56 results on '"Jay T. Lennon"'
Search Results
2. Principles of seed banks and the emergence of complexity from dormancy
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Maite Wilke-Berenguer, Jochen Blath, Jay T. Lennon, and Frank den Hollander
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Light ,Science ,General Physics and Astronomy ,Tree of life ,Review Article ,Environment ,Theoretical ecology ,General Biochemistry, Genetics and Molecular Biology ,Gene Expression Regulation, Plant ,Humans ,Cancer biology ,Ecosystem ,Evolutionary theory ,Cognitive science ,Multidisciplinary ,Temperature ,food and beverages ,Biodiversity ,General Chemistry ,Plant Dormancy ,Applied mathematics ,Seed Bank ,Seedlings ,Seeds ,Dormancy ,Metabolic activity - Abstract
Across the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise to multi-scale structures and networks spanning collections of cells to entire ecosystems. We outline the fundamental attributes and emergent phenomena associated with dormancy and seed banks, with the vision for a unifying and mathematically based framework that can address problems in the life sciences, ranging from global change to cancer biology., Seed banks are generated when individuals enter a dormant state, a phenomenon that has evolved among diverse taxa, but that is also found in stem cells, brains, and tumors. Here, Lennon et al. synthesize the fundamentals of seed-bank theory and the emergence of complex patterns and dynamics in mathematics and the life sciences.
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- 2021
3. Resource heterogeneity structures aquatic bacterial communities
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Mario E. Muscarella, Corey D. Broeckling, Jay T. Lennon, and Claudia M. Boot
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DNA, Bacterial ,Microorganism ,Biology ,Microbiology ,Article ,03 medical and health sciences ,RNA, Ribosomal, 16S ,Dissolved organic carbon ,Ecosystem ,Organic matter ,Relative species abundance ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Bacteria ,030306 microbiology ,Ecology ,Microbiota ,Bacterioplankton ,Lakes ,chemistry ,Species evenness ,Species richness - Abstract
Microorganisms are strongly influenced by the bottom-up effects of resource supply. While many species respond to fluctuations in the concentration of resources, microbial diversity may also be affected by the heterogeneity of the resource pool, which often reflects a mixture of distinct molecules. To test this hypothesis, we examined resource–diversity relationships for bacterioplankton in a set of north temperate lakes that varied in their concentration and composition of dissolved organic matter (DOM), which is an important resource for heterotrophic bacteria. Using 16S rRNA transcript sequencing and ecosystem metabolomics, we documented strong relationships between bacterial alpha-diversity (richness and evenness) and the bulk concentration and the number of molecules in the DOM pool. Similarly, bacterial community beta-diversity was related to both DOM concentration and composition. However, in some lakes the relative abundance of resource generalists, which was inversely related to the DOM concentration, may have reduced the effect of DOM heterogeneity on community composition. Together, our results demonstrate the potential metabolic interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.
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- 2019
4. Microbial community composition is affected by press, but not pulse, seawater intrusion
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Christopher B. Craft, Nathan I. Wisnoski, Merryl Alber, Sarah Widney, Courtney Mobilian, and Jay T. Lennon
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0106 biological sciences ,geography ,Biogeochemical cycle ,Marsh ,geography.geographical_feature_category ,010504 meteorology & atmospheric sciences ,Brackish water ,Ecology ,010604 marine biology & hydrobiology ,Field experiment ,15. Life on land ,01 natural sciences ,6. Clean water ,Microbial population biology ,13. Climate action ,Environmental science ,Seawater ,Ecosystem ,14. Life underwater ,0105 earth and related environmental sciences ,Long-term experiment - Abstract
Tidal freshwater marshes (TFMs) are threatened by seawater intrusion, which can affect microbial communities and alter biogeochemical processes. Here, we report on Seawater Addition Long Term Experiment (SALTEx), a manipulative field experiment that investigated continuous (press) and episodic (pulse, 2 months/yr) inputs of brackish water on microbial communities in a TFM. After 2.5 years, microbial diversity was lower in press treatments than in control (untreated) plots. Sulfate reducers increased in response to both press and pulse treatments whereas methanogens did not differ among treatments. Our results suggest that microbial communities in TFMs are resilient to episodic events, but that continuous seawater intrusion may alter bacterial diversity in ways that affect ecosystem functioning.Scientific Significance StatementSea level rise and seawater intrusion threaten tidal freshwater marshes (TFMs) and the important ecosystem services they provide. Intrusion of seawater in TFMs can occur across a range of timescales, such as episodic events, like storm surges or drought, or continuous intrusion as a result of rising sea level. The effects of these stressors on TFM microbial communities are not well understood. Our multi-year field manipulation of brackish water inputs revealed that microbial communities were resilient to short-term pulses of salinity whereas continuous seawater intrusion led to reduced microbial diversity along with changes in relative abundance of key functional groups. Such alterations may diminish the ability of TFMs to sequester carbon and cycle nutrients.
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- 2020
- Full Text
- View/download PDF
5. Microbial community assembly in a multi-layer dendritic metacommunity
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Nathan I, Wisnoski and Jay T, Lennon
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Microbiota ,Ecosystem ,Phylogeny - Abstract
A major goal of metacommunity ecology is to infer the local- and regional-scale processes that underlie community assembly. In dendritic ecological networks, branching patterns and directional flow can alter the balance between local and regional factors during assembly. Vertical habitat structure may further affect community assembly in dendritic metacommunities. In this study, we analyzed the bacterial metacommunity of a fifth-order mountain stream network to assess differences in community assembly (1) between planktonic and benthic habitats, (2) across spatial scales, and (3) between headwater and downstream regions of the network. Using taxonomic and phylogenetic null modeling, we found habitat-specific spatial patterns of community assembly across the dendritic network. Compositional differences between planktonic and benthic communities were maintained by variable selection, but we also found evidence of local dispersal limitation between the two habitats. Planktonic community assembly was scale dependent, transitioning from homogeneous selection at local scales to variable selection at regional scales, while benthic community assembly was less scale dependent. Variable selection structured headwaters in both habitat types, but downstream communities were primarily structured by homogeneous selection, especially in sediments. Taken together, our results show that vertical habitat structure contributes to the scale-dependent processes of community assembly across the dendritic metacommunity.
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- 2020
6. Microbial Life Deep Underfoot
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Jay T. Lennon
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Range (biology) ,Microorganism ,Ecological and Evolutionary Science ,Biology ,microbial ecology ,complex mixtures ,Microbiology ,03 medical and health sciences ,Soil ,Microbial ecology ,Abundance (ecology) ,Virology ,Ecosystem ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Ecology ,Microbiota ,Biodiversity ,15. Life on land ,respiratory system ,biology.organism_classification ,soil microbiology ,QR1-502 ,Habitat ,North America ,environmental microbiology ,Commentary ,Soil microbiology ,human activities ,Archaea - Abstract
Soil is one of the most diverse microbial habitats on Earth. While the distribution and abundance of microbial taxa in surface soils have been well described, the phylogenetic and functional diversity of bacteria and archaea in deep-soil strata remains unexplored., Soil is one of the most diverse microbial habitats on Earth. While the distribution and abundance of microbial taxa in surface soils have been well described, the phylogenetic and functional diversity of bacteria and archaea in deep-soil strata remains unexplored. Brewer et al. (mBio 10:e01318-19, 2019, https://doi.org/10.1128/mBio.01318-19) documented consistent shifts in the composition and genomic attributes of microbial communities as a function of depth in 20 soil pits that spanned a range of ecosystems across North America. The unique microorganisms found in deep soils appear to be adapted to conditions of low energy based on the recovery of genes that code for traits such as internal resource storage, mixotrophy, and dormancy.
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- 2020
7. Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients
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Breah LaSarre, Jay T. Lennon, James B. McKinlay, and Alexandra L. McCully
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0301 basic medicine ,Nitrogen ,030106 microbiology ,Carboxylic Acids ,Biology ,Models, Biological ,Microbiology ,03 medical and health sciences ,Microbial ecology ,Escherichia coli ,Ecosystem ,Symbiosis ,Nitrogen cycle ,Ecology, Evolution, Behavior and Systematics ,Mutualism (biology) ,Ecology ,Heterotrophic Processes ,biology.organism_classification ,Carbon ,Food web ,Rhodopseudomonas ,Environmental biotechnology ,Fermentation ,Original Article ,Rhodopseudomonas palustris - Abstract
Microbial interactions, including mutualistic nutrient exchange (cross-feeding), underpin the flow of energy and materials in all ecosystems. Metabolic exchanges are difficult to assess within natural systems. As such, the impact of exchange levels on ecosystem dynamics and function remains unclear. To assess how cross-feeding levels govern mutualism behavior, we developed a bacterial coculture amenable to both modeling and experimental manipulation. In this coculture, which resembles an anaerobic food web, fermentative Escherichia coli and photoheterotrophic Rhodopseudomonas palustris obligately cross-feed carbon (organic acids) and nitrogen (ammonium). This reciprocal exchange enforced immediate stable coexistence and coupled species growth. Genetic engineering of R. palustris to increase ammonium cross-feeding elicited increased reciprocal organic acid production from E. coli, resulting in culture acidification. Consequently, organic acid function shifted from that of a nutrient to an inhibitor, ultimately biasing species ratios and decreasing carbon transformation efficiency by the community; nonetheless, stable coexistence persisted at a new equilibrium. Thus, disrupting the symmetry of nutrient exchange can amplify alternative roles of an exchanged resource and thereby alter community function. These results have implications for our understanding of mutualistic interactions and the use of microbial consortia as biotechnology.
