@article{MooijTrolleJeppesenetal.2010,
  author    = {Mooij, Wolf M. and Trolle, Dennis and Jeppesen, Erik and Arhonditsis, George B. and Belolipetsky, Pavel V. and Chitamwebwa, Deonatus B. R. and Degermendzhy, Andrey G. and DeAngelis, Donald L. and Domis, Lisette Nicole de Senerpont and Downing, Andrea S. and Elliott, J. Alex and Fragoso Jr, Carlos Ruberto and Gaedke, Ursula and Genova, Svetlana N. and Gulati, Ramesh D. and H{\aa}kanson, Lars and Hamilton, David P. and Hipsey, Matthew R. and 't Hoen, Jochem and H{\"u}lsmann, Stephan and Los, F. Hans and Makler-Pick, Vardit and Petzoldt, Thomas and Prokopkin, Igor G. and Rinke, Karsten and Schep, Sebastiaan A. and Tominaga, Koji and Van Dam, Anne A. and Van Nes, Egbert H. and Wells, Scott A. and Janse, Jan H.},
  title     = {Challenges and opportunities for integrating lake ecosystem modelling approaches},
  series = {Aquatic ecology},
  volume    = {44},
  journal   = {Aquatic ecology},
  publisher = {Springer Science + Business Media B.V.},
  address   = {Dordrecht},
  issn      = {1573-5125},
  doi       = {10.1007/s10452-010-9339-3},
  pages     = {633 -- 667},
  year      = {2010},
  abstract  = {A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models.},
  language  = {en}
}
@article{GarciaBuckHamiltonetal.2018,
  author    = {Garcia, Sarahi L. and Buck, Moritz and Hamilton, Joshua J. and Wurzbacher, Christian and Grossart, Hans-Peter and McMahon, Katherine D. and Eiler, Alexander},
  title     = {Model communities hint at promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria},
  series = {mSphere},
  volume    = {3},
  journal   = {mSphere},
  number    = {3},
  publisher = {American Society for Microbiology},
  address   = {Washington},
  issn      = {2379-5042},
  doi       = {10.1128/mSphere.00202-18},
  pages     = {8},
  year      = {2018},
  abstract  = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.},
  language  = {en}
}
@article{GarciaBuckMcMahonetal.2015,
  author    = {Garcia, Sarahi L. and Buck, Moritz and McMahon, Katherine D. and Grossart, Hans-Peter and Eiler, Alexander and Warnecke, Falk},
  title     = {Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community},
  series = {Molecular ecology},
  volume    = {24},
  journal   = {Molecular ecology},
  number    = {17},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0962-1083},
  doi       = {10.1111/mec.13319},
  pages     = {4449 -- 4459},
  year      = {2015},
  abstract  = {Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.},
  language  = {en}
}