@article{LANVERS2026125921,

title = {Heterologous production of structurally distinct levans in an optimized Paenibacillus polymyxa chassis},

author = {Pia Lanvers and Jannis Broeker and Severin Pech\'{e} and Claudia Broeker and Luise Ernst and Daniel Wefers and Jochen Schmid},

url = {https://www.sciencedirect.com/science/article/pii/S0144861726010386},

doi = {https://doi.org/10.1016/j.carbpol.2026.125921},

issn = {0144-8617},

year  = {2026},

date = {2026-12-01},

urldate = {2026-12-01},

journal = {Carbohydrate Polymers},

volume = {393},

pages = {125921},

abstract = {Levan is a bacterial β-fructan exopolysaccharide that is highly valued for its applications as a prebiotic, natural sweetener, and adhesive. Levan is synthesized by levansucrases (EC 2.4.1.10), which utilize the energy from sucrose hydrolysis to polymerize fructose. To establish an efficient microbial platform for levan production, we employed the non-pathogenic soil bacterium, Paenibacillus polymyxa, a natural producer of the exopolysaccharides paenan and levan. By sequential deletion of genes involved in paenan biosynthesis, extracellular proteolysis, levan degradation, and foam formation, we created a chassis strain with enhanced levan production. In batch fermentation, the optimized strain produced 30.2 g·L−1 of ultrapure levan (yield: 0.30 g·g−1), which was further increased by 82% using a fed-batch strategy. To expand the structural diversity of levans, levansucrases from various bacterial strains were integrated into the genome of P. polymyxa. Seven of the eight variants successfully produced high-purity levan at titers from 1.8 to 26.3 g·L−1. The obtained levans were structurally diverse, with molecular weights from 5.5 to 30.9 MDa and branching degrees of 9 to 16%. This engineered P. polymyxa chassis enables the production of structurally distinct levans under standardized conditions and provides a versatile platform for recombinant exopolysaccharide biosynthesis.},

keywords = {Chassis, DiP-LeFos, Exopolysaccharides, Fermentation, Levan},

pubstate = {published},

tppubtype = {article}

}

@article{kirsch001,

title = {Strategic Planning of Agroforestry Supply Chains [Preprint]},

author = {Thomas Kirschstein},

url = {https://doi.org/10.21203/rs.3.rs-10756931/v1},

year  = {2026},

date = {2026-10-06},

journal = {In Review [Journal of Industrial Ecology]},

abstract = {Agroforestry systems integrate fast-growing woody perennials into agricultural land. They deliver multiple biomass fractions of differing quality to food, chemical, pulp-and-paper, as well as energy industries. The woody biomass feedstock produced can be used to substitute fossil feedstocks in chemical and energy industry. Additionally, agroforestry increases climate resiliency and sustainability of agricultural production. Agroforestry-based woody biomass shows substantial feedstock potentials as most land is used for agriculture in central Europe. However, agroforestry is only applied in marginal scale in central Europe. A core challenge of agroforestry is to establish economically viable regional bioeconomy networks which connect partners from agriculture and downstream industries. Agroforestry-based supply chains need to be organized such that all partners benefit economically in the long run. This paper presents a supply chain design model that helps to support design decisions for agroforestry-based supply chains. It models agroforestry establishment and harvest scheduling on farm-level in a linear multi-echelon network design model. It relies on biomass growth models describing biomass production in agroforestry systems. These biomass fractions are allocated to chemical, pulp-and-paper, and energy industry depending on quality and demand restrictions. The model is applied in a case study focusing on central Germany. The optimization results indicate that agroforestry-based supply chains can be configured in an economically viable way. Agroforestry systems can serve as feedstock suppliers at a considerable scale. Profitability of agroforestry-based agricultural practice seems to be competitive with traditional agricultural production and provides woody biomass at a competitive cost, provided transports are not too long.},

keywords = {Agroforestry, Biobased production, Bioeconomy network design, Biomass cascading, DiP-SMART Agroforst, Industrial symbiosis, Supply chain optimization},