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- 2016
8. Metabolic insight into bacterial community assembly across ecosystem boundaries
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Nathan I. Wisnoski, Ariane L. Peralta, Jay T. Lennon, Megan L. Larsen, and Mario E. Muscarella
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Metacommunity ,0106 biological sciences ,Niche ,Population ,Biology ,Models, Biological ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Ecosystem ,education ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,High rate ,0303 health sciences ,education.field_of_study ,Bacteria ,Metabolic heterogeneity ,Ecology ,010604 marine biology & hydrobiology ,Aquatic ecosystem ,Species sorting ,15. Life on land ,Habitat ,Biological dispersal - Abstract
The movement of organisms across habitat boundaries has important consequences for populations, communities, and ecosystems. However, because most species are not well adapted to all habitat types, dispersal into suboptimal habitats could induce physiological changes associated with persistence strategies that influence community assembly. For example, high rates of cross-boundary dispersal are thought to maintain sink populations of terrestrial bacteria in aquatic habitats, but these bacteria may also persist by lowering their metabolic activity, introducing metabolic heterogeneity that buffers the population against niche selection. To differentiate between these assembly processes, we analyzed bacterial composition along a hydrological flow path from terrestrial soils through an aquatic reservoir by sequencing the active and total (active + inactive) portions of the community. When metabolic heterogeneity was ignored, our data were consistent with views that cross-boundary dispersal is important for structuring aquatic bacterial communities. In contrast, we found evidence for strong niche selection when metabolic heterogeneity was explicitly considered, suggesting that, relative to persistence strategies, dispersal may have a weaker effect on aquatic community assembly than previously thought. By accounting for metabolic heterogeneity in complex communities, our findings clarify the roles of local- and regional-scale assembly processes in terrestrial-aquatic meta-ecosystems.
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- 2019
- Full Text
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9. Dormancy in Metacommunities
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Nathan I. Wisnoski, Mathew A. Leibold, and Jay T. Lennon
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0106 biological sciences ,Metacommunity ,Ecology ,Plant Dispersal ,010604 marine biology & hydrobiology ,Ecology (disciplines) ,Torpor ,Population Dynamics ,Community structure ,Biology ,Plants ,Plant Dormancy ,010603 evolutionary biology ,01 natural sciences ,Biological Evolution ,Biota ,Seeds ,Biological dispersal ,Dormancy ,Animals ,Animal Distribution ,Ecology, Evolution, Behavior and Systematics ,Ecosystem - Abstract
Although metacommunity ecology has improved our understanding of how dispersal affects community structure and dynamics across spatial scales, it has yet to adequately account for dormancy. Dormancy is a reversible state of reduced metabolic activity that enables temporal dispersal within the metacommunity. Dormancy is also a metacommunity-level process because it can covary with spatial dispersal and affect diversity across spatial scales. We develop a framework to integrate dispersal and dormancy, focusing on the covariation they exhibit, to predict how dormancy modifies the importance of species interactions, dispersal, and historical contingencies in metacommunities. We examine case studies of microcrustaceans in ephemeral ponds, where dormancy is integral to metacommunity dynamics. We analyze traits of bromeliad-dwelling invertebrates and identify constraints on dispersal and dormancy strategies. Using simulations, we demonstrate that dormancy can alter classic metacommunity patterns of diversity in ways that depend on dispersal–dormancy covariation and spatiotemporal environmental variability. We propose that dormancy may also facilitate evolution-mediated priority effects if locally adapted seed banks prevent colonization by more dispersal-limited species. We present theoretically and empirically testable predictions for other possible ecological and evolutionary implications of dormancy in metacommunities, some of which may fundamentally alter our understanding of metacommunity ecology.
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- 2019
10. Species sorting along a subsidy gradient alters bacterial community stability
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Stuart E. Jones, Jay T. Lennon, and Mario E. Muscarella
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0301 basic medicine ,Food Chain ,Bacteria ,Ecology ,Aquatic ecosystem ,Species sorting ,Carbon ,Food web ,03 medical and health sciences ,030104 developmental biology ,Dissolved organic carbon ,Environmental science ,Species evenness ,Ecosystem ,Species richness ,Relative species abundance ,Ecology, Evolution, Behavior and Systematics - Abstract
The movement of resources between terrestrial and aquatic habitats has strong effects on ecological processes in recipient ecosystems. Allochthonous inputs modify the quality and quantity of the available resource pool in ways that may alter the composition and stability of recipient communities. Inputs of terrestrial dissolved organic carbon (tDOC) into aquatic ecosystems represent a large influx of resources that has the potential to affect local communities, especially microorganisms. To evaluate the effects of terrestrial inputs on aquatic bacterial community composition and stability, we manipulated the supply rate of tDOC to a set of experimental ponds. Along the tDOC supply gradient, we measured changes in diversity and taxon-specific changes in relative abundance and activity. We then determined community stability by perturbing each pond using a pulse of inorganic nutrients and measuring changes in composition and activity (i.e., responsiveness) along the gradient. Terrestrial DOC supply significantly altered the composition of the active bacterial community. The composition of the active bacterial community changed via decreases in richness and evenness as well as taxon-specific changes in relative abundance and activity indicating species sorting along the gradient. Likewise, the responsiveness of the active bacterial community decreased along the gradient, which led to a more stable active community. We did not, however, observe these changes in diversity and stability in the total community (i.e., active and inactive organisms), which suggests that tDOC supply modifies bacterial community stability through functional not structural changes. Together, these results show that altered aquatic terrestrial linkages can have profound effects on the activity and stability of the base of the food web and thus can alter ecosystem functioning.
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- 2016
11. A trait-based approach to bacterial biofilms in soil
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Brent K. Lehmkuhl and Jay T. Lennon
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0301 basic medicine ,Ecology ,030106 microbiology ,Biofilm ,biochemical phenomena, metabolism, and nutrition ,Biology ,Microbiology ,03 medical and health sciences ,Niche construction ,030104 developmental biology ,Botany ,Soil water ,Trait ,Ecosystem ,Desiccation ,Water content ,Soil microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
A trait-based approach focuses on attributes of taxa that influence the structure and function of communities. Biofilm production is a common trait among microorganisms in a wide range of environmental, engineered, and host-associated ecosystems. Here, we used Pseudomonas aeruginosa to link biofilm production to moisture availability, a common stressor for microorganisms in soil. First, we demonstrate that biofilm production is a response trait that influences the desiccation phenotype by increasing survivorship, shifting the niche space, and reducing the minimum water potential needed to sustain a net-positive growth rate (Ψ*). Although the allocation of resources to biofilms is thought to be costly, we found no evidence for a trade-off between fitness and biofilm production along a soil moisture gradient. Second, we demonstrated that biofilm production is an effect trait. Specifically, biofilm production increased water retention in soils that were exposed to a series of drying and rewetting cycles. Although this form of niche construction should affect species interactions, we found no evidence that the benefits of biofilm production were extended to another co-occurring soil bacterium. Together, our results support the view that biofilm production is an important trait that may contribute to the distribution, abundance, and functioning of microorganisms in soils.
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- 2016
12. Microbial dormancy improves predictability of soil respiration at the seasonal time scale
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Jeffrey S. Dukes, Alejandro Salazar, and Jay T. Lennon
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010504 meteorology & atmospheric sciences ,Climate change ,01 natural sciences ,Soil respiration ,Abundance (ecology) ,Environmental Chemistry ,Ecosystem ,Earth-Surface Processes ,Water Science and Technology ,0105 earth and related environmental sciences ,2. Zero hunger ,Biomass (ecology) ,Moisture ,biology ,Ecology ,Global warming ,04 agricultural and veterinary sciences ,Soil carbon ,15. Life on land ,biology.organism_classification ,13. Climate action ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Environmental science ,Dormancy ,Bacteria - Abstract
Climate change is accelerating global soil respiration, which could in turn accelerate climate change. The biological mechanisms through which soil carbon (C) responds to climate are not well understood, limiting our ability to predict future global soil respiration rates. As part of a climate manipulation experiment, we tested whether differences in soil heterotrophic respiration driven by season or climate treatment (RH) are linked to 1) relative abundances of microbes in active and dormant metabolic states, 2) net changes in microbial biomass and/or 3) changes in the relative abundances of microbial groups with different C-use strategies. We used a flow-cytometric single-cell metabolic assay to quantify the abundance of active and dormant microbes, and the phospholipid fatty acid (PLFA) method to determine microbial biomass and ratios of fungi:bacteria and Gram-positive:Gram-negative bacteria. RH did not respond to climate treatments but was greater in the warm and dry summer than in the cool and less-dry fall. These dynamics were better explained when microbial data were taken into account compared to when only physical data (temperature and moisture) were used. Overall, our results suggest that RH responses to temperature are stronger when soil contains more active microbes, and that seasonal patterns of RH can be better explained by shifts in microbial activity than by shifts in the relative abundances of fungi and Gram-positive and Gram-negative bacteria. These findings contribute to our understanding of how and under which conditions microbes influence soil C responses to climate.
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- 2018
- Full Text
- View/download PDF
13. Resource diversity structures aquatic bacterial communities
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Jay T. Lennon, Claudia M. Boot, Mario E. Muscarella, and Corey D. Broeckling
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chemistry.chemical_classification ,Resource (biology) ,chemistry ,Ecology ,Microbial diversity ,Species evenness ,Ecosystem ,Organic matter ,Species richness ,Biology ,Generalist and specialist species ,Diversity (business) - Abstract
Microbial diversity is strongly affected by the bottom-up effects of resource availability. However, because resource pools often exist as heterogeneous mixtures of distinct molecules, resource heterogeneity may also affect community diversity. To test this hypothesis, we surveyed bacterial communities in lakes that varied in resource concentration. In addition, we characterized resource heterogeneity in these lakes using an ecosystem metabolomics approach. Overall, resource concentration and resource heterogeneity affected bacterial resource-diversity relationships. We found strong relationships between bacterial alpha-diversity (richness and evenness) and resource concentration and richness, but richness and evenness responded in different ways. Likewise, we found associations between the composition of the bacterial community and both resource concentration and composition, but the relationship with resource composition was stronger. Last, in the surveyed communities the presence of resource generalists may have reduced the effect of resource heterogeneity on community composition. These results have implications for understanding the interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.
