Imperial College London

ProfessorThomasBell

Faculty of Natural SciencesDepartment of Life Sciences (Silwood Park)

Professor of Microbial Ecology
 
 
 
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Contact

 

+44 (0)20 7594 2268thomas.bell

 
 
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Location

 

MunroSilwood Park

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Summary

 

Publications

Publication Type
Year
to

45 results found

Pascual Garcia A, Bell T, 2020, Community-level signatures of ecological succession in natural bacterial communities, Nature Communications, Vol: 11, ISSN: 2041-1723

A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We profiled (16S rRNA sequencing) > 700 semi-aquatic bacterial communities while measuring their functional capacity when grown in laboratory conditions. This approach allowed us to investigate the relationship between composition and function excluding confounding environmental factors. Simulated data allowed us to reject the hypothesis that stochastic processes were responsible for community assembly, suggesting that niche effects prevailed. Consistent with this idea we identified six distinct community classes that contained samples collected from distant locations. Structural equation models showed there was a functional signature associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions (PiCRUST). This approach allowed us to show that the classes contained distinct genetic repertoires reflecting community-level ecological strategies. The ecological strategies resemble the classical distinction between r- and K-strategists, suggesting that bacterial community assembly may be explained by simple ecological mechanisms.

Journal article

Pascual-Garcia A, Bell T, 2020, functionInk: An efficient method to detect functional groups in multidimensional networks reveals the hidden structure of ecological communities, METHODS IN ECOLOGY AND EVOLUTION, Vol: 11, Pages: 804-817, ISSN: 2041-210X

Journal article

Bell T, Pascual Garcia A, Bonhoeffer S, 2020, Metabolically cohesive microbial consortia and ecosystem functioning, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 374, ISSN: 0962-8436

Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in6the context of competition for resources and metabolic complementarity given that, in microbial communities, many excreted by-products of metabolism may also be resources. Microbial communities therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organisation between the species and the community level may be pervasive, where tightly-knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community-, and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild.

Journal article

Scheuerl T, Hopkins M, Nowell R, Rivett D, Barraclough T, Bell Tet al., 2020, Bacterial adaptation is constrained in complex communities, Nature Communications, Vol: 11, ISSN: 2041-1723

A major unresolved question is how bacteria living in complex communities respond to environmental changes. In communities, biotic interactions may either facilitate or constrain evolution depending on whether the interactions expand or contract the range of ecological opportunities. A fundamental challenge is to understand how the surrounding biotic community modifies evolutionary trajectories as species adapt to novel environmental conditions. Here we show that community context can dramatically alter evolutionary dynamics using a novel approach that ‘cages’ individual focal strains within complex communities. We find that evolution of focal bacterial strains depends on properties both of the focal strain and of the surrounding community. In particular, there is a stronger evolutionary response in low-diversity communities, and when the focal species have a larger genome and are initially poorly adapted. We see how community context affects resource usage and detect genetic changes involved in carbon metabolism and inter-specific interaction. The findings demonstrate that adaptation to new environmental conditions should be investigated in the context of interspecific interactions.

Journal article

Smith T, Thomas TJH, Garcia-Carreras B, Sal S, Yvon-Durocher G, Bell T, Pawar Set al., 2019, Community-level respiration of prokaryotic microbes may rise with global warming, Nature Communications, Vol: 10, ISSN: 2041-1723

Understanding how the metabolic rates of prokaryotes respond to temperature is fun-damental to our understanding of how ecosystem functioning will be altered by climatechange, as these micro-organisms are major contributors to global carbon efflux. Ecologicalmetabolic theory suggests that species living at higher temperatures evolve higher growthrates than those in cooler niches due to thermodynamic constraints. Here, using a globalprokaryotic dataset, we find that maximal growth rate at thermal optimum increases withtemperature for mesophiles (temperature optima.45◦C), but not thermophiles (&45◦C).Furthermore, short-term (within-day) thermal responses of prokaryotic metabolic rates aretypically more sensitive to warming than those of eukaryotes. Because climatic warmingwill mostly impact ecosystems in the mesophilic temperature range, we conclude that asmicrobial communities adapt to higher temperatures, their metabolic rates and therefore,biomass-specific CO2production, will inevitably rise. Using a mathematical model, weillustrate the potential global impacts of these findings.