pubstate = {published},

tppubtype = {article}

}

@article{devasahayam2026nanopore,

title = {Nanopore sequencing reveals coordinated host and microbiome responses across barley genotypes},

author = {Bennet Rohan Fernando Devasahayam and Thomas McNeil and Tesfaye Wubet and Thomas Schmutzer},

doi = {10.1186/s12915-026-02688-3},

year  = {2026},

date = {2026-07-29},

urldate = {2026-07-29},

journal = {BMC Biology},

volume = {24},

number = {1},

pages = {177},

abstract = {BackgroundBarley (Hordeum vulgare L.) provides a suitable model for studying domestication-driven plant-microbiome interactions. Although wild, landrace, and modern genotypes host distinct rhizosphere communities, the extent to which roots and microbes reciprocally influence each other remains unclear. Here, we applied an integrated multi-omics approach combining long-read metagenomics, root transcriptomics, and plant genomics to understand genotype-specific host-microbiome coordination.ResultsOxford Nanopore whole metagenome sequencing (WMS) revealed genotype-associated shifts in rhizosphere communities across seasons. Functional profiling showed a conserved metabolic backbone including amino acid metabolism, energy production, and secondary metabolite biosynthesis, alongside genotype-dependent variation in carbohydrate metabolism and transport-associated pathways. Genome-resolved analysis through metagenome-assembled genomes (MAGs) further detailed the taxonomic and functional architecture of key rhizosphere lineages. Root transcriptome profiling identified extensive differential expression associated with microbial perception, signaling, defense, and metabolic processes. Integration of host and microbiome data revealed coordinated molecular patterns, indicating that barley genotypes are associated with distinct microbial assemblages and corresponding transcriptional responses.ConclusionsThese findings indicate that domestication has shaped coordinated associations between barley genotypes and their rhizosphere microbiomes, reflected in both microbial community composition and host transcriptional regulation. This work provides new insights into the evolutionary tuning of plant-microbiome relationships and highlights opportunities for microbiome-informed strategies in barley improvement.},

keywords = {DiP-DIAMANT, Host-microbiome interactions, Long-read nanopore sequencing, Metagenomics, Rhizosphere microbiome, Transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001673578400001,

title = {A novel approach to assessing the tracking accuracy of crop phenology  for multi-orbit and multi-feature Sentinel-1 time series},

author = {Johannes Low and Christopher Conrad and Steven Hill and Michael Thiel and Tobias Ullmann and Insa Otte},

doi = {10.1016/j.srs.2026.100370},

issn = {2666-0172},

year  = {2026},

date = {2026-06-01},

urldate = {2026-06-01},

journal = {SCIENCE OF REMOTE SENSING},

volume = {13},

keywords = {Canola, DEMMIN, DiP-ZAZIkI, InSAR coherence, Phenology, Sugar beet, Wheat},

pubstate = {published},

tppubtype = {article}

}

@article{vonmaydell2026population,

title = {Population structure, genetic diversity and core set construction of an international collection of 256 Melissa officinalis genotypes},

author = {Daniel Maydell and Johannes Schwerdt and Heike Lehnert and Yvonne P\"{o}schl-Grau and Thomas Schmutzer and Frank Marthe},