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- 2018
14. How, When, and Where Relic DNA Affects Microbial Diversity
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Sarah A Placella, Brent K. Lehmkuhl, Mario E. Muscarella, and Jay T. Lennon
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0301 basic medicine ,DNA, Bacterial ,Biodiversity ,Biology ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Abundance (ecology) ,Virology ,RNA, Ribosomal, 16S ,Ecosystem ,Gene ,Relative species abundance ,Phylogeny ,biodiversity ,sampling theory ,Bacteria ,Microbiota ,phylogenetic analysis ,mathematical modeling ,15. Life on land ,Models, Theoretical ,QR1-502 ,Phylogenetic diversity ,030104 developmental biology ,chemistry ,13. Climate action ,Evolutionary biology ,Evolutionary ecology ,ecology ,Extracellular Space ,DNA ,Research Article ,extracellular DNA - Abstract
Extracellular or “relic” DNA is one of the largest pools of nucleic acids in the biosphere. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also affect estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SADs) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33% of the total bacterial DNA pool but exceeded 80% in some samples. Despite its abundance, relic DNA had a minimal effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Our findings are consistent with the expectation that relic DNA from different taxa degrades at a constant and equal rate, suggesting that it may not fundamentally alter estimates of microbial diversity., IMPORTANCE The ability to rapidly obtain millions of gene sequences and transcripts from a range of environments has greatly advanced understanding of the processes that regulate microbial communities. However, nucleic acids extracted from complex samples do not come only from viable microorganisms. Dead microorganisms can generate large pools of relic DNA that distort insight into the ecology and evolution of microbial systems. Here, we develop a conceptual and quantitative framework for understanding how relic DNA influences the structure of microbiomes. Our theoretical models and empirical results demonstrate that a large relic DNA pool does not automatically lead to biased estimates of microbial diversity. Rather, relic DNA effects emerge in combination with microscale processes that alter the commonness and rarity of sequences found in heterogeneous DNA pools.
- Published
- 2018
15. Crop rotational diversity increases disease suppressive capacity of soil microbiomes
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Jay T. Lennon, Ariane L. Peralta, Marshall D. McDaniel, and Yanmei Sun
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0106 biological sciences ,Biodiversity ,structure–function relationships ,Biology ,01 natural sciences ,crop rotation ,disease suppression ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,QH540-549.5 ,2. Zero hunger ,Ecology ,Soil organic matter ,fungi ,food and beverages ,04 agricultural and veterinary sciences ,15. Life on land ,Crop rotation ,respiratory system ,Microbial population biology ,Crop diversity ,Agronomy ,microbial diversity ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Monoculture ,Soil fertility ,human activities ,010606 plant biology & botany - Abstract
Microbiomes can aid in the protection of hosts from infection and disease, but the mechanisms underpinning these functions in complex environmental systems remain unresolved. Soils contain microbiomes that influence plant performance, including their susceptibility to disease. For example, some soil microorganisms produce antimicrobial compounds that suppress the growth of plant pathogens, which can provide benefits for sustainable agricultural management. Evidence shows that crop rotations increase soil fertility and tend to promote microbial diversity, and it has been hypothesized that crop rotations can enhance disease suppressive capacity, either through the influence of plant diversity impacting soil bacterial composition or through the increased abundance of disease suppressive microorganisms. In this study, we used a long‐term field experiment to test the effects of crop diversity through time (i.e., rotations) on soil microbial diversity and disease suppressive capacity. We sampled soil from seven treatments along a crop diversity gradient (from monoculture to five crop species rotation) and a spring fallow (non‐crop) treatment to examine crop diversity influence on soil microbiomes including bacteria that are capable of producing antifungal compounds. Crop diversity significantly influenced bacterial community composition, where the most diverse cropping systems with cover crops and fallow differed from bacterial communities in the 1–3 crop species diversity treatments. While soil bacterial diversity was about 4% lower in the most diverse crop rotation (corn–soybean–wheat + 2 cover crops) compared to monoculture corn, crop diversity increased disease suppressive functional group prnD gene abundance in the more diverse rotation by about 9% compared to monocultures. In addition, disease suppressive potential was significantly diminished in the (non‐crop) fallow treatment compared to the most diverse crop rotation treatments. The composition of the microbial community could be more important than diversity to disease suppressive function in our study. Identifying patterns in microbial diversity and ecosystem function relationships can provide insight into microbiome management, which will require manipulating soil nutrients and resources mediated through plant diversity.
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- 2018
16. A test of the subsidy–stability hypothesis: the effects of terrestrial carbon in aquatic ecosystems
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Stuart E. Jones and Jay T. Lennon
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Ecological stability ,Nutrient ,Ecology ,Aquatic ecosystem ,Dissolved organic carbon ,Primary production ,Growing season ,Environmental science ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,Ecosystem services - Abstract
Global change is altering the movement of materials across landscapes in ways that likely have major consequences for the functioning and stability of ecosystems. For example, the export of dissolved organic carbon (DOC) from terrestrial to aquatic ecosystems is increasing globally. This browning phenomenon is expected to alter the stability of recipient aquatic ecosystems, but theory provides contrasting predictions about the form and direction of this response. We created a gradient in terrestrial DOC supply by adding humic substances on weekly basis to 10 experimental ponds (10 6 L each) over a growing season. The manipulation of terrestrial DOC supply had strong effects on the chemical, physical, and biological properties of the pond ecosystems. Light attenuation linearly increased with terrestrial DOC supply, which created a shading effect that negatively influenced whole-pond gross primary production and respiration. Despite this, bacterial contributions to basal energy mobilization and respiration increased with terrestrial DOC supply indicating that aquatic food webs were subsidized by terrestrial inputs. After establishing the DOC gradient, we used dynamic linear models to test the subsidy-stability hypothesis by measuring the resilience and sensitivity of each pond to a pulse nutrient perturbation. We found that recovery from the perturbation decreased nonlinearly along a gradient in terrestrial DOC supply. Reciprocal transplant experiments indicated that owing primarily to its light attenuating properties and recalcitrant nature, terrestrial DOC diminished aquatic ecosystem stability by reducing nutrient turnover rates (NTR). Together, our results demonstrate that global-change- mediated alterations in the movement of material and energy between habitats can have unpredictable and dramatic impacts on the reliability of ecosystem services.
- Published
- 2015
17. Ecosystem Consequences of Changing Inputs of Terrestrial Dissolved Organic Matter to Lakes: Current Knowledge and Future Challenges
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Jan Karlsson, Jasmine E. Saros, Brian C. Weidel, Jordan S. Read, Stuart E. Jones, Christopher T. Solomon, Steven Sadro, Soren H. H. Larsen, Megan L. Fork, Jay T. Lennon, and Ishi Buffam
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Ecology ,Environmental change ,ved/biology ,Ecology (disciplines) ,ved/biology.organism_classification_rank.species ,Lake ecosystem ,Current (stream) ,Terrestrial plant ,Dissolved organic carbon ,Environmental Chemistry ,Environmental science ,Ecosystem ,Ecology, Evolution, Behavior and Systematics - Abstract
Lake ecosystems and the services that they provide to people are profoundly influenced by dissolved organic matter derived from terrestrial plant tissues. These terrestrial dissolved organic matter (tDOM) inputs to lakes have changed substantially in recent decades, and will likely continue to change. In this paper, we first briefly review the substantial literature describing tDOM effects on lakes and ongoing changes in tDOM inputs. We then identify and provide examples of four major challenges which limit predictions about the implications of tDOM change for lakes, as follows: First, it is currently difficult to forecast future tDOM inputs for particular lakes or lake regions. Second, tDOM influences ecosystems via complex, interacting, physical-chemical-biological effects and our holistic understanding of those effects is still rudimentary. Third, non-linearities and thresholds in relationships between tDOM inputs and ecosystem processes have not been well described. Fourth, much understanding of tDOM effects is built on comparative studies across space that may not capture likely responses through time. We conclude by identifying research approaches that may be important for overcoming those challenges in order to provide policy- and management-relevant predictions about the implications of changing tDOM inputs for lakes.
- Published
- 2015
18. A social–ecological framework for 'micromanaging' microbial services
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Diana Stuart, Jay T. Lennon, Ariane L. Peralta, and Angela D. Kent
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Micromanagement ,Resource (biology) ,Ecology ,business.industry ,Social system ,Environmental resource management ,Ecosystem ,business ,Ecological systems theory ,Socioeconomic status ,Ecology, Evolution, Behavior and Systematics ,Ecosystem services - Abstract
Despite playing a central role in the regulation of ecosystem services, microorganisms are often neglected when evaluating feedbacks between social and ecological systems. A social–ecological framework is a tool for evaluating how social factors affect ecosystems through human actions and how ecological factors in turn affect social systems through ecosystem services. Here, we consider linkages and trade-offs between social and biophysical factors that arise when unique microbial attributes such as complexity, dispersal, and rapid evolution are integrated into a social–ecological framework. Using case studies from food production systems, wastewater treatment facilities, and synthetic biology, we show that unintended dis-services can arise when microbial information is limited or is ignored as a result of socioeconomic policies and practices. In contrast, when knowledge about microorganisms is integrated into a social–ecological framework, we can identify how to best maximize microbial services. New scientific tools used to characterize microbial traits, communities, and functions will enhance our ability to monitor microorganisms in diverse systems. However, communication and collaboration among stakeholders – including policy makers, landowners, resource managers, and scientists – are also needed to foster more effective “micromanagement” of microbial services.
- Published
- 2014
19. How, when, and where relic DNA biases estimates of microbial diversity
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Sarah A Placella, Brent K. Lehmkuhl, Jay T. Lennon, and Mario E. Muscarella
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0303 health sciences ,030306 microbiology ,Ecology ,Biodiversity ,15. Life on land ,Biology ,DNA sequencing ,03 medical and health sciences ,chemistry.chemical_compound ,Phylogenetic diversity ,chemistry ,13. Climate action ,Abundance (ecology) ,Ecosystem ,Gene ,Relative species abundance ,DNA ,030304 developmental biology - Abstract
Extracellular or “relic” DNA is one of the largest pools of nucleic acids in the mbiosphere1,2. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also bias estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SAD) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33 % of the total bacterial DNA pool, but exceeded 80 % in some samples. Despite its abundance, relic DNA had no effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Rather, our findings are consistent with the expectation that relic DNA sequences degrade in proportion to their abundance and therefore may contribute minimally to estimates of microbial diversity.
