Publications

For a full list see below or go to Google Scholar , ResearcherID

Highlights

Quantifying microbial growth and carbon use efficiency in dry soil environments via 18O water vapor equilibration

We developed a unique method that allows for the first time to introduce stable isotope in soil without direct water addition. This has generated enourmous developments for measuring microbial growth in soil, from application to drought studies to intact soil cores, from community level measurements to taxa specific growth rates.

Canarini A., Wanek W., Watzka M., Sandén T., Spiegel H., Šantrůček J. and Schnecker J.

Global Change Biology 26(9), 5333–5341 (2020)

Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community

We discovered that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

Canarini A., Schmidt H., Fuchslueger L., Martin V., Herbold C. W., Zezula D., Gündler P., Hasibeder R., Jecmenica M., Bahn M., and Richter A.

Nature Communications, 12(1), 5308 (2021)

Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions

We applied the vapor equilibration method in combination with the qSIP to obtain taxa-specific growth rates. We found that during drought fewer taxa grow but they sustain high growth rates, and that future climate conditions (higher temperatures and atmospheric CO2) modified these taxa.

Metze D., Schnecker J., Canarini A., Fuchslueger L., Koch B. J., Stone B. W., Hungate B. A., Hausmann B., Schmidt H., Schaumberger A., Bahn M., Kaiser C., and Richter A.

Nature Communications, 14(1), 1–12 (2023)

Preprints

Canarini, A., Fuchslueger, L., Schnecker, J., Metze, D., Nelson, D., Kahmen, A., Watzka, M., Poetsch, E. M., Schaumberger, A., Bahn, M., & Richter, A. (2023). Soil fungi remain active and invest in storage compounds during drought independent of future climate conditions. bioRxiv; Pages: 2023.10.23.563577 Section: New Results. https://www.biorxiv.org/content/10.1101/2023.10.23.563577v1

@misc{canarini_soil_2023,
  title = {Soil fungi remain active and invest in storage compounds during drought independent of future climate conditions},
  copyright = {© 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
  url = {https://www.biorxiv.org/content/10.1101/2023.10.23.563577v1},
  doi = {10.1101/2023.10.23.563577},
  language = {en},
  urldate = {2023-10-24},
  publisher = {bioRxiv},
  author = {Canarini, Alberto and Fuchslueger, Lucia and Schnecker, Joerg and Metze, Dennis and Nelson, Daniel and Kahmen, Ansgar and Watzka, Margarete and Poetsch, Erich M. and Schaumberger, Andreas and Bahn, Michael and Richter, Andreas},
  month = oct,
  year = {2023},
  note = {Pages: 2023.10.23.563577
  Section: New Results},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\QLZ33XMW\\Canarini et al. - 2023 - Soil fungi remain active and invest in storage com.pdf:application/pdf}
}

Microbial growth is central to soil carbon cycling. However, how microbial communities grow under climate change is still largely unexplored. In an experiment simulating future climate conditions (increased atmospheric CO2 and temperature) and drought, we traced 2H or 18O applied via water-vapor exchange into fatty acids or DNA, respectively, allowing to measure community- and group-level adjustments in soil microbial physiology (replication, storage product synthesis, and carbon use efficiency, CUE). We show, that while overall community-level growth decreased by half during drought, fungal growth remained stable demonstrating an astonishing resistance of fungal activity against soil moisture changes. In addition, fungal investment into storage triglycerides increased more than five-fold under drought. CUE (the balance between anabolism and catabolism) was unaffected by drought but decreased in future climate conditions. Our results highlight that accounting for different growth strategies can foster our understanding of soil microbial contribution to C cycling and feedback to climate change.

Refereed journal articles

2024

Martin, V., Schmidt, H., Canarini, A., Koranda, M., Hausmann, B., Müller, C. W., & Richter, A. (2024). Soil cover shapes organic matter pools and microbial communities in soils of maritime Antarctica. Geoderma, 446, 116894. https://www.sciencedirect.com/science/article/pii/S001670612400123X

@article{martin_soil_2024,
  title = {Soil cover shapes organic matter pools and microbial communities in soils of maritime {Antarctica}},
  volume = {446},
  issn = {0016-7061},
  url = {https://www.sciencedirect.com/science/article/pii/S001670612400123X},
  doi = {10.1016/j.geoderma.2024.116894},
  urldate = {2024-05-12},
  journal = {Geoderma},
  author = {Martin, Victoria and Schmidt, Hannes and Canarini, Alberto and Koranda, Marianne and Hausmann, Bela and Müller, Carsten W. and Richter, Andreas},
  month = jun,
  year = {2024},
  keywords = {Biocrusts, Biological soil cover, Maritime Antarctica, Mass-specific microbial activity, Mosses, SOM fingerprint},
  pages = {116894},
  file = {ScienceDirect Snapshot:C\:\\Users\\alber\\Zotero\\storage\\NP9KSANN\\S001670612400123X.html:text/html}
}

Bryophytes and biological soil crusts (biocrusts) are the two major biological soil cover types of maritime Antarctica and play a crucial role for key ecosystem functions in the barely vegetated and little developed soils. Besides their profound impacts on nutrient cycling, they also provide habitats and activity hotspots for unique soil microbial communities. Yet, the effects of biological soil cover on the physical and chemical soil environment and belowground microbial communities have not been comprehensively studied in this fragile ecosystem. We here address the research question how biocrusts and mosses shape the quantity and structure of the soil organic matter pool, and the activity and composition of subjacent microbial communities. Towards this end, we sampled soils under two common, but physiologically distinct moss species, Polytrichastrum alpinum and Sanionia unicinata, and adjacent biological soil crusts at two sites on Deception Island, South Shetland Islands. We found that biocrusts and mosses differentially influenced central soil properties and subjacent soil microbial communities. All major SOM compound groups (carbohydrates, aromatics and phenols, lipids, N-containing polymers) as well as microbial biomass were more abundant in soil under biocrusts. However, microbial mass-specific growth rates were higher in soil under mosses. Our results showed moss-species-specific effects in addition to effects of soil cover type, as P. alpinum affected the activity and structure of soil microbial communities and the composition of soil organic matter stronger than S. unicinata. Our study highlights the interconnectedness between soil cover and soil biogeochemistry, which is crucial for deepening our understanding of belowground functioning in Antarctic soils. This linkage is of particular importance in the context of ongoing rapid climate change on the Antarctic Peninsula, as future shifts in the distribution and abundance of soil cover may substantially impact multiple soil processes in this vulnerable ecosystem.

Yang, L., Canarini, A., Zhang, W., Lang, M., Chen, Y., Cui, Z., Kuzyakov, Y., Richter, A., Chen, X., Zhang, F., & Tian, J. (2024). Microbial life-history strategies mediate microbial carbon pump efficacy in response to N management depending on stoichiometry of microbial demand. Global Change Biology, 30(5), e17311. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.17311. https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.17311

@article{yang_microbial_2024,
  title = {Microbial life-history strategies mediate microbial carbon pump efficacy in response to {N} management depending on stoichiometry of microbial demand},
  volume = {30},
  copyright = {© 2024 John Wiley \& Sons Ltd.},
  issn = {1365-2486},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.17311},
  doi = {10.1111/gcb.17311},
  language = {en},
  number = {5},
  urldate = {2024-05-15},
  journal = {Global Change Biology},
  author = {Yang, Liyang and Canarini, Alberto and Zhang, Wushuai and Lang, Ming and Chen, Yuanxue and Cui, Zhenling and Kuzyakov, Yakov and Richter, Andreas and Chen, Xinping and Zhang, Fusuo and Tian, Jing},
  year = {2024},
  note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.17311},
  keywords = {growth yield, microbial carbon pump efficacy, microbial life-history strategies, nitrogen addition, resource acquisition, SOC stability},
  pages = {e17311},
  annote = {e17311 GCB-23-3048.R1},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\NQQ2QMCV\\Yang et al. - 2024 - Microbial life-history strategies mediate microbia.pdf:application/pdf;Snapshot:C\:\\Users\\alber\\Zotero\\storage\\HULYKIH8\\gcb.html:text/html}
}

The soil microbial carbon pump (MCP) is increasingly acknowledged as being directly linked to soil organic carbon (SOC) accumulation and stability. Given the close coupling of carbon (C) and nitrogen (N) cycles and the constraints imposed by their stoichiometry on microbial growth, N addition might affect microbial growth strategies with potential consequences for necromass formation and carbon stability. However, this topic remains largely unexplored. Based on two multi-level N fertilizer experiments over 10 years in two soils with contrasting soil fertility located in the North (Cambisol, carbon-poor) and Southwest (Luvisol, carbon-rich), we hypothesized that different resource demands of microorganism elicit a trade-off in microbial growth potential (Y-strategy) and resource-acquisition (A-strategy) in response to N addition, and consequently on necromass formation and soil carbon stability. We combined measurements of necromass metrics (MCP efficacy) and soil carbon stability (chemical composition and mineral associated organic carbon) with potential changes in microbial life history strategies (assessed via soil metagenomes and enzymatic activity analyses). The contribution of microbial necromass to SOC decreased with N addition in the Cambisol, but increased in the Luvisol. Soil microbial life strategies displayed two distinct responses in two soils after N amendment: shift toward A-strategy (Cambisol) or Y-strategy (Luvisol). These divergent responses are owing to the stoichiometric imbalance between microbial demands and resource availability for C and N, which presented very distinct patterns in the two soils. The partial correlation analysis further confirmed that high N addition aggravated stoichiometric carbon demand, shifting the microbial community strategy toward resource-acquisition which reduced carbon stability in Cambisol. In contrast, the microbial Y-strategy had the positive direct effect on MCP efficacy in Luvisol, which greatly enhanced carbon stability. Such findings provide mechanistic insights into the stoichiometric regulation of MCP efficacy, and how this is mediated by site-specific trade-offs in microbial life strategies, which contribute to improving our comprehension of soil microbial C sequestration and potential optimization of agricultural N management.

