publications

2025

1. 

   Evolution induced state shifts in a long-term microbial community experiment

   Mikko Kivikoski, Johannes Cairns, Shane L Hogle, and 4 more authors

   bioRxiv, 2025

   Abs DOI

   Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evolution shapes these systems through eco-evolutionary feedbacks is a central challenge in ecology and evolution. Experimental studies using simplified microbial assemblages have yielded important insights into the ecological principles governing community states. However, an important knowledge gap is how selection within member species drives changes of community state in multispecies systems. Here, we present a fouryear evolution experiment involving a 23-species synthetic bacterial community propagated in two environments: a control medium and the same medium supplemented with the antibiotic streptomycin. Through combined analyses of community composition and genome evolution, we quantified the temporal changes in species abundances and the evolutionary trajectories of individual community members. The extended duration of the experiment enabled the detection of adaptive mutations and community state shifts that occur only over long evolutionary timescales. We show that community dynamics are environment dependent and reproducible across replicates, and that evolution of streptomycin resistance in a previously streptomycin-sensitive species on its own can induce abrupt community state shifts. Our results provide a direct demonstration of eco-evolutionary feedbacks within a multi-species community, revealing how a single adaptive mutation can reorganize complex ecological networks.Competing Interest StatementThe authors have declared no competing interest.Research Council of Finland, https://ror.org/05k73zm37, #346126, #330886, #327741, #346128, #364234

2. 

   Universal bacterial clade dynamics dominate under predation despite altered phenotypes and mutation targets

   Dovydas Kičiatovas, Johannes Cairns, Veera Partanen, and 4 more authors

   bioRxiv, 2025

   Abs DOI

   Recent studies have revealed bacterial genome-wide evolution to be complex and dynamic even in a constant environment. The evolution is characterized by the emergence of new clades competing or temporarily coexisting as each clade undergoes evolutionary change. Previous studies on predator-prey dynamics tracking simple ecological and phenotypic metrics have shown predation to fundamentally alter prey evolution, facilitating defense evolution followed by coevolution and frequency dependent selection between defended and undefended prey genotypes. Moreover, these dynamics can differ between prey species depending, for example, on mutation rate and the physiological and fitness effects of the mutations available. Here we sought to consolidate these fields by examining genome-wide evolution in five bacterial prey species separately subjected to long-term evolution under ciliate predation. For all species, we found mutational signals of prey adaptation, with genomic and phenotypic data demonstrating changes in composition between the experimental treatments. Mutational targets and dynamics also differed between prey species. Intriguingly, however, overall temporal molecular dynamics across the prey species were strikingly similar to those of bacteria evolving alone, with constant emergence, competition and quasi-stable coexistence of clades. This makes molecular evolution more interesting and less predictable than we might expect based on existing coevolutionary theories.Competing Interest StatementThe authors have declared no competing interest.Research Council of Finland, 346126, 330886, 327741, 346128Deutsche Forschungsgemeinschaft, BE 4135/12-1

3. 

   Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities

   Johannes Cairns, Shane Hogle, Elizaveta Alitupa, and 2 more authors

   Nature Ecology & Evolution, 2025

   DOI

2024

1. 

   Quantifying massively parallel microbial growth with spatially mediated interactions

   Florian Borse, Dovydas Kičiatovas, Teemu Kuosmanen, and 5 more authors

   PLOS Computational Biology, 2024

2023

1. 

   Towards evolutionary predictions: Current promises and challenges

   Meike T Wortel, Deepa Agashe, Susan F Bailey, and 8 more authors

   Evolutionary applications, 2023

2. 

   Understanding and applying biological resilience, from genes to ecosystems

   Rose Thorogood, Ville Mustonen, Alexandre Aleixo, and 8 more authors

   npj Biodiversity, 2023

3. 

   Understanding cellular growth strategies via optimal control

   Tommi Mononen, Teemu Kuosmanen, Johannes Cairns, and 1 more author

   Journal of the Royal Society Interface, 2023

4. 

   Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function

   Shane L Hogle, Liisa Ruusulehto, Johannes Cairns, and 2 more authors

   The ISME Journal, 2023

5. 