- Published
- 2017
20. A macroecological theory of microbial biodiversity
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William R. Shoemaker, Jay T. Lennon, and Kenneth J. Locey
- Subjects
0106 biological sciences ,0301 basic medicine ,0303 health sciences ,Ecology ,030306 microbiology ,Scale (chemistry) ,Biodiversity ,Biology ,15. Life on land ,Ecological systems theory ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Microbial ecology ,Abundance (ecology) ,13. Climate action ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,Macroecology ,Relative abundance distribution ,030304 developmental biology - Abstract
Microorganisms are the most abundant, diverse, and functionally important organisms on Earth. Over the past decade, microbial ecologists have produced the largest ever community datasets. However, these data are rarely used to uncover law-like patterns of commonness and rarity, test theories of biodiversity, or explore unifying explanations for the structure of microbial communities. Using a global-scale compilation of >20,000 samples from environmental, engineered, and host-related ecosystems, we test the power of competing theories to predict distributions of microbial abundance and diversity-abundance scaling laws. We show that these patterns are best explained by the synergistic interaction of stochastic processes that are captured by lognormal dynamics. We demonstrate that lognormal dynamics have predictive power across scales of abundance, a criterion that is essential to biodiversity theory. By understanding the multiplicative and stochastic nature of ecological processes, scientists can better understand the structure and dynamics of Earth’s largest and most diverse ecological systems.
- Published
- 2016
21. Understanding how microbiomes influence the systems they inhabit
- Author
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Mark A. Bradford, Emily B. Graham, Raven L. Bier, Kenneth J. Locey, Paul A. del Giorgio, Jay T. Lennon, Jennifer D. Rocca, Emily S. Bernhardt, Mark P. Waldrop, Claudia M. Boot, Joshua P. Schimel, Stuart E. Jones, Diana R. Nemergut, Matthew D. Wallenstein, Sarah E. Evans, James B. Cotner, Brooke B. Osborne, and Edward K. Hall
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0301 basic medicine ,Microbiology (medical) ,Correlative ,Bacteria ,Computer science ,Microbiota ,Immunology ,Inference ,Cell Biology ,Common framework ,Applied Microbiology and Biotechnology ,Microbiology ,Data science ,Field (geography) ,03 medical and health sciences ,030104 developmental biology ,Conceptual framework ,Microbial ecology ,Genetics ,Microbiome ,Built environment ,Ecosystem - Abstract
Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.
- Published
- 2016
22. Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes
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Donald P. Breakwell, Tylan W. Magnusson, Zachary T. Aanderud, Alan R. Harker, Joshua C. Vert, and Jay T. Lennon
- Subjects
0301 basic medicine ,Microbiology (medical) ,biology ,Ecology ,030106 microbiology ,Great Salt Lake ,Alphaproteobacteria ,Lake ecosystem ,biology.organism_classification ,Microbiology ,salinity ,Actinobacteria ,Salinity ,03 medical and health sciences ,Extremophile ,Dormancy ,Ecosystem ,phosphorus ,Rhodobacteraceae ,seed banks ,extremophiles ,Original Research - Abstract
Bacteria employ a diverse array of strategies to survive under extreme environmental conditions but maintaining these adaptations comes at an energetic cost. If energy reserves drop too low, extremophiles may enter a dormant state to persist. We estimated bacterial dormancy and identified the environmental variables influencing our activity proxy in 10 hypersaline and freshwater lakes across the Western United States. Using ribosomal RNA:DNA ratios as an indicator for bacterial activity, we found that the proportion of the community exhibiting dormancy was 16% lower in hypersaline than freshwater lakes. Based on our indicator variable multiple regression results, saltier conditions in both freshwater and hypersaline lakes increased activity, suggesting that salinity was a robust environmental filter structuring bacterial activity in lake ecosystems. To a lesser degree, higher total phosphorus concentrations reduced dormancy in all lakes. Thus, even under extreme conditions, the competition for resources exerted pressure on activity. Within the compositionally distinct and less diverse hypersaline communities, abundant taxa were disproportionately active and localized in families Microbacteriaceae (Actinobacteria), Nitriliruptoraceae (Actinobacteria), and Rhodobacteraceae (Alphaproteobacteria). Our results are consistent with the view that hypersaline communities are able to capitalize on a seemingly more extreme, yet highly selective, set of conditions and finds that extremophiles may need dormancy less often to thrive and survive.
- Published
- 2016
23. Rapid responses of soil microorganisms improve plant fitness in novel environments
- Author
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Jennifer A. Lau and Jay T. Lennon
- Subjects
Time Factors ,Environmental change ,Climate Change ,Biodiversity ,Plant Development ,Climate change ,Environment ,Bacterial Physiological Phenomena ,Plant Physiological Phenomena ,Ecosystem ,Symbiosis ,Soil Microbiology ,Multidisciplinary ,Ecology ,fungi ,Fungi ,Correction ,food and beverages ,Plants ,Adaptation, Physiological ,Biological Evolution ,Droughts ,Agronomy ,Microbial population biology ,Wetlands ,Environmental science ,Adaptation ,Soil microbiology - Abstract
Global change is challenging plant and animal populations with novel environmental conditions, including increased atmospheric CO 2 concentrations, warmer temperatures, and altered precipitation regimes. In some cases, contemporary or “rapid” evolution can ameliorate the effects of global change. However, the direction and magnitude of evolutionary responses may be contingent upon interactions with other community members that also are experiencing novel environmental conditions. Here, we examine plant adaptation to drought stress in a multigeneration experiment that manipulated aboveground–belowground feedbacks between plants and soil microbial communities. Although drought stress reduced plant growth and accelerated plant phenologies, surprisingly, plant evolutionary responses to drought were relatively weak. In contrast, plant fitness in both drought and nondrought environments was linked strongly to the rapid responses of soil microbial community structure to moisture manipulations. Specifically, plants were most fit when their contemporary environmental conditions (wet vs. dry soil) matched the historical environmental conditions (wet vs. dry soil) of their associated microbial community. Together, our findings suggest that, when faced with environmental change, plants may not be limited to “adapt or migrate” strategies; instead, they also may benefit from association with interacting species, especially diverse soil microbial communities, that respond rapidly to environmental change.
- Published
- 2012
24. Nitrogen transformations in a through-flow wetland revealed using whole-ecosystem pulsed 15 N additions
- Author
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Stephen K. Hamilton, Lauren E Kinsman-Costello, Nathaniel E. Ostrom, Jonathan M. O'Brien, and Jay T. Lennon
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Hydrology ,Denitrification ,chemistry.chemical_element ,Aquatic Science ,Oceanography ,Nitrogen ,chemistry.chemical_compound ,Water column ,Nitrate ,chemistry ,Environmental chemistry ,Ammonium ,Nitrification ,Ecosystem ,Autotroph - Abstract
We used pulsed and continuous additions of 15N together with whole-ecosystem metabolism measurements to elucidate the mechanisms of nitrogen (N) transformations in a small (1170 m2) through-flow wetland situated along a stream. From measurements of the wetland inflow and outflow, we observed a consistent decrease in nitrate (by 10% of inflow concentrations), while ammonium increased by an order of magnitude. Outflow ammonium concentrations oscillated in a diel cycle, inverse to the concentration of dissolved oxygen (i.e., greater ammonium export at night). The pulsed 15N additions showed little uptake of nitrate over time in the wetland and rapid daytime uptake of ammonium from the water column (rate constant, kt 5 0.11 h21). A steady-state 15Nammonium addition demonstrated a similar rate of ammonium uptake (kt 5 0.067 h21), no detectable nitrification, and highlighted the spatial pattern of ammonium and nitrate uptake within the wetland. Porewater concentration profiles suggest high rates of net ammonium diffusion from the sediments. Ecosystem metabolism measurements indicate that release was attenuated during the day by autotrophic uptake, resulting in lower ammonium export during the day. Denitrification rates were modeled from dissolved N2 : Ar ratios, but they were not sufficient to account for the observed loss in nitrate. Nitrate was removed near the pond inflow but not actively cycled throughout the pond, while the balance between sediment release and subsequent uptake of ammonium from the water-column dominated N cycling in this wetland.
- Published
- 2012
25. Microbial contributions to subterranean methane sinks
- Author
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Kevin D. Webster, Dương Nguyễn-Thùy, Thomas Streil, Jay T. Lennon, Agnieszka Drobniak, T. M. Phạm, P. H. Tạ, Arndt Schimmelmann, and N. Ð. Phạm
- Subjects
0301 basic medicine ,Biogeochemical cycle ,010504 meteorology & atmospheric sciences ,030106 microbiology ,Microbial metabolism ,Biology ,01 natural sciences ,Sink (geography) ,Methane ,Mesocosm ,03 medical and health sciences ,chemistry.chemical_compound ,Cave ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,General Environmental Science ,0105 earth and related environmental sciences ,Abiotic component ,0303 health sciences ,geography ,geography.geographical_feature_category ,Bacteria ,030306 microbiology ,Ecology ,Atmospheric methane ,Global warming ,15. Life on land ,Tundra ,Caves ,Vietnam ,chemistry ,13. Climate action ,Greenhouse gas ,Environmental chemistry ,General Earth and Planetary Sciences ,Environmental science ,Climate model ,Oxidation-Reduction - Abstract
Sources and sinks of methane (CH4 ) are critical for understanding global biogeochemical cycles and their role in climate change. A growing number of studies have reported that CH4 concentrations in cave ecosystems are depleted, leading to the notion that these subterranean environments may act as sinks for atmospheric CH4 . Recently, it was hypothesized that this CH4 depletion may be caused by radiolysis, an abiotic process whereby CH4 is oxidized via interactions with ionizing radiation derived from radioactive decay. An alternate explanation is that the depletion of CH4 concentrations in caves could be due to biological processes, specifically oxidation by methanotrophic bacteria. We theoretically explored the radiolysis hypothesis and conclude that it is a kinetically constrained process that is unlikely to lead to the rapid loss of CH4 in subterranean environments. We present results from a controlled laboratory experiment to support this claim. We then tested the microbial oxidation hypothesis with a set of mesocosm experiments that were conducted in two Vietnamese caves. Our results reveal that methanotrophic bacteria associated with cave rocks consume CH4 at a rate of 1.3-2.7 mg CH4 · m-2 · d-1 . These CH4 oxidation rates equal or exceed what has been reported in other habitats, including agricultural systems, grasslands, deciduous forests, and Arctic tundra. Together, our results suggest that depleted concentrations of CH4 in caves are most likely due to microbial activity, not radiolysis as has been recently claimed. Microbial methanotrophy has the potential to oxidize CH4 not only in caves, but also in smaller-size open subterranean spaces, such as cracks, fissures, and other pores that are connected to and rapidly exchange with the atmosphere. Future studies are needed to understand how subterranean CH4 oxidation scales up to affect local, regional, and global CH4 cycling.
