reid G., Steenwerth, Kerri L., Mills, David A., Cantu, Dario, and Bokulich, Nicholas A.
- Subjects
WINE flavor & odor ,MICROBIAL communities ,VINEYARDS ,WINES ,PHENOMENOLOGICAL biology ,PLANT-microbe relationships ,GRAPES - Abstract
Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
20. Adapting metacommunity theory to the human gastrointestinal microbiome
- Abstract
The human microbiome is composed of a diversity of bacteria, fungi, protists and viruses, and what’s more, it’s dynamic ! It changes according to what we eat, the medicines we take or the illnesses we may suffer from. In this respect, it is interesting to study how microbial taxa disperse and change in different parts of the body. To tackle this problem, we have drawn on the theory of metacommunities, which was originally developed to study macroecological systems, but has recently been suggested to study microbiomes. Metacommunity theory states that taxonomic composition at different locations differs according to known and well-defined mechanisms resulting from interactions between taxa, the impact of the environment and the ability of different taxa to disperse. In this project, I propose to adapt the theory of metacommunities to the particularities of the human gastrointestinal system. Specifically, I have developed a multivariate Lotka- Volterra competition-diffusion model that evolves dynamically over time and considers the gastrointestinal system as a one-dimensional transect in which taxa disperse. By studying how the new multivariate Lotka-Volterra competition-diffusion model behaves in various contexts, it becomes possible to develop new hypotheses about what is happening throughout the gastrointestinal system in sections that are difficult to sample. To understand the mechanisms that structure the gastrointestinal microbiome, we need to parameterise the multivariate Lotka-Volterra competition-diffusion model that I have developed on data so that we can study the behaviour of the model under realistic conditions. To achieve this, I developed a Bayesian statistical model that estimates each parameter of the theoretical model using data collected in the gastrointestinal tract. I relied on simulations to validate this new statistical model., Le microbiome humain est composé d’une diversité de bactéries, de champignons, protistes et de virus et, en plus il est dynamique ! Il change en fonction de ce que nous mangeons, des médicaments que nous prenons ou des maladies que nous pouvons avoir. À cet égard, il est intéressant d’étudier comment les microorganismes se dispersent et changent dans les différentes parties de notre corps. Pour aborder ce problème, nous nous sommes appuyés sur la théorie des métacommunautés, qui a été développée à l’origine pour étudier les systèmes macroécologiques, mais qui a récemment été suggérée pour étudier les microbiomes. La théorie des métacommunautés stipule que la composition taxonomique à différente localisation diffère en fonction de mécanismes connus et bien déőnit résultant des interactions entre taxons, de l’impact de l’environnement et de l’habileté des différents taxons à se disperser. Dans ce projet, je propose d’adapter la théorie des métacommunautés aux particularités du système gastro-intestinal humain. Spéciőquement, j’ai développé un modèle multivarié de compétition-diffusion de Lotka-Volterra qui évolue dans le temps de façon dynamique et qui considère le système gastro-intestinal comme un transect unidimensionnel dans lequel les taxons se dispersent. En étudiant comment se comporte le nouveau modèle multivarié de compétition-diffusion de Lotka-Volterra dans divers contextes, il devient possible de développer de nouvelles hypothèses sur ce qui se passe à travers le système gastro-intestinal dans des sections difficiles à échantillonner. Pour comprendre les mécanismes qui structurent le microbiote gastro-intestinal, il faut paramétrer le modèle multivarié de compétition-diffusion de Lotka-Volterra sur des données réel. Pour y arriver, j’ai développé un modèle statistique bayésien qui permet d’estimer chaque paramètre du modèle théorique en utilisant des données amassées dans le système gastro-intestinal. J’ai utilisé ds simulations pour valider ce nouveau mod
- Published
- 2023
21. Major imprint of surface plankton on deep ocean prokaryotic structure and activity.
- Author
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Ruiz‐González, Clara, Mestre, Mireia, Estrada, Marta, Sebastián, Marta, Salazar, Guillem, Agustí, Susana, Moreno‐Ostos, Enrique, Reche, Isabel, Álvarez‐Salgado, Xosé Antón, Morán, Xosé Anxelu G., Duarte, Carlos M., Sala, M. Montserrat, and Gasol, Josep M.
- Subjects
- *
PLANKTON , *PROKARYOTES , *OCEAN mining , *OCEAN , *WATER , *DISSOLVED organic matter , *MICROBIAL communities - Abstract
Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean, yet it remains unknown whether surface processes determine the assembly and function of bathypelagic prokaryotes to a larger extent than deep‐sea physicochemical conditions. Here, we explored whether variations in surface phytoplankton assemblages across Atlantic, Pacific and Indian ocean stations can explain structural changes in bathypelagic (ca. 4,000 m) free‐living and particle‐attached prokaryotic communities (characterized through 16S rRNA gene sequencing), as well as changes in prokaryotic activity and dissolved organic matter (DOM) quality. We show that the spatial structuring of prokaryotic communities in the bathypelagic strongly followed variations in the abundances of surface dinoflagellates and ciliates, as well as gradients in surface primary productivity, but were less influenced by bathypelagic physicochemical conditions. Amino acid‐like DOM components in the bathypelagic reflected variations of those components in surface waters, and seemed to control bathypelagic prokaryotic activity. The imprint of surface conditions was more evident in bathypelagic than in shallower mesopelagic (200–1,000 m) communities, suggesting a direct connectivity through fast‐sinking particles that escape mesopelagic transformations. Finally, we identified a pool of endemic deep‐sea prokaryotic taxa (including potentially chemoautotrophic groups) that appear less connected to surface processes than those bathypelagic taxa with a widespread vertical distribution. Our results suggest that surface planktonic communities shape the spatial structure of the bathypelagic microbiome to a larger extent than the local physicochemical environment, likely through determining the nature of the sinking particles and the associated prokaryotes reaching bathypelagic waters. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
22. Freezing Tolerance of Thermophilic Bacterial Endospores in Marine Sediments
- Author
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Margaret A. Cramm, Anirban Chakraborty, Carmen Li, S. Emil Ruff, Bo Barker Jørgensen, and Casey R. J. Hubert
- Subjects
thermophiles ,endospores ,microbial ecology ,extremophiles ,microbial dispersal ,panspermia ,Microbiology ,QR1-502 - Abstract
Dormant endospores of anaerobic, thermophilic bacteria found in cold marine sediments offer a useful model for studying microbial biogeography, dispersal, and survival. The dormant endospore phenotype confers resistance to unfavorable environmental conditions, allowing dispersal to be isolated and studied independently of other factors such as environmental selection. To study the resilience of thermospores to conditions relevant for survival in extreme cold conditions, their viability following different freezing treatments was tested. Marine sediment was frozen at either −80°C or −20°C for 10 days prior to pasteurization and incubation at +50°C for 21 days to assess thermospore viability. Sulfate reduction commenced at +50°C following both freezing pretreatments indicating persistence of thermophilic endospores of sulfate-reducing bacteria. The onset of sulfate reduction at +50°C was delayed in −80°C pretreated microcosms, which exhibited more variability between triplicates, compared to −20°C pretreated microcosms and parallel controls that were not frozen in advance. Microbial communities were evaluated by 16S rRNA gene amplicon sequencing, revealing an increase in the relative sequence abundance of thermophilic endospore-forming Firmicutes in all microcosms. Different freezing pretreatments (−80°C and −20°C) did not appreciably influence the shift in overall bacterial community composition that occurred during the +50°C incubations. Communities that had been frozen prior to +50°C incubation showed an increase in the relative sequence abundance of operational taxonomic units (OTUs) affiliated with the class Bacilli, relative to unfrozen controls. These results show that freezing impacts but does not obliterate thermospore populations and their ability to germinate and grow under appropriate conditions. Indeed the majority of the thermospore OTUs detected in this study (21 of 22) could be observed following one or both freezing treatments. These results are important for assessing thermospore viability in frozen samples and following cold exposure such as the very low temperatures that would be encountered during panspermia.