   Microbiological and physicochemical quality of groundwater and risk factors for Its pollution in Ouagadougou, Burkina Faso

   Oumar Traoré, Dissinviel Stéphane Kpoda, René Dembélé, and 4 more authors

   Water, 2023

2022

1. 

   Effect of mutation supply on population dynamics and trait evolution in an experimental microbial community

   Johannes Cairns, Alexandre Jousset, Lutz Becks, and 1 more author

   Ecology Letters, 2022

2. 

   Strong selective environments determine evolutionary outcome in time-dependent fitness seascapes

   Johannes Cairns, Florian Borse, Tommi Mononen, and 2 more authors

   Evolution Letters, 2022

3. 

   Effects of phenotypic variation on consumer coexistence and prey community structure

   Shane L Hogle, Iina Hepolehto, Lasse Ruokolainen, and 2 more authors

   Ecology Letters, 2022

4. 

   Biological units of antimicrobial resistance and strategies for their containment in animal production

   Johanna Muurinen, Johannes Cairns, John Eddie Ekakoro, and 3 more authors

   FEMS Microbiology Ecology, 2022

2021

1. 

   Drug-induced resistance evolution necessitates less aggressive treatment

   Teemu Kuosmanen, Johannes Cairns, Robert Noble, and 3 more authors

   PLoS computational biology, 2021

2020

1. 

   Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation

   Johannes Cairns, Roosa Jokela, Lutz Becks, and 2 more authors

   Nature Ecology & Evolution, 2020

2. 

   Evolution in interacting species alters predator life-history traits, behaviour and morphology in experimental microbial communities

   Johannes Cairns, Felix Moerman, Emanuel A Fronhofer, and 2 more authors

   Proceedings of the Royal Society B, 2020

2019

1. 

   Predator coevolution and prey trait variability determine species coexistence

   Thomas Scheuerl, Johannes Cairns, Lutz Becks, and 1 more author

   Proceedings of the Royal Society B, 2019

2. 

   Contrasting the impact of cytotoxic and cytostatic drug therapies on tumour progression

   Jani V Anttila, Mikhail Shubin, Johannes Cairns, and 6 more authors

   PLoS computational biology, 2019

2018

1. 

   Dual-stressor selection alters eco-evolutionary dynamics in experimental communities

   Teppo Hiltunen, Johannes Cairns, Jens Frickel, and 6 more authors

   Nature Ecology & Evolution, 2018

2. 

   Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes

   Johannes Cairns, Lasse Ruokolainen, Jenni Hultman, and 3 more authors

   Communications biology, 2018

3. 

   Black queen evolution and trophic interactions determine plasmid survival after the disruption of the conjugation network

   Johannes Cairns, Katariina Koskinen, Reetta Penttinen, and 8 more authors

   Msystems, 2018

4. 

   Construction and characterization of synthetic bacterial community for experimental ecology and evolution

   Johannes Cairns, Roosa Jokela, Jenni Hultman, and 3 more authors

   Frontiers in genetics, 2018

5. 

   Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent

   Jenni Hultman, Manu Tamminen, Katariina Pärnänen, and 3 more authors

   FEMS microbiology ecology, 2018

2017

1. 

   Genomic evolution of bacterial populations under coselection by antibiotics and phage

   Johannes Cairns, Jens Frickel, Matti Jalasvuori, and 2 more authors

   Molecular Ecology, 2017

2. 

   Sublethal streptomycin concentrations and lytic bacteriophage together promote resistance evolution

   Johannes Cairns, Lutz Becks, Matti Jalasvuori, and 1 more author

   Philosophical Transactions of the Royal Society B: Biological Sciences, 2017

2016

1. 

   Conjugation is necessary for a bacterial plasmid to survive under protozoan predation

   Johannes Cairns, Matti Jalasvuori, Ville Ojala, and 2 more authors

   Biology letters, 2016

2. 

   Evolving interactions between diazotrophic cyanobacterium and phage mediate nitrogen release and host competitive ability

   Johannes Cairns, Sebastián Coloma, Kaarina Sivonen, and 1 more author

   Royal Society open science, 2016