- Published
- 2015
26. Species sorting along a subsidy gradient alters community stability
- Author
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Mario E. Muscarella, Stuart E. Jones, and Jay T. Lennon
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0106 biological sciences ,0303 health sciences ,Ecology ,Aquatic ecosystem ,Species sorting ,Biology ,010603 evolutionary biology ,01 natural sciences ,Food web ,03 medical and health sciences ,Microbial population biology ,Abundance (ecology) ,Species evenness ,Ecosystem ,14. Life underwater ,Species richness ,030304 developmental biology - Abstract
The movement of resources between terrestrial and aquatic habitats has strong effects on ecological processes in recipient ecosystems. Allochthonous inputs modify the quality and quantity of the available resource pool in ways that may alter the composition and stability of recipient communities. Inputs of terrestrial dissolved organic carbon (tDOC) into aquatic ecosystems represent a large influx of resources that has the potential to affect local communities, especially microorganisms. To evaluate the effects terrestrial inputs on aquatic microbial community composition and stability, we manipulated the supply rate of tDOC to a set of experimental ponds. Along the tDOC supply gradient, we measured changes in diversity and taxon-specific changes in abundance and activity. We then determined community stability by perturbing each pond using a pulse of inorganic nutrients and measuring changes in composition and activity (i.e., responsiveness) along the gradient. Terrestrial DOC supply significantly altered the composition of the active microbial community. The composition of the active bacterial community changed via decreases in richness and evenness as well as taxon-specific changes in abundance and activity indicating species sorting along the gradient. Likewise, the responsiveness of the active bacterial community decreased along the gradient, which led to a more stable active community. We did not, however, observe these changes in diversity and stability in the total community (i.e., active and inactive organisms), which suggests that tDOC supply modifies microbial community stability through functional not structural changes. Together, these results show that altered aquatic terrestrial linkages can have profound effects on the activity and stability of the base of the food web and thus can alter ecosystem functioning.
- Published
- 2015
27. Crop diversity increases disease suppressive capacity of soil microbiomes
- Author
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McDaniel, Ariane L. Peralta, Sun Y, and Jay T. Lennon
- Subjects
0106 biological sciences ,2. Zero hunger ,fungi ,food and beverages ,04 agricultural and veterinary sciences ,15. Life on land ,Crop rotation ,Biology ,respiratory system ,010603 evolutionary biology ,01 natural sciences ,Agronomy ,Crop diversity ,Abundance (ecology) ,Soil water ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Ecosystem ,Monoculture ,Soil fertility ,Cover crop ,human activities - Abstract
Microbiomes can aid in the protection of hosts from infection and disease, but the mechanisms underpinning these functions in complex environmental systems remain unresolved. Soils contain microbiomes that influence plant performance, including their susceptibility to disease. For example, some soil microorganisms produce antimicrobial compounds that suppress the growth of plant pathogens, which can provide benefits for sustainable agricultural management. Evidence shows that crop rotations increase soil fertility and tend to promote microbial diversity, and it has been hypothesized that crop rotations can enhance disease suppressive capacity, either through the influence of plant diversity impacting soil bacterial composition or through the increased abundance of disease suppressive microorganisms. In this study, we used a long-term field experiment to test the effects of crop diversity through time (i.e., rotations) on soil microbial diversity and disease suppressive capacity. We sampled soil from seven treatments along a crop diversity gradient (from monoculture to five crop species rotation) and a spring fallow (non-crop) treatment to examine crop diversity influence on soil microbiomes including bacteria that are capable of producing antifungal compounds. Crop diversity significantly influenced bacterial community composition, where the most diverse cropping systems with cover crops and fallow differed from bacterial communities in the 1-3 crop species diversity treatments. While soil bacterial diversity was about 4% lower in the most diverse crop rotation (corn-soy-wheat + 2 cover crops) compared to monoculture corn, crop diversity increased disease suppressive functional group prnD gene abundance in the more diverse rotation by about 9% compared to monocultures. Identifying patterns in microbial diversity and ecosystem function relationships can provide insight into microbiome management, which will require manipulating soil nutrients and resources mediated through plant diversity.
- Published
- 2015
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28. Integrating microbial ecology into ecosystem models: challenges and priorities
- Author
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Eric A. Dubinsky, Kirsten S. Hofmockel, Uri Y. Levine, Eoin L. Brodie, Valerie T. Eviner, Jennifer Pett-Ridge, Teri C. Balser, Barbara J. MacGregor, Mark A. Bradford, Jay T. Lennon, Kathleen K. Treseder, and Mark P. Waldrop
- Subjects
Biogeochemical cycle ,Functional ecology ,Microbial ecology ,Environmental change ,Ecology ,Environmental Chemistry ,Environmental science ,Global change ,Ecosystem ,Biogeosciences ,Phylogenetic distribution ,Earth-Surface Processes ,Water Science and Technology - Abstract
Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ—sometimes substantially—from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment.
- Published
- 2011
29. Microbial seed banks: the ecological and evolutionary implications of dormancy
- Author
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Jay T. Lennon and Stuart E. Jones
- Subjects
education.field_of_study ,General Immunology and Microbiology ,Environmental change ,Rare biosphere ,Ecology ,Population ,Biology ,Microbiology ,Infectious Diseases ,Microbial ecology ,Dormancy ,Ecosystem ,education ,Evolutionary dynamics ,Organism - Abstract
Dormancy is a bet-hedging strategy used by a wide range of taxa, including microorganisms. It refers to an organism's ability to enter a reversible state of low metabolic activity when faced with unfavourable environmental conditions. Dormant microorganisms generate a seed bank, which comprises individuals that are capable of being resuscitated following environmental change. In this Review, we highlight mechanisms that have evolved in microorganisms to allow them to successfully enter and exit a dormant state, and discuss the implications of microbial seed banks for evolutionary dynamics, population persistence, maintenance of biodiversity, and the stability of ecosystem processes.
- Published
- 2011
30. Evidence for a temperature acclimation mechanism in bacteria: an empirical test of a membrane-mediated trade-off
- Author
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Martin J. Kainz, Gabriel Singer, Jay T. Lennon, and Edward K. Hall
- Subjects
Ecology ,Epilimnion ,Respiration ,Niche ,Membrane fluidity ,Ecosystem ,Bacterioplankton ,Biology ,Adaptation ,Acclimatization ,Ecology, Evolution, Behavior and Systematics - Abstract
Summary 1. Shifts in bacterial community composition along temporal and spatial temperature gradients occur in a wide range of habitats and have potentially important implications for ecosystem functioning. However, it is often challenging to empirically link an adaptation or acclimation that defines environmental niche or biogeography with a quantifiable phenotype, especially in micro-organisms. 2. Here we evaluate a possible mechanistic explanation for shifts in bacterioplankton community composition in response to temperature by testing a previously hypothesized membrane mediated trade-off between resource acquisition and respiratory costs. 3. We isolated two strains of Flavobacterium sp. at two temperatures (cold isolate and warm isolate) from the epilimnion of a small temperate lake in North Central Minnesota. 4. Compared with the cold isolate the warm isolate had higher growth rate, higher carrying capacity, lower lag time and lower respiration at the high temperature and lower phosphorus uptake at the low temperature. We also observed significant differences in membrane lipid composition between isolates and between environments that were consistent with adjustments necessary to maintain membrane fluidity at different temperatures. 5. Our results suggest that temperature acclimation in planktonic bacteria is, in part, a resource-dependent membrane-facilitated phenomenon. This study provides an explicit example of how a quantifiable phenotype can be linked through physiology to competitive ability and environmental niche.
- Published
- 2010
31. Dormancy contributes to the maintenance of microbial diversity
- Author
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Stuart E. Jones and Jay T. Lennon
- Subjects
DNA, Bacterial ,Multidisciplinary ,Bacteria ,Rare biosphere ,Ecology ,Molecular Sequence Data ,Lake ecosystem ,Biodiversity ,Species diversity ,Fresh Water ,Biological Sciences ,Biology ,Models, Biological ,Microbial ecology ,Environmental Microbiology ,Dormancy ,Ecosystem ,Species richness - Abstract
Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible state of low metabolic activity, dormant individuals become members of a seed bank, which can determine community dynamics in future generations. Although microbiologists have documented dormancy in both clinical and natural settings, the importance of seed banks for the diversity and functioning of microbial communities remains untested. Here, we develop a theoretical model demonstrating that microbial communities are structured by environmental cues that trigger dormancy. A molecular survey of lake ecosystems revealed that dormancy plays a more important role in shaping bacterial communities than eukaryotic microbial communities. The proportion of dormant bacteria was relatively low in productive ecosystems but accounted for up to 40% of taxon richness in nutrient-poor systems. Our simulations and empirical data suggest that regional environmental cues and dormancy synchronize the composition of active communities across the landscape while decoupling active microbes from the total community at local scales. Furthermore, we observed that rare bacterial taxa were disproportionately active relative to common bacterial taxa, suggesting that microbial rank-abundance curves are more dynamic than previously considered. We propose that repeated transitions to and from the seed bank may help maintain the high levels of microbial biodiversity that are observed in nearly all ecosystems.