Journal article

Vila JCC, Jones ML, Patel M, Bell T, Rosindell Jet al., 2019, Uncovering the rules of microbial community invasion, Nature Ecology and Evolution, Vol: 3, Pages: 1162-1171, ISSN: 2397-334X

Understanding the ecological and evolutionary processes determining the outcome of biological invasions has been the subject of decades of research with most work focusing on macro-organisms. In the context of microbes, invasions remain poorly understood despite being increasingly recognised as important. To shed light on the factors affecting the success of microbial community invasions, we perform simulations using an individual-based nearly neutral model that combines ecological and evolutionary processes. Our simulations qualitatively recreate numerous empirical patterns and lead to a description of five general rules of invasion: 1) larger communities evolve better invaders and better defenders; 2) where invader and resident fitness difference is large invasion success is essentially deterministic; 3) propagule pressure contributes to invasion success if and only if invaders and residents are competitively similar; 4) increasing the diversity of invaders has a similar effect to increasing the number of invaders; 5) more diverse communities better resist invasion.

Journal article

Zhang F-G, Bell T, Zhang Q-G, 2019, Experimental testing of dispersal limitation in soil bacterial communities with a propagule addition approach, Microbial Ecology, Vol: 77, Pages: 905-912, ISSN: 0095-3628

The role of dispersal in the assembly of microbial communities remains contentious. This study tested the importance of dispersal limitation for the structuring of local soil bacterial communities using an experimental approach of propagule addition. Microbes extracted from soil pooled from samples collected at 20 localities across ~ 400 km in a temperate steppe were added to microcosms of local soils at three sites; the microcosms were then incubated in situ for 3 months. We then assessed the composition and diversity of bacterial taxa in the soils using 16S rRNA gene amplicon sequencing. The addition of the regional microbial pool did not cause significant changes in the overall composition or diversity of the total bacterial community, although a very small number of individual taxa may have been affected by the addition treatment. Our results suggest a negligible role of dispersal limitation in structuring soil bacterial communities in our study area.

Journal article

Bell T, 2019, Next-generation experiments linking community structure and ecosystem functioning, Environmental Microbiology Reports, Vol: 11, Pages: 20-22, ISSN: 1758-2229

Journal article

Tiegs SD, Costello DM, Isken MW, Woodward G, McIntyre PB, Gessner MO, Chauvet E, Griffiths NA, Flecker AS, Acuna V, Albarino R, Allen DC, Alonso C, Andino P, Arango C, Aroviita J, Barbosa MVM, Barmuta LA, Baxter CV, Bell TDC, Bellinger B, Boyero L, Brown LE, Bruder A, Bruesewitz DA, Burdon FJ, Callisto M, Canhoto C, Capps KA, Castillo MM, Clapcott J, Colas F, Colon-Gaud C, Cornut J, Crespo-Perez V, Cross WF, Culp JM, Danger M, Dangles O, de Eyto E, Derry AM, Diaz Villanueva V, Douglas MM, Elosegi A, Encalada AC, Entrekin S, Espinosa R, Ethaiya D, Ferreira V, Ferriol C, Flanagan KM, Fleituch T, Shah JJF, Frainer A, Friberg N, Frost PC, Garcia EA, Lago LG, Garcia Soto PE, Ghate S, Giling DP, Gilmer A, Goncalves JF, Gonzales RK, Graca MAS, Grace M, Grossart H-P, Guerold F, Gulis V, Hepp LU, Higgins S, Hishi T, Huddart J, Hudson J, Imberger S, Iniguez-Armijos C, Iwata T, Janetski DJ, Jennings E, Kirkwood AE, Koning AA, Kosten S, Kuehn KA, Laudon H, Leavitt PR, Lemes da Silva AL, Leroux SJ, Leroy CJ, Lisi PJ, MacKenzie R, Marcarelli AM, Masese FO, Mckie BG, Oliveira Medeiros A, Meissner K, Milisa M, Mishra S, Miyake Y, Moerke A, Mombrikotb S, Mooney R, Moulton T, Muotka T, Negishi JN, Neres-Lima V, Nieminen ML, Nimptsch J, Ondruch J, Paavola R, Pardo I, Patrick CJ, Peeters ETHM, Pozo J, Pringle C, Prussian A, Quenta E, Quesada A, Reid B, Richardson JS, Rigosi A, Rincon J, Risnoveanu G, Robinson CT, Rodriguez-Gallego L, Royer TV, Rusak JA, Santamans AC, Selmeczy GB, Simiyu G, Skuja A, Smykla J, Sridhar KR, Sponseller R, Stoler A, Swan CM, Szlag D, Teixeira-de Mello F, Tonkin JD, Uusheimo S, Veach AM, Vilbaste S, Vought LBM, Wang C-P, Webster JR, Wilson PB, Woelfl S, Xenopoulos MA, Yates AG, Yoshimura C, Yule CM, Zhang YX, Zwart JAet al., 2019, Global patterns and drivers of ecosystem functioning in rivers and riparian zones, Science Advances, Vol: 5, ISSN: 2375-2548

