Soil fungal : Bacterial ratios are linked to altered carbon cycling

Acknowledgments We thank Steffen Ruehlow, Agnes Fastnacht, Karl Kuebler, Iris Kuhlmann, Heike Geilmann, and Petra Linke for technical support in establishing the experiment and with stable isotope analyses. We also thank Markus Lange, Daniel Read, and Hyun Gweon for helpful discussions. Funding AM has received funding from Max Planck Society and the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 655240. AM has also received a career orientation grant from the Jena School for Microbial Communication (JSMC) that funded the laboratory visits. DFG SFB Aquadiva funded part of this work.Peer reviewedPublisher PD

Soil microbial communities with greater investment in resource acquisition have lower growth yield

Resource acquisition and growth yield are fundamental microbial traits that affect biogeochemical processes and have consequences for ecosystem functioning. However, there is a lack of empirical observations linking these traits. Using a landscape-scale survey of temperate near-neutral pH soils, we show tradeoffs in key community-level parameters linked to these traits. Increased investment into extracellular enzymes estimated using specific potential enzyme activity was associated with reduced growth yield obtained using carbon use efficiency measures from stable isotope tracing. Reduction in growth yield was linked more to carbon than nitrogen acquisition highlighting smaller stoichiometric than energetic constraints on community metabolism in examined soils

Rhizosphere bacterial carbon turnover is higher in nucleic acids than membrane lipids : Implications for understanding soil carbon cycling

Acknowledgments We thank Agnes Fastnacht, Karl Kuebler, Steffen Ruehlow, Iris Kuhlmann, Heike Geilmann, Petra Linke, and Willi Brand for technical support in establishing the experimental setup and/or with stable isotope analyses. We also thank Bernhard Ahrens and Daniel Read for helpful discussions. This project was funded by the Max-Planck-Gesellschaft. We acknowledge Deutsche Forschungsgemeinschaft (DFG) for the fellowship to AAM in the research training group 1257 ‘Alteration and element mobility at microbe-mineral interface’ that is part of the Jena School for Microbial Communication (JSMC). AAM was also supported by the International Max Planck Research School for Global Biogeochemical Cycles (IMPRS-gBGC).Peer reviewedPublisher PD

Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics

This project was funded by the UK Natural Environment Research Council (standard grant NE/E006353/1 to R.I.G., A.S.W., and M.B. and Soil Security grant NE/M017125/1 to R.I.G.). A.A.M. has received funding from the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodowska-Curie grant no. 655240. We wish to further acknowledge the lab assistance of Phillip James and the staff at the NERC Biomolecular Analysis Facility, University of Liverpool, United Kingdom.Peer reviewedPublisher PD

Plants with arbuscular mycorrhizal fungi efficiently acquire Nitrogen from substrate additions by shaping the decomposer community composition and their net plant carbon demand

Acknowledgements SC received funding from long term DAAD scholarship to carry out the research. ML is funded by the German Research Foundation (DFG; FOR 456, FOR 1451 – “The Jena Experiment”) and by the “Zwillenberg-Tietz Stiftung”. We acknowledge help from Agnes Fastnacht with greenhouse resources and monitoring of the experiment. Special thanks to Karl Kübler for construction and deployment of the pulse labelling setup in the greenhouse. We acknowledge Heike Geilmann and Steffen Ruehlow for help with stable isotope measurements, and Maria Foerster for helping with fatty acid analysis. We also thank Erika Kothe, Ruchira Mukherji, Elisa Catao and Huei Ying Gan for helpful comments and discussions and Simon Benk for proof reading the MS. Funding Open Access funding enabled and organized by Projekt DEAL.Peer reviewedPublisher PD

Land use effects on soil microbiome composition and traits with consequences for soil carbon cycling