- Published
- 2010
32. Evidence for limited microbial transfer of methane in a planktonic food web
- Author
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Jay T. Lennon and Stuart E. Jones
- Subjects
biology ,Ecology ,Aquatic ecosystem ,fungi ,Aquatic Science ,Plankton ,biology.organism_classification ,Zooplankton ,Daphnia ,Food web ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,Trophic level ,Isotope analysis - Abstract
Methane-derived carbon may be an important, but overlooked source of energy fueling food webs in a variety of aquatic ecosystems. Although it is commonly assumed that the flow of methane-derived carbon is regulated by aquatic invertebrate consumption of methane-oxidizing bacteria (MOB), few studies have characterized this trophic interaction. We used stable isotope analysis, bioassay experiments, and PCR-based molecular techniques to investigate the interactions between Daphnia and MOB in the pelagic region of a humic lake located in southwestern Michigan, USA. We observed moderate depletion of 13 C in the plankton, but these data alone could not provide evidence for the consumption of MOB by Daphnia. Using quantitative PCR, we determined that MOB attained relatively high densities in the water column (3% of the bacterial community), but we found no evidence that they were grazed upon by Daphnia. Moreover, our results do not support the hypothesis that Daphnia harbored symbiotic MOB. Therefore, the isotopic composition of Daphnia could not be explained by direct trophic interactions with MOB, suggesting the potential importance of indirect trophic interactions (e.g. consumption of MOB-feeding protists) or other processes that alter the isotopic composition of zooplankton resources (e.g. CO2 recycling).
- Published
- 2009
33. Rapid evolution buffers ecosystem impacts of viruses in a microbial food web§
- Author
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Jennifer B. H. Martiny and Jay T. Lennon
- Subjects
Biomass (ecology) ,Nutrient cycle ,education.field_of_study ,Microbial food web ,Community ,Ecology ,Microorganism ,Population ,Ecosystem ,Biology ,education ,Ecology, Evolution, Behavior and Systematics ,Food web - Abstract
Predation and parasitism often regulate population dynamics, community interactions, and ecosystem functioning. The strength of these top-down pressures is variable, however, and may be influenced by both ecological and evolutionary processes. We conducted a chemostat experiment to assess the direct and indirect effects of viruses on a marine microbial food web comprised of an autotrophic host (Synechococcus) and non-target heterotrophic bacteria. Viruses dramatically altered the host population dynamics, which in turn influenced phosphorus resource availability and the stoichiometric allocation of nutrients into microbial biomass. These virus effects diminished with time, but could not be attributed to changes in the abundance or composition of heterotrophic bacteria. Instead, attenuation of the virus effects coincided with the detection of resistant host phenotypes, suggesting that rapid evolution buffered the effect of viruses on nutrient cycling. Our results demonstrate that evolutionary processes are important for community dynamics and ecosystem processes on ecologically relevant time scales.
- Published
- 2008
34. MICROBIAL PRODUCTIVITY IN VARIABLE RESOURCE ENVIRONMENTS
- Author
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Kathryn L. Cottingham and Jay T. Lennon
- Subjects
chemistry.chemical_classification ,Time Factors ,Resource (biology) ,Bacteria ,Ecology ,Reproduction ,Simulation modeling ,Fresh Water ,Models, Biological ,Carbon ,Microbial Physiology ,Productivity (ecology) ,chemistry ,Dissolved organic carbon ,Environmental science ,Computer Simulation ,Ecosystem ,Organic matter ,Terrestrial ecosystem ,Water Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
The rate, timing, and quality of resource supply exert strong controls on a wide range of ecological processes. In particular, resource-mediated changes in microbial activity have the potential to alter ecosystem processes, including the production and respiration of organic matter. In this study, we used field experiments and simulation modeling to explore how aquatic heterotrophic bacteria respond to variation in resource quality (low vs. high) and resource schedule (pulse vs. press). Field experiments revealed that one-time pulse additions of resources in the form of dissolved organic carbon (DOC) caused short-lived (or =48 h) peaks in bacterial productivity (BP), which translated into large differences across treatments: cumulative BP was twice as high in the pulse vs. press treatment under low resource quality, and five times as high under high resource quality. To gain a more mechanistic understanding of microbial productivity in variable resource environments, we constructed a mathematical model to explore the attributes of bacterial physiology and DOC supply that might explain the patterns observed in our field experiments. Model results suggest that the mobilization rate of refractory to labile carbon, an index of resource quality, was critical in determining cumulative differences in BP between pulse and press resource environments (BPPu:Pr ratios). Moreover, BPPu:Pr ratios were substantially larger when our model allowed for realistic changes in bacterial growth efficiency as a function of bacterial carbon consumption. Together, our field and modeling results imply that resource schedule is important in determining the flow of material and energy from microbes to higher trophic levels in aquatic food webs, and that the effects of resource quality are conditional upon resource schedule. An improved understanding of the effects of resource variability on microorganisms is therefore critical for predicting potential changes in ecosystem functioning in response to environmental change, such as altered DOC fluxes from terrestrial to aquatic ecosystems.
- Published
- 2008
35. Evolutionary Ecology of Microorganisms: From the Tamed to the Wild
- Author
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Jay T. Lennon and Vincent J. Denef
- Subjects
Functional ecology ,Experimental evolution ,Abundance (ecology) ,Ecology ,Biodiversity ,Evolutionary ecology ,Ecosystem ,Biology ,Ecology and Evolutionary Biology ,System dynamics - Abstract
An overarching goal of biology is to understand how evolutionary and ecological processes generate and maintain biodiversity. While evolutionary biologists interested in biodiversity tend to focus on the mechanisms controlling rates of evolution and how this influences the phylogenetic relationship among species, ecologists attempt to explain the distribution and abundance of taxa based upon interactions among species and their environment. Recently, a more concerted effort has been made to integrate some of the theoretical and empirical approaches from the fields of ecology and evolutionary biology. This integration has been motivated in part by the growing evidence that evolution can happen on “rapid” or contemporary time scales, suggesting that eco-evolutionary feedbacks can alter system dynamics in ways that cannot be predicted based on ecological principles alone. As such, it may be inappropriate to ignore evolutionary processes when attempting to understand ecological phenomena in natural and managed ecosystems. In this chapter, we highlight why it is particularly important to consider eco-evolutionary feedbacks for microbial populations. We emphasize some of the major processes that are thought to influence the strength of eco-evolutionary dynamics, provide an overview of methods used to quantify the relative importance of ecology and evolution, and showcase the importance of considering evolution in a community context and how this may influence the dynamics and stability of microbial systems under novel environmental conditions.
- Published
- 2015
36. Fungal Traits That Drive Ecosystem Dynamics on Land
- Author
-
Jay T. Lennon and Kathleen K. Treseder
- Subjects
Technology ,Reviews ,Biology ,Medical and Health Sciences ,Microbiology ,Decomposer ,Environmental ,Soil ,Phylogenetics ,Botany ,Ecosystem ,Taxonomic rank ,Molecular Biology ,Nitrogen cycle ,Phylogeny ,Soil Microbiology ,Genome ,Phylum ,Ecology ,Fungi ,Soil carbon ,Biological Sciences ,Nitrogen Cycle ,Carbon ,Fungal ,Infectious Diseases ,Biodegradation, Environmental ,Biodegradation ,Microbial Interactions ,Genome, Fungal ,Soil microbiology - Abstract
SUMMARY Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance—β-glucan synthesis, trehalose production, and cold-induced RNA helicases—were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter—lignin peroxidases, cellobiohydrolases, and crystalline cellulases—were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming.
- Published
- 2015
37. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes
- Author
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Charles A. Stock, K. Eric Wommack, Alison Buchan, Bradford P. Taylor, William H. Wilson, Jed A. Fuhrman, Luis F. Jover, Derek L. Sonderegger, Joshua S. Weitz, Michael J. Follows, Steven W. Wilhelm, Mathias Middelboe, Jay T. Lennon, Lydia Bourouiba, Curtis A. Suttle, Maureen L. Coleman, and T. Frede Thingstad
- Subjects
Nutrient cycle ,Biomass (ecology) ,Food Chain ,Bacteria ,Ecology ,Oceans and Seas ,Community structure ,Primary production ,Biology ,Cyanobacteria ,Microbiology ,Carbon ,Zooplankton ,Food chain ,Marine bacteriophage ,Viruses ,Animals ,Microbial Interactions ,Ecosystem ,Original Article ,Biomass ,Water Microbiology ,Ecology, Evolution, Behavior and Systematics ,Trophic level - Abstract
Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.
- Published
- 2015
38. Resuscitation of the rare biosphere contributes to pulses of ecosystem activity
- Author
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Jay T. Lennon, Zachary T. Aanderud, Stuart E. Jones, and Noah Fierer
- Subjects
Microbiology (medical) ,dormancy ,Rare biosphere ,lcsh:QR1-502 ,Stable-isotope probing ,Biodiversity ,CO2 pulses ,dominance ,Microbiology ,lcsh:Microbiology ,seed bank ,desiccation ,rarity ,Ecosystem ,Original Research Article ,Oxalobacteraceae ,2. Zero hunger ,biology ,Ecology ,15. Life on land ,biology.organism_classification ,Deciduous ,13. Climate action ,soil rewetting ,Dormancy ,stable isotope probing (SIP) ,Rank abundance curve - Abstract
Dormancy is a life history trait that may have important implications for linking microbial communities to the functioning of natural and managed ecosystems. Rapid changes in environmental cues may resuscitate dormant bacteria and create pulses of ecosystem activity. In this study, we used heavy-water (H(18) 2O) stable isotope probing (SIP) to identify fast-growing bacteria that were associated with pulses of trace gasses (CO2, CH4, and N2O) from different ecosystems [agricultural site, grassland, deciduous forest, and coniferous forest (CF)] following a soil-rewetting event. Irrespective of ecosystem type, a large fraction (69-74%) of the bacteria that responded to rewetting were below detection limits in the dry soils. Based on the recovery of sequences, in just a few days, hundreds of rare taxa increased in abundance and in some cases became dominant members of the rewetted communities, especially bacteria belonging to the Sphingomonadaceae, Comamonadaceae, and Oxalobacteraceae. Resuscitation led to dynamic shifts in the rank abundance of taxa that caused previously rare bacteria to comprise nearly 60% of the sequences that were recovered in rewetted communities. This rapid turnover of the bacterial community corresponded with a 5-20-fold increase in the net production of CO2 and up to a 150% reduction in the net production of CH4 from rewetted soils. Results from our study demonstrate that the rare biosphere may account for a large and dynamic fraction of a community that is important for the maintenance of bacterial biodiversity. Moreover, our findings suggest that the resuscitation of rare taxa from seed banks contribute to ecosystem functioning.