- Published
- 2019
- Full Text
- View/download PDF
23. Testing the contribution of dispersal to microbial succession following a wildfire.
- Author
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Barbour KM, Weihe C, Walters KE, and Martiny JBH
- Subjects
- Bacteria, Soil Microbiology, Wildfires, Microbiota, Mycobiome
- Abstract
Importance: Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change., Competing Interests: The authors declare no conflict of interest.
- Published
- 2023
- Full Text
- View/download PDF
24. Freezing Tolerance of Thermophilic Bacterial Endospores in Marine Sediments.
- Author
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Cramm, Margaret A., Chakraborty, Anirban, Li, Carmen, Ruff, S. Emil, Jørgensen, Bo Barker, and Hubert, Casey R. J.
- Subjects
MARINE sediments ,BACTERIAL spores ,THERMOPHILIC bacteria ,SULFATE-reducing bacteria ,MICROBIAL communities ,REDUCTION of sulfates ,FREEZING - Abstract
Dormant endospores of anaerobic, thermophilic bacteria found in cold marine sediments offer a useful model for studying microbial biogeography, dispersal, and survival. The dormant endospore phenotype confers resistance to unfavorable environmental conditions, allowing dispersal to be isolated and studied independently of other factors such as environmental selection. To study the resilience of thermospores to conditions relevant for survival in extreme cold conditions, their viability following different freezing treatments was tested. Marine sediment was frozen at either −80°C or −20°C for 10 days prior to pasteurization and incubation at +50°C for 21 days to assess thermospore viability. Sulfate reduction commenced at +50°C following both freezing pretreatments indicating persistence of thermophilic endospores of sulfate-reducing bacteria. The onset of sulfate reduction at +50°C was delayed in −80°C pretreated microcosms, which exhibited more variability between triplicates, compared to −20°C pretreated microcosms and parallel controls that were not frozen in advance. Microbial communities were evaluated by 16S rRNA gene amplicon sequencing, revealing an increase in the relative sequence abundance of thermophilic endospore-forming Firmicutes in all microcosms. Different freezing pretreatments (−80°C and −20°C) did not appreciably influence the shift in overall bacterial community composition that occurred during the +50°C incubations. Communities that had been frozen prior to +50°C incubation showed an increase in the relative sequence abundance of operational taxonomic units (OTUs) affiliated with the class Bacilli , relative to unfrozen controls. These results show that freezing impacts but does not obliterate thermospore populations and their ability to germinate and grow under appropriate conditions. Indeed the majority of the thermospore OTUs detected in this study (21 of 22) could be observed following one or both freezing treatments. These results are important for assessing thermospore viability in frozen samples and following cold exposure such as the very low temperatures that would be encountered during panspermia. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
25. Corrigendum: Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean
- Author
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Eva Mayol, María A. Jiménez, Gerhard J. Herndl, Carlos M. Duarte, and Jesús M. Arrieta
- Subjects
airborne microbes ,microbial dispersal ,air-sea exchange ,bioaerosols ,Atlantic Ocean ,Microbiology ,QR1-502 - Published
- 2017
- Full Text
- View/download PDF
26. Microbial ecology of the atmosphere
- Abstract
The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.
- Published
- 2022
27. Infant and Adult Gut Microbiome and Metabolome in Rural Bassa and Urban Settlers from Nigeria.
- Author
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Ayeni, Funmilola A., Biagi, Elena, Rampelli, Simone, Fiori, Jessica, Soverini, Matteo, Audu, Haruna J., Cristino, Sandra, Caporali, Leonardo, Schnorr, Stephanie L., Carelli, Valerio, Brigidi, Patrizia, Candela, Marco, and Turroni, Silvia
- Abstract
Summary We assessed the subsistence-related variation of the human gut microbiome at a fine resolution for two of the main dimensions of microbiome variation, age and geography. For this, we investigated the fecal microbiome and metabolome in rural Bassa and urbanized individuals from Nigeria, including infants, and compared data with worldwide populations practicing varying subsistence. Our data highlight specific microbiome traits that are progressively lost with urbanization, such as the dominance of pristine fiber degraders and the low inter-individual variation. For the Bassa, this last feature is the result of their subsistence-related practices favoring microbial dispersal, such as their extensive environmental contact and the usage of untreated waters from the Usuma River. The high degree of microbial dispersal observed in the Bassa meta-community nullifies the differences between infant and adult intestinal ecosystems, suggesting that the infant-type microbiome in Western populations could be the result of microbiome-associated neotenic traits favored by urbanization. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
28. Variation in range size and dispersal capabilities of microbial taxa.
- Author
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Choudoir, Mallory J., Fierer, Noah, Barberán, Albert, Menninger, Holly L., and Dunn, Rob R.
