| 1. |
- Teixeira, Pedro P.C., et al.
(författare)
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Decoding the rhizodeposit-derived carbon's journey into soil organic matter
- 2024
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Ingår i: Geoderma. - 0016-7061. ; 443
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Tidskriftsartikel (refereegranskat)abstract
- Net rhizodeposition corresponds to the portion of living root carbon (C) that remains in the soil after microbial processing and partial decomposition. Although it is assumed that this C input exerts an important role in the formation of soil organic matter (SOM), its contribution to distinct SOM pools is still not fully understood. In this study, we aimed to (i) quantify the retention of net rhizodeposition C in the different SOM fractions and in reactive Al and Fe mineral phases and (ii) investigate how rhizodeposition drives the spatial distribution of microbial communities in the rhizosphere. To track the transfer of net rhizodeposition into the soil, we used artificially labeled eucalypt (Eucalyptus spp.) seedlings under a 13C-CO2 atmosphere (multiple-pulse labeling). Combining physical SOM fractionation and the chemical extraction of aluminum (Al) and iron (Fe) reactive phases, we studied the distribution of net rhizodeposition into different soil fractions. We also assessed the 13C incorporation into microbial phospholipid fatty acids (PLFAs) at different distances from the roots. Our results show that 76 % of the net rhizodeposition 13C was retained within the mineral-associated organic matter (MAOM) fraction. About 28 % of net rhizodeposition 13C within the MAOM fraction was retained within the Al and Fe reactive phases, indicating that this is a sizeable mechanism for the retention of net rhizodeposition in soil. Rhizodeposition increased the abundance of microbial PLFAs exclusively in the soil close to the roots (0–4 mm), with prominent incorporation of net rhizodeposition 13C into fungal biomarkers. Overall, our findings underscore the importance of mineral associations for the retention of net rhizodeposition in the soil. We also highlight the role of fungi in transferring the root-derived C beyond the root vicinity and promoting the formation of occluded SOM.
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| 2. |
- Camenzind, Tessa, et al.
(författare)
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Arbuscular mycorrhizal fungal and soil microbial communities in African Dark Earths
- 2018
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 94:4
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Tidskriftsartikel (refereegranskat)abstract
- The socio-economic values of fertile and carbon-rich Dark Earth soils are well described from the Amazon region. Very recently, Dark Earth soils were also identified in tropical West Africa, with comparable beneficial soil properties and plant growth-promoting effects. The impact of this management technique on soil microbial communities, however, is less well understood, especially with respect to the ecologically relevant group of arbuscular mycorrhizal (AM) fungi. Thus, we tested the hypotheses that (1) improved soil quality in African Dark Earth (AfDE) will increase soil microbial biomass and shift community composition and (2) concurrently increased nutrient availability will negatively affect AM fungal communities. Microbial communities were distinct in AfDE in comparison to adjacent sites, with an increased fungal:bacterial ratio of 71%, a pattern mainly related to shifts in pH. AM fungal abundance and diversity, however, did not differ despite clearly increased soil fertility in AfDE, with 3.7 and 1.7 times greater extractable P and total N content, respectively. The absence of detrimental effects on AM fungi, often seen following applications of inorganic fertilizers, and the enhanced role of saprobic fungi relevant for mineralization and C sequestration support previous assertions of this management type as a sustainable alternative agricultural practice.
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| 3. |
- Caruso, Tancredi, et al.