- Published
- 2015
39. Relative importance of CO2 recycling and CH4 pathways in lake food webs along a dissolved organic carbon gradient
- Author
-
Jay T. Lennon, Anthony M. Faiia, Xiahong Feng, and Kathryn L. Cottingham
- Subjects
Ecology ,Stable isotope ratio ,Aquatic ecosystem ,Phytoplankton ,Dissolved organic carbon ,Environmental science ,Ecosystem ,Terrestrial ecosystem ,Aquatic Science ,Plankton ,Oceanography ,Zooplankton - Abstract
Terrestrial ecosystems export large quantities of dissolved organic carbon (DOC) to aquatic ecosystems. This DOC can serve as a resource for heterotrophic bacteria and influence whether lakes function as sources or sinks of atmospheric CO2. However, it remains unclear as to how terrestrial carbon moves through lake food webs. We addressed this topic by conducting a comparative lake survey in the northeastern U.S. along a gradient of terrestrial-derived DOC. We used naturally occurring carbon stable isotopes of CO2, particulate organic matter (POM), and crustacean zooplankton, as well as gas measurements and culture-independent assessments of microbial community composition to make inferences about the flow of terrestrial carbon in lake food webs. Stable isotope ratios of POM and zooplankton decreased with DOC and were often depleted in 13C relative to terrestrial carbon, suggesting the importance of an isotopically light carbon source. It has been proposed that the incorporation of biogenic methane (CH4) into plankton food webs would account for such trends in stable isotope ratios, but we found weak evidence for this hypothesis, on the basis of relationships of CH4, methanogenic archaebacteria, and methanotrophic bacteria in our lakes. Instead, our results are consistent with the view that phytoplankton increase their use of heterotrophically respired CO2 with increasing concentrations of terrestrialderived DOC. The effect of this CO2 recycling can be detected in the stable isotope composition of crustacean zooplankton, suggesting that the direct transfer of terrestrial DOC inputs to higher trophic levels may be relatively inefficient.
- Published
- 2006
40. Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed
- Author
-
Emily B. Graham, Diana R. Nemergut, Jennifer D. Rocca, Jay T. Lennon, Sarah E. Evans, Mark P. Waldrop, Matthew D. Wallenstein, James B. Cotner, and Edward K. Hall
- Subjects
Genetics ,Enzyme function ,Transcription, Genetic ,Nitrogen ,Gene Expression Profiling ,Gene Dosage ,Gene Expression Regulation, Bacterial ,Biology ,Microbiology ,Gene dosage ,Carbon ,Catalysis ,Transcriptome ,Gene expression profiling ,Transcription (biology) ,Dosage Compensation, Genetic ,Biocatalysis ,Positive relationship ,Ecosystem ,Gene ,Ecology, Evolution, Behavior and Systematics ,Perspectives - Abstract
For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.
- Published
- 2014
41. Source and supply of terrestrial organic matter affects aquatic microbial metabolism
- Author
-
Liza E. Pfaff and Jay T. Lennon
- Subjects
Ecology ,Aquatic ecosystem ,Dissolved organic carbon ,Ecological stoichiometry ,Biogeochemistry ,Ecosystem ,Bacterioplankton ,Aquatic Science ,Plankton ,Biology ,Microcosm ,Ecology, Evolution, Behavior and Systematics - Abstract
Aquatic ecosystems are connected to their surrounding watersheds through inputs of terrestrial-derived dissolved organic matter (DOM). The assimilation of this allochthonous resource by recipient bacterioplankton has consequences for food webs and the biogeochemistry of aquatic ecosystems. We used laboratory batch experiments to examine how variation in the source and supply (i.e. concentration) of DOM affects the productivity, respiration and growth efficiency of heterotrophic lake bacterioplankton. We created 6 different DOM sources from soils beneath near- monotypic tree stands in a temperate deciduous-coniferous forest. We then exposed freshwater microcosms containing a natural microbial community to a 1100 µM supply gradient of each DOM source. Bacterial productivity (BP) and bacterial respiration (BR) increased linearly over the broad gradient, on average consuming 7% of the standing pool of dissolved organic carbon (DOC). Bacter- ial metabolism was also influenced by the chemical composition of the DOM source. Carbon-specific productivity declined exponentially with an increase in the carbon:phosphorus (C:P) ratio of the dif- ferent DOM sources, consistent with the predictions of ecological stoichiometry. Together, our short- term laboratory experiments quantitatively describe the metabolic responses of freshwater bacterio- plankton to variation in the supply of terrestrial-derived DOM. Furthermore, our results suggest that dissolved organic phosphorus (DOP) content, which may be linked to the identity of terrestrial vege- tation, is indicative of DOM quality and influences the productivity of freshwater bacterioplankton.
- Published
- 2005
42. Experimental evidence that terrestrial carbon subsidies increase CO 2 flux from lake ecosystems
- Author
-
Jay T. Lennon
- Subjects
Ecology ,Aquatic ecosystem ,Lake ecosystem ,Fresh Water ,Carbon Dioxide ,Biology ,Plankton ,Carbon ,Mesocosm ,Nutrient ,Environmental chemistry ,Dissolved organic carbon ,Humans ,Soil Pollutants ,Terrestrial ecosystem ,Ecosystem ,Ecology, Evolution, Behavior and Systematics - Abstract
Subsidies are donor-controlled inputs of nutrients and energy that can affect ecosystem-level processes in a recipient environment. Lake ecosystems receive large inputs of terrestrial carbon (C) in the form of dissolved organic matter (DOM). DOM inputs may energetically subsidize heterotrophic bacteria and determine whether lakes function as sources or sinks of atmospheric CO(2). I experimentally tested this hypothesis using a series of mesocosm experiments in New England lakes. In the first experiment, I observed that CO(2) flux increased by 160% 4 days following a 1,000 microM C addition in the form of DOM. However, this response was relatively short lived, as there was no effect of DOM enrichment on CO(2) flux beyond 8 days. In a second experiment, I demonstrated that peak CO(2) flux from mesocosms in two lakes increased linearly over a broad DOM gradient (slope for both lakes=0.02+/-0.001 mM CO(2).m(-2) day(-1) per microM DOC, mean+/-SE). Concomitant changes in bacterial productivity and dissolved oxygen strengthen the inference that increasing CO(2) flux resulted from the metabolism of DOM. I conducted two additional studies to test whether DOM-correlated attributes were responsible for the observed change in plankton metabolism along the subsidy gradient. First, terrestrial DOM reduced light transmittance, but experimental shading revealed that this was not responsible for the observed patterns of CO(2) flux. Second, organically bound nitrogen (N) and phosphorus (P) accompanied DOM inputs, but experimental nutrient additions (without organic C) caused mesocosms to be saturated with CO(2). Together, these results suggest that C content of terrestrial DOM may be an important subsidy for freshwater bacteria that can influence whether recipient aquatic ecosystems are sources or sinks of atmospheric CO(2).
- Published
- 2004
43. Invasibility of plankton food webs along a trophic state gradient
- Author
-
Val H. Smith, Andrew R. Dzialowski, and Jay T. Lennon
- Subjects
Ecology ,fungi ,Species diversity ,Daphnia lumholtzi ,Introduced species ,Ecosystem ,Biology ,Plankton ,biology.organism_classification ,Zooplankton ,Ecology, Evolution, Behavior and Systematics ,Food web ,Trophic level - Abstract
Biological invasions are becoming more common, yet the majority of introduced exotic species fail to establish viable populations in new environments. Current ecological research suggests that invasion success may be determined by properties of the native ecosystem, such as the supply rate of limiting nutrients (i.e. trophic state). We examined how trophic state influences invasion success by introducing an exotic zooplankter, Daphnia lumholtzi into native plankton communities in a series of experimental mesocosms exposed to a strong nutrient gradient. We predicted that the attributes of nutrient-enriched communities would increase the likelihood of a successful invasion attempt by D. lumholtzi. Contrary to our original predictions, we found that D. lumholtzi was often absent from mesocosms that developed under high nutrient supply rates. Instead, the presence of D. lumholtzi was associated with systems that had low nutrients, low zooplankton biomass, and high zooplankton species diversity. Using generalized estimating equations (GEE) and multivariate species data, we found that the presence-absence of D. lumholtzi could be explained by variations in zooplankton community structure, which was itself strongly influenced by nutrient supply rate. We argue that the apparent invasion success of D. lumholtzi was inhibited by the dominance of another cladoceran species, Chydorus sphaericus. These results suggest that the interaction between trophic state and species identity influenced the invasion success of introduced D. lumholtzi.
