Visualization of metabolic interaction networks in microbial communities using VisANT 5.0

The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues.This work was supported by the National Institutes of Health, R01GM103502-05 to CD, ZH and DS. Partial support was also provided by grants from the Office of Science (BER), U.S. Department of Energy (DE-SC0004962), the Joslin Diabetes Center (Pilot & Feasibility grant P30 DK036836), the Army Research Office under MURI award W911NF-12-1-0390, National Institutes of Health (1RC2GM092602-01, R01GM089978 and 5R01DE024468), NSF (1457695), and Defense Advanced Research Projects Agency Biological Technologies Office (BTO), Program: Biological Robustness In Complex Settings (BRICS), Purchase Request No. HR0011515303, Program Code: TRS-0 Issued by DARPA/CMO under Contract No. HR0011-15-C-0091. Funding for open access charge: National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (R01GM103502-05 - National Institutes of Health; 1RC2GM092602-01 - National Institutes of Health; R01GM089978 - National Institutes of Health; 5R01DE024468 - National Institutes of Health; DE-SC0004962 - Office of Science (BER), U.S. Department of Energy; P30 DK036836 - Joslin Diabetes Center; W911NF-12-1-0390 - Army Research Office under MURI; 1457695 - NSF; HR0011515303 - Defense Advanced Research Projects Agency Biological Technologies Office (BTO), Program: Biological Robustness In Complex Settings (BRICS); HR0011-15-C-0091 - DARPA/CMO; National Institutes of Health)Published versio

Volatile codes: Correlation of olfactory signals and reception in Drosophila-yeast chemical communication.

Drosophila have evolved strong mutualistic associations with yeast communities that best support their growth and survival, resulting in the development of novel niches. It has been suggested that flies recognize their cognate yeasts primarily based on the rich repertoire of volatile organic compounds (VOCs) derived from the yeasts. Thus, it remained an exciting avenue to study whether fly spp. detect and discriminate yeast strains based on odor alone, and if so, how such resolution is achieved by the olfactory system in flies. We used two fly species known to exploit different niches and harboring different yeasts, D. suzukii (a pest of fresh fruit) and D. melanogaster (a saprophytic fly and a neurogenetic model organism). We initially established the behavioral preference of both fly species to six Drosophila-associated yeasts; then chemically analyzed the VOC profile of each yeast which revealed quantitative and qualitative differences; and finally isolated and identified the physiologically active constituents from yeast VOCs for each drosophilid that potentially define attraction. By employing chemical, behavioral, and electrophysiological analyses, we provide a comprehensive portrait of the olfactory neuroethological correlates underlying fly-yeast coadaptation in two drosophilids with distinct habitats

Informatics Technology Mimics Ecology: Dense, Mutualistic Collaboration Networks Are Associated with Higher Publication Rates

Information technology (IT) adoption enables biomedical research. Publications are an accepted measure of research output, and network models can describe the collaborative nature of publication. In particular, ecological networks can serve as analogies for publication and technology adoption. We constructed network models of adoption of bioinformatics programming languages and health IT (HIT) from the literature

Investigations into stability in the fig/ fig-wasp mutualism

Fig trees (Ficus, Moraceae) and their pollinating wasps (Chalcidoidea, Agaonidae) are involved in an obligate mutualism where each partner relies on the other in order to reproduce: the pollinating fig wasps are a fig tree’s only pollen disperser whilst the fig trees provide the wasps with places in which to lay their eggs. Mutualistic interactions are, however, ultimately genetically selfish and as such, are often rife with conflict. Fig trees are either monoecious, where wasps and seeds develop together within fig fruit (syconia), or dioecious, where wasps and seeds develop separately. In interactions between monoecious fig trees and their pollinating wasps, there are conflicts of interest over the relative allocation of fig flowers to wasp and seed development. Although fig trees reap the rewards associated with wasp and seed production (through pollen and seed dispersal respectively), pollinators only benefit directly from flowers that nurture the development of wasp larvae, and increase their fitness by attempting to oviposit in as many ovules as possible. If successful, this oviposition strategy would eventually destroy the mutualism; however, the interaction has lasted for over 60 million years suggesting that mechanisms must be in place to limit wasp oviposition. This thesis addresses a number of factors to elucidate how stability may be achieved in monoecious fig systems. Possible mechanisms include: 1) a parasitoidcentred short ovipositor hypothesis in Ficus rubiginosa, which suggests that a subset of flowers are out of reach to parasitoid ovipositors making these ovules the preferred choice for ovipositing pollinators and allowing seeds to develop in less preferred ovules; 2) the presence of third-party mutualists such as non-pollinating fig wasps (F. burkei) and patrolling green tree ants on the fig surface (F. racemosa) that limit pollinator and parasitoid oviposition respectively; and 3) selection on fig morphology which constrains the size (and therefore fecundity) of the associated pollinators. I discuss the lack of evidence for a single unifying theory for mutualism stability and suggest that a more likely scenario is the presence of separate, and perhaps multiple, stabilising strategies in different fig/ fig-wasp partnerships

Cucurbit Pollination: Mechanisms and Management to Optimise Field Quality and Quantity

