Abstract

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「大規模相互作用網の再構成に関するノンパラメトリック手法の日本語解説」

三木健（龍谷大学）

生態学にとどまらず、「力学方程式」・「数理モデル」を用いた理論によって発展してきた研究分野においては、なかなか「モデル数式」(Theoretical Dynamic Modeling: TDM)から離れて事象を理解しその動態を定量化しようという機運がなかなか高まらない。21世紀に入って、Cross-Convergence Mapping (CCM)やS-mapと言った具体的なモデル数式に依存しない「ノンパラメトリック」な手法で相互作用する要素間の因果関係を明らかにするEmpirical Dynamic Modeling (EDM)が勃興した現在においても、TDMの呪縛から逃れられない人は多い。斯く言う私もEDMに初めて出会った（というか謝志豪氏に出会った）2005年以来、TDMの支配から逃れるのに10数年以上もかかってしまったし、その心変わりの原因を言語化するのも難しい。本講演では、参加者の心の呪縛を少しでも解けるよう、EDMの基盤的コンセプトの解説から始めた上で、英語セッションのChang博士の講演についての平易な紹介を行いたい。現状のEDMの手法では「次元の呪い」のせいで100ノードを超えるような大規模ネットワーク（たとえば100種が相互作用する生物群集）に適用する際の正確さについての性能評価が行われておらず、実データへの適用の有効性に疑問が残る（最適埋め込み次元がノード数よりもだいぶ小さいからである）。この問題を解決するために講演者も参加してChang博士が主導した研究によって開発された、“multiview distance regularized S-map”について、みなさんに紹介する予定である。

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“The multitude of microbial interactions: the need for new molecular tools and theoretical concepts”

Prof. Hans-Peter Grossart (Leibniz Institute of Freshwater Ecology and Inland Fisheries, IGB-Berlin, Germany)

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Microbes are basically everywhere on earth and greatly interact with their abiotic and biotic environment. In particular, interactions with organisms - including us humans - are of great interest since they can shape many important physiological functions and behavior of organisms and thus can to a large extent shape food web structure and functioning. These interactions often include the intensive exchange of signaling molecules, hormone like substance, vitamins, trace metals and metabolic products such as sugars and proteins. As such microbes can greatly interlink organisms and create trophic links which would otherwise not exist. To disentangle the multitude of possible interactions, new molecular tools are of great value. On the one hand, genomic features can be used to discover interaction traits via bioinformatics, which then can be specifically searched for by using various OMICS tools. On the other hand, we are lacking profound theoretical understanding on how these interactions shape food web structure and biogeochemical cycles. New concepts and models are needed to account for the central role microbes play in many environments. Lately, cross feedings has been accepted as an important ecological concept which can be well implemented into theoretical food web models. Also, it has been shown that microbes being parasites or saprophytes are crucial for community assembly and hence ecosystem functions. In times of rapid global, such knowledge is urgently needed to mitigate arising negative consequences, e.g. due to increasing temperatures and anthropogenic interferences.

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“The effect of global change on phytoplankton disease, and consequences for the rest of the aquatic food web”

Dr. Thijs Frenken (Netherlands Institute of Ecology, NIOO-KNAW, The Netherlands)

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Aquatic systems are generally warming and receive an increased nutrient supply. During these conditions harmful phytoplankton can proliferate and form dense surface blooms that often consist of large-sized phytoplankton taxa, such as diatoms or filamentous cyanobacteria. In many cases these are inedible to zooplankton and thus form trophic bottlenecks, preventing efficient transfer of energy and elements to higher trophic levels. Just as any other organism cyanobacteria and diatoms can also get infected by pathogens, including fungal parasites and viruses. However, it remains unclear how warming and changes in nutrient supply affect these parasites. Here, we show how changes in temperature and stoichiometry may affect epidemic development in phytoplankton. Using large 1000-L mesocosms with a natural community we show that warming advances timing of aquatic viruses, and accelerates termination of a phytoplankton bloom by fungal parasites. Also, temperature led to changes in the stoichiometry of primary producers, which may have consequences for reproduction and stoichiometry of parasites. Indeed, by synthesizing literature, and with laboratory experiments, we confirm that changes in nutrient supply may create or alleviate stoichiometric mismatches between primary producers and their pathogens. This may have consequences for herbivores that rely on phytoplankton and parasites as food. Fungal parasites may not only provide zooplankton with a complementary food source in the form of fungal zoospores, they also fragmentate cyanobacterial filaments making them more edible. This work highlights the need to incorporate the complex dynamics between infections, stoichiometry and grazing to better understand how future aquatic food webs and their phytoplankton communities will respond to climate change.