- Published
- 2003
44. Trait-based approaches for understanding microbial biodiversity and ecosystem functioning
- Author
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Sascha eKrause, Xavier eLe Roux, Pascal Alex Niklaus, Peter Van Bodegom, Jay T Lennon, Stefan eBertilsson, Hans-Peter eGrossart, Laurent ePhilippot, Paul eBodelier, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), University of Zurich, Krause, Sascha, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Netherlands Organization for Scientific Research (NWO) [855.01.150], German Science Foundation [GR 1540/17-1], National Science Foundation [DEB 1146149], US Department of Agriculture [2013-02775], Systems Ecology, Amsterdam Global Change Institute, and Microbial Ecology (ME)
- Subjects
Microbiology (medical) ,functional traits ,ecosystem function ,ecological theory ,study designs ,microbial diversity ,[SDV]Life Sciences [q-bio] ,Microbial diversity ,trait fonctionnel ,lcsh:QR1-502 ,Biodiversity ,Review Article ,Biology ,Ecological systems theory ,Microbiology ,lcsh:Microbiology ,2726 Microbiology (medical) ,10127 Institute of Evolutionary Biology and Environmental Studies ,Microbial ecology ,diversité microbienne ,Ecosystem ,Institut für Biochemie und Biologie ,business.industry ,Ecology ,2404 Microbiology ,Environmental resource management ,Trait based ,15. Life on land ,Microbial biodiversity ,13. Climate action ,international ,Trait ,théorie écologique ,570 Life sciences ,biology ,590 Animals (Zoology) ,business - Abstract
In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology. © 2014 Krause, Le Roux, Niklaus, Van Bodegom, Lennon, Bertilsson, Grossart, Philippot and Bodelier.
- Published
- 2014
45. Phosphorus resource heterogeneity in microbial food webs
- Author
-
K. C. Bird, Sarah A Placella, Megan L. Larsen, Jay T. Lennon, Mario E. Muscarella, Department of Biology, Indiana University System, Cary Institute of Ecosystem Studies, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), National Science Foundation [DEB-0743402, DEB-0842441], Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
- Subjects
0106 biological sciences ,Algae ,[SDV]Life Sciences [q-bio] ,cyanobactérie ,Generalist ,Aquatic Science ,Biology ,Specialist ,Generalist and specialist species ,010603 evolutionary biology ,01 natural sciences ,service écosystémique ,03 medical and health sciences ,Nutrient ,Biodiversity ,Bacterial community composition ,Metabolism ,Ecosystem function ,Eutrophication ,Ecosystem ,mésocosme aquatique ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,Biomass (ecology) ,communauté microbienne ,Ecology ,Aquatic ecosystem ,15. Life on land ,Food web ,phosphore ,écosystème aquatique ,Eukariota ,Productivity (ecology) ,13. Climate action ,eutrophisation - Abstract
All code for sequence processing and statistical analyses is available at https://github.com/LennonLab/p-meso.Présentation orale au 'SAME 13: progress and perspectives in aquatic microbial ecology', Stresa, Italy, 8-13 septembre 2013; Food webs are often regulated by the bottom-up effects of resource supply rate. However, heterogeneity within a resource pool may also affect the structure and function of communities. To test this hypothesis, we measured the responses of aquatic microbial food webs in experimental mesocosms to the addition of 4 different phosphorus (P) sources: orthophosphate (PO43-), 2-aminoethylphosphonate (AEP), adenosine triphosphate (ATP), and phytic acid (PA). Based on 16S rRNA gene sequencing, we found that P resource heterogeneity altered community assembly for bacteria and eukaryotic algae, suggesting that these microbial functional groups may be comprised of P-specialists. In contrast, cyanobacteria were relatively unaffected by our treatments, suggesting that these microorganisms may adopt a more generalist strategy for P-acquisition. Furthermore, our results revealed that P resource heterogeneity affected food web and ecosystem attributes such as nutrient concentrations, bacterial productivity, algal biomass, and ecosystem respiration. Lastly, we found no evidence for non-additive effects of resource heterogeneity based on a treatment where a set of mesocosms received all 4 sources of P. Instead, our results support the view that there may be non-substitutable classes of P in aquatic ecosystems. Specifically, microbial food webs were more sensitive to P-containing biomolecules (PO43- and ATP) than P-containing structural or storage molecules (AEP and PA). Our results demonstrate that not all P resources are the same; although historically overlooked, P resource heterogeneity may have important implications for understanding and predicting the structure and function of aquatic communities.
- Published
- 2014
46. Biodiversity may regulate the temporal variability of ecological systems
- Author
-
Kathryn L. Cottingham, Bryan L. Brown, and Jay T. Lennon
- Subjects
education.field_of_study ,Biomass (ecology) ,Empirical research ,Ecology ,Population ,Biodiversity ,Ecosystem ,Species richness ,Biology ,education ,Ecological systems theory ,Ecology, Evolution, Behavior and Systematics ,Global biodiversity - Abstract
The effect of biodiversity on natural communities has recently emerged as a topic of considerable ecological interest. We review studies that explicitly test whether the number of species in a community (species richness) regulates the temporal variability of aggregate community (total biomass, productivity, nutrient cycling) and population (density, biomass) properties. Theoretical studies predict that community variability should decline with increasing species richness, while population variability should increase. Many, but not all, empirical studies support these expectations. However, a closer look reveals that several empirical studies have either imperfect experimental designs or biased methods of calculating variability. Furthermore, most theoretical studies rely on highly unrealistic assumptions. We conclude that evidence to support the claim that biodiversity regulates temporal variability is accumulating, but not unequivocal. More research, in a broader array of ecosystem types and with careful attention to methodological considerations, is needed before we can make definitive statements regarding richness-variability relationships.
- Published
- 2001
47. The under-ice microbiome of seasonally frozen lakes
- Author
-
Cayelan C. Carey, Hans-Peter Grossart, Stefan Bertilsson, Lorena M. Grubisic, Ian D. Jones, Georgiy Kirillin, Robyn Smyth, Ashley Shade, Jay T. Lennon, Samuel B. Fey, and Amy J. Burgin
- Subjects
Open water ,Biology and Microbiology ,Phenology ,Ecology ,Water Movements ,Physics ,Temperate climate ,Ecosystem ,Microbiome ,Aquatic Science ,Biology ,Oceanography ,Ecology and Environment - Abstract
Compared to the well-studied open water of the ‘‘growing’’ season, under-ice conditions in lakes are characterized by low and rather constant temperature, slow water movements, limited light availability, and reduced exchange with the surrounding landscape. These conditions interact with ice-cover duration to shape microbial processes in temperate lakes and ultimately influence the phenology of community and ecosystem processes. We review the current knowledge on microorganisms in seasonally frozen lakes. Specifically, we highlight how under-ice conditions alter lake physics and the ways that this can affect the distribution and metabolism of auto- and heterotrophic microorganisms. We identify functional traits that we hypothesize are important for understanding under-ice dynamics and discuss how these traits influence species interactions. As ice coverage duration has already been seen to reduce as air temperatures have warmed, the dynamics of the underice microbiome are important for understanding and predicting the dynamics and functioning of seasonally frozen lakes in the near future.
- Published
- 2013
48. A source of terrestrial organic carbon to investigate the browning of aquatic ecosystems
- Author
-
Stuart E. Jones, Stephen K. Hamilton, Jay T. Lennon, Mario E. Muscarella, Kyle Wickings, and A. Stuart Grandy
- Subjects
0106 biological sciences ,010504 meteorology & atmospheric sciences ,lcsh:Medicine ,01 natural sciences ,Daphnia ,Zooplankton ,Dissolved organic carbon ,Ecosystem ,14. Life underwater ,lcsh:Science ,Humic Substances ,0105 earth and related environmental sciences ,Total organic carbon ,Multidisciplinary ,biology ,Chemistry ,Ecology ,010604 marine biology & hydrobiology ,Aquatic ecosystem ,lcsh:R ,15. Life on land ,biology.organism_classification ,Carbon ,13. Climate action ,Terrestrial ecosystem ,lcsh:Q ,Surface water ,Research Article - Abstract
There is growing evidence that terrestrial ecosystems are exporting more dissolved organic carbon (DOC) to aquatic ecosystems than they did just a few decades ago. This “browning” phenomenon will alter the chemistry, physics, and biology of inland water bodies in complex and difficult-to-predict ways. Experiments provide an opportunity to elucidate how browning will affect the stability and functioning of aquatic ecosystems. However, it is challenging to obtain sources of DOC that can be used for manipulations at ecologically relevant scales. In this study, we evaluated a commercially available source of humic substances (“Super Hume”) as an analog for natural sources of terrestrial DOC. Based on chemical characterizations, comparative surveys, and whole-ecosystem manipulations, we found that the physical and chemical properties of Super Hume are similar to those of natural DOC in aquatic and terrestrial ecosystems. For example, Super Hume attenuated solar radiation in ways that will not only influence the physiology of aquatic taxa but also the metabolism of entire ecosystems. Based on its chemical properties (high lignin content, high quinone content, and low C:N and C:P ratios), Super Hume is a fairly recalcitrant, low-quality resource for aquatic consumers. Nevertheless, we demonstrate that Super Hume can subsidize aquatic food webs through 1) the uptake of dissolved organic constituents by microorganisms, and 2) the consumption of particulate fractions by larger organisms (i.e., Daphnia). After discussing some of the caveats of Super Hume, we conclude that commercial sources of humic substances can be used to help address pressing ecological questions concerning the increased export of terrestrial DOC to aquatic ecosystems.
- Published
- 2013
49. Temporal variability in soil microbial communities across land-use types
- Author
-
Kelly S. Ramirez, Christian L. Lauber, Zach Aanderud, Jay T. Lennon, and Noah Fierer
- Subjects
Michigan ,Time Factors ,Biodiversity ,Biology ,Environment ,Bacterial Physiological Phenomena ,Microbiology ,complex mixtures ,Grassland ,Soil ,Microbial ecology ,RNA, Ribosomal, 16S ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,Soil Microbiology ,geography ,geography.geographical_feature_category ,Land use ,Bacteria ,Ecology ,Plant community ,Soil classification ,Agriculture ,Plants ,Soil water ,Original Article - Abstract
Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.
- Published
- 2012
50. Mapping the niche space of soil microorganisms using taxonomy and traits
- Author
-
Jay T. Lennon, Donald R. Schoolmaster, B. K. Lehmkuhl, and Zachary T. Aanderud
- Subjects
Moisture ,Bacteria ,Ecology ,Niche ,Microbial metabolism ,Fungi ,Moisture stress ,Biodiversity ,Biology ,Generalist and specialist species ,Botany ,Ecosystem ,Water content ,Soil microbiology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Soil Microbiology - Abstract
The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.
- Published
- 2012
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