| 1. |
- Bösch, Yvonne, et al.
(författare)
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Distribution and Environmental Drivers of Fungal Denitrifiers in Global Soils
- 2023
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Ingår i: Microbiology Spectrum. - 2165-0497. ; 11, s. e00061-23
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Tidskriftsartikel (refereegranskat)abstract
- The microbial process of denitrification is the primary source of the greenhouse gas nitrous oxide (N2O) from terrestrial ecosystems. Fungal denitrifiers, unlike many bacteria, lack the N2O reductase, and thereby are sources of N2O. Still, their diversity, global distribution, and environmental determinants, as well as their relative importance, compared to bacterial and archaeal denitrifiers, remain unresolved. Employing a phylogenetically informed approach to analyze 1,980 global soil and rhizosphere metagenomes for the denitrification marker gene nirK, which codes for the copper dependent nitrite reductase in denitrification, we show that fungal denitrifiers are sparse, yet cosmopolitan and that they are dominated by saprotrophs and pathogens. Few showed biome-specific distribution patterns, although members of the Fusarium oxysporum species complex, which are known to produce substantial amounts of N2O, were proportionally more abundant and diverse in the rhizosphere than in other biomes. Fungal denitrifiers were most frequently detected in croplands, but they were most abundant in forest soils when normalized to metagenome size. Nevertheless, the overwhelming dominance of bacterial and archaeal denitrifiers suggests a much lower fungal contribution to N2O emissions than was previously estimated. In relative terms, they could play a role in soils that are characterized by a high carbon to nitrogen ratio and a low pH, especially in the tundra as well as in boreal and temperate coniferous forests. Because global warming predicts the proliferation of fungal pathogens, the prevalence of potential plant pathogens among fungal denitrifiers and the cosmopolitan distribution of these organisms suggest that fungal denitrifier abundance may increase in terrestrial ecosystems.IMPORTANCE Fungal denitrifiers, in contrast to their bacterial counterparts, are a poorly studied functional group within the nitrogen cycle, even though they produce the greenhouse gas N2O. To curb soil N2O emissions, a better understanding of their ecology and distribution in soils from different ecosystems is needed. Here, we probed a massive amount of DNA sequences and corresponding soil data from a large number of samples that represented the major soil environments for a broad understanding of fungal denitrifier diversity at the global scale. We show that fungal denitrifiers are predominantly cosmopolitan saprotrophs and opportunistic pathogens. Fungal denitrifiers constituted, on average, 1% of the total denitrifier community. This suggests that earlier estimations of fungal denitrifier abundance, and, thereby, it is also likely that the contributions of fungal denitrifiers to N2O emissions have been overestimated. Nevertheless, with many fungal denitrifiers being plant pathogens, they could become increasingly relevant, as soilborne pathogenic fungi are predicted to increase with ongoing climate change.Fungal denitrifiers, in contrast to their bacterial counterparts, are a poorly studied functional group within the nitrogen cycle, even though they produce the greenhouse gas N2O. To curb soil N2O emissions, a better understanding of their ecology and distribution in soils from different ecosystems is needed.
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| 2. |
- Graf, Daniel, et al.
(författare)
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Lucerne (Medicago sativa) alters N2O-reducing communities associated with cocksfoot (Dactylis glomerata) roots and promotes N2O production in intercropping in a greenhouse experiment
- 2019
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 137
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Tidskriftsartikel (refereegranskat)abstract
- Lower emissions of the greenhouse gas nitrous oxide (N2O) are generally observed from intercropped compared to sole cropped systems. This could be due to better N-use efficiency, but differences in microbial communities establishing in the rhizosphere may also play a role as the only known biological sink for N2O is its reduction to nitrogen gas (N-2) by bacteria and archaea that possess the nosZ gene encoding the N2O reductase. Nitrous oxide reducing communities can be divided into two clades, I and II, and their relative abundance and diversity may have important consequences for N2O emissions. Here, we examine how intercropping with a legume (Medicago sativa, "lucerne") and a grass (Dactylis glomerata, "cocksfoot") species, compared to sole cropping of each species, affects the N2O emission potential, and the structure and abundance of root-associated N2O-reducing microbial communities. In a rhizobox experiment, we show that intercropping resulted in higher total shoot biomass compared to sole cropping. Further, N2O production rates were significantly higher in intercropped cocksfoot roots compared to sole cropping of either species. This coincided with lower abundances of nosZ Glade II communities in intercropped compared to sole cropped cocksfoot roots, suggesting that these organisms likely act as a N2O sink. Phylogenetic placement of sequencing reads placed root-associated nosZ Glade II reads close to Ignavibacteria and Opitutaceae, which harbour non-denitrifying N2O reducers with the genetic capacity to also perform dissimilatory nitrate reduction to ammonium (DNRA). We observed a shift in the composition of the cocksfoot root-associated nosZI communities towards incomplete denitrifiers terminating with N2O in intercropped roots. Overall, we hypothesize that such alterations of plant-microbe and/or microbe-microbe interactions contributed to the higher potential N2O emission rate observed in intercropped cocksfoot roots. Understanding the nature of these interactions would represent an important step forward for the design of management practices that minimize N2O emissions.
