Martin Hartmann

Last Name

Hartmann

First Name

Martin

ORCID

0000-0001-8069-5284

Organisational unit

03982 - Six, Johan / Six, Johan

Show all metadata

Search Results

Publications 1 - 10 of 72

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
Bengtsson-Palme, Johan; Ryberg, Martin; Hartmann, Martin; et al. (2013)
Methods in Ecology and Evolution
Crop genotype modulates root rot resistance-associated microbial community composition and abundance of key taxa
Gfeller, Valentin; Schneider, Michael; Bodenhausen, Natacha; et al. (2025)
bioRxiv
Plants are constantly challenged by pathogens, which can cause substantial yield losses. The aggressiveness of and damage by pathogens depends on the host-associated microbiome, which might be shaped by plant genetics to improve resistance. How different crop genotypes modulate their microbiota when challenged by a complex of pathogens is largely unknown. Here, we investigate if and how pea (Pisum sativum L.) genotypes shape their root microbiota upon challenge by soil-borne pathogens and how this relates to a genotype’s resistance. Building on the phenotyping efforts of 252 pea genotypes grown in naturally infested soil, we characterized root fungi and bacteria by ITS region and 16S rRNA gene amplicon sequencing, respectively. Pea genotype markedly affected both fungal and bacterial community composition, and these genotype-specific microbiota were associated with root rot resistance. For example, genotype resistance was correlated (R2 = 19%) with root fungal community composition. Further, several key microbes, showing a high relative abundance, heritability, connectedness with other microbes, and correlation with plant resistance, were identified. Our findings highlight the importance of crop genotype-specific root microbiota under root rot stress and the potential of the plant to shape its associated microbiota as a second line of defense.
Drought increases root and rhizodeposition carbon inputs into soils
Kost, Elena; Kundel, Dominika; Barthel, Matti; et al. (2026)
Plant and Soil
Aims Increasing droughts affect crop yield and health. Plants can respond to drought by adapting their root biomass, root morphology, and quality and quantity of rhizodeposition to improve water and nutrient uptake. Besides droughts, agricultural management influences roots and rhizodeposition; however, it is not well studied how agricultural management can affect the response of roots and rhizodeposition to drought. Methods A semi-continuous 13CO2 isotope labelling experiment was performed in a long-term field experiment comparing biodynamic, mixed conventional, and mineral conventional cropping systems. Rainout shelters were installed to induce drought. Root, net rhizodeposition, and the rhizosphere microbiome were determined at ripening of wheat. Results Drought enhanced the total root carbon mainly through the increase of fine roots. Fine root carbon under drought was primarily enhanced in the mixed conventional and biodynamic cropping system, both receiving farmyard manure, whereas no increase was measured in the mineral fertilized conventional system. Net rhizodeposition carbon was enhanced in all cropping systems under drought, particularly in the first 0.25 m. While some plant-growth-promoting genera such as Streptomyces and Rhizophagus showed relative increases under drought, other plant growth-promoting genera often involved in nitrogen fixation such as Rhodoferax and Mesorhizobium were decreased. Conclusion This field trial suggests that drought increases total belowground carbon input via fine root and net rhizodeposition carbon inputs. Since fine root carbon increased under drought in cropping systems with farmyard manure, adding manure under future drought periods could be advantageous to increase soil carbon inputs and improve nutrient foraging.
Drought resistance and resilience of rhizosphere communities in forest soils from the cellular to ecosystem scale – insights from ¹³C pulse labeling
Gao, Decai; Luster, Jörg; Zürcher, Alois; et al. (2024)
New Phytologist