- Subjects
- *
MICROBIAL aggregation , *DUST & the environment , *MICROBIAL diversity , *TAXONOMY , *ACTINOBACTERIA - Abstract
Abstract: Geographic range size can span orders of magnitude for plant and animal species, with the study of why range sizes vary having preoccupied biogeographers for decades. In contrast, there have been few comparable studies of how range size varies across microbial taxa and what traits may be associated with this variation. We determined the range sizes of 74,134 bacterial and archaeal taxa found in settled dust collected from 1,065 locations across the United States. We found that most microorganisms have small ranges and few have large ranges, a pattern similar to the range size distributions commonly observed for macrobes. However, contrary to expectations, those microbial taxa that were locally abundant did not necessarily have larger range sizes. The observed differences in microbial range sizes were generally predictable from taxonomic identity, phenotypic traits, genomic attributes, and habitat preferences, findings that provide insight into the factors shaping patterns of microbial biogeography. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
29. Contribution of soil bacteria to the atmosphere across biomes
- Author
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Stephen D.J. Archer, Kevin C. Lee, Tancredi Caruso, Antonio Alcami, Jonathan G. Araya, S. Craig Cary, Don A. Cowan, Claudia Etchebehere, Batdelger Gantsetseg, Benito Gomez-Silva, Sean Hartery, Ian D. Hogg, Mayada K. Kansour, Timothy Lawrence, Charles K. Lee, Patrick K.H. Lee, Matthias Leopold, Marcus H.Y. Leung, Teruya Maki, Christopher P. McKay, Dina M. Al Mailem, Jean-Baptiste Ramond, Alberto Rastrojo, Tina Šantl-Temkiv, Henry J. Sun, Xinzhao Tong, Bryan Vandenbrink, Kimberley A. Warren-Rhodes, Stephen B. Pointing, and UAM. Departamento de Biología
- Subjects
Environmental Engineering ,Biogeography ,Atmospheric Microbiology ,Environmental Chemistry ,Source Tracking ,Biología y Biomedicina / Biología ,Pollution ,Waste Management and Disposal ,Microbial dispersal ,Soil Microbiology - Abstract
Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, los autores pertenecientes a la UAM y el nombre del grupo de colaboración, si lo hubiere, The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity, This work was supported by the Singapore Ministry of Education and Yale-NUS College, grant number R-607-265-331-121
- Published
- 2023
30. Corrigendum: Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean.
- Subjects
AIRBORNE infection ,MICROBIAL diversity ,MICROBIOLOGICAL aerosols - Published
- 2017
- Full Text
- View/download PDF
31. Contribution of soil bacteria to the atmosphere across biomes.
- Author
-
Archer, Stephen D.J., Lee, Kevin C., Caruso, Tancredi, Alcami, Antonio, Araya, Jonathan G., Cary, S. Craig, Cowan, Don A., Etchebehere, Claudia, Gantsetseg, Batdelger, Gomez-Silva, Benito, Hartery, Sean, Hogg, Ian D., Kansour, Mayada K., Lawrence, Timothy, Lee, Charles K., Lee, Patrick K.H., Leopold, Matthias, Leung, Marcus H.Y., Maki, Teruya, and McKay, Christopher P.
- Published
- 2023
- Full Text
- View/download PDF
32. Microbial ecology of the atmosphere
- Author
-
Tina Šantl-Temkiv, Pierre Amato, Emilio O Casamayor, Patrick K H Lee, Stephen B Pointing, Department of Bioscience [Aarhus], Stellar Astrophysics Centre [Aarhus] (SAC), Aarhus University [Aarhus], iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, Institut de Chimie de Clermont-Ferrand (ICCF), SIGMA Clermont (SIGMA Clermont)-Institut de Chimie du CNRS (INC)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Centre d'Estudis Avançats de Blanes (CEAB), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), and Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA)
- Subjects
microbial ice nucleation ,Atmosphere ,Microbial biogeography ,Microbiota ,Microbiology ,Microbial ecology ,Ecosystems ecology ,Atmospheric microbiology ,aeromicrobiology ,Infectious Diseases ,bioaerosols ,microbial dispersal ,FEMS Microbiology Reviews Aeromicrobiology ,[SDE]Environmental Sciences ,[CHIM]Chemical Sciences ,Metagenomics ,One Health ,microbial biogeography ,Microbial dispersal - Abstract
Este artículo contiene 18 páginas, 7 figuras., The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed., This work was supported by the following research grants: TST was supported by the Danish National Research Foundation [grant number DNRF106], the Aarhus University Research Foundation Nova programme [grant number AUFF-E-2015-FLS- 9-10], the Villum Foundation [grant numbers 23175 and 37435], the NOVO Interdisciplinary Synergy Programme [grant number NNF19OC0056963] and the Independent Research Fund Denmark [grant number 9145-00001B]. PA was supported by the French National Research Agency Make Our Planet Great Again (MOPGA) programme [grant number ANR-17-MOPGA-0013]. EOC was supported by the Spanish State Research Agency [grant number AEI- MICINN] and European Regional Development Fund [grant number INTERACTOMA RTI2018-101205-B-I00]. PKHL was supported by the Environment Conservation Fund of theGovernment of Hong Kong [grant number 2019–12]. SBP was supported by the Ministry of Education - SingaporeandYale-NUS College [grant number R-607-265-331-121].
- Published
- 2022
33. Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems.
- Author
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Bell, Thomas and Tylianakis, Jason M.