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| 3. |
- Hallin, Sara, et al.
(författare)
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Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts
- 2022
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Ingår i: Nature ecology & evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 6, s. 1145-1154
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Tidskriftsartikel (refereegranskat)abstract
- Combining field data and greenhouse experiments, the authors show how agricultural management practices like fungicide applications can affect the degree to which arbuscular mycorrhizal fungi in the soil provision phosphorus to plants.Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-European gradient. In a greenhouse experiment, we tested the ability of AMF in these soils to forage for the radioisotope P-33 from a hyphal compartment. AMF communities in grassland soils were much more efficient in acquiring P-33 and transferred 64% more P-33 to plants compared with AMF in cropland soils. Fungicide application best explained hyphal P-33 transfer in cropland soils. The use of fungicides and subsequent decline in AMF richness in croplands reduced P-33 uptake by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the functioning and natural nutrient uptake capacity of AMF in agroecosystems.
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| 4. |
- Hallin, Sara, et al.
(författare)
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Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity
- 2022
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Ingår i: Environmental Microbiome. - : Springer Science and Business Media LLC. - 2524-6372. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. Results We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. Conclusions Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.
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| 5. |
- Pold, Grace, et al.
(författare)
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Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles
- 2024
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Ingår i: ISME Communications. - 2730-6151. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- The two evolutionarily unrelated nitric oxide-producing nitrite reductases, NirK and NirS, are best known for their redundant role in denitrification. They are also often found in organisms that do not perform denitrification. To assess the functional roles of the two enzymes and to address the sequence and structural variation within each, we reconstructed robust phylogenies of both proteins with sequences recovered from 6973 isolate and metagenome-assembled genomes and identified 32 well-supported clades of structurally distinct protein lineages. We then inferred the potential niche of each clade by considering other functional genes of the organisms carrying them as well as the relative abundances of each nir gene in 4082 environmental metagenomes across diverse aquatic, terrestrial, host-associated, and engineered biomes. We demonstrate that Nir phylogenies recapitulate ecology distinctly from the corresponding organismal phylogeny. While some clades of the nitrite reductase were equally prevalent across biomes, others had more restricted ranges. Nitrifiers make up a sizeable proportion of the nitrite-reducing community, especially for NirK in marine waters and dry soils. Furthermore, the two reductases showed distinct associations with genes involved in oxidizing and reducing other compounds, indicating that the NirS and NirK activities may be linked to different elemental cycles. Accordingly, the relative abundance and diversity of NirS versus NirK vary between biomes. Our results show the divergent ecological roles NirK and NirS-encoding organisms may play in the environment and provide a phylogenetic framework to distinguish the traits associated with organisms encoding the different lineages of nitrite reductases.
