@article{LiAbdulkadirSchattenbergetal.2022,
  author    = {Li, Shuang and Abdulkadir, Nafi'u and Schattenberg, Florian and da Rocha, Ulisses Nunes and Grimm, Volker and M{\"u}ller, Susann and Liu, Zishu},
  title     = {Stabilizing microbial communities by looped mass transfer},
  series = {Proceedings of the National Academy of Sciences of the United States of America : PNAS},
  volume    = {119},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America : PNAS},
  number    = {17},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.2117814119},
  pages     = {11},
  year      = {2022},
  abstract  = {Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates mu'. Subsets of cells that did not show net growth mu'SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.},
  language  = {en}
}
@article{KrauzeKaempfHornetal.2017,
  author    = {Krauze, Patryk and K{\"a}mpf, Horst and Horn, Fabian and Liu, Qi and Voropaev, Andrey and Wagner, Dirk and Alawi, Mashal},
  title     = {Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic},
  series = {Frontiers in microbiology},
  volume    = {8},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2017.02446},
  pages     = {16},
  year      = {2017},
  abstract  = {The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO2 at the surface that occurs in the form of CO2-rich mineral springs and wet and dry mofettes. So far, the influence of CO2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas) and iron (e.g., Gallionella, Sideroxydans) cycling shaped the core community. Additionally, CO2-influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments.},
  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{BaunachChowdhuryStallforthetal.2021,
  author    = {Baunach, Martin and Chowdhury, Somak and Stallforth, Pierre and Dittmann-Th{\"u}nemann, Elke},
  title     = {The landscape of recombination events that create nonribosomal peptide diversity},
  series = {Molecular biology and evolution : MBE},
  volume    = {38},
  journal   = {Molecular biology and evolution : MBE},
  number    = {5},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0737-4038},
  doi       = {10.1093/molbev/msab015},
  pages     = {2116 -- 2130},
  year      = {2021},
  abstract  = {Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing andmatching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the A(core) domains, yet domain interfaces and the flexible A(sub) domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches.},
  language  = {en}
}
@article{BachmannHeimbachHassenruecketal.2018,
  author    = {Bachmann, Jennifer and Heimbach, Tabea and Hassenr{\"u}ck, Christiane and Kopprio, German A. and Iversen, Morten Hvitfeldt and Grossart, Hans-Peter and G{\"a}rdes, Astrid},
  title     = {Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System},
  series = {Frontiers in microbiology},
  volume    = {9},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2018.02836},
  pages     = {13},
  year      = {2018},
  abstract  = {Saharan dust input and seasonal upwelling along North-West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; > 3.0 mu m) and free-living (FL; 0.2-3.0 mu m) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.},
  language  = {en}
}