2023

Gorka, S., Darcy, S., Horak, J., Imai, B., Mohrlok, M., Salas, E., Richter, A., Schmidt, H., Wanek, W., Kaiser, C., & Canarini, A. (2023). Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities. Soil Biology and Biochemistry, 187, 109205. https://www.sciencedirect.com/science/article/pii/S0038071723002675

@article{gorka_beyond_2023,
  title = {Beyond {PLFA}: {Concurrent} extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities},
  volume = {187},
  issn = {0038-0717},
  shorttitle = {Beyond {PLFA}},
  url = {https://www.sciencedirect.com/science/article/pii/S0038071723002675},
  doi = {10.1016/j.soilbio.2023.109205},
  urldate = {2023-10-16},
  journal = {Soil Biology and Biochemistry},
  author = {Gorka, Stefan and Darcy, Sean and Horak, Julia and Imai, Bruna and Mohrlok, Moritz and Salas, Erika and Richter, Andreas and Schmidt, Hannes and Wanek, Wolfgang and Kaiser, Christina and Canarini, Alberto},
  month = dec,
  year = {2023},
  keywords = {Phospholipid fatty acids, NLFA, Ergosterol, GLFA, Soil lipids},
  pages = {109205},
  file = {ScienceDirect Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\BNV3T7WL\\Gorka et al. - 2023 - Beyond PLFA Concurrent extraction of neutral and .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\alber\\Zotero\\storage\\6NRPCHSE\\S0038071723002675.html:text/html}
}

The analysis of phospholipid fatty acids (PLFAs) is one of the most common methods used to quantify the abundance, and analyse the community structure, of soil microbes. The PLFA extraction method can yield two additional lipid fractions—neutral lipids and glycolipids—which potentially hold additional, valuable information on soil microbial communities. Yet its quantitative sensitivity on complete neutral lipid (NLFA) and glycolipid fatty acid (GLFA) profiles has never been validated. In this study we tested (i) if the high-throughput PLFA method can be expanded to concurrently extract complete NLFA and GLFA profiles, as well as sterols, (ii) whether taxonomic specificities of signature fatty acids are retained across the three lipid fractions in pure culture strains, and (iii) whether NLFAs and GLFAs allow soil-specific fingerprinting to the same extent as PLFA analysis. By adjusting the polarity of chloroform with 2% ethanol for solid phase extraction, pure lipid standards were fully fractionated into neutral lipids, glycolipids, and phospholipids. Sterols eluted in the neutral lipid fraction, and a betaine lipid co-eluted with phospholipids. We found consistent taxonomic specificities of fatty acid markers across the three lipid fractions by analysing pure culture extracts representative of soil microbes. Fatty acid profiles from soil extracts, however, showed stronger differences between PLFAs, NLFAs, and GLFAs than between soil types. This indicates that PLFAs and NLFAs signify different community properties (biomass vs. carbon storage, putatively), and that GLFAs are sensitive markers for community traits which behave differently than PLFAs. Although we consistently found high abundances of characteristic sterols in fungal extracts, the PLFA extraction method only yielded miniscule amounts of ergosterol from soil extracts. We argue that concomitant measurement of fatty acid profiles from all three lipid fractions is a low-effort and potentially information-rich addition to the PLFA method, and discuss its applicability for soil microbial community analyses.

Metze, D., Schnecker, J., Canarini, A., Fuchslueger, L., Koch, B. J., Stone, B. W., Hungate, B. A., Hausmann, B., Schmidt, H., Schaumberger, A., Bahn, M., Kaiser, C., & Richter, A. (2023). Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nature Communications, 14(1), 1–12. Number: 1 Publisher: Nature Publishing Group. https://www.nature.com/articles/s41467-023-41524-y
```
@article{metze_microbial_2023,
  title = {Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions},
  volume = {14},
  copyright = {2023 Springer Nature Limited},
  issn = {2041-1723},
  url = {https://www.nature.com/articles/s41467-023-41524-y},
  doi = {10.1038/s41467-023-41524-y},
  language = {en},
  number = {1},
  urldate = {2023-09-22},
  journal = {Nature Communications},
  author = {Metze, Dennis and Schnecker, Jörg and Canarini, Alberto and Fuchslueger, Lucia and Koch, Benjamin J. and Stone, Bram W. and Hungate, Bruce A. and Hausmann, Bela and Schmidt, Hannes and Schaumberger, Andreas and Bahn, Michael and Kaiser, Christina and Richter, Andreas},
  month = sep,
  year = {2023},
  note = {Number: 1
  Publisher: Nature Publishing Group},
  keywords = {Microbial ecology, Climate-change ecology, Soil microbiology, Stable isotope analysis},
  pages = {1--12}
}
```
```
Climate change increases the frequency and intensity of drought events, affecting soil functions driven by microorganisms. Here, Metze et al. develop a method to estimate microbial growth rates in dry soils, and provide insights into the response of active microbes to drought today and in potential future climate conditions (high temperatures and CO2 levels).
```
Fujita, H., Ushio, M., Suzuki, K., Abe, M. S., Yamamichi, M., Iwayama, K., Canarini, A., Hayashi, I., Fukushima, K., Fukuda, S., Kiers, E. T., & Toju, H. (2023). Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics. Microbiome, 11(1), 63. https://doi.org/10.1186/s40168-023-01474-5
```
@article{fujita_alternative_2023,
  title = {Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics},
  volume = {11},
  issn = {2049-2618},
  url = {https://doi.org/10.1186/s40168-023-01474-5},
  doi = {10.1186/s40168-023-01474-5},
  number = {1},
  journal = {Microbiome},
  author = {Fujita, Hiroaki and Ushio, Masayuki and Suzuki, Kenta and Abe, Masato S. and Yamamichi, Masato and Iwayama, Koji and Canarini, Alberto and Hayashi, Ibuki and Fukushima, Keitaro and Fukuda, Shinji and Kiers, E. Toby and Toju, Hirokazu},
  month = mar,
  year = {2023},
  pages = {63}
}
```
```
Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as “dysbiosis” in human microbiomes.
```

Zheng, J., Canarini, A., Fujii, K., Mmari, W. N., Kilasara, M. M., & Funakawa, S. (2023). Cropland intensification mediates the radiative balance of greenhouse gas emissions and soil carbon sequestration in maize systems of sub-Saharan Africa. Global Change Biology, 29(6), 1514–1529. Publisher: John Wiley & Sons, Ltd. https://doi.org/10.1111/gcb.16550

@article{zheng_cropland_2023,
  title = {Cropland intensification mediates the radiative balance of greenhouse gas emissions and soil carbon sequestration in maize systems of sub-{Saharan} {Africa}},
  volume = {29},
  issn = {1354-1013},
  url = {https://doi.org/10.1111/gcb.16550},
  doi = {10.1111/gcb.16550},
  number = {6},
  urldate = {2023-06-13},
  journal = {Global Change Biology},
  author = {Zheng, Jinsen and Canarini, Alberto and Fujii, Kazumichi and Mmari, William N. and Kilasara, Method M. and Funakawa, Shinya},
  month = mar,
  year = {2023},
  note = {Publisher: John Wiley \& Sons, Ltd},
  keywords = {crop residue, global warming potential, greenhouse gas emission, N fertilizer, soil C sequestration, soil type, sub-Saharan Africa},
  pages = {1514--1529},
  annote = {https://doi.org/10.1111/gcb.16550}
}

Abstract Sub-Saharan Africa (SSA) must undertake proper cropland intensification for higher crop yields while minimizing climate impacts. Unfortunately, no studies have simultaneously quantified greenhouse gas (GHG; CO2, CH4, and N2O) emissions and soil organic carbon (SOC) change in SSA croplands, leaving it a blind spot in the accounting of global warming potential (GWP). Here, based on 2-year field monitoring of soil emissions of CO2, CH4, and N2O, as well as SOC changes in two contrasting soil types (sandy vs. clayey), we provided the first, full accounting of GWP for maize systems in response to cropland intensifications (increasing nitrogen rates and in combination with crop residue return) in SSA. To corroborate our field observations on SOC change (i.e., 2-year, a short duration), we implemented a process-oriented model parameterized with field data to simulate SOC dynamic over time. We further tested the generality of our findings by including a literature synthesis of SOC change across maize-based systems in SSA. We found that nitrogen application reduced SOC loss, likely through increased biomass yield and consequently belowground carbon allocation. Residue return switched the direction of SOC change from loss to gain; such a benefit (SOC sequestration) was not compromised by CH4 emissions (negligible) nor outweighed by the amplified N2O emissions, and contributed to negative net GWP. Overall, we show encouraging results that, combining residue and fertilizer-nitrogen input allowed for sequestering 82?284?kg of CO2-eq per Mg of maize grain produced across two soils. All analyses pointed to an advantage of sandy over clayey soils in achieving higher SOC sequestration targets, and thus call for a re-evaluation on the potential of sandy soils in SOC sequestration across SSA croplands. Our findings carry important implications for developing viable intensification practices for SSA croplands in mitigating climate change while securing food production.