- Subjects
- *
MICROORGANISMS , *ANTHROPOCENE Epoch , *ECOSYSTEMS , *SOIL microbial ecology , *SOIL microbiology , *BIOLOGICAL adaptation - Abstract
Soil microbial communities are enormously diverse, with at least millions of species and trillions of genes unknown to science or poorly described. Soil microbial communities are key components of agriculture, for example, in provisioning nitrogen and protecting crops from pathogens, providing overall ecosystem services in excess of $1000bn per year. It is important to know how humans are affecting this hidden diversity. Much is known about the negative consequences of agricultural intensification on higher organisms, but almost nothing is known about how alterations to landscapes affect microbial diversity, distributions and processes. We review what is known about spatial flows of microbes and their response to land-use change, and outline nine hypotheses to advance research of microbiomes across landscapes. We hypothesize that intensified agriculture selects for certain taxa and genes, which then 'spill over' into adjacent unmodified areas and generate a halo of genetic differentiation around agricultural fields. Consequently, the spatial configuration and management intensity of different habitats combines with the dispersal ability of individual taxa to determine the extent of spillover, which can impact the functioning of adjacent unmodified habitats. When landscapes are heterogeneous and dispersal rates are high, this will select for large genomes that allow exploitation of multiple habitats, a process that may be accelerated through horizontal gene transfer. Continued expansion of agriculture will increase genotypic similarity, making microbial community functioning increasingly variable in human-dominated landscapes, potentially also impacting the consistent provisioning of ecosystem services. While the resulting economic costs have not been calculated, it is clear that dispersal dynamics of microbes should be taken into consideration to ensure that ecosystem functioning and services are maintained in agri-ecosystem mosaics. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
34. The aerobiome uncovered:Multi-marker metabarcoding reveals potential drivers of turn-over in the full microbial community in the air
- Abstract
Air is a major conduit for the dispersal of organisms at the local and the global scale. Most research has focused on the dispersal of plants, vertebrates and human disease agents. However, the air represents a key dispersal medium also for bacteria, fungi and protists. Many of those represent potential pathogens of animals and plants and have until now gone largely unrecorded. Here we studied the turnover in composition of the entire aerobiome, the collective diversity of airborne microorganisms. For that we performed daily analyses of all prokaryotes and eukaryotes (including plants) using multi-marker high-throughput sequencing for a total of three weeks. We linked the resulting communities to local weather conditions, to assess determinants of aerobiome composition and distribution. We observed hundreds of microbial taxa, mostly belonging to spore-forming organisms including fungi, but also protists. Additionally, we detected many potential human- and plant-pathogens. Community composition fluctuated on a daily basis and was linked to concurrent weather conditions, particularly air pressure and temperature. Using network analyses, we identified taxonomically diverse groups of organisms with correlated temporal dynamics. In part, this was due to co-variation with environmental conditions, while we could also detect specific host-parasite interactions. This study provides the first full inventory of the aerobiome and identifies putative drivers of its dynamics in terms of taxon composition. This knowledge can help develop early warning systems against pathogens and improve our understanding of microbial dispersal.
- Published
- 2021
35. The aerobiome uncovered:Multi-marker metabarcoding reveals potential drivers of turn-over in the full microbial community in the air
- Abstract
Air is a major conduit for the dispersal of organisms at the local and the global scale. Most research has focused on the dispersal of plants, vertebrates and human disease agents. However, the air represents a key dispersal medium also for bacteria, fungi and protists. Many of those represent potential pathogens of animals and plants and have until now gone largely unrecorded. Here we studied the turnover in composition of the entire aerobiome, the collective diversity of airborne microorganisms. For that we performed daily analyses of all prokaryotes and eukaryotes (including plants) using multi-marker high-throughput sequencing for a total of three weeks. We linked the resulting communities to local weather conditions, to assess determinants of aerobiome composition and distribution. We observed hundreds of microbial taxa, mostly belonging to spore-forming organisms including fungi, but also protists. Additionally, we detected many potential human- and plant-pathogens. Community composition fluctuated on a daily basis and was linked to concurrent weather conditions, particularly air pressure and temperature. Using network analyses, we identified taxonomically diverse groups of organisms with correlated temporal dynamics. In part, this was due to co-variation with environmental conditions, while we could also detect specific host-parasite interactions. This study provides the first full inventory of the aerobiome and identifies putative drivers of its dynamics in terms of taxon composition. This knowledge can help develop early warning systems against pathogens and improve our understanding of microbial dispersal.
- Published
- 2021
36. The aerobiome uncovered: Multi-marker metabarcoding reveals potential drivers of turn-over in the full microbial community in the air
- Abstract
Air is a major conduit for the dispersal of organisms at the local and the global scale. Most research has focused on the dispersal of plants, vertebrates and human disease agents. However, the air represents a key dispersal medium also for bacteria, fungi and protists. Many of those represent potential pathogens of animals and plants and have until now gone largely unrecorded. Here we studied the turnover in composition of the entire aerobiome, the collective diversity of airborne microorganisms. For that we performed daily analyses of all prokaryotesand eukaryotes (including plants) using multi-marker high-throughput sequencing for a total of three weeks. We linked the resulting communities to local weather conditions, to assess determinants of aerobiome composition and distribution. We observed hundreds of microbial taxa, mostly belonging to spore-forming organisms including fungi, but also protists. Additionally, we detected many potential human- and plantpathogens. Community composition fluctuated on a daily basis and was linked to concurrent weather conditions, particularly air pressure and temperature. Using network analyses, we identified taxonomically diverse groups of organisms with correlated temporal dynamics. In part, this was due to co-variation with environmental conditions, while we could also detect specific host-parasite interactions. This study provides the first full inventoryof the aerobiome and identifies putative drivers of its dynamics in terms of taxon composition. This knowledge can help develop early warning systems against pathogens and improve our understanding of microbial dispersal.
- Published
- 2021
37. The aerobiome uncovered: Multi-marker metabarcoding reveals potential drivers of turn-over in the full microbial community in the air
- Author
-
de Groot, G Arjen, Geisen, Stefan, Wubs, E R Jasper, Meulenbroek, Liz, Laros, Ivo, Snoek, L Basten, Lammertsma, Dennis R, Hansen, Lars H, Slim, Pieter A, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Sub Bioinformatics, and Theoretical Biology and Bioinformatics
- Subjects
010504 meteorology & atmospheric sciences ,Microorganism ,Bos- en Landschapsecologie ,010501 environmental sciences ,Biology ,01 natural sciences ,Human disease ,Meteorology ,Environmental Science(all) ,Early-warning system ,Humans ,Forest and Landscape Ecology ,GE1-350 ,Microbiome ,Laboratorium voor Nematologie ,Vegetatie ,0105 earth and related environmental sciences ,General Environmental Science ,Vegetation ,Bacteria ,Ecology ,Microbiota ,fungi ,Fungi ,Allergens ,Plants ,PE&RC ,Environmental sciences ,Taxon ,Microbial population biology ,Community composition ,Turnover ,Aerobiome monitoring ,Microbial dispersal ,Potential pathogens ,Co-dispersal ,Dierecologie ,Biological dispersal ,Vegetatie, Bos- en Landschapsecologie ,Animal Ecology ,Vegetation, Forest and Landscape Ecology ,Laboratory of Nematology - Abstract
Air is a major conduit for the dispersal of organisms at the local and the global scale. Most research has focused on the dispersal of plants, vertebrates and human disease agents. However, the air represents a key dispersal medium also for bacteria, fungi and protists. Many of those represent potential pathogens of animals and plants and have until now gone largely unrecorded. Here we studied the turnover in composition of the entire aerobiome, the collective diversity of airborne microorganisms. For that we performed daily analyses of all prokaryotes and eukaryotes (including plants) using multi-marker high-throughput sequencing for a total of three weeks. We linked the resulting communities to local weather conditions, to assess determinants of aerobiome composition and distribution. We observed hundreds of microbial taxa, mostly belonging to spore-forming organisms including fungi, but also protists. Additionally, we detected many potential human- and plant-pathogens. Community composition fluctuated on a daily basis and was linked to concurrent weather conditions, particularly air pressure and temperature. Using network analyses, we identified taxonomically diverse groups of organisms with correlated temporal dynamics. In part, this was due to co-variation with environmental conditions, while we could also detect specific host-parasite interactions. This study provides the first full inventory of the aerobiome and identifies putative drivers of its dynamics in terms of taxon composition. This knowledge can help develop early warning systems against pathogens and improve our understanding of microbial dispersal., Environment International, 154, ISSN:0160-4120, ISSN:1873-6750