River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth’s biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented “next-generation biomonitoring” by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.

Journal article

Rivett DW, Bell T, 2018, Abundance determines the functional role of bacterial phylotypes in complex communities., Nature microbiology, Vol: 3, Pages: 767-772, ISSN: 2058-5276

Bacterial communities are essential for the functioning of the Earth's ecosystems 1 . A key challenge is to quantify the functional roles of bacterial taxa in nature to understand how the properties of ecosystems change over time or under different environmental conditions 2 . Such knowledge could be used, for example, to understand how bacteria modulate biogeochemical cycles 3 , and to engineer bacterial communities to optimize desirable functional processes 4 . Communities of bacteria are, however, extraordinarily complex with hundreds of interacting taxa in every gram of soil and every millilitre of pond water 5 . Little is known about how the tangled interactions within natural bacterial communities mediate ecosystem functioning, but high levels of bacterial diversity have led to the assumption that many taxa are functionally redundant 6 . Here, we pinpoint the bacterial taxa associated with keystone functional roles, and show that rare and common bacteria are implicated in fundamentally different types of ecosystem functioning. By growing hundreds of bacterial communities collected from a natural aquatic environment (rainwater-filled tree holes) under the same environmental conditions, we show that negative statistical interactions among abundant phylotypes drive variation in broad functional measures (respiration, metabolic potential, cell yield), whereas positive interactions between rare phylotypes influence narrow functional measures (the capacity of the communities to degrade specific substrates). The results alter our understanding of bacterial ecology by demonstrating that unique components of complex communities are associated with different types of ecosystem functioning.

Journal article

Rivett D, Jones M, Ramoneda J, Mombrikotb S, Ransome E, Bell TDCet al., 2018, Elevated success of multispecies bacterial invasions impacts community composition during ecological succession, Ecology Letters, Vol: 21, Pages: 516-524, ISSN: 1461-023X

Successful microbial invasions are determined by a species’ ability to occupy a niche in the new habitat whilst resisting competitive exclusion by the resident community. Despite the recognised importance of biotic factors in determining the invasiveness of microbial communities, the success and impact of multiple concurrent invaders on the resident community has not been examined. Simultaneous invasions might have synergistic effects, for example if resident species need to exhibit divergent phenotypes to compete with the invasive populations. We used three phylogenetically diverse bacterial species to invade two compositionally distinct communities in a controlled, naturalised in vitro system. By initiating the invader introductions at different stages of succession, we could disentangle the relative importance of resident community structure, invader diversity and time pre‐invasion. Our results indicate that multiple invaders increase overall invasion success, but do not alter the successional trajectory of the whole community.

Journal article

Jones ML, Ramoneda JM, Rivett DW, Bell TDet al., 2017, Biotic resistance shapes the influence of propagule pressure on invasion success in bacterial communities, Ecology, ISSN: 1939-9170

The number of invaders and the timing of invasion are recognized as key determinants of successful invasions. Despite the recognized importance of “propagule pressure,” invasion ecology has largely focused on how characteristics of the native community confer invasion resistance. We simultaneously manipulated community composition and invader propagule pressure in microcosm communities of freshwater bacteria. We show that high propagule pressures can be necessary to establish an invader population, but that the influence of propagule pressure depends on the composition of the resident species. In particular, the number of individuals invading was most important to invasion success when one of the species in a resident community is a strong competitor against other species. By contrast, the timing of invasion was most important when communities had lower growth rates. The results suggest that the importance of propagule pressure varies both between communities and within the same community over time, and therefore have implications for the way we understand the relationship between biotic resistance and invasion success.

