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

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

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

Aims: We investigated the role of plants and their plant-derived carbon in shaping the microbial community that decomposes substrates and traced the return of nutrients from decomposition back to plant shoots in order to understand the importance of plants for ecosystem element cycling. Methods: We performed a greenhouse experiment having plant communities with and without arbuscular mycorrhizal fungi (AMF) and ingrowth cores that held different 15N labeled substrates. We determined the microbial community structure using molecular sequencing and the net assimilation of plant carbon into soil microorganisms using a 13CO2 pulse and 13C measurements of microbial biomarkers. We determined the return of nitrogen back to the shoots using the 15N signal, which was provided from the decomposition of the substrate added to the ingrowth cores. Results: We observed that the microbial community composition in the ingrowth cores and their net 13C assimilation depended on the presence of AMF and the added substrate. Both plant communities had similar 15N uptake into their shoots, but the net N uptake cost was significantly lower in presence of AMF. In the presence of AMF also lower net N uptake cost was observed for the decomposition of plant-derived and microorganism-derived substrates compared to inorganic nitrogen suggesting that AMF actively controls the decomposer comunity and their carbon demand. Conclusion: Our results identify for the first time a functional overlap of soil microorganisms as identical substrate is decomposed by different microorganisms suggesting functional redundancy of microbial communities. In consequence a better understanding of ecosystem element cycling can only be achieved when the whole plant-microorganism-organic matter-soil continuum is investigated