- Published
- 2021
38. Testing the passive sampling hypothesis: The role of dispersal in shaping microbial species-area relationship.
- Author
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Deng W, Yu GB, Yang XY, and Xiao W
- Abstract
Dispersal is one of the key processes determining biodiversity. The passive sampling hypothesis, which emphasizes dispersal processes, suggests that larger habitats receive more species from the species pool as the main mechanism leading to more species in larger habitats than in smaller habitats (i.e., species-area relationships). However, the specific mechanisms by which dispersion shapes biodiversity still need to be discovered due to the difficulties of quantifying dispersal and the influence of multiple factors. Solving the above problem with a designed experiment is necessary to test the passive sampling hypothesis. This study designed a passive sampling experiment using sterile filter paper to quantify the microbial diffusion process, excluding the effects of pure sampling effects, habitat heterogeneity, and extinction processes. The results of high-throughput sequencing showed that a larger filter paper could receive more colonists, and the passive sampling hypothesis of SAR was confirmed. Dispersal shaped SAR by increasing species richness, especially rare species, and increasing the species replacement rate between habitats. These two processes are the mechanisms by which dispersal shapes biodiversity patterns. Compared with the results of this study, the commonly used mathematical model of passive sampling was able to predict the richness of non-rare species accurately but underestimated the richness of rare species. Underestimating rare species by mathematical models of passive sampling is more severe in small habitats. These findings provide new insights into the study of dispersal processes and the mechanism of species-area relationships., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Deng, Yu, Yang and Xiao.)
- Published
- 2023
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- View/download PDF
39. Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion.
- Author
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Ruan, Chujin, Ramoneda, Josep, Gogia, Guram, Wang, Gang, and Johnson, David R.
- Subjects
- *
PLASMIDS , *BACTERIAL diversity , *DISPERSAL (Ecology) , *HORIZONTAL gene transfer , *DRUG resistance in bacteria , *BACTERIAL communities , *BACTERIAL population , *URBAN growth , *SYNTROPHISM - Abstract
The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains. This is true regardless of the type of interaction (competition or resource cross-feeding) imposed between the bacterial strains. We further show that the underlying cause is that flagellar motility drives bacterial dispersal along the hyphal network, which counteracts the purifying effects of ecological drift at the expansion frontier. We finally demonstrate that hyphae-mediated spatial intermixing increases the conjugation-mediated spread of plasmid-encoded antibiotic resistance. In conclusion, fungal hyphae are important regulators of bacterial diversity and promote plasmid-mediated functional novelty during range expansion in an interaction-independent manner. [Display omitted] • Fungal hyphae promote and maintain bacterial diversity during range expansion • Fungal hyphae increase bacterial dispersal and counteract ecological drift • This increases the spatial intermixing of different bacterial populations • The increased spatial intermixing promotes plasmid-mediated functional novelty Ruan et al. demonstrate that fungal hyphae can promote and maintain bacterial diversity during range expansion. Fungal hyphae increase bacterial dispersal, which counteracts the effects of ecological drift at the expansion frontier. This increases the spatial intermixing of different populations and promotes plasmid-mediated functional novelty. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
40. Biodiversity gradients in obligate symbiotic organisms: exploring the diversity and traits of lichen propagules across the United States.
- Author
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Tripp, Erin A., Lendemer, James C., Barberán, Albert, Dunn, Robert R., and Fierer, Noah
- Subjects
- *
SYMBIOSIS , *LICHENS , *URBANIZATION , *BIOGEOGRAPHY - Abstract
Aim Large-scale distributions of plants and animals have been studied extensively and form the foundation for core concepts and paradigms in biogeography and macroecology. Much less attention has been given to other groups of organisms, particularly obligate symbiotic organisms. We present the first quantitative assessment of how spatial and environmental variables shape the abundance and distribution of obligate symbiotic organisms across nearly an entire subcontinent, using lichen propagules as an example. Location The contiguous United States (excluding Alaska and Hawaii). Methods We use DNA sequence-based analyses of lichen reproductive propagules from settled dust samples collected from nearly 1300 home exteriors to reconstruct biogeographical correlates of lichen taxonomic and functional diversity. Results Contrary to expectations, we found a weak but significant reverse latitudinal gradient in lichen propagule diversity. Diversity was not impacted by urbanization or human population density. We show that propagules of asexually reproducing species have wider geographical ranges than propagules from sexually reproducing species, likely reflecting the lichenized nature of asexual spores that disperse both the mycobiont and photobiont versus non-lichenized sexual spores, which disperse only the mycobiont. Main Conclusions Our findings of a reverse latitudinal gradient and a relative lack of impact of urbanization on lichen propagules and/or lichen-forming fungal spores suggest that core concepts in biogeography are better informed via consideration of additional patterns from other, less well studied groups of organisms. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
41. Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean.
- Author
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Mayol, Eva, Jiménez, María A., Herndl, Gerhard J., Duarte, Carlos M., and Arrieta, Jesús M.