Journal article

Bell T, Tylianakis JM, 2016, Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems, Proceedings of the Royal Society B: Biological Sciences, Vol: 283, ISSN: 0962-8452

Soil microbial communities are enormously diverse, with at least millions of species and trillions of genes unknown to science or poorly described. Soil microbial communities are key components of agriculture, for example in provisioning nitrogen and protecting crops from pathogens, providing overall ecosystem services in excess of $1000bn per year. It is important to know how humans are affecting this hidden diversity. Much is known about the negative consequences of agricultural intensification on higher-organisms, but almost nothing is known about how alterations to landscapes affect microbial diversity, distributions and processes. Wereview what is known about spatial flows of microbes and their response to land use change, and outline nine hypotheses to advance research of microbiomes across landscapes. We hypothesise that intensified agriculture selects for certain taxa and genes, which then “spill over” into adjacent unmodified areas and generate a halo of genetic differentiation around agricultural fields.Consequently, the spatial configuration and management intensityof different habitats combines with the dispersal ability of individual taxa to determine the extent of spillover, which canimpact the functioning of adjacent unmodified habitats. When landscapes are heterogeneous and dispersal rates are high, this will select for large genomes that allow exploitation of multiple habitats, a process that may be accelerated through horizontal gene transfer.Continued expansion of agriculture will increase genotypic similarity, making microbial community functioning increasingly variable in human-dominated landscapes, potentially also impactingthe consistent provisioning of ecosystem services.While the resulting economic costs have not been calculated, it is clear that dispersal dynamics of microbes s

Journal article

Lehmann K, Bell T, Bowes MJ, Amos GCA, Gaze WH, Wellington EMH, Singer ACet al., 2016, Trace levels of sewage effluent are sufficient to increase class 1 integron prevalence in freshwater biofilms without changing the core community, WATER RESEARCH, Vol: 106, Pages: 163-170, ISSN: 0043-1354

Journal article

Dupont AOC, Griffiths RI, Bell T, Bass Det al., 2016, Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs, ENVIRONMENTAL MICROBIOLOGY, Vol: 18, Pages: 2010-2024, ISSN: 1462-2912

Journal article

Barraclough TG, Bell TDC, Rivett D, Scheuerl T, Mombrikotb S, Culbert C, Johnstone Eet al., 2016, Resource-dependent attenuation of species interactions during bacterial succession, ISME Journal, Vol: 10, Pages: 2259-2268, ISSN: 1751-7362

Bacterial communities are vital for many economically and ecologically important processes. The role of bacterial community composition in determining ecosystem functioning depends critically on interactions among bacterial taxa. Several studies have shown that, despite a predominance of negative interactions in communities, bacteria are able to display positive interactions given the appropriate evolutionary or ecological conditions. We were interested in how interspecific interactions develop over time in a naturalistic setting of low resource supply rates. We assembled aquatic bacterial communities in microcosms and assayed the productivity (respiration and growth) and substrate degradation while tracking community composition. The results demonstrated that while bacterial communities displayed strongly negative interactions during the early phase of colonisation and acclimatisation to novel biotic and abiotic factors, this antagonism declined over time towards a more neutral state. This was associated with a shift from use of labile substrates in early succession to use of recalcitrant substrates later in succession, confirming a crucial role of resource dynamics in linking interspecific interactions with ecosystem functioning.

Journal article

Fisher RM, Bell T, West SA, 2016, Multicellular group formation in response to predators in the alga Chlorella vulgaris, Journal of Evolutionary Biology, Vol: 29, Pages: 551-559, ISSN: 1420-9101

A key step in the evolution of multicellular organisms is the formation of cooperative multicellular groups. It has been suggested that predation pressure may promote multicellular group formation in some algae and bacteria, with cells forming groups to lower their chance of being eaten. We use the green alga Chlorella vulgaris and the protist Tetrahymena thermophila to test whether predation pressure can initiate the formation of colonies. We found that: (1) either predators or just predator exoproducts promote colony formation; (2) higher predator densities cause more colonies to form; and (3) colony formation in this system is facultative, with populations returning to being unicellular when the predation pressure is removed. These results provide empirical support for the hypothesis that predation pressure promotes multicellular group formation. The speed of the reversion of populations to unicellularity suggests that this response is due to phenotypic plasticity and not evolutionary change.