Zheng, J., Fujii, K., Koba, K., Wanek, W., Müller, C., Jansen-Willems, A. B., Nakajima, Y., Wagai, R., & Canarini, A. (2023). Revisiting process-based simulations of soil nitrite dynamics: Tighter cycling between nitrite and nitrate than considered previously. Soil Biology and Biochemistry, 178, 108958. https://www.sciencedirect.com/science/article/pii/S0038071723000202

@article{zheng_revisiting_2023,
  title = {Revisiting process-based simulations of soil nitrite dynamics: {Tighter} cycling between nitrite and nitrate than considered previously},
  volume = {178},
  issn = {0038-0717},
  url = {https://www.sciencedirect.com/science/article/pii/S0038071723000202},
  doi = {10.1016/j.soilbio.2023.108958},
  journal = {Soil Biology and Biochemistry},
  author = {Zheng, Jinsen and Fujii, Kazumichi and Koba, Keisuke and Wanek, Wolfgang and Müller, Christoph and Jansen-Willems, Anne B. and Nakajima, Yasuhiro and Wagai, Rota and Canarini, Alberto},
  month = mar,
  year = {2023},
  keywords = {N tracing, Nitrate reduction, Nitrite dynamic, Nitrite re-oxidation, Numerical simulation},
  pages = {108958}
}

Nitrite is an important precursor of many environmentally hazardous compounds (e.g., nitrate, nitrous oxide, and nitrous acid). However, its dynamics in the soil environment are not yet fully understood. The NtraceNitrite tool has been successful in analyzing 15N tracing data. Here, based on a 15N tracing experiment (under aerobic condition) where either the nitrite, the nitrate, or the ammonium pool was labelled, we developed an extended model (NO2Trace), which was featured by the addition of coupled nitrate reduction and nitrite re-oxidation and the separation of the nitrate pool in two sub-pools. With 5 additional parameters optimized, NO2Trace was able to achieve a superior fit to the data, as compared to the NtraceNitrite tool. The additional features might offer a suitable explanation for the isotopic composition of nitrate produced via nitrification in terrestrial ecosystems. Our results carry two important implications: (i) a key assumption of the classical isotope pool dilution technique (i.e., no reflux of tracer) for estimating gross nitrate fluxes is violated, leading to considerable underestimations (22–99% in the datasets tested); (ii) re-oxidation can dominate the consumption (∼75%) of nitrite derived from nitrate reduction, indicating the potential of this process as a target for nitrogen retention mechanism against gaseous nitrogen losses (through nitrite reduction). The additional features of the extended model show a tighter cycle between soil nitrite and nitrate than considered previously and provide a more comprehensive description of soil nitrite transformations. This study also highlights that more work is needed to develop methods capable of separating process- and pathways-specific nitrate and nitrite pools.

Fujita, H., Ushio, M., Suzuki, K., Abe, M. S., Yamamichi, M., Okazaki, Y., Canarini, A., Hayashi, I., Fukushima, K., Fukuda, S., Kiers, E. T., & Toju, H. (2023). Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics. Frontiers in Microbiology, 14. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1261137

@article{fujita_metagenomic_2023,
  title = {Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics},
  volume = {14},
  issn = {1664-302X},
  url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1261137},
  doi = {https://doi.org/10.3389/fmicb.2023.1261137},
  urldate = {2023-12-01},
  journal = {Frontiers in Microbiology},
  author = {Fujita, Hiroaki and Ushio, Masayuki and Suzuki, Kenta and Abe, Masato S. and Yamamichi, Masato and Okazaki, Yusuke and Canarini, Alberto and Hayashi, Ibuki and Fukushima, Keitaro and Fukuda, Shinji and Kiers, E. Toby and Toju, Hirokazu},
  year = {2023},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\WQ7V836R\\Fujita et al. - 2023 - Metagenomic analysis of ecological niche overlap a.pdf:application/pdf}
}

Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).

Fujita, H., Ushio, M., Suzuki, K., Abe, M. S., Yamamichi, M., Okazaki, Y., Canarini, A., Hayashi, I., Fukushima, K., Fukuda, S., Kiers, E. T., & Toju, H. (2023). Facilitative interaction networks in experimental microbial community dynamics. Frontiers in Microbiology, 14. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1153952

@article{fujita_facilitative_2023,
  title = {Facilitative interaction networks in experimental microbial community dynamics},
  volume = {14},
  issn = {1664-302X},
  url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1153952},
  doi = {https://doi.org/10.3389/fmicb.2023.1153952},
  urldate = {2023-12-01},
  journal = {Frontiers in Microbiology},
  author = {Fujita, Hiroaki and Ushio, Masayuki and Suzuki, Kenta and Abe, Masato S. and Yamamichi, Masato and Okazaki, Yusuke and Canarini, Alberto and Hayashi, Ibuki and Fukushima, Keitaro and Fukuda, Shinji and Kiers, E. Toby and Toju, Hirokazu},
  year = {2023},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\I5CX8KK7\\Fujita et al. - 2023 - Facilitative interaction networks in experimental .pdf:application/pdf}
}

Facilitative interactions between microbial species are ubiquitous in various types of ecosystems on the Earth. Therefore, inferring how entangled webs of interspecific interactions shift through time in microbial ecosystems is an essential step for understanding ecological processes driving microbiome dynamics. By compiling shotgun metagenomic sequencing data of an experimental microbial community, we examined how the architectural features of facilitative interaction networks could change through time. A metabolic modeling approach for estimating dependence between microbial genomes (species) allowed us to infer the network structure of potential facilitative interactions at 13 time points through the 110-day monitoring of experimental microbiomes. We then found that positive feedback loops, which were theoretically predicted to promote cascade breakdown of ecological communities, existed within the inferred networks of metabolic interactions prior to the drastic community-compositional shift observed in the microbiome time-series. We further applied “directed-graph” analyses to pinpoint potential keystone species located at the “upper stream” positions of such feedback loops. These analyses on facilitative interactions will help us understand key mechanisms causing catastrophic shifts in microbial community structure.

2022

Verbrigghe, N., Meeran, K., Bahn, M., Canarini, A., Fransen, E., Fuchslueger, L., Ingrisch, J., Janssens, I. A., Richter, A., Sigurdsson, B. D., Soong, J. L., & Vicca, S. (2022). Long-term warming reduced microbial biomass but increased recent plant-derived C in microbes of a subarctic grassland. Soil Biology and Biochemistry, 167, 108590. https://www.sciencedirect.com/science/article/pii/S0038071722000475

@article{verbrigghe_long-term_2022,
  title = {Long-term warming reduced microbial biomass but increased recent plant-derived {C} in microbes of a subarctic grassland},
  volume = {167},
  issn = {0038-0717},
  url = {https://www.sciencedirect.com/science/article/pii/S0038071722000475},
  doi = {10.1016/j.soilbio.2022.108590},
  urldate = {2023-10-05},
  journal = {Soil Biology and Biochemistry},
  author = {Verbrigghe, Niel and Meeran, Kathiravan and Bahn, Michael and Canarini, Alberto and Fransen, Erik and Fuchslueger, Lucia and Ingrisch, Johannes and Janssens, Ivan A. and Richter, Andreas and Sigurdsson, Bjarni D. and Soong, Jennifer L. and Vicca, Sara},
  month = apr,
  year = {2022},
  keywords = {Microbial community structure, 13CO2 pulse labelling, Long-term warming, Microbial biomass, N addition},
  pages = {108590},
  file = {ScienceDirect Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\HUYFU5EG\\Verbrigghe et al. - 2022 - Long-term warming reduced microbial biomass but in.pdf:application/pdf}
}

Long-term soil warming and nitrogen (N) availability have been shown to affect microbial biomass and community composition. Altered assimilation patterns of recent plant-derived C and changes in soil C stocks following warming as well as increased N availability are critical in mediating the direction and magnitude of these community shifts. A 13C pulse labelling experiment was done on a warming gradient in an Icelandic grassland (Sigurdsson et al., 2016), to investigate the role of recent plant-derived C and warming on the microbial community structure and size. We observed an overall increase of microbial 13C (e.g., root-exudate) uptake, while warming led to significant microbial biomass loss in all microbial groups. The increase of microbial 13C uptake with warming differed between microbial groups: an increase was only observed in the general and Gram-positive bacterial phospholipid fatty acid (PLFA) markers and in the PLFA and neutral lipid fatty acid (NLFA) markers of arbuscular mycorrhizal fungi (AMF). Nitrogen addition of 50 kg ha−1 y−1 for two years had no effect on the microbial uptake, microbial biomass or community composition, indicating that microbes were not N limited, and no plant-mediated N addition effects occurred. Additionally, we show that both warming and soil C depletion were responsible for the microbial biomass loss. Soil warming caused stronger loss in microbial groups with higher 13C uptake. In our experiment, warming caused a general reduction of microbial biomass, despite a relative increase in microbial 13C uptake, and altered microbial community composition. The warming effects on microbial biomass and community composition were partly mediated through soil C depletion with warming and changes in recent plant-derived C uptake patterns of the microbial community.