- Subjects
MICROORGANISMS ,MICROBIAL diversity ,SURFACE of the earth ,MICROBIOLOGICAL aerosols ,BOUNDARY layer (Aerodynamics) - Abstract
Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of diversity in aquatic systems and in meteorological processes such as cloud formation. Yet, there is almost no information about the abundance and fate of microbes over the oceans, which cover >70% of the Earth's surface and are the likely source and final destination of a large fraction of airborne microbes. We measured the abundance of microbes in the lower atmosphere over a transect covering 17° of latitude in the North Atlantic Ocean and derived estimates of air-sea exchange of microorganisms from meteorological data. The estimated load of microorganisms in the atmospheric boundary layer ranged between 6 × 104 and 1.6 × 107 microbes per m2 of ocean, indicating a very dynamic air-sea exchange with millions of microbes leaving and entering the ocean per m
2 every day. Our results show that about 10% of the microbes detected in the boundary layer were still airborne 4 days later and that they could travel up to 11,000km before they entered the ocean again. The size of the microbial pool hovering over the North Atlantic indicates that it could play a central role in the maintenance of microbial diversity in the surface ocean and contribute significantly to atmospheric processes. [ABSTRACT FROM AUTHOR]- Published
- 2014
- Full Text
- View/download PDF
42. Significant changes in the skin microbiome mediated by the sport of roller derby
- Author
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James F. Meadow, Ashley C. Bateman, Keith M. Herkert, Timothy K. O’Connor, and Jessica L. Green
- Subjects
Microbial biogeography ,Contact sport ,Human microbiome ,Microbial ecology ,Skin microbiology ,Microbial dispersal ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Diverse bacterial communities live on and in human skin. These complex communities vary by skin location on the body, over time, between individuals, and between geographic regions. Culture-based studies have shown that human to human and human to surface contact mediates the dispersal of pathogens, yet little is currently known about the drivers of bacterial community assembly patterns on human skin. We hypothesized that participation in a sport involving skin to skin contact would result in detectable shifts in skin bacterial community composition. We conducted a study during a flat track roller derby tournament, and found that teammates shared distinct skin microbial communities before and after playing against another team, but that opposing teams’ bacterial communities converged during the course of a roller derby bout. Our results are consistent with the hypothesis that the human skin microbiome shifts in composition during activities involving human to human contact, and that contact sports provide an ideal setting in which to evaluate dispersal of microorganisms between people.
- Published
- 2013
- Full Text
- View/download PDF
43. Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks.
- Author
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Ebrahimi, Ali N. and Or, Dani
- Subjects
DISPERSAL of microorganisms ,UNSATURATED compounds ,BACTERIAL cells ,WATER pollution ,WATER supply ,POROUS materials ,HYDRATION - Abstract
The dispersal rates of self-propelled microorganisms affect their spatial interactions and the ecological functioning of microbial communities. Microbial dispersal rates affect risk of contamination of water resources by soil-borne pathogens, the inoculation of plant roots, or the rates of spoilage of food products. In contrast with the wealth of information on microbial dispersal in water replete systems, very little is known about their dispersal rates in unsaturated porous media. The fragmented aqueous phase occupying complex soil pore spaces suppress motility and limits dispersal ranges in unsaturated soil. The primary objective of this study was to systematically evaluate key factors that shape microbial dispersal in model unsaturated porous media to quantify effects of saturation, pore space geometry, and chemotaxis on characteristics of principles that govern motile microbial dispersion in unsaturated soil. We constructed a novel 3-D angular pore network model (PNM) to mimic aqueous pathways in soil for different hydration conditions; within the PNM, we employed an individual-based model that considers physiological and biophysical properties of motile and chemotactic bacteria. The effects of hydration conditions on first passage times in different pore networks were studied showing that fragmentation of aquatic habitats under dry conditions sharply suppresses nutrient transport and microbial dispersal rates in good agreement with limited experimental data. Chemotactically biased mean travel speed of microbial cells across 9 mm saturated PNM was ∼3 mm/h decreasing exponentially to 0.45 mm/h for the PNM at matric potential of [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
44. Major imprint of surface plankton on deep ocean prokaryotic structure and activity
- Author
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Josep M. Gasol, Susana Agustí, Xosé Anxelu G. Morán, Enrique Moreno-Ostos, Isabel Reche, M. Montserrat Sala, Guillem Salazar, Xosé Antón Álvarez-Salgado, Carlos M. Duarte, Marta Sebastián, Clara Ruiz-González, Mireia Mestre, Marta Estrada, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, King Abdullah University of Science and Technology, Universidad de Las Palmas de Gran Canaria, Comisión Nacional de Investigación Científica y Tecnológica (Chile), and Agencia Estatal de Investigación (España)
- Subjects
0106 biological sciences ,0301 basic medicine ,Deep ocean ,Mesopelagic zone ,Particle sinking ,Surface phytoplankton ,Particle-attached ,Biology ,010603 evolutionary biology ,01 natural sciences ,Deep sea ,Bathyal zone ,03 medical and health sciences ,RNA, Ribosomal, 16S ,Carbon export ,Dissolved organic carbon ,Phytoplankton ,Genetics ,Organic matter ,Fluorescent dissolved ,Seawater ,Ciliophora ,Atlantic Ocean ,Indian Ocean ,Bacterial activity ,Ecology, Evolution, Behavior and Systematics ,Total organic carbon ,chemistry.chemical_classification ,Pacific Ocean ,Marine prokaryotic communities ,Plankton ,Microbial dispersal, Particle-attached ,030104 developmental biology ,Oceanography ,chemistry ,Fluorescent dissolved organic matter ,Dinoflagellida ,Microbial dispersal - Abstract
Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean, yet it remains unknown whether surface processes determine the assembly and function of bathypelagic prokaryotes to a larger extent than deep-sea physicochemical conditions. Here, we explored whether variations in surface phytoplankton assemblages across Atlantic, Pacific and Indian ocean stations can explain structural changes in bathypelagic (ca. 4,000 m) free-living and particle-attached prokaryotic communities (characterized through 16S rRNA gene sequencing), as well as changes in prokaryotic activity and dissolved organic matter (DOM) quality. We show that the spatial structuring of prokaryotic communities in the bathypelagic strongly followed variations in the abundances of surface dinoflagellates and ciliates, as well as gradients in surface primary productivity, but were less influenced by bathypelagic physicochemical conditions. Amino acid-like DOM components in the bathypelagic reflected variations of those components in surface waters, and seemed to control bathypelagic prokaryotic activity. The imprint of surface conditions was more evident in bathypelagic than in shallower mesopelagic (200–1,000 m) communities, suggesting a direct connectivity through fast-sinking particles that escape mesopelagic transformations. Finally, we identified a pool of endemic deep-sea prokaryotic taxa (including potentially chemoautotrophic groups) that appear less connected to surface processes than those bathypelagic taxa with a widespread vertical distribution. Our results suggest that surface planktonic communities shape the spatial structure of the bathypelagic microbiome to a larger extent than the local physicochemical environment, likely through determining the nature of the sinking particles and the associated prokaryotes reaching bathypelagic waters., Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio program (Malaspina 2010 Expedition) (FEDER funds) CSD2008-00077 CTM2015-70340R CTM2015-65720-R CTM2015-69936-P RTI2018-101025-B-I00 UCE.PP2017.03 CTM2015-69392-C3-2-R, King Abdullah University of Science & Technology, Juan de la Cierva fellowship, GRAMMI project IJCI-2015-23505 RTI2018-099740-J-I00, Viera y Clavijo contract - ACIISI, ULPGC, Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) FONDAP-IDEAL15150003 FONDECYT-POSTDOCTORADO 3190369
- Published
- 2020
45. The effect of microbial communities on soil hydrological processes: A microcosm study utilising simulated rainfall
- Author
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Allton, Kathryn E., Harris, James A., Rickson, R. Jane, and Ritz, Karl
- Subjects
- *
MICROORGANISM populations , *RAINFALL , *PLANT biomass , *PHOSPHOLIPIDS - Abstract
Abstract: The effects of soil microbial communities upon hydrological processes in relation to water holding capacity, run-off and percolation were assessed using sterile and non-sterile microcosms subjected to simulated rainfall. The treatments comprised a non-sterile field soil, soil sterilised by gamma-irradiation and sterile soil re-inoculated with field soil. Microbial biomass C was determined by chloroform fumigation–extraction and community structure by phospholipid fatty acid (PLFA) analysis. These properties were measured at the top, middle and bottom regions of the sloped (12°) microcosms. The field soil treatment had a significantly greater water holding capacity than the sterilised treatments. There was no significant difference in mean volumes of run-off or percolate between the treatments, although our results suggest a trend to a lower probability of run-off losses from a soil with higher microbial biomass and a greater potential for percolation of water. In re-inoculated treatments, microbial biomass was greater at the bottom of the slopes after rainfall, suggesting that the nascent community was relatively mobile. This effect did not occur in the field soil, although the community profiles in the re-inoculated and field soils were significantly different between the tops and bottoms of slope after rainfall. The soil microbial communities observed before and after rainfall application were significantly different for all treatments. The microbial community profiles associated with the run-off and percolate were significantly different to those found in the soil and also those found in the rainwater prior to application. Run-off and percolate community profiles were similar to one another, suggesting a consistency in the phenotypic structure of the phase of the microbial communities that was “water mobile”. This may be of significance when considering how microbial populations and communities disperse, and in relation to microbial quality of surface and groundwaters. [Copyright &y& Elsevier]
- Published
- 2007
- Full Text
- View/download PDF
46. Freezing Tolerance of Thermophilic Bacterial Endospores in Marine Sediments
- Author
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Bo Barker Jørgensen, M Cramm, S. Emil Ruff, Carmen Li, Anirban Chakraborty, and Casey R. J. Hubert
- Subjects
Microbiology (medical) ,Firmicutes ,spores ,lcsh:QR1-502 ,microbial ecology ,Endospore ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,Microbial ecology ,microbial dispersal ,DISPERSAL ,Extremophile ,SPACE ,Food science ,PROTECTION ,panspermia ,Incubation ,TEMPERATURE ,extremophiles ,030304 developmental biology ,Original Research ,0303 health sciences ,ENVIRONMENT ,biology ,030306 microbiology ,Chemistry ,MARS ,endospores ,biology.organism_classification ,BACILLUS-SUBTILIS SPORES ,Spore ,frozen environments ,13. Climate action ,SURVIVAL ,ACID-SOLUBLE PROTEINS ,Microcosm ,Bacteria ,RESISTANCE ,thermophiles - Abstract
Dormant endospores of anaerobic, thermophilic bacteria found in cold marine sediments offer a useful model for studying microbial biogeography, dispersal, and survival. The dormant endospore phenotype confers resistance to unfavorable environmental conditions, allowing dispersal to be isolated and studied independently of other factors such as environmental selection. To study the resilience of thermospores to conditions relevant for survival in extreme cold conditions, their viability following different freezing treatments was tested. Marine sediment was frozen at either -80 degrees C or -20 degrees C for 10 days prior to pasteurization and incubation at +50 degrees C for 21 days to assess thermospore viability. Sulfate reduction commenced at +50 degrees C following both freezing pretreatments indicating persistence of thermophilic endospores of sulfate-reducing bacteria. The onset of sulfate reduction at +50 degrees C was delayed in -80 degrees C pretreated microcosms, which exhibited more variability between triplicates, compared to -20 degrees C pretreated microcosms and parallel controls that were not frozen in advance. Microbial communities were evaluated by 16S rRNA gene amplicon sequencing, revealing an increase in the relative sequence abundance of thermophilic endospore-forming Firmicutes in all microcosms. Different freezing pretreatments (-80 degrees C and -20 degrees C) did not appreciably influence the shift in overall bacterial community composition that occurred during the +50 degrees C incubations. Communities that had been frozen prior to +50 degrees C incubation showed an increase in the relative sequence abundance of operational taxonomic units (OTUs) affiliated with the class Bacilli, relative to unfrozen controls. These results show that freezing impacts but does not obliterate thermospore populations and their ability to germinate and grow under appropriate conditions. Indeed the majority of the thermospore OTUs detected in this study (21 of 22) could be observed following one or both freezing treatments. These results are important for assessing thermospore viability in frozen samples and following cold exposure such as the very low temperatures that would be encountered during panspermia.