“Reconstructing large networks with time-varying interactions”

Dr. Chun-Wei Chang (National Taiwan University, Taiwan)

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Reconstructing interactions from observational data is a critical need for investigating natural biological networks, wherein network dimensionality (ie number of interacting components) is usually high and interactions are time-varying. These pose a challenge to existing methods that can quantify only small interaction networks or assume static interactions under steady state. Here, we proposed a novel approach to reconstruct high-dimensional, time-varying interaction networks using empirical time series. This method, named" multiview distance regularized S-map", generalized the state space reconstruction to accommodate high dimensionality and overcome difficulties in quantifying massive interactions with limited data. When we evaluated this method using the time series generated from a large theoretical model involving hundreds of interacting species, estimated interaction strengths were in good agreement with theoretical expectations. As a result, reconstructed networks preserved important topological properties, such as centrality, strength distribution and derived stability measures. Moreover, our method effectively forecasted the dynamic behavior of network nodes. Applying this method to a natural bacterial community helped identify keystone species from the interaction network and revealed the mechanisms governing the dynamical stability of bacterial community. Our method overcame the challenge of high dimensionality and disentangled complex time-varying interactions in large natural dynamical systems.

 

“A high-throughput synthetic microbial ecosystem: stochastic community dynamics, inter-ecosystem interactions, predictions and controls”

Dr. Kazufumi Hosoda (RIKEN, Japan)

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Experiments on ecosystems have intrinsic difficulties in handling, reproducibility, and experimental commonality compared with individual organisms, where large-scale experiments using some “model organisms” have been commonly conducted. Synthetic assemblage of microorganisms that is axenically-culturable and cryopreservable is a type of ideal model ecosystems. However, most of previously-reported this type of synthetic ecosystems with trophic relationships had little diversity (typically each single species of producer, decomposer, and predator). Here we developed a synthetic ecosystem of 12 cryopreservable microbial species with diverse interactions as an experimental “model ecosystem.” We created a machine learning model that noninvasively distinguished the 12 species on micrographs. Our developments enable high-throughput experiments, for example, one researcher can simultaneously run 10,000 synthetic ecosystems in an ordinary experimental laboratory. This synthetic ecosystem was simple, but stochastic phenomena due to keystone species were observed, suggesting that it had some complexity as an ecosystem. In my talk, I will show some results about stochastic community dynamics, inter-ecosystem interactions, and predictions and controls of ecosystems.

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"Comments & Announcement; Methological applications to investigate microbial trophic interactions"

Dr. Serena Rasconi (INRAE CARRTEL, Alpine Centre for Research on Lake Ecosystems and Food Webs, Thonon les Bains, France)

 

Recent insights into aquatic diversity revealed the importance of overlooked trophic interactions (parasitism, saprophytism, mixotrophy...), carrying an enormous related potential for ecological functions. These different interactions can affect and govern ecological processes such as organic matter transfer, trophic upgrading, and nutrient cycling. A new view into aquatic food webs, which have otherwise focused on predation, herbivory and bacterivory is now contributing knowledge of ecosystem metabolism and functioning.

In particular, microbial parasites (fungi and fungal-like organisms) are major infectious agents in pelagic ecosystems and also can be novel food sources that sustain consumer growth. Similarly, parasites can not only affect host population dynamics and predator-prey interactions but they play an important role in ecological processes such as organic matter transfer, trophic upgrading, and nutrient cycling. In this talk we will focus on the application of methods in trophic ecology (fatty acids, stable isotopes…) to study microbial interactions. We will particularly explore recent studies applying these methods to investigate the functional role of microbial parasites in natural ecosystems and the related insights we are getting from the recently modified view of how the microbial loop is organized.