(författare)
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Assessing soil ecosystem processes – biodiversity relationships in a nature reserve in Central Europe
- 2018
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Ingår i: Plant and Soil. - : Springer Science and Business Media LLC. - 0032-079X .- 1573-5036. ; 424:1-2, s. 491-501
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Tidskriftsartikel (refereegranskat)abstract
- Background and aims: Plant diversity – ecosystem processes relationships are essential to our understanding of ecosystem functioning. We aimed at disentangling the nature of such relationships in a mesotrophic grassland that was highly heterogeneous with regards to nutrient availability. Methods: Rather than targeting primary productivity, like most existing reports do, we focused our study on belowground ecosystem processes. We tested three, largely mutually exclusive, hypotheses of ecosystem processes relationships: the redundancy hypothesis, the insurance hypothesis and the centrifugal model hypothesis. We sampled the grassland twice within a single plant growing season in a spatially explicit way and assayed the soil for nitrification, urease activity, relative bacterial activity and a microbial community profile based on respiration while we simultaneously assessed plant diversity. Results: Results supported the centrifugal model. We justify the lack of support for the other two hypotheses on the basis of having conducted an observational study in an environmentally heterogeneous site. Conclusions: The centrifugal model hypothesis appears to be a very good predictive model for explaining diversity in observational, heterogeneous studies. The specific study represents one of the few observational studies that consider measures of ecosystem functioning other than primary productivity.
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| 4. |
- Ilardi, Marco O., et al.
(författare)
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Scavenging beetles control the temporal response of soil communities to carrion decomposition
- 2021
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Ingår i: Functional Ecology. - : Wiley. - 0269-8463 .- 1365-2435. ; 35:9, s. 2033-2044
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Tidskriftsartikel (refereegranskat)abstract
- Carrion is a frequent but overlooked source of nutrients to the soil. The decomposition of carrion is accelerated by invertebrate scavengers, but the impact of the scavengers on below-ground biota and its functions is scarcely known. We conducted a laboratory experiment to investigate the effects of the burying beetle Nicrophorus vespilloides on the soil community of a temperate broadleaved forest. We assembled microcosms from soil collected from an oak woodland and treated them with mouse Mus musculus carcasses and mating pairs of burying beetles (♀+♂) in a factorial design with control soils. We sampled independent replicates over time to investigate how the beetles affect soil microarthropods and microbial biomass (bacteria and fungi) in relation to soil pH and organic matter content. The beetle treatment initially reduced the total microbial biomass and abundance of major groups of microarthropods relative to the control soil. At the same time, organic matter increased in the beetle treatment and then dropped to the pre-beetle level (i.e. soil baseline) at the end of the beetle breeding cycle (2 weeks). The rapid temporal changes in organic matter were mimicked by the relative abundances of the dominant microarthropod groups, with Oribatida relatively more abundant than Collembola and predaceous mites in the beetle treatment. The overall final effect of the beetle (relative to the laboratory control) on microarthropods was negative but the beetle kept these variables within the levels observed for freshly collected soil (baseline), while the final effect on pH was positive, and most likely driven by the surplus of nutrients from the carcass and biochemical changes triggered by the decomposition process. In nature, scavenging invertebrates are widespread. Our study demonstrates that beetles breeding in carcasses regulate the dynamics of key components of the soil food web, including microbial biomass, changes in the relative abundances of dominant microarthropods and soil organic matter and pH. Given the abundance of these beetles in nature, the study implies that the distribution of these beetles is a key driver of variation in soil nutrient cycling in woodlands. A free Plain Language Summary can be found within the Supporting Information of this article.
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| 5. |
- Aleklett, Kristin, et al.
(författare)
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Build your own soil : exploring microfluidics to create microbial habitat structures
- 2018
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 12:2, s. 312-319
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Forskningsöversikt (refereegranskat)abstract
- Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.The ISME Journal advance online publication, 14 November 2017; doi:10.1038/ismej.2017.184.
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| 6. |
- Aleklett, Kristin, et al.
(författare)
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Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips
- 2021
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Ingår i: The Isme Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370.