Gavazov, K., Canarini, A., Jassey, V. E. J., Mills, R., Richter, A., Sundqvist, M. K., Väisänen, M., Walker, T. W. N., Wardle, D. A., & Dorrepaal, E. (2022). Plant-microbial linkages underpin carbon sequestration in contrasting mountain tundra vegetation types. Soil Biology and Biochemistry, 165, 108530. https://www.sciencedirect.com/science/article/pii/S0038071721004041

@article{gavazov_plant-microbial_2022,
  title = {Plant-microbial linkages underpin carbon sequestration in contrasting mountain tundra vegetation types},
  volume = {165},
  issn = {0038-0717},
  url = {https://www.sciencedirect.com/science/article/pii/S0038071721004041},
  doi = {10.1016/j.soilbio.2021.108530},
  urldate = {2023-10-05},
  journal = {Soil Biology and Biochemistry},
  author = {Gavazov, Konstantin and Canarini, Alberto and Jassey, Vincent E. J. and Mills, Robert and Richter, Andreas and Sundqvist, Maja K. and Väisänen, Maria and Walker, Tom W. N. and Wardle, David A. and Dorrepaal, Ellen},
  month = feb,
  year = {2022},
  keywords = {Carbon use efficiency, Above- and belowground interactions, C:N stoichiometry, Elevation gradient, Microbial physiology, Primary productivity},
  pages = {108530},
  file = {ScienceDirect Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\J7BZTGKA\\Gavazov et al. - 2022 - Plant-microbial linkages underpin carbon sequestra.pdf:application/pdf}
}

Tundra ecosystems hold large stocks of soil organic matter (SOM), likely due to low temperatures limiting rates of microbial SOM decomposition more than those of SOM accumulation from plant primary productivity and microbial necromass inputs. Here we test the hypotheses that distinct tundra vegetation types and their carbon supply to characteristic rhizosphere microbes determine SOM cycling independent of temperature. In the subarctic Scandes, we used a three-way factorial design with paired heath and meadow vegetation at each of two elevations, and with each combination of vegetation type and elevation subjected during one growing season to either ambient light (i.e., ambient plant productivity), or 95% shading (i.e., reduced plant productivity). We assessed potential above- and belowground ecosystem linkages by uni- and multivariate analyses of variance, and structural equation modelling. We observed direct coupling between tundra vegetation type and microbial community composition and function, which underpinned the ecosystem’s potential for SOM storage. Greater primary productivity at low elevation and ambient light supported higher microbial biomass and nitrogen immobilisation, with lower microbial mass-specific enzymatic activity and SOM humification. Congruently, larger SOM at lower elevation and in heath sustained fungal-dominated microbial communities, which were less substrate-limited, and invested less into enzymatic SOM mineralisation, owing to a greater carbon-use efficiency (CUE). Our results highlight the importance of tundra plant community characteristics (i.e., productivity and vegetation type), via their effects on soil microbial community size, structure and physiology, as essential drivers of SOM turnover. The here documented concerted patterns in above- and belowground ecosystem functioning is strongly supportive of using plant community characteristics as surrogates for assessing tundra carbon storage potential and its evolution under climate and vegetation changes.

Maxwell, T. L., Canarini, A., Bogdanovic, I., Böckle, T., Martin, V., Noll, L., Prommer, J., Séneca, J., Simon, E., Piepho, H.-P., Herndl, M., Pötsch, E. M., Kaiser, C., Richter, A., Bahn, M., & Wanek, W. (2022). Contrasting drivers of belowground nitrogen cycling in a montane grassland exposed to a multifactorial global change experiment with elevated CO2, warming, and drought. Global Change Biology, 28(7), 2425–2441. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.16035. https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.16035

@article{maxwell_contrasting_2022,
  title = {Contrasting drivers of belowground nitrogen cycling in a montane grassland exposed to a multifactorial global change experiment with elevated {CO2}, warming, and drought},
  volume = {28},
  copyright = {© 2021 The Authors. Global Change Biology published by John Wiley \& Sons Ltd.},
  issn = {1365-2486},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.16035},
  doi = {10.1111/gcb.16035},
  language = {en},
  number = {7},
  urldate = {2023-10-05},
  journal = {Global Change Biology},
  author = {Maxwell, Tania L. and Canarini, Alberto and Bogdanovic, Ivana and Böckle, Theresa and Martin, Victoria and Noll, Lisa and Prommer, Judith and Séneca, Joana and Simon, Eva and Piepho, Hans-Peter and Herndl, Markus and Pötsch, Erich M. and Kaiser, Christina and Richter, Andreas and Bahn, Michael and Wanek, Wolfgang},
  year = {2022},
  note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.16035},
  keywords = {drought, climate warming, elevated CO2, amino acid consumption, protein depolymerization, soil nitrogen cycling, T-FACE},
  pages = {2425--2441},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\UK98GJ7U\\Maxwell et al. - 2022 - Contrasting drivers of belowground nitrogen cyclin.pdf:application/pdf;Snapshot:C\:\\Users\\alber\\Zotero\\storage\\ESEIGMGN\\gcb.html:text/html}
}

Depolymerization of high-molecular weight organic nitrogen (N) represents the major bottleneck of soil N cycling and yet is poorly understood compared to the subsequent inorganic N processes. Given the importance of organic N cycling and the rise of global change, we investigated the responses of soil protein depolymerization and microbial amino acid consumption to increased temperature, elevated atmospheric CO2, and drought. The study was conducted in a global change facility in a managed montane grassland in Austria, where elevated CO2 (eCO2) and elevated temperature (eT) were stimulated for 4 years, and were combined with a drought event. Gross protein depolymerization and microbial amino acid consumption rates (alongside with gross organic N mineralization and nitrification) were measured using 15N isotope pool dilution techniques. Whereas eCO2 showed no individual effect, eT had distinct effects which were modulated by season, with a negative effect of eT on soil organic N process rates in spring, neutral effects in summer, and positive effects in fall. We attribute this to a combination of changes in substrate availability and seasonal temperature changes. Drought led to a doubling of organic N process rates, which returned to rates found under ambient conditions within 3 months after rewetting. Notably, we observed a shift in the control of soil protein depolymerization, from plant substrate controls under continuous environmental change drivers (eT and eCO2) to controls via microbial turnover and soil organic N availability under the pulse disturbance (drought). To the best of our knowledge, this is the first study which analyzed the individual versus combined effects of multiple global change factors and of seasonality on soil organic N processes and thereby strongly contributes to our understanding of terrestrial N cycling in a future world.

2021

Canarini, A., Schmidt, H., Fuchslueger, L., Martin, V., Herbold, C. W., Zezula, D., Gündler, P., Hasibeder, R., Jecmenica, M., Bahn, M., & Richter, A. (2021). Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community. Nature Communications, 12(1), 5308. Number: 1 Publisher: Nature Publishing Group. https://www.nature.com/articles/s41467-021-25675-4

@article{canarini_ecological_2021,
  title = {Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community},
  volume = {12},
  copyright = {2021 The Author(s)},
  issn = {2041-1723},
  url = {https://www.nature.com/articles/s41467-021-25675-4},
  doi = {10.1038/s41467-021-25675-4},
  language = {en},
  number = {1},
  urldate = {2023-03-02},
  journal = {Nature Communications},
  author = {Canarini, Alberto and Schmidt, Hannes and Fuchslueger, Lucia and Martin, Victoria and Herbold, Craig W. and Zezula, David and Gündler, Philipp and Hasibeder, Roland and Jecmenica, Marina and Bahn, Michael and Richter, Andreas},
  month = sep,
  year = {2021},
  note = {Number: 1
  Publisher: Nature Publishing Group},
  keywords = {Microbial ecology, Climate-change ecology, Carbon cycle},
  pages = {5308},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\CN45N6U2\\Canarini et al. - 2021 - Ecological memory of recurrent drought modifies so.pdf:application/pdf}
}

Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

Alteio, L. V., Séneca, J., Canarini, A., Angel, R., Jansa, J., Guseva, K., Kaiser, C., Richter, A., & Schmidt, H. (2021). A critical perspective on interpreting amplicon sequencing data in soil ecological research. Soil Biology and Biochemistry, 160, 108357. https://www.sciencedirect.com/science/article/pii/S0038071721002303

@article{alteio_critical_2021,
  title = {A critical perspective on interpreting amplicon sequencing data in soil ecological research},
  volume = {160},
  issn = {0038-0717},
  url = {https://www.sciencedirect.com/science/article/pii/S0038071721002303},
  doi = {10.1016/j.soilbio.2021.108357},
  language = {en},
  urldate = {2022-07-15},
  journal = {Soil Biology and Biochemistry},
  author = {Alteio, Lauren V. and Séneca, Joana and Canarini, Alberto and Angel, Roey and Jansa, Jan and Guseva, Ksenia and Kaiser, Christina and Richter, Andreas and Schmidt, Hannes},
  month = sep,
  year = {2021},
  keywords = {notion, Amplicon sequencing, Compositional data, Soil complexity, Soil metabarcoding, Soil microbial diversity, Soil microorganisms},
  pages = {108357},
  file = {ScienceDirect Snapshot:C\:\\Users\\alber\\Zotero\\storage\\V4K2G5GI\\S0038071721002303.html:text/html}
}

Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation, and availability to improve the rigor of future studies.

