How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation

Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.

Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation

Root exudation contributes to soil carbon allocation and also to microbial C and energy supply, which subsequently impacts soil aggregation around roots. Biologically-driven soil structural formation is an important driver of soil fertility. Plant genetic determinants of exudation and more generally of factors promoting rhizosphere soil aggregation are largely unknown. Here, we characterized rhizosphere aggregation in a panel of 86 pearl millet inbred lines using a ratio of root-adhering soil dry mass per root tissue dry mass (RAS/RT). This ratio showed significant variations between lines, with a roughly 2-fold amplitude between lowest and highest average values. For 9 lines with contrasting aggregation properties, we then compared the bacterial diversity and composition in root-adhering soil. Bacterial α-diversity metrics increased with the "RAS/RT ratio." Regarding taxonomic composition, the Rhizobiales were stimulated in lines showing high aggregation level whereas Bacillales were more abundant in lines with low ratio. 184 strains of cultivable exopolysaccharides-producing bacteria have been isolated from the rhizosphere of some lines, including members from Rhizobiales and Bacillales. However, at this stage, we could not find a correlation between abundance of EPS-producing species in bacterial communities and the ratio RAS/RT. These results illustrated the impact of cereals genetic trait variation on soil physical properties and microbial diversity. This opens the possibility of considering plant breeding to help management of soil carbon content and physical characteristics through carbon rhizodeposition in soil.

Nitrous Oxide (N2O) Emissions by Termites: Does the Feeding Guild Matter?

In the tropics, termites are major players in the mineralization of organic matter leading to the production of greenhouse gases including nitrous oxide (N₂O). Termites have a wide trophic diversity and their N-metabolism depends on the feeding guild. This study assessed the extent to which N₂O emission levels were determined by termite feeding guild and tested the hypothesis that termite species feeding on a diet rich in N emit higher levels of N₂O than those feeding on a diet low in N. An in-vitro incubation approach was used to determine the levels of N₂O production in 14 termite species belonging to different feeding guilds, collected from a wide range of biomes. Fungus-growing and soil-feeding termites emit N₂O. The N₂O production levels varied considerably, ranging from 13.14 to 117.62 ng N₂O-N d^-1 (g dry wt.)^-1 for soil-feeding species, with Cubitermes spp. having the highest production levels, and from 39.61 to 65.61 ng N₂O-N d^-1 (g dry wt.)^-1 for fungus-growing species. Wood-feeding termites were net N₂O consumers rather than N₂O producers with a consumption ranging from 16.09 to 45.22 ng N₂O-N d^-1 (g dry wt.)^-1. Incubating live termites together with their mound increased the levels of N₂O production by between 6 and 13 fold for soil-feeders, with the highest increase in Capritermes capricornis, and between 14 and 34 fold for fungus-growers, with the highest increase in Macrotermes muelleri. Ammonia-oxidizing (amoA-AOB and amoA-AOA) and denitrifying (nirK, nirS, nosZ) gene markers were detected in the guts of all termite species studied. No correlation was found between the abundance of these marker genes and the levels of N₂O production from different feeding guilds. Overall, these results support the hypothesis that N₂O production rates were higher in termites feeding on substrates with higher N content, such as soil and fungi, compared to those feeding on N-poor wood.

Plant Roots Increase Bacterivorous Nematode Dispersion through Nonuniform Glass-bead Media

Dispersion of bacterivorous nematodes in soil is a crucial ecological process that permits settlement and exploitation of new bacterial-rich patches. Although plant roots, by modifying soil structure, are likely to influence this process, they have so far been neglected. In this study, using an original three-compartment microcosm experimental design and polyvinyl chloride (PVC) bars to mimic plant roots, we tested the ability of roots to improve the dispersion of bacterivorous nematode populations through two wet, nonuniform granular (glass bead) media imitating contrasting soil textures. We showed that artificial roots increased migration time of bacterivorous nematode populations in the small-bead medium, suggesting that plant roots may play an important role in nematode dispersion in fine-textured soils or when soil compaction is high.

Modification of a commercial DNA extraction kit for safe and rapid recovery of DNA and RNA simultaneously from soil, without the use of harmful solvents

An optimized method, based on the coupling of two commercial kits, is described for the extraction of soil nucleic acids, with simultaneous extraction and purification of DNA and RNA following a cascade scheme and avoiding the use of harmful solvents. The protocol canmonitor the variations in the recovery yield of DNA and RNA from soils of various types.The quantitative version of the protocol was obtained by testing the starting soil quantity, the grinding parameters and the final elution volumes, in order to avoid saturation of both kits.

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A first soil-crushing step in liquid nitrogen could be added for the assessment of fungal parameters.

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The protocol was efficienton different tropical soils, including Andosol, while their high contents of clays, including poorly crystalline clays, and Fe and Al oxides usually make the nucleic acid extraction more difficult.

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The RNA recovery yield from the previous tropical soils appeared to correlate better to soil respiration than DNA, which is positively influenced by soil clay content.