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Abstract Numerous 13CO 2 labeling studies have traced the flow of carbon from fresh plant exudates into rhizosphere bacterial communities. However, the succession of the uptake of carbon leaving the roots by distinct rhizosphere microbiota has rarely been resolved between microbial kingdoms. This can provide valuable insights on the niche partitioning of primary rhizodeposit consumption, as well as on community interactions in plant-derived carbon flows in soil. Here, we have traced the flow of fresh plant assimilates to rhizosphere microbiota of maize (Zea mays L.) by rRNA-stable isotope probing (SIP). Carbon flows involving bacteria, unicellular fungi, as well as protists were observed over 5 and 8 days. Surprisingly, labeling of Paraglomerales and several bacteria including Opitutus, Mucliaginibacter and Massilia spp. was especially apparent in soil surrounding the strict rhizosphere after 5 d. This highlights the central role of arbuscular mycorrhizal fungi (AMF) as a shunt for fresh plant assimilates to soil microbes not directly influenced by root exudation. Distinct trophic webs involving different flagellates, amoeba and ciliates were also observed in rhizosphere and surrounding soil, while labeling of filamentous saprotrophic Ascomycota or Basidiomycota was not apparent. This challenges the proposed "sapro-rhizosphere" concept and demonstrates the utility of rRNA-SIP to disentangle inter-kingdom microbial relationships in the rhizosphere. Graphical abstract Image 1 Highlights • rRNA-SIP was used to trace plant-derived carbon flows in the rhizosphere of maize. • 13C-labeling of mycorrhiza was stronger in surrounding soil than in the rhizosphere. • Labelling of bacteria incl. Opitutus spp. was also stronger in surrounding soil. • AMF are a shunt of plant assimilates to microbes outside the strict rhizosphere. [ABSTRACT FROM AUTHOR]

This study assessed the carbon (C) budget and the C stocks in major compartments of the soil food web (bacteria, fungi, protists, nematodes, meso- and macrofauna) in an arable field with/without litter addition. The C stocks in the food web were more than three times higher in topsoil (0–10 cm) compared to subsoil (>40 cm). Microorganisms contained over 95% of food web C, with similar contributions of bacteria and fungi in topsoil. Litter addition did not alter C pools of soil biota after one growing season, except for the increase of fungi and fungal feeding nematodes in the topsoil. However, the C budget for functional groups changed with depth, particularly in the microfauna. This suggests food web resilience to litter amendment in terms of C pool sizes after one growing season. In contrast, the distinct depth dependent pattern indicates specific metacommunities, likely shaped by dominant abiotic and biotic habitat properties. [ABSTRACT FROM AUTHOR]

Decomposition of organic matter is crucial for ecosystem functioning. Microorganisms, which are responsible for the mineralization of organic matter, are usually treated as a homogeneous functional guild, despite mineralization capacity can differ profoundly between taxa. In addition, a significant part of the microbial community is top-down controlled by microbial grazers, such as protist. Since protist grazing is selective, and selectivity differs among species, we hypothesized that protist taxa complement each other in grazing intensity and thereby affect bacterial community structure and mineralization rate. In a laboratory experiment the species richness of protist communities was manipulated in an arable field soil and the mineralization rate of maize litter residues followed during the decomposition of the labile (4 days) and recalcitrant (3 weeks) carbon (C) fractions. Mineralization rate overall increased in the presence of protists. Changes in microbial function could be related to changes in microbial community composition (measured by phospholipid fatty acids pattern). During microbial decomposition, different protist grazers gained influence on mineralization rates over consecutive time intervals, indicating that a succession of protists caused an enhanced bacterial C-mineralization of plant detritus. Protist identity and species richness affected the microbial community composition, but not the magnitude of its mineralization function. In general, protist identity appeared to be more relevant for the composition of the microbial communities at the beginning of decomposition while the protist species richness appeared to be more critical in the later, slow phase of decomposition. This study provides an example that the overall outcome of ecosystem processes, such as mineralization rate is regulated by the sum of positive and negative effects of complex species interactions operating at a very fine spatial and temporal scales. [ABSTRACT FROM AUTHOR]

Soil protists are commonly suggested being solely bacterivorous, serving together with bacterivorous nematodes as the main controllers of the bacterial energy channel in soil food webs. In contrast, the fungal energy channel is assumed to be controlled by arthropods and mycophagous nematodes. This perspective accepted by most soil biologists is, however, challenged by functional studies conducted by taxonomists that revealed a range of mycophagous protists. In order to increase the knowledge on the functional importance of mycophagous protists we isolated and initiated cultures of protist taxa and tested eight for facultative feeding on diverse fungi in microcosm experiments. Two different flagellate species of the genus Cercomonas , the testate amoeba Cryptodifflugia operculata and four genera of naked amoebae ( Acanthamoeba sp., Leptomyxa sp., two Mayorella spp. and Thecamoeba spp.) fed and grew on yeasts with four taxa ( Cercomonas sp., Leptomyxa sp., Mayorella sp., and Thecamoeba sp.) also thriving on spores of the plant pathogenic hyphal-forming fungus Fusarium culmorum . To identify the potential importance of mycophagous protists in the environment we applied a data-mining approach targeting small subunit (SSU) rRNA data obtained in metatranscriptomes of five fundamentally different terrestrial samples. We focused our analyses on the distribution and relative abundances of two well-studied mycophagous protist groups, vampyrellid amoebae and grossglockneriid ciliates. Both groups were detected in all of the highly contrasting terrestrial samples, comprising up to 3% of all protist SSU rRNA transcripts. SSU transcripts of these two groups, in contrast to all remaining protist SSU transcripts, showed strong correlations with the relative abundance of fungal sequences indicating close direct trophic interactions. Taken together, this study provides evidence that mycophagy among soil protists is common and might be of substantial but hitherto overlooked ecological importance in terrestrial ecosystems. Future studies should aim at evaluating taxon-specific (facultative) mycophagy, decipher changes caused in the fungal community and quantitatively evaluate the functional importance of this trophic position in soil ecosystems. [ABSTRACT FROM AUTHOR]

Abstract: Soil food webs are important determinants for the carbon flow through terrestrial systems, with the trophic networks between microbes and microfaunal grazers forming the basis for processing plant resources. At an agricultural field site cropped with maize or wheat, plant carbon input to soil was experimentally manipulated by amendment with maize litter. The community structure of dominant micro-food web components, the bacteria, fungi, protozoa and nematodes, was investigated across a depth gradient comprising plough layer, rooted soil below plough horizon, and deeper root free soil. The community composition and diversity within micro-food webs, and the response to resource supply, were assessed in summer, the vegetation period with highest root exudation. In the plough layer amendment with plant residues increased microbial biomass as well as density of fan shaped amoeba morphotypes and of bacterial- and fungal-feeding nematodes. Diversity of food web assemblages was assessed by operational taxonomic units (OTU) for bacteria and fungi, protozoa morphotypes and nematode families. Changes in diversity were either not apparent (fungi, protozoa), negatively related to litter (bacteria) or positively linked to the presence of a specific crop plant (bacteria, nematodes). Based on nematode functional guilds and the related enrichment and structure index, general food web conditions were assigned as nutrient enriched, with a high degree of disturbance, and a dominance of the bacterial energy channel. In sum, litter amendment fostered the abundance but not the diversity of organisms as food webs remained bottom heavy with only small amounts of carbon conserved at higher trophic levels. Food web structure was more affected by the abiotic (soil profile) and biotic (crop plant) environment than by the supply with litter resources. [Copyright &y& Elsevier]