doi = {10.1186/s12870-026-08853-8},

issn = {1471-2229},

year  = {2026},

date = {2026-05-01},

urldate = {2026-05-01},

journal = {BMC Plant Biology},

volume = {26},

number = {1},

pages = {794},

abstract = {BackgroundMelissa officinalis (balm) is a perennial medicinal. Climate change and high cultivation costs necessitate the breeding of new cultivars with improved stress tolerance and high metabolite content. However, the high costs of phenotyping large collections limit breeding progress. This study characterized the genetic diversity and population structure of 256 genotypes from 215 international accessions using flow cytometry and genotyping by sequencing (GBS). The primary objective was to identify untapped genetic resources and establish core sets to streamline future breeding and research efforts.ResultsMorphological characterization and flow cytometry revealed a clear division by ploidy and subspecies. The collection comprised 209 diploid and three polyploid genotypes of ssp. officinalis (2C = 1.79 pg) and 44 tetraploid genotypes of ssp. altissima (4C = 3.57 pg). GBS generated 29,307 and 9,909 SNPs for the entire collection and a subset of ssp. officinalis genotypes, respectively. We identified significant genetic differentiation between the subspecies, as confirmed by PCA (PC1 = 69.9%), STRUCTURE, and hierarchical clustering. With 21,770 private alleles and HE = 0.38 subspecies altissima exhibited greater genetic divergence than ssp. officinalis (2,953 private alleles},

keywords = {DiP-DIAMANT, DiP-OptiLamia, Domestication, Gene flow, Gene pool, Genetic diversity, Identification (biology), Melissa officinalis, Officinalis, Population, Subspecies},

pubstate = {published},

tppubtype = {article}

}

@article{fierlej2026zmsweet,

title = {ZmSWEET Sucrose transporters expressed in the endosperm adjacent to the maize embryo are necessary for carbon partitioning and embryo growth [Preprint]},

author = {Yannick Fierlej and Laurine Grazer and Abdelsabour G. A. Khaled and Matthias Langer and \'{E}milie Montes and Thibaut Perez and Laura Gallo and Beno\^{i}t Lacombe and Philippe Nacry and H\'{e}l\`{e}ne Duplus-Bottin and Nicolas M. Doll and Ljudmilla Borisjuk and Hardy Rolletschek and Gwyneth Ingram and Peter M. Rogowsky and Thomas Widiez},

doi = {10.64898/2026.02.24.707659},

year  = {2026},

date = {2026-02-25},

urldate = {2026-02-25},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Abstract In cereals such as maize, the kernel accumulates large quantities of storage compounds, including carbohydrates, lipids, and proteins, a process that requires tight regulation of nutrient transport. Seeds are composed of distinct tissues: the embryo, the endosperm, and maternal tissues that are symplastically isolated (not connected through plasmodesmata), necessitating specialized nutrient transfer mechanisms. In maize, nutrient transfer from maternal tissues to the endosperm via specialized basal endosperm transfer layer (BETL) cells is well characterized. However, nutrient transfer at the endosperm/embryo interface remains poorly understood. Consequently, the routes by which maternal carbon-derived sugars support embryo growth are still unclear. Our previous transcriptomic profiling uncovered a novel Endosperm domain Adjacent to the embryo Scutellum (EAS) with strong enrichment for transporter genes. Notably, genes encoding three sugar transporters from the SWEET (Sugars Will Eventually be Exported Transporters) family are highly and preferentially expressed in the EAS, suggesting the existence of a specialized sugar transfer mechanism at this interface. We show that the ZmSWEET proteins encoded by these genes are membrane-localized sucrose transporters and are functionally important for kernel development. A gene-edited triple zmsweet14a/14b/15a knock-out mutant exhibits reduced kernel weight and embryo size, significantly decreased embryo oil accumulation at maturity, and altered carbon partitioning within the kernel. In addition to these defects, mutant kernels display a significant reduction in primary root length during germination, indicating either lasting physiological consequences of disrupted sucrose transport during seed development or an additional role for these SWEET transporters during germination. Together, our findings demonstrate that sucrose transport at the endosperm/embryo interface is critical for proper carbon allocation, embryo development, and seed vigor, and identify the EAS as a key functional domain and potential target for improving seed composition.},

keywords = {DiP-Magdi, EAS, Embryo, Endosperm, Mutant, Scutellum, Sucrose, Transporter},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001681509300001,

title = {Fast barcode calling based on k-mer distances},

author = {Riko Corwin Uphoff and Steffen Schuler and Ivo Grosse and Matthias Muller-Hannemann},

doi = {10.1093/pnasnexus/pgag001},

year  = {2026},

date = {2026-02-01},

urldate = {2026-02-01},

journal = {PNAS NEXUS},

volume = {5},

number = {2},

keywords = {Algorithm engineering, DiP-Hyperspace, DNA barcode calling, Spatial transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001643722100001,