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| 6. |
- Saghai, Aurélien
(författare)
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A Novel Microbialite-Associated Phototrophic Chloroflexi Lineage Exhibiting a Quasi-Clonal Pattern along Depth
- 2020
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 12, s. 1207-1216
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Tidskriftsartikel (refereegranskat)abstract
- Chloroflexales (Chloroflexi) are typical members of the anoxygenic photosynthesizing component of microbial mats and have mostly been characterized from communities associated to hot springs. Here, we report the assembly of five metagenome-assembled genomes (MAGs) of a novel lineage of Chloroflexales found in mesophilic lithifying microbial mats (microbialites) in Lake Alchichica (Mexico). Genomic and phylogenetic analyses revealed that the bins shared 92% of their genes, and these genes were nearly identical despite being assembled from samples collected along a depth gradient (1-15m depth). We tentatively name this lineage Candidatus Lithoflexus mexicanus. Metabolic predictions based on the MAGs suggest that these chlorosome-lacking mixotrophs share features in central carbon metabolism, electron transport, and adaptations to life under oxic and anoxic conditions, with members of two related lineages, Chloroflexineae and Roseiflexineae. Contrasting with the other diverse microbialite community members, which display much lower genomic conservation along the depth gradient, Ca. L. mexicanus MAGs exhibit remarkable similarity. This might reflect a particular flexibility to acclimate to varying light conditions with depth or the capacity to occupy a very specific spatial ecological niche in microbialites from different depths. Alternatively, Ca. L. mexicanus may also have the ability to modulate its gene expression as a function of the local environmental conditions during diel cycles in microbialites along the depth gradient.
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| 7. |
- Saghai, Aurélien
(författare)
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Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient
- 2021
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 23, s. 51-68
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Tidskriftsartikel (refereegranskat)abstract
- Microbialites are usually carbonate-rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analysed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. Microbialite size and community structure correlated with lake physicochemical parameters, notably alkalinity. Although microbial community composition varied across lake microbialites, major taxa-associated functions appeared quite stable with both, oxygenic and anoxygenic photosynthesis and, to less extent, sulphate reduction, as major putative carbonatogenic processes. Despite interlake microbialite community differences, we identified a microbial core of 247 operational taxonomic units conserved across lake microbialites, suggesting a prominent ecological role in microbialite formation. This core mostly encompassed Cyanobacteria and their typical associated taxa (Bacteroidetes, Planctomycetes) and diverse anoxygenic photosynthetic bacteria, notably Chloroflexi, Alphaproteobacteria (Rhodobacteriales, Rhodospirilalles), Gammaproteobacteria (Chromatiaceae) and minor proportions of Chlorobi. The conserved core represented up to 40% (relative abundance) of the total community in lakes Alchichica and Atexcac, displaying the highest alkalinities and the most conspicuous microbialites. Core microbialite communities associated with carbonatogenesis might be relevant for inorganic carbon sequestration purposes.
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| 8. |
- Saghai, Aurélien, et al.
(författare)
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Crop cover is more important than rotational diversity for soil multifunctionality and cereal yields in European cropping systems
- 2021
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Ingår i: Nature Food. - : Springer Science and Business Media LLC. - 2662-1355. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- In natural ecosystems, positive effects of plant diversity on ecosystem functioning have been widely observed, yet whether this is true in cropping systems remains unclear. Here we assessed the impact of crop diversification on soil microbial diversity, soil multifunctionality (SMF) and crop yields in 155 cereal fields across a 3,000 km north-south European gradient. Overall, crop diversity showed a relatively minor effect on soil microbial diversity, SMF and yields. In contrast, the proportion of time with crop cover (including cash crops, cover crops or forage leys) during the past ten-year crop rotation had a much stronger impact. This suggests that increasing crop cover can enhance both yields and soil functioning, while also providing habitat for soil microorganisms. We found that SMF did not positively contribute to crop yields, highlighting that care must be taken to balance the provision of food with environmentally beneficial functions and services, since they do not always go hand in hand.System-level analysis on the effects of soil biodiversity on cropping system is lacking. Across conventionally managed European fields, the proportion of time with crop cover during the past ten-year rotation has a greater impact than crop diversity on soil microbial diversity, soil multifunctionality and crop yield.
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| 9. |
- Saghai, Aurélien, et al.
(författare)
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Diversity and ecology of NrfA-dependent ammonifying microorganisms
- 2024
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Ingår i: Trends in Microbiology. - 0966-842X .- 1878-4380. ; 32, s. 602-613
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Forskningsöversikt (refereegranskat)abstract
- Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.
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| 10. |
- Saghai, Aurélien, et al.
(författare)
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Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils
- 2021
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 24, s. 341-356
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Tidskriftsartikel (refereegranskat)abstract
- Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.
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