Meeran, K., Ingrisch, J., Reinthaler, D., Canarini, A., Müller, L., Pötsch, E. M., Richter, A., Wanek, W., & Bahn, M. (2021). Warming and elevated CO2 intensify drought and recovery responses of grassland carbon allocation to soil respiration. Global Change Biology, 27(14), 3230–3243. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15628. https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.15628

@article{meeran_warming_2021,
  title = {Warming and elevated {CO2} intensify drought and recovery responses of grassland carbon allocation to soil respiration},
  volume = {27},
  issn = {1365-2486},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.15628},
  doi = {10.1111/gcb.15628},
  language = {en},
  number = {14},
  urldate = {2022-07-24},
  journal = {Global Change Biology},
  author = {Meeran, Kathiravan and Ingrisch, Johannes and Reinthaler, David and Canarini, Alberto and Müller, Lena and Pötsch, Erich M. and Richter, Andreas and Wanek, Wolfgang and Bahn, Michael},
  year = {2021},
  note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15628},
  keywords = {notion, drought, soil respiration, 13C labeling, carbon allocation, climate warming, elevated CO2, gross primary productivity, temperate grassland},
  pages = {3230--3243}
}

Photosynthesis and soil respiration represent the two largest fluxes of CO2 in terrestrial ecosystems and are tightly linked through belowground carbon (C) allocation. Drought has been suggested to impact the allocation of recently assimilated C to soil respiration; however, it is largely unknown how drought effects are altered by a future warmer climate under elevated atmospheric CO2 (eT_eCO2). In a multifactor experiment on managed C3 grassland, we studied the individual and interactive effects of drought and eT_eCO2 (drought, eT_eCO2, drought × eT_eCO2) on ecosystem C dynamics. We performed two in situ 13CO2 pulse-labeling campaigns to trace the fate of recent C during peak drought and recovery. eT_eCO2 increased soil respiration and the fraction of recently assimilated C in soil respiration. During drought, plant C uptake was reduced by c. 50% in both ambient and eT_eCO2 conditions. Soil respiration and the amount and proportion of 13C respired from soil were reduced (by 32%, 70% and 30%, respectively), the effect being more pronounced under eT_eCO2 (50%, 84%, 70%). Under drought, the diel coupling of photosynthesis and SR persisted only in the eT_eCO2 scenario, likely caused by dynamic shifts in the use of freshly assimilated C between storage and respiration. Drought did not affect the fraction of recent C remaining in plant biomass under ambient and eT_eCO2, but reduced the small fraction remaining in soil under eT_eCO2. After rewetting, C uptake and the proportion of recent C in soil respiration recovered more rapidly under eT_eCO2 compared to ambient conditions. Overall, our findings suggest that in a warmer climate under elevated CO2 drought effects on the fate of recent C will be amplified and the coupling of photosynthesis and soil respiration will be sustained. To predict the future dynamics of terrestrial C cycling, such interactive effects of multiple global change factors should be considered.

2020

Séneca, J., Pjevac, P., Canarini, A., Herbold, C. W., Zioutis, C., Dietrich, M., Simon, E., Prommer, J., Bahn, M., Pötsch, E. M., Wagner, M., Wanek, W., & Richter, A. (2020). Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought. The ISME Journal, 14(12), 3038–3053. Number: 12 Publisher: Nature Publishing Group. https://www.nature.com/articles/s41396-020-00735-7

@article{seneca_composition_2020,
  title = {Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and {CO2}, but strongly affected by drought},
  volume = {14},
  copyright = {2020 The Author(s)},
  issn = {1751-7370},
  url = {https://www.nature.com/articles/s41396-020-00735-7},
  doi = {10.1038/s41396-020-00735-7},
  language = {en},
  number = {12},
  urldate = {2022-07-24},
  journal = {The ISME Journal},
  author = {Séneca, Joana and Pjevac, Petra and Canarini, Alberto and Herbold, Craig W. and Zioutis, Christos and Dietrich, Marlies and Simon, Eva and Prommer, Judith and Bahn, Michael and Pötsch, Erich M. and Wagner, Michael and Wanek, Wolfgang and Richter, Andreas},
  month = dec,
  year = {2020},
  note = {Number: 12
  Publisher: Nature Publishing Group},
  keywords = {Microbial ecology, notion, Climate-change ecology, Biogeochemistry},
  pages = {3038--3053},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\2SMV27CM\\Séneca et al. - 2020 - Composition and activity of nitrifier communities .pdf:application/pdf;Snapshot:C\:\\Users\\alber\\Zotero\\storage\\DGUK2D9L\\s41396-020-00735-7.html:text/html}
}

Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO2, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO2 and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH4+ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO2 have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.

Simon, E., Canarini, A., Martin, V., Séneca, J., Böckle, T., Reinthaler, D., Pötsch, E. M., Piepho, H.-P., Bahn, M., Wanek, W., & Richter, A. (2020). Microbial growth and carbon use efficiency show seasonal responses in a multifactorial climate change experiment. Communications Biology, 3(1), 1–10. Number: 1 Publisher: Nature Publishing Group. https://www.nature.com/articles/s42003-020-01317-1

@article{simon_microbial_2020,
  title = {Microbial growth and carbon use efficiency show seasonal responses in a multifactorial climate change experiment},
  volume = {3},
  copyright = {2020 The Author(s)},
  issn = {2399-3642},
  url = {https://www.nature.com/articles/s42003-020-01317-1},
  doi = {10.1038/s42003-020-01317-1},
  language = {en},
  number = {1},
  urldate = {2022-07-24},
  journal = {Communications Biology},
  author = {Simon, Eva and Canarini, Alberto and Martin, Victoria and Séneca, Joana and Böckle, Theresa and Reinthaler, David and Pötsch, Erich M. and Piepho, Hans-Peter and Bahn, Michael and Wanek, Wolfgang and Richter, Andreas},
  month = oct,
  year = {2020},
  note = {Number: 1
  Publisher: Nature Publishing Group},
  keywords = {Microbial ecology, notion, Climate-change ecology, Ecophysiology, Carbon cycle},
  pages = {1--10},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\SNCDLGGI\\Simon et al. - 2020 - Microbial growth and carbon use efficiency show se.pdf:application/pdf;Snapshot:C\:\\Users\\alber\\Zotero\\storage\\VXSMFTIV\\s42003-020-01317-1.html:text/html}
}

Microbial growth and carbon use efficiency (CUE) are central to the global carbon cycle, as microbial remains form soil organic matter. We investigated how future global changes may affect soil microbial growth, respiration, and CUE. We aimed to elucidate the soil microbial response to multiple climate change drivers across the growing season and whether effects of multiple global change drivers on soil microbial physiology are additive or interactive. We measured soil microbial growth, CUE, and respiration at three time points in a field experiment combining three levels of temperature and atmospheric CO2, and a summer drought. Here we show that climate change-driven effects on soil microbial physiology are interactive and season-specific, while the coupled response of growth and respiration lead to stable microbial CUE (average CUE = 0.39). These results suggest that future research should focus on microbial growth across different seasons to understand and predict effects of global changes on soil carbon dynamics.

Canarini, A., Wanek, W., Watzka, M., Sandén, T., Spiegel, H., Šantrůček, J., & Schnecker, J. (2020). Quantifying microbial growth and carbon use efficiency in dry soil environments via 18O water vapor equilibration. Global Change Biology, 26(9), 5333–5341. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15168. https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.15168

@article{canarini_quantifying_2020,
  title = {Quantifying microbial growth and carbon use efficiency in dry soil environments via {18O} water vapor equilibration},
  volume = {26},
  copyright = {© 2020 The Authors. Global Change Biology published by John Wiley \& Sons Ltd},
  issn = {1365-2486},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.15168},
  doi = {10.1111/gcb.15168},
  language = {en},
  number = {9},
  urldate = {2023-07-31},
  journal = {Global Change Biology},
  author = {Canarini, Alberto and Wanek, Wolfgang and Watzka, Margarete and Sandén, Taru and Spiegel, Heide and Šantrůček, Jiří and Schnecker, Jörg},
  year = {2020},
  note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15168},
  keywords = {Birch effect, carbon use efficiency, drought, microbial growth, soil microbial physiology},
  pages = {5333--5341},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\XVNH47UT\\Canarini et al. - 2020 - Quantifying microbial growth and carbon use effici.pdf:application/pdf;Snapshot:C\:\\Users\\alber\\Zotero\\storage\\LNBJ2C8J\\gcb.html:text/html}
}

Soil microbial physiology controls large fluxes of C to the atmosphere, thus, improving our ability to accurately quantify microbial physiology in soil is essential. However, current methods to determine microbial C metabolism require liquid water addition, which makes it practically impossible to measure microbial physiology in dry soil samples without stimulating microbial growth and respiration (namely, the “Birch effect”). We developed a new method based on in vivo 18O-water vapor equilibration to minimize soil rewetting effects. This method allows the isotopic labeling of soil water without direct liquid water addition. This was compared to the main current method (direct 18O-liquid water addition) in moist and air-dry soils. We determined the time kinetics and calculated the average 18O enrichment of soil water over incubation time, which is necessary to calculate microbial growth from 18O incorporation in genomic DNA. We tested isotopic equilibration patterns in three natural and six artificially constructed soils covering a wide range of soil texture and soil organic matter content. We then measured microbial growth, respiration and carbon use efficiency (CUE) in three natural soils (either air-dry or moist). The proposed 18O-vapor equilibration method provided similar results as the current method of liquid 18O-water addition when used for moist soils. However, when applied to air-dry soils the liquid 18O-water addition method overestimated growth by up to 250%, respiration by up to 500%, and underestimated CUE by up to 40%. We finally describe the new insights into biogeochemical cycling of C that the new method can help uncover, and we consider a range of questions regarding microbial physiology and its response to global change that can now be addressed.