The link between above- and belowground communities is a key uncertainty in drought and rewetting effects on forest carbon (C) cycle. In young beech model ecosystems and mature naturally dry pine forest exposed to 15-yr-long irrigation, we performed ¹³C pulse labeling experiments, one during drought and one 2 wk after rewetting, tracing tree assimilates into rhizosphere communities. The ¹³C pulses applied in tree crowns reached soil microbial communities of the young and mature forests one and 4 d later, respectively. Drought decreased the transfer of labeled assimilates relative to the irrigation treatment. The ¹³C label in phospholipid fatty acids (PLFAs) indicated greater drought reduction of assimilate incorporation by fungi (−85%) than by gram-positive (−43%) and gram-negative bacteria (−58%). ¹³C label incorporation was more strongly reduced for PLFAs (cell membrane) than for microbial cytoplasm extracted by chloroform. This suggests that fresh rhizodeposits are predominantly used for osmoregulation or storage under drought, at the expense of new cell formation. Two weeks after rewetting, ¹³C enrichment in PLFAs was greater in previously dry than in continuously moist soils. Drought and rewetting effects were greater in beech systems than in pine forest. Belowground C allocation and rhizosphere communities are highly resilient to drought.
Potential consequences of water limitation and drought-induced tree mortality on carbon and nitrogen cycling
Solly, Emily F.; Jaeger, Astrid C.H.; Six, Johan; et al. (2020)
EGUsphere
Water limiting conditions for the growth and physiology of trees as well as episodes of tree mortality triggered by drought have recently been documented in several bioregions across the world. In parallel to these major vegetation alterations, the impact of water scarcity also has prominent effects on soil processes mediated by the microbiome such as the transformation of organic matter, heterotrophic respiration, microbial uptake as well as nutrient mineralization. Although currently little explored, shifts in the interplay occurring between tree functioning and soil microbial processes may be crucial during tree mortality events and may feed back on ecosystem carbon and nitrogen cycling. We will present a multidisciplinary setup to mechanistically explore how water limitation acts synergistically on the interplay between trees and soil microorganisms, with potential consequences for ecosystem biogeochemical fluxes. The experimental setup focusses on a key temperate forest species, Scots pine (Pinus sylvestris L.), which is currently facing high mortality rates in several inner-Alpine valleys of Europe due to drier climatic conditions during parts of the year. We make use of small scale mesocosms featuring young trees and soil collected from a drought-affected natural forest. The mesocosms are treated with different levels of water availability under controlled conditions. Plant growth and physiological changes related to water limitation are investigated in parallel to various soil properties. State-of-the-art isotopic labelling techniques are used to trace alterations in carbon and nitrogen transfers within the plant-soil-microbe continuum. We will specifically test whether extended periods of drought suppress the flux of carbon from plants to soil and lead plants to invest more in the maintenance of fine root systems. Moreover, we will follow the potential changes in the rates of decomposition, mineralization and incorporation of plant debris into soil organic matter over time and link them to potential alterations of the soil microbiota. These experimental observations will be validated by measurements in drought-affected Scots pine forests in inner-Alpine valleys. We expect the outcomes of this work to advance the fundamental understanding of the alterations occurring in the plant-soil-microbe system related to drought as well as to improve the detection of mechanisms leading to Scots pine mortality.
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
Bengtsson-Palme, Johan; Richardson, Rodney T.; Meola, Marco; et al. (2018)
Bioinformatics
Motivation Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data. Results We evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.
Potential relevance between soybean nitrogen uptake and rhizosphere prokaryotic communities under waterlogging stress
Lian, Tengxiang; Cheng, Lang; Liu, Qi; et al. (2023)
ISME Communications