Journal article

Barraclough TG, Lawrence D, Bell T, 2015, The effect of immigration on the adaptation of microbial communities to warming, American Naturalist, Vol: 187, ISSN: 1537-5323

Theory predicts that immigration can either enhance or impair the rate at which species and whole communities adapt to environmental change, depending on the traits of genotypes and species in the source pool relative to local conditions. These responses in turn will determine how well whole communities function in changing environments. We tested the effects of immigration and experimental warming on microbial communities during an 81 day field experiment. The effects of immigration depended on the warming treatment. In warmed communities immigration was detrimental to community growth whereas in ambient communities it was beneficial. This result is explained if colonists came from a local species pool pre-adapted to ambient conditions. Loss of metabolic diversity, however, was buffered by immigration in both environments. Communities showed increasing local adaptation to temperature conditions during the experiment and this was independent of whether or not they received immigration. Genotypes that comprised the communities were not locally adapted, however, indicating that community local adaptation can be independent of adaptation of component genotypes. Our results are consistent with a greater role for species interactions rather than adaptation of constituent species in determining local adaptation of whole communities, and confirm that immigration can either enhance or impair community responses to environmental change depending on the environmental context.

Journal article

Lehmann K, Singer A, Bowes MJ, Ings NL, Field D, Bell Tet al., 2015, 16S rRNA assessment of the influence of shading on early-successional biofilms in experimental streams, FEMS Microbiology Ecology, Vol: 91, Pages: 1-11, ISSN: 0168-6496

Elevated nutrient levels can lead to excessive biofilm growth, but reducing nutrient pollution is often challenging. There is therefore interest in developing control measures for biofilm growth in nutrient-rich rivers that could act as complement to direct reductions in nutrient load. Shading of rivers is one option that can mitigate blooms, but few studies have experimentally examined the differences in biofilm communities grown under shaded and unshaded conditions. We investigated the assembly and diversity of biofilm communities using in situ mesocosms within the River Thames (UK). Biofilm composition was surveyed by 454 sequencing of 16S amplicons (∼400 bp length covering regions V6/V7). The results confirm the importance of sunlight for biofilm community assembly; a resource that was utilized by a relatively small number of dominant taxa, leading to significantly less diversity than in shaded communities. These differences between unshaded and shaded treatments were either because of differences in resource utilization or loss of diatom-structures as habitats for bacteria. We observed more co-occurrence patterns and network interactions in the shaded communities. This lends further support to the proposal that increased river shading can help mitigate the effects from macronutrient pollution in rivers.

Journal article

Slade EM, Roslin T, Santalahti M, Bell Tet al., 2015, Disentangling the "brown world' faecal-detritus interaction web: dung beetle effects on soil microbial properties, Oikos, Vol: 125, Pages: 629-635, ISSN: 0030-1299

Many ecosystem services are sustained by the combined action of microscopic and macroscopic organisms, and shaped by interactions between the two. However, studies tend to focus on only one of these two components. We combined the two by investigating the impact of macrofauna on microbial community composition and functioning in the context of a major ecosystem process: the decomposition of dung. We compared bacterial communities of pasture soil and experimental dung pats inhabited by one (Aphodius), two (Aphodius and Geotrupes), or no dung beetle genera. Overall, we found distinct microbial communities in soil and dung samples, and that the communities converged over the course of the experiment. Characterising the soil microbial communities underlying the dung pats revealed a significant interactive effect between the microflora and macrofauna, where the diversity and composition of microbial communities was significantly affected by the presence or absence of dung beetles. e specific identity of the beetles had no detectable impact, but the microbial evenness was lower in the presence of both Aphodius and Geotrupes than in the presence of Aphodius alone. Differences in microbial community composition were associated with differences in substrate usage as measured by Ecoplates. More-over, microbial communities with similar compositions showed more similar substrate usage. Our study suggests that the presence of macrofauna (dung beetles) will modify the microflora (bacteria) of both dung pats and pasture soil, including community diversity and functioning. In particular, the presence of dung beetles promotes the transfer of bacteria across the soil–dung interface, resulting in increased similarity in community structure and functioning. e results demonstrate that to understand how microbes contribute to the ecosystem process of dung decomposition, there is a need to understand their interactions with larger co-occurring fauna.

