Protists regulate microbially-mediated organic carbon turnover in soil aggregates
Data files
Dec 22, 2023 version files 25.91 KB
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Dataset_GCB-23-1723.R2.csv
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README.md
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Abstract
Soil protists, the major predator of bacteria and fungi, shape the taxonomic and functional structure of soil microbiome via trophic regulation. However, how trophic interactions between protists and their prey influence microbially mediated soil organic carbon turnover remains largely unknown. Here, we investigated the protistan communities and microbial trophic interactions across different aggregates-size fractions in agricultural soil with long-term fertilization regimes. Our results showed that aggregate sizes significantly influenced the protistan community and microbial hierarchical interactions. Bacterivores were the predominant protistan functional group and were more abundant in macroaggregates and silt + clay than in microaggregates, while omnivores showed an opposite distribution pattern. Furthermore, partial least square path modeling revealed positive impacts of omnivores on the C-decomposition genes and soil organic matter (SOM) contents, while bacterivores displayed negative impacts. Microbial trophic interactions were intensive in macroaggregates and silt + clay but were restricted in microaggregates, as indicated by the intensity of protistan-bacterial associations and network complexity and connectivity. Cercozoan taxa were consistently identified as the keystone species in SOM degradation-related ecological clusters in macroaggregates and silt + clay, indicating the critical roles of protists in SOM degradation by regulating bacterial and fungal taxa. Chemical fertilization had a positive effect on soil C sequestration through suppressing SOM degradation-related ecological clusters in macroaggregate and silt + clay. Conversely, the associations between the trophic interactions and SOM contents were decoupled in microaggregates, suggesting limited microbial contributions to SOM turnovers. Our study demonstrates the importance of protists-driven trophic interactions on soil C cycling in agricultural ecosystems.
README
Sample information
Id
Sample_ID
Aggregate: LA, macroaggregates (250-2000 μm); MA, microaggregates (53-25 μm); SA, silt + clay (< 53 μm).
Fertilization type: Control, non-fertilization; NPK, chemical fertilization; M, organic manure; MNPK, a combination of chemical and organic fertilization.
Abiotic factors
- The abiotic factors of of different soil aggregates were determined.
TC: total carbon (g/kg); TN:total nitrogen (g/kg); C/N: the ratio of soil total carbon to total nitrogen;
SOM: soil organic matter (g/kg); AN: ammonium-nitrogen (mg/kg); TP: total phosphor (g/kg); AP:
available phosphorus (mg/kg); pH: soil pH.
Protistan functional groups
- The protistan ASVs were assigned into functional groups based on their feeding modes. Then, the relative abundances of the protistan functional groups in soil aggregates were caculated, including:
Bacterivore, Eukaryvore, Omnivore, Parasites, Phototrophs, Plantpathogens, Saprotrophs, and uncertain.
Protistan groups (at class level)
- The relative abundances of the majority of protistan classes in soil aggregates were analysed by high-throughput sequencing (protistan 18S rRNA gene V4 region), including:
Filosa-Sarcomonadea, Variosea, Filosa-Thecofilosea, Oomycota, Colpodea, Tubulinea, Spirotrichea, Chrysophyceae, Filosa-Imbricate, and the other classes.
C-decomposition genes
- The signal intensities of C-cycling functional genes involveded in organic C decompositions in soil aggregates were examined by GeoChip 5.0 (60K), including:
Starch, Inulin, Hemicellulose, Pectin, Cellulose, Cutin, Chitin, Vanillin and Lignin.
Bacterial groups (at phylum level)
- The relative abundances of the majority of bacterial phylum/class in soil aggregates were analysed by high-throughput sequencing (bacterial 16S rRNA gene V4 region), including:
Actinobacteria, Alphaproteobacteria, Gemmatimonadetes, Acidobacteria, Betaproteobacteria, Chloroflexi, Gammaproteobacteria, Deltaproteobacteria, Verrucomicrobia, Bacteroidetes, Planctomycetes, Nitrospirae, and the others.
Fungal groups (at class level)
- The relative abundances of the majority of fungal class in soil aggregates were analysed by high-throughput sequencing (fungal ITS 1 gene), including:
Sordariomycetes, Zygomycota_Incertae_sedis, Dothideomycetes, Leotiomycetes, Tremellomycetes, Ascomycota_unidentified,
and the others.