Negative impacts from intensifying agriculture have generated concerns that pollinator-dependent crop species, such as courgette Cucurbita pepo L., may be experiencing a pollination deficit. This thesis explores the extent to which pollination influences fruit set; how pollination could be improved; and how in doing so growers’ profits and agricultural resilience could increase, using UK field-grown courgettes as a model system. Inspired by evidence of parthenocarpy (fruit set in the absence of fertilisation) in courgette, a systematic review showed extensive use of parthenocarpy to circumvent the need for pollination in other ‘pollinator-dependent’ crop species across the globe. Nonetheless, pollination significantly increased yield and pollinators were abundant enough to fulfil the pollination requirements of courgette, which if extrapolated to the rest of the UK, equates to pollinators contributing approximately £2.7 million to annual UK courgette production. Furthermore, wild flowers within fields were shown to be effective at increasing the abundance of bumblebees and solitary bees. Further exploration of the mutualistic relationship between courgettes and pollinators showed that courgette can improve populations of Bombus terrestris (using the Bumble-BEEHAVE model), an important pollinator of courgette. This thesis concludes that pollination is a vital mechanism for ensuring optimal courgette yields and that whilst pollination levels were maximal at study sites, simple management, such as encouraging wild flowers within courgette fields could help to attract pollinators to courgette flowers and support bees’ nutritional requirements beyond the extensive, yet transient, resource provided by courgette. Understanding a crop’s requirement for pollinators can also aid growers in their decision making about what varieties and sites should be used which could increase their agricultural resilience and further their economic advantage. Further work is needed to understand how other environmental factors interact with pollination to influence fruit set so that growers can prioritise key regulating services in their management for optimal crop yields.Agriculture and Horticulture Development Boar

Bombus terrestris in a mass‐flowering pollinator‐dependent crop: A mutualistic relationship? (article)

This is the final version. Available on open access from Wiley via the DOI in this recordThe dataset associated with this article is in ORE at https://doi.org/10.24378/exe.823Bumblebees (Bombus spp.) rely on an abundant and diverse selection of floral resources to meet their nutritional requirements. In farmed landscapes, mass‐flowering crops can provide an important forage resource for bumblebees, with increased visitation from bumblebees into mass‐flowering crops having an additional benefit to growers who require pollination services. This study explores the mutualistic relationship between Bombus terrestris L. (buff‐tailed bumblebee), a common species in European farmland, and the mass‐flowering crop courgette (Cucurbita pepo L.) to see how effective B. terrestris is at pollinating courgette and in return how courgette may affect B. terrestris colony dynamics. By combining empirical data on nectar and pollen availability with model simulations using the novel bumblebee model Bumble‐BEEHAVE, we were able to quantify and simulate for the first time, the importance of courgette as a mass‐flowering forage resource for bumblebees. Courgette provides vast quantities of nectar to ensure a high visitation rate, which combined with abundant pollen grains, enables B. terrestris to have a high pollination potential. While B. terrestris showed a strong fidelity to courgette flowers for nectar, courgette pollen was not found in any pollen loads from returning foragers. Nonetheless, model simulations showed that early season courgette (nectar) increased the number of hibernating queens, colonies, and adult workers in the modeled landscapes. Synthesis and applications. Courgette has the potential to improve bumblebee population dynamics; however, the lack of evidence of the bees collecting courgette pollen in this study suggests that bees can only benefit from this transient nectar source if alternative floral resources, particularly pollen, are also available to fulfill bees’ nutritional requirements in space and time. Therefore, providing additional forage resources could simultaneously improve pollination services and bumblebee populations.Natural Environment Research Council (NERC)Agriculture and Horticulture Development Boar

An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots.

The phytohormones jasmonate, gibberellin, salicylate, and ethylene regulate an interconnected reprogramming network integrating root development with plant responses against microbes. The establishment of mutualistic ectomycorrhizal symbiosis requires the suppression of plant defense responses against fungi as well as the modification of root architecture and cortical cell wall properties. Here, we investigated the contribution of phytohormones and their crosstalk to the ontogenesis of ectomycorrhizae (ECM) between grey poplar (Populus tremula x alba) roots and the fungus Laccaria bicolor. To obtain the hormonal blueprint of developing ECM, we quantified the concentrations of jasmonates, gibberellins, and salicylate via liquid chromatography-tandem mass spectrometry. Subsequently, we assessed root architecture, mycorrhizal morphology, and gene expression levels (RNA sequencing) in phytohormone-treated poplar lateral roots in the presence or absence of L. bicolor. Salicylic acid accumulated in mid-stage ECM. Exogenous phytohormone treatment affected the fungal colonization rate and/or frequency of Hartig net formation. Colonized lateral roots displayed diminished responsiveness to jasmonate but regulated some genes, implicated in defense and cell wall remodelling, that were specifically differentially expressed after jasmonate treatment. Responses to salicylate, gibberellin, and ethylene were enhanced in ECM. The dynamics of phytohormone accumulation and response suggest that jasmonate, gibberellin, salicylate, and ethylene signalling play multifaceted roles in poplar L. bicolor ectomycorrhizal development