Journal article

Barraclough TG, Bell T, Scheuerl T, 2015, Saturating effects of species diversity on life-history evolution in bacteria, Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol: 282, ISSN: 0080-4649

Species interactions can play a major role in shaping evolution in new environments. In theory, species interactions can either stimulate evolution by promoting coevolution or inhibit evolution by constraining ecological opportunity. The relative strength of these effects should vary as species richness increases, and yet there has been little evidence for evolution of component species in communities. We evolved bacterial microcosms containing between 1 and 12 species in three different environments. Growth rates and yields of isolates that evolved in communities were lower than those that evolved in monocultures, consistent with recent theory that competition constrains species to specialize on narrower sets of resources. This effect saturated or reversed at higher levels of richness, consistent with theory that directional effects of species interactions should weaken in more diverse communities. Species varied considerably, however, in their responses to both environment and richness levels. Mechanistic models and experiments are now needed to understand and predict joint evolutionary dynamics of species in diverse communities.

Journal article

Friman V-P, Guzman LM, Reuman DC, Bell Tet al., 2015, Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 282, ISSN: 0962-8452

Journal article

Fiegna F, Moreno-Letelier A, Bell T, Barraclough TGet al., 2015, Evolution of species interactions determines microbial community productivity in new environments, ISME JOURNAL, Vol: 9, Pages: 1235-1245, ISSN: 1751-7362

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Samani P, Low-Decarie E, McKelvey K, Bell T, Burt A, Koufopanou V, Landry CR, Bell Get al., 2015, Metabolic variation in natural populations of wild yeast, Ecology and Evolution, Vol: 5, Pages: 722-732, ISSN: 2045-7758

Ecological diversification depends on the extent of genetic variation and on the pattern of covariation with respect to ecological opportunities. We investigated the pattern of utilization of carbon substrates in wild populations of budding yeast Saccharomyces paradoxus. All isolates grew well on a core diet of about 10 substrates, and most were also able to grow on a much larger ancillary diet comprising most of the 190 substrates we tested. There was substantial genetic variation within each population for some substrates. We found geographical variation of substrate use at continental, regional, and local scales. Isolates from Europe and North America could be distinguished on the basis of the pattern of yield across substrates. Two geographical races at the North American sites also differed in the pattern of substrate utilization. Substrate utilization patterns were also geographically correlated at local spatial scales. Pairwise genetic correlations between substrates were predominantly positive, reflecting overall variation in metabolic performance, but there was a consistent negative correlation between categories of substrates in two cases: between the core diet and the ancillary diet, and between pentose and hexose sugars. Such negative correlations in the utilization of substrate from different categories may indicate either intrinsic physiological trade‐offs for the uptake and utilization of substrates from different categories, or the accumulation of conditionally neutral mutations. Divergence in substrate use accompanies genetic divergence at all spatial scales in S. paradoxus and may contribute to race formation and speciation.

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Poisot T, Bell T, Martinez E, Gougat-Barbera C, Hochberg MEet al., 2013, Terminal investment induced by a bacteriophage in a rhizosphere bacterium., F1000Res, Vol: 1, Pages: 1-21, ISSN: 2046-1402

Despite knowledge about microbial responses to abiotic stress, few studies have investigated stress responses to antagonistic species, such as competitors, predators and pathogens. While it is often assumed that interacting populations of bacteria and phage will coevolve resistance and exploitation strategies, an alternative is that individual bacteria tolerate or evade phage predation through inducible responses to phage presence. Using the microbial model Pseudomonas fluorescens SBW25 and its lytic DNA phage SBW25Φ2, we demonstrate the existence of an inducible response in the form of a transient increase in population growth rate, and found that the response was induced by phage binding. This response was accompanied by a decrease in bacterial cell size, which we propose to be an associated cost. We discuss these results in the context of bacterial ecology and phage-bacteria co-evolution.