title = {Machine Learning-Driven Enzyme Mining: Opportunities, Challenges, and  Future Perspectives},

author = {Felix Moorhoff and Yanzi Zhang and Sizhe Qiu and Wenjuan Dong and David Medina-Ortiz and Jing Zhao and Mehdi D. Davari},

doi = {10.1021/acscatal.5c04814},

issn = {2155-5435},

year  = {2026},

date = {2026-01-01},

urldate = {2026-01-01},

journal = {ACS CATALYSIS},

volume = {16},

number = {1},

pages = {12-30},

keywords = {Biocatalysis, DiP-BioCasNavi, Enzyme discovery, Machine learning},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001631204600001,

title = {Whole-genome resequencing of the wild barley diversity collection: a  resource for identifying and exploiting genetic variation for cultivated  barley improvement},

author = {Rebecca Spanner and Ahmad H. Sallam and Yu Guo and Murukarthick Jayakodi and Axel Himmelbach and Anne Fiebig and Jamie Simmons and Gerit Bethke and Yoonjung Lee and Luis Willian Pacheco Arge and Yinjie Qiu and Ana Badea and Michael Baum and Francois Belzile and Roi Ben-David and Robert Brueggeman and Austin Case and Luigi Cattivelli and Michael Davis and Christoph Dockter and Jaroslav Dolezel and Antonin Dreiseitl and Ryan Gavin and Lior Glick and Stephan Greiner and Ruth Hamilton and Patrick M. Hayes and Scott Heisel and Cynthia Henson and Benjamin Kilian and Takao Komatsuda and Chengdao Li and Cheng Liu and Ramamurthy Mahalingam and Maren Maruschewski and Oadi Matny and Andreas Maurer and Klaus F. X. Mayer and Itay Mayrose and Matthew Moscou and Gary J. Muehlbauer and Youko Oono and Frank Ordon and Hakan Ozkan and Ales Pecinka and Dragan Perovic and Klaus Pillen and Mohammad Pourkheirandish and Joanne Russell and Jan Safar and Silvio Salvi and Miguel Sanchez-Garcia and Kazuhiro Sato and Thomas Schmutzer and Uwe Scholz and Jeness Scott and Gurcharn Singh Brar and Kevin P. Smith and Mark E. Sorrells and Manuel Spannagl and Nils Stein and Alessandro Tondelli and Roberto Tuberosa and James Tucker and Thomas Turkington and Jan Valkoun and Ramesh Pal Singh Verma and Marcus A. Vinje and Maria Korff and Jason G. Walling and Robbie Waugh and Roger P. Wise and Brande B. H. Wulff and Shengming Yang and Guoping Zhang and Peter L. Morrell and Martin Mascher and Brian J. Steffenson},

doi = {10.1093/g3journal/jkaf261},

issn = {2160-1836},

year  = {2026},

date = {2026-01-01},

urldate = {2026-01-01},

journal = {G3-GENES GENOMES GENETICS},

volume = {16},

number = {1},

abstract = {To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the 

 Wild Barley Diversity Collection was subjected to paired-end Illumina 

 sequencing at similar to 9 x depth and evaluated for several agronomic 

 traits. We discovered 240.2 million single nucleotide polymorphisms 

 (SNPs) after alignment to the Morex V3 assembly and 24.4 million short 

 (1 to 50 bp) insertions and deletions. A genome-wide association study 

 of lemma color identified one marker-trait association (MTA) on 

 chromosome 1H close to HvBlp, the cloned gene controlling black lemma. 

 Four MTAs were identified for seedling stem rust resistance, including 2 

 novel loci on chromosomes 1H and 6H and one co-locating to the complex 

 RMRL1-RMRL2 locus on 5H. The whole-genome sequence data described herein 

 will facilitate the identification and utilization of new alleles for 

 barley improvement.},

keywords = {Genomic data, Sequencing, Variant analysis},

pubstate = {published},

tppubtype = {article}

}