2019

Canarini, A., Kaiser, C., Merchant, A., Richter, A., & Wanek, W. (2019). Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli. Frontiers in Plant Science, 10. https://www.frontiersin.org/articles/10.3389/fpls.2019.00157

@article{canarini_root_2019,
  title = {Root {Exudation} of {Primary} {Metabolites}: {Mechanisms} and {Their} {Roles} in {Plant} {Responses} to {Environmental} {Stimuli}},
  volume = {10},
  issn = {1664-462X},
  shorttitle = {Root {Exudation} of {Primary} {Metabolites}},
  url = {https://www.frontiersin.org/articles/10.3389/fpls.2019.00157},
  urldate = {2023-10-05},
  journal = {Frontiers in Plant Science},
  author = {Canarini, Alberto and Kaiser, Christina and Merchant, Andrew and Richter, Andreas and Wanek, Wolfgang},
  year = {2019},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\EK42EI68\\Canarini et al. - 2019 - Root Exudation of Primary Metabolites Mechanisms .pdf:application/pdf}
}

Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO2 emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.

2018

Canarini, A., Mariotte, P., Ingram, L., Merchant, A., & Dijkstra, F. A. (2018). Mineral-Associated Soil Carbon is Resistant to Drought but Sensitive to Legumes and Microbial Biomass in an Australian Grassland. Ecosystems, 21(2), 349–359. https://doi.org/10.1007/s10021-017-0152-x

@article{canarini_mineral-associated_2018,
  title = {Mineral-{Associated} {Soil} {Carbon} is {Resistant} to {Drought} but {Sensitive} to {Legumes} and {Microbial} {Biomass} in an {Australian} {Grassland}},
  volume = {21},
  issn = {1435-0629},
  url = {https://doi.org/10.1007/s10021-017-0152-x},
  doi = {10.1007/s10021-017-0152-x},
  language = {en},
  number = {2},
  urldate = {2022-06-17},
  journal = {Ecosystems},
  author = {Canarini, Alberto and Mariotte, Pierre and Ingram, Lachlan and Merchant, Andrew and Dijkstra, Feike A.},
  month = mar,
  year = {2018},
  keywords = {notion, carbon inputs, carbon storage, microbial biomass carbon, organo-mineral carbon, plant functional groups, plant–soil interactions, rainout shelter},
  pages = {349--359},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\64IS2HE6\\Canarini et al. - 2018 - Mineral-Associated Soil Carbon is Resistant to Dro.pdf:application/pdf}
}

Drought is predicted to increase in many areas of the world with consequences for soil carbon (C) dynamics. Plant litter, root exudates and microbial biomass can be used as C substrates to form organo-mineral complexes. Drought effects on plants and microbes could potentially compromise these relative stable soil C pools, by reducing plant C inputs and/or microbial activity. We conducted a 2-year drought experiment using rainout shelters in a semi-natural grassland. We measured aboveground biomass and C and nitrogen (N) in particulate organic matter (Pom), the organo-mineral fraction (Omin), and microbial biomass within the first 15 cm of soil. Aboveground plant biomass was reduced by 50% under drought in both years, but only the dominant C4 grasses were significantly affected. Soil C pools were not affected by drought, but were significantly higher in the relatively wet second year compared to the first year. Omin-C was positively related to microbial C during the first year, and positively related to clay and silt content in the second year. Increases in Omin-C in the second year were explained by increases in legume biomass and its effect on Pom-N and microbial biomass N (MBN) through structural equation modeling. In conclusion, soil C pools were unaffected by the drought treatment. Drought resistant legumes enhanced formation of organo-mineral complexes through increasing Pom-N and MBN. Our findings also indicate the importance of microbes for the formation of Omin-C as long as soil minerals have not reached their maximum capacity to bind with C (that is, saturation).

2017

Canarini, A., Kiær, L. P., & Dijkstra, F. A. (2017). Soil carbon loss regulated by drought intensity and available substrate: A meta-analysis. Soil Biology and Biochemistry, 112, 90–99. https://www.sciencedirect.com/science/article/pii/S0038071716306198

@article{canarini_soil_2017,
  title = {Soil carbon loss regulated by drought intensity and available substrate: {A} meta-analysis},
  volume = {112},
  issn = {0038-0717},
  shorttitle = {Soil carbon loss regulated by drought intensity and available substrate},
  url = {https://www.sciencedirect.com/science/article/pii/S0038071716306198},
  doi = {10.1016/j.soilbio.2017.04.020},
  urldate = {2023-10-05},
  journal = {Soil Biology and Biochemistry},
  author = {Canarini, Alberto and Kiær, Lars Pødenphant and Dijkstra, Feike A.},
  month = sep,
  year = {2017},
  keywords = {Microbial community, Soil respiration, Soil organic matter, Dry-rewetting cycles, F:B ratio, Metabolic quotient},
  pages = {90--99},
  file = {ScienceDirect Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\LVXBG26X\\Canarini et al. - 2017 - Soil carbon loss regulated by drought intensity an.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\alber\\Zotero\\storage\\VAS7EJUC\\S0038071716306198.html:text/html}
}

Drought is one of the most important climate change factors, but its effects on ecosystems are little understood. While known to influence soil carbon (C) cycling, it remains unresolved if altered rainfall patterns induced by climate change will stimulate positive feedbacks of CO2 into the atmosphere. Using a meta-analysis frame-work including 1495 observations from 60 studies encompassing a variety of ecosystems and soil types, we investigated drought effects on respiration rates, cumulative respiration during drying-rewetting cycles, metabolic quotient (qCO2), dissolved organic C (DOC), microbial biomass and fungi to bacteria (F:B) ratios from laboratory and field experiments. We show that C-rich soils (\textgreater2% organic carbon) increase CO2 release into the atmosphere after intense droughts, but that C-poor soils show a net decline in C losses. We explain this self-reinforcing mechanism of climate change in C-rich soils by: (i) high substrate availability that magnify bursts of CO2 release after drought events and (ii) a shift in microbial community with increased loss of C per unit of biomass. These findings shed light on important responses of soil CO2 emissions to drought, which could either offset or facilitate positive feedbacks to global warming. Our results should be considered in global climate models, as even small changes in soil CO2 emission have large repercussions for global warming.

Carrillo, Y., Bell, C., Koyama, A., Canarini, A., Boot, C. M., Wallenstein, M., & Pendall, E. (2017). Plant traits, stoichiometry and microbes as drivers of decomposition in the rhizosphere in a temperate grassland. Journal of Ecology, 105(6), 1750–1765. _eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.12772. https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.12772

@article{carrillo_plant_2017,
  title = {Plant traits, stoichiometry and microbes as drivers of decomposition in the rhizosphere in a temperate grassland},
  volume = {105},
  copyright = {© 2017 The Authors. Journal of Ecology © 2017 British Ecological Society},
  issn = {1365-2745},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.12772},
  doi = {10.1111/1365-2745.12772},
  language = {en},
  number = {6},
  urldate = {2023-10-05},
  journal = {Journal of Ecology},
  author = {Carrillo, Yolima and Bell, Colin and Koyama, Akihiro and Canarini, Alberto and Boot, Claudia M. and Wallenstein, Matthew and Pendall, Elise},
  year = {2017},
  note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.12772},
  keywords = {microbial communities, bacteria, rhizosphere, decomposition, soil carbon, enzymes, plant traits, priming, root morphology, stoichiometry},
  pages = {1750--1765},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\ZAS45KLH\\Carrillo et al. - 2017 - Plant traits, stoichiometry and microbes as driver.pdf:application/pdf}
}

It is becoming increasingly clear that plant roots can impact the decomposition of existing soil C in the rhizosphere. Studies under controlled conditions suggest this impact may be plant species dependent, but whether this is the case in natural conditions or what factors underlie this variation is mostly unknown. With a novel field-based isotopic approach combining 13C-enriched glucose and 5-bromo-2-deoxyuridine additions, we compared in situ C decomposition of added labile C and native soil C (priming) among eight semi-arid grassland species’ rhizospheres to investigate the factors driving inter-species variation. We examined the influence of several rhizosphere factors related to soil chemistry, microbial activity, microbial community, microbial stoichiometry, plant chemistry and root morphology. Plant species generated distinct microbial and chemical rhizosphere environments, which translated into differences in the direction, magnitude and temporal dynamics of the soil C priming. Soil C decomposition was positively related to soil C/P and soil N/P (via its influence on the bacterial community), which in turn were positively related to plant N/P. Plant C/N was also a significant factor via its negative influence on soil N/P. In contrast, the main direct predictors of labile C decomposition were microbial biomass, microbial C/N and the C-degrading enzymes, which in turn were linked to root morphology and C chemistry. Synthesis. Within this community, plant species’ rhizospheres can vary in their susceptibility to C loss in response to changes in C availability. Soil stoichiometry, driven by plant chemical traits, appeared to be the strongest driver of priming. Our study suggests that shifts in plant communities involving increases in N relative to P have the greatest potential to lead to C loss. We provide evidence of root morphology and C chemistry as drivers of labile C processing in soil, a novel empirical contribution to our understanding of the role of plant traits below-ground. The contrasting regulation of different pools of soil C suggests observations of the regulation of simple C compounds should not be extrapolated to the whole C pool. Our findings provide support for rhizosphere-driven mechanisms by which shifts in plant community composition could have implications on the ecosystem-level C balance.