Waterlogging in soil can limit the availability of nitrogen to plants by promoting denitrification and reducing nitrogen fixation and nitrification. The root-associated microorganisms that determine nitrogen availability at the root-soil interface can be influenced by plant genotype and soil type, which potentially alters the nitrogen uptake capacity of plants in waterlogged soils. In a greenhouse experiment, two soybean genotypes with contrasting capacities to resist waterlogging stress were grown in Udic Argosol and Haplic Alisol soils with and without waterlogging, respectively. Using isotope labeling, high-throughput amplicon sequencing and qPCR, we show that waterlogging negatively affects soybean yield and nitrogen absorption from fertilizer, atmosphere, and soil. These effects were soil-dependent and more pronounced in the waterlogging-sensitive than tolerant genotype. The tolerant genotype harbored more ammonia oxidizers and less nitrous oxide reducers. Anaerobic, nitrogen-fixing, denitrifying and iron-reducing bacteria such as Geobacter/Geomonas, Sphingomonas, Candidatus Koribacter, and Desulfosporosinus were proportionally enriched in association with the tolerant genotype under waterlogging. These changes in the rhizosphere microbiome might ultimately help the plant to improve nitrogen uptake under waterlogged, anoxic conditions. This research contributes to a better understanding of the adaptability of soybean genotypes under waterlogging stress and might help to formulate fertilization strategies that improve nitrogen use efficiency of soybean.
Drought-induced tree mortality in Scots pine mesocosms promotes changes in soil microbial communities and trophic groups
Jaeger, Astrid C.H.; Hartmann, Martin; Conz, Rafaela Feola; et al. (2024)
Applied Soil Ecology
Increased tree mortality related to water limitation is documented for various species at different sites globally. Nevertheless, our understanding of tree mortality effects on soil microbial communities remains scarce. Therefore, we conducted a mesocosm experiment with young Scots pine saplings and natural forest soil with differing drought legacies to follow changes in soil microbial communities during tree mortality. Scots pine saplings were completely deprived of water during the experiment until they died. Shifts in soil microbial communities during tree mortality were assessed by metabarcoding in parallel with measurements of tree vitality and physicochemical soil properties. Drought history influenced the rate at which trees died, although high individual differences were observed. Tree death was accompanied by reduced stomatal conductance, discoloring of needles, increased defoliation, and shrinkage of the stem diameter. Soil NO3− concentrations increased after tree death, potentially through diminished plant uptake and increased microbial nitrification. Microbial abundance and community composition were affected by tree death and drought legacy. Copiotrophic bacterial taxa decreased during tree mortality, while oligotrophic taxa increased, probably slowing down soil carbon turnover. Fungal saprotrophs decreased, while symbiotrophs, such as ectomycorrhizal (ECM) fungi, increased in abundance, potentially through facultative saprothrophy and as a survival strategy of the trees in the initial phase of dying. Overall, our results indicate that drought-induced tree mortality promotes changes in soil prokaryotic and fungal communities, potentially affecting soil processes in forest ecosystems.
Worldwide diversity of endophytic fungi and insects associated with dormant tree twigs
Franić, Iva; Prospero, Simone; Adamson, Kalev; et al. (2022)
Scientific Data
International trade in plants and climate change are two of the main factors causing damaging tree pests (i.e. fungi and insects) to spread into new areas. To mitigate these risks, a large-scale assessment of tree-associated fungi and insects is needed. We present records of endophytic fungi and insects in twigs of 17 angiosperm and gymnosperm genera, from 51 locations in 32 countries worldwide. Endophytic fungi were characterized by high-throughput sequencing of 352 samples from 145 tree species in 28 countries. Insects were reared from 227 samples of 109 tree species in 18 countries and sorted into taxonomic orders and feeding guilds. Herbivorous insects were grouped into morphospecies and were identified using molecular and morphological approaches. This dataset reveals the diversity of tree-associated taxa, as it contains 12,721 fungal Amplicon Sequence Variants and 208 herbivorous insect morphospecies, sampled across broad geographic and climatic gradients and for many tree species. This dataset will facilitate applied and fundamental studies on the distribution of fungal endophytes and insects in trees.
Are traded forest tree seeds a potential source of nonnative pests?
Franic, Iva; Prospero, Simone; Hartmann, Martin; et al. (2019)
Ecological Applications

Publications 1 - 10 of 72

Martin Hartmann

Last Name

First Name

ORCID

Organisational unit

Filters

Search Results