Journal article

Connolly J, Bell T, Bolger T, Brophy C, Carnus T, Finn JA, Kirwan L, Isbell F, Levine J, Luescher A, Picasso V, Roscher C, Teresa Sebastia M, Suter M, Weigelt Aet al., 2013, An improved model to predict the effects of changing biodiversity levels on ecosystem function, JOURNAL OF ECOLOGY, Vol: 101, Pages: 344-355, ISSN: 0022-0477

Journal article

Gravel D, Bell T, Barbera C, Combe M, Pommier T, Mouquet Net al., 2012, Phylogenetic constraints on ecosystem functioning, Nature Communications, Vol: 3

There is consensus that biodiversity losses will result in declining ecosystem functioning if species have different functional traits. Phylogenetic diversity has recently been suggested as a predictor of ecosystem functioning because it could approximate the functional complementarity among species. Here we describe an experiment that takes advantage of the rapid evolutionary response of bacteria to disentangle the role of phylogenetic and species diversity. We impose a strong selection regime on marine bacterial lineages and assemble the ancestral and evolved lines in microcosms of varying lineage and phylogenetic diversity. We find that the relationship between phylogenetic diversity and productivity is strong for the ancestral lineages but brakes down for the evolved lineages. Our results not only emphasize the potential of using phylogeny to evaluate ecosystem functioning, but also they warn against using phylogenetics as a proxy for functional diversity without good information on species evolutionary history

Journal article

Foster K, Bell T, 2012, Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species, Current Biology, Vol: 22, Pages: 1845-1850

Microbial cells secrete numerous enzymes, scavenging molecules, and signals that can promote the growth and survival of other cells around them [ [1], [2], [3] and [4]]. This observation is consistent with the evolution of cooperation within species [5], and there is now an increasing emphasis on the importance of cooperation between different microbial species [ [4], [5] and [6]]. We lack, however, a systematic test of the importance of mutually positive interactions between different species, which is vital for assessing the commonness and importance of cooperative evolution in natural communities. Here, we study the extent of mutually positive interaction among bacterial strains isolated from a common aquatic environment. Using data collected from two independent experiments evaluating community productivity across diversity gradients, we show that (1) in pairwise species combinations, the great majority of interactions are net negative and (2) there is no evidence that strong higher-order positive effects arise when more than two species are mixed together. Our data do not exclude the possibility of positive effects in one direction where one species gains at the expense of another, i.e., predator-prey-like interactions. However, these do not constitute cooperation and our analysis suggests that the typical result of adaptation to other microbial species will be competitive, rather than cooperative, phenotypes.

Journal article

Lawrence D, Fiegna F, Behrends V, Bundy JG, Phillimore AB, Bell T, Barraclough TGet al., 2012, Species interactions alter evolutionary responses to a novel environment., PLoS Biol, Vol: 10

Studies of evolutionary responses to novel environments typically consider single species or perhaps pairs of interacting species. However, all organisms co-occur with many other species, resulting in evolutionary dynamics that might not match those predicted using single species approaches. Recent theories predict that species interactions in diverse systems can influence how component species evolve in response to environmental change. In turn, evolution might have consequences for ecosystem functioning. We used experimental communities of five bacterial species to show that species interactions have a major impact on adaptation to a novel environment in the laboratory. Species in communities diverged in their use of resources compared with the same species in monocultures and evolved to use waste products generated by other species. This generally led to a trade-off between adaptation to the abiotic and biotic components of the environment, such that species evolving in communities had lower growth rates when assayed in the absence of other species. Based on growth assays and on nuclear magnetic resonance (NMR) spectroscopy of resource use, all species evolved more in communities than they did in monocultures. The evolutionary changes had significant repercussions for the functioning of these experimental ecosystems: communities reassembled from isolates that had evolved in polyculture were more productive than those reassembled from isolates that had evolved in monoculture. Our results show that the way in which species adapt to new environments depends critically on the biotic environment of co-occurring species. Moreover, predicting how functioning of complex ecosystems will respond to an environmental change requires knowing how species interactions will evolve.

Journal article

Poroyko V, Morowitz M, Bell T, Ulanov A, Wang M, Donovan S, Bao N, Gu S, Hong L, Alverdy JC, Bergelson J, Liu DCet al., 2011, Diet creates metabolic niches in the "inmature gut" that shape microbial communities, NUTRICION HOSPITALARIA, Vol: 26, Pages: 1283-1295, ISSN: 0212-1611

Journal article

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