Mariotte, P., Canarini, A., & Dijkstra, F. A. (2017). Stoichiometric N:P flexibility and mycorrhizal symbiosis favour plant resistance against drought. Journal of Ecology, 105(4), 958–967. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.12731. https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.12731

@article{mariotte_stoichiometric_2017,
  title = {Stoichiometric {N}:{P} flexibility and mycorrhizal symbiosis favour plant resistance against drought},
  volume = {105},
  issn = {1365-2745},
  shorttitle = {Stoichiometric {N}},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.12731},
  doi = {10.1111/1365-2745.12731},
  language = {en},
  number = {4},
  urldate = {2022-06-17},
  journal = {Journal of Ecology},
  author = {Mariotte, Pierre and Canarini, Alberto and Dijkstra, Feike A.},
  year = {2017},
  note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.12731},
  keywords = {notion, drought, climate change, arbuscular mycorrhizal fungi, grassland, N:P stoichiometry, plant mineral nutrition, plant–soil (below-ground) interactions, subordinate species, water-use efficiency},
  pages = {958--967},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\4E9WUBXU\\Mariotte et al. - 2017 - Stoichiometric NP flexibility and mycorrhizal sym.pdf:application/pdf;Snapshot:C\:\\Users\\alber\\Zotero\\storage\\EB5SMALI\\1365-2745.html:text/html}
}

Drought induces changes in the nitrogen (N) and phosphorus (P) cycle but most plant species have limited flexibility to take up nutrients under such variable or unbalanced N and P availability. Both the degree of flexibility in plant N:P ratio and of root symbiosis with arbuscular mycorrhizal fungi might control plant resistance to drought-induced changes in nutrient availability, but this has not been directly tested. Here, we examined the role of plant N:P stoichiometric status and mycorrhizal symbiosis in the drought-resistance of dominant and subordinate species in a semi-natural grassland. We reduced water availability using rainout shelters (control vs. drought) and measured how plant biomass responded for the dominant and subordinate species. We then selected a dominant (Paspalum dilatatum) and a subordinate species (Cynodon dactylon), for which we investigated the N:P stoichiometric status, mycorrhizal root colonization and water-use efficiency. The biomass of all dominant plant species, but not subordinate species, decreased under drought. Drought increased soil available nitrogen, and thus increased soil N:P ratio, due to decreasing plant N uptake. The dominant P. dilatatum showed a high degree of plant N:P homeostasis and a considerable reduction in biomass under drought. At the opposite, the more flexible subordinate species C. dactylon increased its N uptake and water-use efficiency, apparently due to stronger symbiosis with mycorrhizae, and maintained its biomass. Synthesis. We conclude that the maintenance of N:P homeostasis in dominant species, possibly because of a large root nutrient foraging capacity, becomes inefficient when water stress limits N mobility in the soil. By contrast, we demonstrate that higher stoichiometric N:P flexibility coupled with stronger mutualistic association with mycorrhizae allow subordinate species to better withstand drought perturbations. Using a stoichiometric approach in a field experiment, our study provides for the first time clear and novel understandings of the mechanisms involved in drought-resistance within the plant-mycorrhizae-soil system.

2016

Canarini, A., Merchant, A., & Dijkstra, F. A. (2016). Drought effects on Helianthus annuus and Glycine max metabolites: from phloem to root exudates. Rhizosphere, 2, 85–97. https://www.sciencedirect.com/science/article/pii/S2452219816300647

@article{canarini_drought_2016,
  title = {Drought effects on {Helianthus} annuus and {Glycine} max metabolites: from phloem to root exudates},
  volume = {2},
  issn = {2452-2198},
  shorttitle = {Drought effects on {Helianthus} annuus and {Glycine} max metabolites},
  url = {https://www.sciencedirect.com/science/article/pii/S2452219816300647},
  doi = {10.1016/j.rhisph.2016.06.003},
  urldate = {2023-10-05},
  journal = {Rhizosphere},
  author = {Canarini, Alberto and Merchant, Andrew and Dijkstra, Feike A.},
  month = dec,
  year = {2016},
  keywords = {Dry-rewetting, Metabolomics, Multivariate analysis, Rhizodeposition, Root biomass, Soil-hydroponic method, Soybean, Sunflower},
  pages = {85--97},
  file = {ScienceDirect Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\6TQ287JZ\\Canarini et al. - 2016 - Drought effects on Helianthus annuus and Glycine m.pdf:application/pdf}
}

Numerous compounds are exuded by roots that play a central role in microbial decomposition and stabilization of soil carbon. The release of root exudates is sensitive to drought, but it is unclear how compound-specific exudates are related to drought-induced changes in plant metabolism. We investigated drought effects on root exudate quality and quantity for sunflower (Helianthus annuus) and soybean (Glycine max). We analyzed metabolites in phloem and root biomass extracts, to investigate whether root exudation is controlled by above- or below-ground processes. Sunflower and soybean showed different drought responses. Sunflower increased rates of exudation after rewetting (+330% in C) but the composition of metabolites remained unchanged compared to the control (constant moisture). Soybean did not change rates but the composition of metabolites changed with increased concentrations of osmolites (proline and pinitol). For specific groups, positive relationships were observed between exudates and phloem (amino-acids and organic acids) and between exudates and root biomass (sugars). Our results indicate that drought can induce different responses in plant metabolism causing changes in the quantity or composition of root exudates following rewetting. Furthermore, our results suggest that metabolism in shoots can influence exudation of organic acids and amino acids, while roots have a stronger control over exudation of sugars.

Canarini, A., Carrillo, Y., Mariotte, P., Ingram, L., & Dijkstra, F. A. (2016). Soil microbial community resistance to drought and links to C stabilization in an Australian grassland. Soil Biology and Biochemistry, 103, 171–180. https://www.sciencedirect.com/science/article/pii/S0038071716302097

@article{canarini_soil_2016,
  title = {Soil microbial community resistance to drought and links to {C} stabilization in an {Australian} grassland},
  volume = {103},
  issn = {0038-0717},
  url = {https://www.sciencedirect.com/science/article/pii/S0038071716302097},
  doi = {10.1016/j.soilbio.2016.08.024},
  language = {en},
  urldate = {2023-08-02},
  journal = {Soil Biology and Biochemistry},
  author = {Canarini, Alberto and Carrillo, Yolima and Mariotte, Pierre and Ingram, Lachlan and Dijkstra, Feike A.},
  month = dec,
  year = {2016},
  keywords = {Compost, Grassland, Organo-mineral carbon, Path-analysis, Rain out shelter, Reduced precipitation},
  pages = {171--180},
  file = {ScienceDirect Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\ZLU5IEEZ\\Canarini et al. - 2016 - Soil microbial community resistance to drought and.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\alber\\Zotero\\storage\\IKEHHKIU\\S0038071716302097.html:text/html}
}

Drought is predicted to increase in many areas of the world, which can greatly influence soil microbial community structure and C stabilization. Increasing soil carbon (C) stabilization is an important strategy to mitigate climate change effects, but the underlying processes promoting C stabilization are still unclear. Microbes are an important contributor of C stabilization through the adsorption of microbial-derived compounds on organo-mineral complexes. Management practices, such as addition of organic amendments might increase soil C stock and mitigate drought impacts, especially in agro-ecosystems where large losses of C have been reported. Here, we conducted a drought experiment where we tested whether the addition of organic amendments mitigates drought effects on soil C stabilization and its links to microbial community changes. In a semi-natural grassland system of eastern Australia, we combined a management treatment (compost vs. inorganic fertilizer addition) and a drought treatment using rainout shelters (half vs. ambient precipitation). We measured soil moisture, soil nitrogen and phosphorus, particulate organic C (Pom-C) and organo-mineral C (Min-C). Microbial community composition and biomass were assessed with PLFA analyses. A structural equation modeling (SEM) approach was used to examine the controls of soil moisture, Pom-C and nutrients on soil microbial biomass and community structure and changes in Min-C. Overall, the drought treatment did not affect microbial community structure and Min-C, while fertilizer only marginally increased Min-C, highlighting the resistance to these treatments in this grassland soil. In the surface soil (0–5 cm) Min-C was strongly associated with fungi that may have been stimulated by root exudates, and by gram-negative bacteria in the deep soil (5–15 cm) that were more affected by Pom-C and soil moisture. . We conclude that the grassland microbial community and its effect on Min-C at our field-site were non-responsive to our drought treatment, but sensitive to variability in soil moisture and microbial community structure. Our findings also show that surface compost application can moderately increase soil C stabilization under drought, representing a useful tool for improving soil C stability.

Dijkstra, F. A., Carrillo, Y., Aspinwall, M. J., Maier, C., Canarini, A., Tahaei, H., Choat, B., & Tissue, D. T. (2016). Water, nitrogen and phosphorus use efficiencies of four tree species in response to variable water and nutrient supply. Plant and Soil, 406(1), 187–199. https://doi.org/10.1007/s11104-016-2873-6

@article{dijkstra_water_2016,
  title = {Water, nitrogen and phosphorus use efficiencies of four tree species in response to variable water and nutrient supply},
  volume = {406},
  issn = {1573-5036},
  url = {https://doi.org/10.1007/s11104-016-2873-6},
  doi = {10.1007/s11104-016-2873-6},
  language = {en},
  number = {1},
  urldate = {2023-10-05},
  journal = {Plant and Soil},
  author = {Dijkstra, Feike A. and Carrillo, Yolima and Aspinwall, Michael J. and Maier, Chelsea and Canarini, Alberto and Tahaei, Hero and Choat, Brendan and Tissue, David T.},
  month = sep,
  year = {2016},
  keywords = {Microbial immobilisation, Nutrient limitation, Trade-off, Tree species, Water stress},
  pages = {187--199},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\6K5JYTKA\\Dijkstra et al. - 2016 - Water, nitrogen and phosphorus use efficiencies of.pdf:application/pdf}
}

The commonly observed trade-off between plant water use efficiency (WUE) and nitrogen use efficiency (NUE) has been attributed to physiological constraints in the leaf. We examined if a similar trade-off can occur between WUE and phosphorus use efficiency (PUE) and if changes in NUE and PUE in response to water and nutrient supply can be related to microbial N and P immobilisation.