The soil microbiome determines the fate of plant-fixed carbon. The shifts in soil properties caused by land use change leads to modifications in microbiome function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated using metaproteomics, metabarcoding and a 13C labelled litter decomposition experiment across two temperate sites with differing soil pH each with a paired land use intensity contrast. 13C incorporation into microbial biomass increased with land use intensification in low pH soil but decreased in high pH soil, with potential impact on carbon use efficiency (CUE) in opposing directions. Reduction in biosynthesis traits was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. We observed divergent pH-controlled pathways of SOC cycling. In low-pH soil, land use intensification alleviates microbial abiotic stress resulting in increased biomass production but promotes decomposition and SOC loss. In contrast, in high-pH soil, land use intensification increases microbial physiological constraints and decreases biomass production, leading to reduced necromass build-up and SOC stabilisation. We demonstrate how microbial biomass production and respiration dynamics and therefore CUE can be decoupled from SOC highlighting the need for its careful consideration in managing SOC storage for soil health and climate change mitigation

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

We acknowledge funding from the US DOE Genomic Science Program, BER, Office of Science project DE-SC0016410. We thank Bin Wang for discussion and inputs on trait-based modelling.Peer reviewedPublisher PD

Differential Response of Bacterial Microdiversity to Simulated Global Change

ACKNOWLEDGMENTS UC Irvine and the LRGCE are located on the ancestral homelands of the Indigenous Kizh and Acjachemen nations. We thank Alejandra Rodriguez Verdugo, Katrine Whiteson, Kendra Walters, Cynthia Rodriguez, Kristin Barbour, Alberto Barron Sandoval, Joanna Wang, Joia Kai Capocchi, Pauline Uyen Phuong Nguyen, Khanh Thuy Huynh, and Clara Barnosky for their input on analyses and previous drafts and for laboratory help. This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research grants DE-SC0016410 and DE-SC0020382.Peer reviewedPublisher PD

Linking molecular size, composition and carbon turnover of extractable soil microbial compounds

Microbial contribution to the maintenance and turnover of soil organic matter is significant. Yet, we do not have a thorough understanding of how biochemical composition of soil microbial biomass is related to carbon turnover and persistence of different microbial components. Using a suite of state-of-the-art analytical techniques, we investigated the molecular characteristics of extractable microbial biomass and linked it to its carbon turnover time. A 13CO2 plant pulse labelling experiment was used to trace plant carbon into rhizosphere soil microbial biomass, which was obtained by chloroform fumigation extraction (CFE). 13C content in molecular size classes of extracted microbial compounds was analysed using size exclusion chromatography (SEC) coupled online to high performance liquid chromatography–isotope ratio mass spectrometry (SEC-HPLC-IRMS). Molecular characterization of microbial compounds was performed using complementary approaches, namely SEC-HPLC coupled to Fourier transform infrared spectroscopy (SEC-HPLC-FTIR) and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). SEC-HPLC-FTIR suggests that mid to high molecular weight (MW) microbial compounds were richer in aliphatic CH bonds, carbohydrate-like compounds and possibly Pdouble bond; length as m-dashO derivatives from phospholipids. On the contrary, the lower size range was characterized by more oxidised compounds with hydroxyl, carbonyl, ether and/or carboxyl groups. ESI-FT-ICR-MS suggests that microbial compounds were largely aliphatic and richer in N than the background detrital material. Both molecular characterization tools suggest that CFE derived microbial biomass was largely lipid, carbohydrate and protein derived. SEC-HPLC-IRMS analysis revealed that 13C enrichment decreased with increasing MW of microbial compounds and the turnover time was deduced as 12.8 ± 0.6, 18.5 ± 0.6 and 22.9 ± 0.7 days for low, mid and high MW size classes, respectively. We conclude that low MW compounds represent the rapidly turned-over metabolite fraction of extractable soil microbial biomass consisting of organic acids, alcohols, amino acids and sugars; whereas, larger structural compounds are part of the cell envelope (likely membrane lipids, proteins or polysaccharides) with a much lower renewal rate. This relation of microbial carbon turnover to its molecular size, structure and composition thus highlights the significance of cellular biochemistry in determining the microbial contribution to soil carbon cycling and specifically soil organic matter formation