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Tidskriftsartikel (refereegranskat)abstract
- How do fungi navigate through the complex microscopic maze-like structures found in the soil? Fungal behaviour, especially at the hyphal scale, is largely unknown and challenging to study in natural habitats such as the opaque soil matrix. We monitored hyphal growth behaviour and strategies of seven Basidiomycete litter decomposing species in a micro-fabricated "Soil Chip" system that simulates principal aspects of the soil pore space and its micro-spatial heterogeneity. The hyphae were faced with micrometre constrictions, sharp turns and protruding obstacles, and the species examined were found to have profoundly different responses in terms of foraging range and persistence, spatial exploration and ability to pass obstacles. Hyphal behaviour was not predictable solely based on ecological assumptions, and our results obtained a level of trait information at the hyphal scale that cannot be fully explained using classical concepts of space exploration and exploitation such as the phalanx/guerrilla strategies. Instead, we propose a multivariate trait analysis, acknowledging the complex trade-offs and microscale strategies that fungal mycelia exhibit. Our results provide novel insights about hyphal behaviour, as well as an additional understanding of fungal habitat colonisation, their foraging strategies and niche partitioning in the soil environment.
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| 7. |
- Arellano-Caicedo, Carlos, et al.
(författare)
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Habitat complexity affects microbial growth in fractal maze
- 2023
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Ingår i: Current biology : CB. - : Elsevier BV. - 1879-0445 .- 0960-9822. ; 33:8, s. 4-1458
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Tidskriftsartikel (refereegranskat)abstract
- The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.
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| 8. |
- Arellano-Caicedo, Carlos, et al.
(författare)
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Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation
- 2021
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth, interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by sharper angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, since hyphae branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization.
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| 9. |
- Arellano-Caicedo, Carlos, et al.
(författare)
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Quantification of growth and nutrient consumption of bacterial and fungal cultures in microfluidic microhabitat models
- 2024
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Ingår i: STAR Protocols. - 2666-1667. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Understanding microbes in nature requires consideration of their microenvironment. Here, we present a protocol for quantifying biomass and nutrient degradation of bacterial and fungal cultures (Pseudomonas putida and Coprinopsis cinerea, respectively) in microfluidics. We describe steps for mask design and fabrication, master printing, polydimethylsiloxane chip fabrication, and chip inoculation and imaging using fluorescence microscopy. We include procedures for image analysis, plotting, and statistics. For complete details on the use and execution of this protocol, please refer to Arellano-Caicedo et al. (2023).1
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| 10. |
- Barin, Mohsen, et al.
(författare)
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Optimization of Biofertilizer Formulation for Phosphorus Solubilizing by Pseudomonas fluorescens Ur21 via Response Surface Methodology
- 2022
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Ingår i: Processes. - : MDPI AG. - 2227-9717. ; 10:4
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Tidskriftsartikel (refereegranskat)abstract
- This study aimed to analyze and quantify the effect of different ratios of vermicompost, phosphate rock, and sulfur on P solubilization and release by Pseudomonas fluorescens Ur21, and to identify optimal levels of those variables for an efficient biofertilizer. Twenty experiments were defined by surface response methodology based on a central composite design (CCD), and the effects of various quantities of vermicompost, phosphate rock, and sulfur (encoded by −1, 0, or +1) on P solubilization was explored. The results show that the CCD model had high efficiency for predicting P solubilization (R2 = 0.9035). The strongest effects of the included variables on the observed P solubilization were linear effects of sulfur and organic matter (vermicompost), a quadratic effect of phosphate rock, and an interactive effect of organic matter × phosphate rock. Statistical analysis of the coefficients in the CCD model revealed that vermicompost, vermicompost × phosphate rock, and phosphate rock × phosphate rock treatments increased P solubilization. The optimal predicted composition for maximal P solubilization by P. fluorescens Ur21 (at 1684.39 mg·kg−1, with more than 90% of the added phosphate dissolved) was 58.8% vermicompost, 35.3% phosphate rock, and 5.8% sulfur. ANOVA analysis confirmed the model’s accuracy and validity in terms of F value (10.41), p value (<0.001), and non-significant lack of fit.
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