- Published
- 2019
47. Particle foraging strategies promote microbial diversity in marine environments.
- Author
-
Ebrahimi A, Goyal A, and Cordero OX
- Subjects
- Animals, Ecosystem, Fresh Water, Models, Theoretical, Oceans and Seas, Environment, Predatory Behavior
- Abstract
Microbial foraging in patchy environments, where resources are fragmented into particles or pockets embedded in a large matrix, plays a key role in natural environments. In the oceans and freshwater systems, particle-associated bacteria can interact with particle surfaces in different ways: some colonize only during short transients, while others form long-lived, stable colonies. We do not yet understand the ecological mechanisms by which both short- and long-term colonizers can coexist. Here, we address this problem with a mathematical model that explains how marine populations with different detachment rates from particles can stably coexist. In our model, populations grow only while on particles, but also face the increased risk of mortality by predation and sinking. Key to coexistence is the idea that detachment from particles modulates both net growth and mortality, but in opposite directions, creating a trade-off between them. While slow-detaching populations show the highest growth return (i.e., produce more net offspring), they are more susceptible to suffer higher rates of mortality than fast-detaching populations. Surprisingly, fluctuating environments, manifesting as blooms of particles (favoring growth) and predators (favoring mortality) significantly expand the likelihood that populations with different detachment rates can coexist. Our study shows how the spatial ecology of microbes in the ocean can lead to a predictable diversification of foraging strategies and the coexistence of multiple taxa on a single growth-limiting resource., Competing Interests: AE, AG, OC No competing interests declared, (© 2022, Ebrahimi et al.)
- Published
- 2022
- Full Text
- View/download PDF
48. Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function
- Abstract
Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities. Soil bacterial assemblages showed a strong influence of tree composition, but such community differences were not reflected in the structure of lake communities that developed during the experiment. Bacterial taxa showing the largest abundance increases during incubation were initially present in both lake water and across most soils, and were related to Cytophagales, Burkholderiales and Rhizobiales. No clear metabolic profiles based on inoculum source were found, yet soil-amended communities used 60% more substrate than non-inoculated communities. Overall, we show that terrestrial inputs influence aquatic communities by stimulating the growth and activity of certain ubiquitous taxa distributed across the terrestrial-aquatic continuum, yet different forest soils did not cause predictable changes in lake bacterioplankton assemblages
- Published
- 2018
49. Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function
- Author
-
Charles A. Nock, Clara Ruiz-González, Beatrix E. Beisner, Esther Archambault, Christian Messier, Isabelle Laforest-Lapointe, Paul A. del Giorgio, Steven W. Kembel, and Natural Sciences and Engineering Research Council of Canada
- Subjects
0301 basic medicine ,Aquatic Organisms ,Terrestrial inputs ,Forests ,Applied Microbiology and Biotechnology ,Microbiology ,Freshwater ecosystem ,Trees ,Soil ,03 medical and health sciences ,Rhizobiaceae ,RNA, Ribosomal, 16S ,Burkholderiales ,Soil Microbiology ,Biolog Ecoplates ,Ecology ,biology ,Bacteroidetes ,Illumina sequencing ,Freshwater ecosystems ,Community structure ,Soil chemistry ,Bacterioplankton ,Plankton ,biology.organism_classification ,Bacterial communities ,Rhizobiales ,Lakes ,030104 developmental biology ,IDENT ,Soil water ,Soil microbiology ,Microbial dispersal - Abstract
15 pages, 6 figures, 3 tables, supplementary data https://doi.org/10.1093/femsec/fiy115, Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities. Soil bacterial assemblages showed a strong influence of tree composition, but such community differences were not reflected in the structure of lake communities that developed during the experiment. Bacterial taxa showing the largest abundance increases during incubation were initially present in both lake water and across most soils, and were related to Cytophagales, Burkholderiales and Rhizobiales. No clear metabolic profiles based on inoculum source were found, yet soil-amended communities used 60% more substrate than non-inoculated communities. Overall, we show that terrestrial inputs influence aquatic communities by stimulating the growth and activity of certain ubiquitous taxa distributed across the terrestrial-aquatic continuum, yet different forest soils did not cause predictable changes in lake bacterioplankton assemblages, This work was supported by the Natural Science and Engineering Research Council of Canada (NSERC) and Hydro-Quebec, as well as by the Fons de Reserche Nature et Technologies (FRQNT) and the Canada Research Chairs program
- Published
- 2018
50. Infant and Adult Gut Microbiome and Metabolome in Rural Bassa and Urban Settlers from Nigeria
- Author
-
Jessica Fiori, Haruna J. Audu, Stephanie L. Schnorr, Patrizia Brigidi, Leonardo Caporali, Sandra Cristino, Marco Candela, Valerio Carelli, Funmilola A. Ayeni, Matteo Soverini, Simone Rampelli, Silvia Turroni, Elena Biagi, Ayeni, Funmilola A., Biagi, Elena, Rampelli, Simone, Fiori, Jessica, Soverini, Matteo, Audu, Haruna J., Cristino, Sandra, Caporali, Leonardo, Schnorr, Stephanie L., Carelli, Valerio, Brigidi, Patrizia, Candela, Marco, and Turroni, Silvia
- Subjects
0301 basic medicine ,Adult ,Rural Population ,Adolescent ,Urban Population ,Nigeria ,urbanization ,Gut flora ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Feces ,Young Adult ,human evolution ,microbial dispersal ,Urbanization ,Metabolome ,Humans ,Ecosystem ,Microbiome ,Child ,Neoteny ,Aged ,Principal Component Analysis ,Biochemistry, Genetics and Molecular Biology (all) ,biology ,gut microbiota ,Geography ,Ecology ,Subsistence agriculture ,Infant ,subsistence pattern ,Biodiversity ,Middle Aged ,biology.organism_classification ,Diet ,Gastrointestinal Microbiome ,030104 developmental biology ,Socioeconomic Factors ,Child, Preschool ,Biological dispersal ,infant microbiome - Abstract
We assessed the subsistence-related variation of the human gut microbiome at a fine resolution for two of the main dimensions of microbiome variation, age and geography. For this, we investigated the fecal microbiome and metabolome in rural Bassa and urbanized individuals from Nigeria, including infants, and compared data with worldwide populations practicing varying subsistence. Our data highlight specific microbiome traits that are progressively lost with urbanization, such as the dominance of pristine fiber degraders and the low inter-individual variation. For the Bassa, this last feature is the result of their subsistence-related practices favoring microbial dispersal, such as their extensive environmental contact and the usage of untreated waters from the Usuma River. The high degree of microbial dispersal observed in the Bassa meta-community nullifies the differences between infant and adult intestinal ecosystems, suggesting that the infant-type microbiome in Western populations could be the result of microbiome-associated neotenic traits favored by urbanization. Ayeni et al. characterize the fecal microbiome and metabolome of rural Bassa and urban individuals from Nigeria, including infants. Their findings stress the loss of ancient signatures along with urbanization and support distinct trajectories of development of the intestinal ecosystem in early life, depending on human subsistence.
- Published
- 2018
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