2015

Canarini, A., & Dijkstra, F. A. (2015). Dry-rewetting cycles regulate wheat carbon rhizodeposition, stabilization and nitrogen cycling. Soil Biology and Biochemistry, 81, 195–203. https://www.sciencedirect.com/science/article/pii/S0038071714004003

@article{canarini_dry-rewetting_2015,
  title = {Dry-rewetting cycles regulate wheat carbon rhizodeposition, stabilization and nitrogen cycling},
  volume = {81},
  issn = {0038-0717},
  url = {https://www.sciencedirect.com/science/article/pii/S0038071714004003},
  doi = {10.1016/j.soilbio.2014.11.014},
  urldate = {2023-10-05},
  journal = {Soil Biology and Biochemistry},
  author = {Canarini, Alberto and Dijkstra, Feike A.},
  month = feb,
  year = {2015},
  keywords = {Drought, Rhizodeposition, Carbon stabilization, Plant–microbe interactions, Rewatering, Wheat},
  pages = {195--203},
  file = {ScienceDirect Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\APJPRC8U\\Canarini and Dijkstra - 2015 - Dry-rewetting cycles regulate wheat carbon rhizode.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\alber\\Zotero\\storage\\5HGPQCUF\\S0038071714004003.html:text/html}
}

Drying and rewetting of soil can have large effects on carbon (C) and nitrogen (N) dynamics. Drying-rewetting effects have mostly been studied in the absence of plants, although it is well known that plant–microbe interactions can substantially alter soil C and N dynamics. We investigated for the first time how drying and rewetting affected rhizodeposition, its utilization by microbes, and its stabilization into soil (C associated with soil mineral phase). We also investigated how drying and rewetting influenced N mineralization and loss. We grew wheat (Triticum aestivum) in a controlled environment under constant moisture and under dry-rewetting cycles, and used a continuous 13C-labeling method to partition plant and soil organic matter (SOM) contribution to different soil pools. We applied a 15N label to the soil to determine N loss. We found that dry-rewetting decreased total input of plant C in microbial biomass (MB) and in the soil mineral phase, mainly due to a reduction of plant biomass. Plant derived C in MB and in the soil mineral phase were positively correlated (R2 = 0.54; P = 0.0012). N loss was reduced with dry rewetting cycles, and mineralization increased after each rewetting event. Overall drying and rewetting reduced rhizodeposition and stabilization of new C, primary through biomass reduction. However, frequency of rewetting and intensity of drought may determine the fate of C in MB and consequently into the soil mineral phase. Frequency and intensity may also be crucial in stimulating N mineralization and reducing N loss in agricultural soils.

2010

Salvucci, M. E., Barta, C., Byers, J. A., & Canarini, A. (2010). Photosynthesis and assimilate partitioning between carbohydrates and isoprenoid products in vegetatively active and dormant guayule: physiological and environmental constraints on rubber accumulation in a semiarid shrub. Physiologia Plantarum, 140(4), 368–379. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2010.01409.x. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.2010.01409.x

@article{salvucci_photosynthesis_2010,
  title = {Photosynthesis and assimilate partitioning between carbohydrates and isoprenoid products in vegetatively active and dormant guayule: physiological and environmental constraints on rubber accumulation in a semiarid shrub},
  volume = {140},
  copyright = {Copyright © Physiologia Plantarum 2010},
  issn = {1399-3054},
  shorttitle = {Photosynthesis and assimilate partitioning between carbohydrates and isoprenoid products in vegetatively active and dormant guayule},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.2010.01409.x},
  doi = {10.1111/j.1399-3054.2010.01409.x},
  language = {en},
  number = {4},
  urldate = {2023-10-05},
  journal = {Physiologia Plantarum},
  author = {Salvucci, Michael E. and Barta, Csengele and Byers, John A. and Canarini, Alberto},
  year = {2010},
  note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2010.01409.x},
  pages = {368--379},
  file = {Snapshot:C\:\\Users\\alber\\Zotero\\storage\\F6Y5AEQM\\j.1399-3054.2010.01409.html:text/html}
}

The stems and roots of the semiarid shrub guayule, Parthenium argentatum, contain a significant amount of natural rubber. Rubber accumulates in guayule when plants are vegetatively and reproductively dormant, complicating the relationship between growth/reproduction and product synthesis. To evaluate the factors regulating the partitioning of carbon to rubber, carbon assimilation and partitioning were measured in guayule plants that were grown under simulated summer- and winter-like conditions and under winter-like conditions with CO2 enrichment. These conditions were used to induce vegetatively active and dormant states and to increase the source strength of vegetatively dormant plants, respectively. Rates of CO2 assimilation, measured under growth temperatures and CO2, were similar for plants grown under summer- and winter-like conditions, but were higher with elevated CO2. After 5 months, plants grown under summer-like conditions had the greatest aboveground biomass, but the lowest levels of non-structural carbohydrates and rubber. In contrast, the amount of resin in the stems was similar under all growth conditions. Emission of biogenic volatile compounds was more than three-fold higher in plants grown under summer- compared with winter-like conditions. Taken together, the results show that guayule plants maintain a high rate of photosynthesis and accumulate non-structural carbohydrates and rubber in the vegetatively dormant state, but emit volatile compounds at a lower rate when compared with more vegetatively active plants. Enrichment with CO2 in the vegetatively dormant state increased carbohydrate content but not the amount of rubber, suggesting that partitioning of assimilate to rubber is limited by sink strength in guayule.

Book Chapters and Editorials

Canarini, A., Fuchslueger, L., Joly, F.-X., & Richter, A. (2023). Climate change impacts on soil biology. In M. J. Goss & M. Oliver (Eds.), Encyclopedia of Soils in the Environment (Second Edition) (pp. 578–586). Academic Press. https://www.sciencedirect.com/science/article/pii/B9780128229743002445

@incollection{canarini_climate_2023,
  address = {Oxford},
  title = {Climate change impacts on soil biology},
  isbn = {978-0-323-95133-3},
  url = {https://www.sciencedirect.com/science/article/pii/B9780128229743002445},
  urldate = {2023-10-05},
  booktitle = {Encyclopedia of {Soils} in the {Environment} ({Second} {Edition})},
  publisher = {Academic Press},
  author = {Canarini, Alberto and Fuchslueger, Lucia and Joly, François-Xavier and Richter, Andreas},
  editor = {Goss, Michael J. and Oliver, Margaret},
  month = jan,
  year = {2023},
  doi = {10.1016/B978-0-12-822974-3.00244-5},
  keywords = {Climate change, Climate feedbacks, Drought, Ecological interactions, Elevated CO, Soil fauna, Soil food-web, Soil microorganisms, Soil processes, Warming},
  pages = {578--586},
  file = {ScienceDirect Snapshot:C\:\\Users\\alber\\Zotero\\storage\\J98TPA8S\\B9780128229743002445.html:text/html}
}

Human activities have caused a rapid climate change affecting all parts of the biosphere, including soils. Soil organisms from all three domains of life, their interactions, and all soil processes for which they are responsible are influenced by and in turn respond to climate change. The understanding of how soil organisms and their processes react to climate changes, is thus central to our ability to manage ecosystems and develop strategies to mitigate climate change. This chapter examines the current state of soil biology (from organisms and communities to the processes they control) in the context of climate change and identifies current gaps in knowledge and promising ways forward.

Preece, C., Canarini, A., Verbruggen, E., & Fuchslueger, L. (2021). Editorial: Exchanges at the Root-Soil Interface: Resource Trading in the Rhizosphere That Drives Ecosystem Functioning. In Frontiers in Forests and Global Change (Vol. 4). https://www.frontiersin.org/articles/10.3389/ffgc.2021.747492
```
@incollection{preece_editorial_2021,
  title = {Editorial: {Exchanges} at the {Root}-{Soil} {Interface}: {Resource} {Trading} in the {Rhizosphere} {That} {Drives} {Ecosystem} {Functioning}},
  volume = {4},
  issn = {2624-893X},
  shorttitle = {Editorial},
  url = {https://www.frontiersin.org/articles/10.3389/ffgc.2021.747492},
  doi = {https://doi.org/10.3389/ffgc.2021.747492},
  urldate = {2023-10-05},
  journal = {Frontiers in Forests and Global Change},
  author = {Preece, Catherine and Canarini, Alberto and Verbruggen, Erik and Fuchslueger, Lucia},
  year = {2021},
  file = {Full Text PDF:C\:\\Users\\alber\\Zotero\\storage\\353A4AMM\\Preece et al. - 2021 - Editorial Exchanges at the Root-Soil Interface R.pdf:application/pdf}
}
```