Small world below ground: Microbial ecology ¶

Earthworms and enchytraeids play an important role in biogeochemical cycles and are good indicators of soil fertility. However, assessing their assemblages is difficult, mainly because the methods to identify them require expert knowledge, which becomes a technical challenge when surveying large areas. Soil DNA metabarcoding is a promising method that enables the identification of individual species directly from a bulk composite sample in large field experiments. Here, we investigated in parallel both earthworm (family Lumbricidae) and enchytraeid (family Enchytraeidae) assemblages in three land-use types (arable land, grassland, forest) across 29 Swiss Soil Monitoring Network (NABO) sites, using high-throughput amplicon sequencing of marker genes. For both earthworms and enchytraeids, α-diversity was higher in grasslands than in arable land and forests, and it was significantly affected by soil physico-chemical, climate and biological properties, especially pH and climate properties. In addition, we found negative correlations between earthworms α-diversity and soil total carbon (TC) content and the soil carbon to nitrogen ratio. Using the DNA metabarcoding, we observed sequences of Aporrectodea nocturna in soils with low pH, while other Aporrectodea species occurred in soils with high pH. We identified Bimastos rubidus in soils with low pH but higher TC, total nitrogen, organic C, and low silt content, while the enchytraeids Cognettia sphagnetorum and Cernosvitoviella atrata occurred in forest soils with high water and organic matter contents. We identified some indicator taxa for the different land-use types, for grassland: Aporrectodea icterica, Lumbricus rubellus, Marionina communis, Fridericia bisetosa and Fridericia connata; arable land: Allolobophora chlorotica, Enchytraeus dichaetus, Achaeta iberica, Prodtodrilus antipae and Fridericia tuberosa; and for forest: Octolasion cyaneum, Octolasion lacteum and Cognettia chlorophila. Although these indicator taxa are unlikely to provide information about the effect of land-use change on soil biodiversity at large spatial scales, these species do drive assemblage differences between land-use types. Soil DNA metabarcoding could therefore assist land managers in monitoring soil biodiversity and quality.

Background: Phosphorus (P) availability in soils regulates forest productivity. However, the drivers of soil P dynamics following forest management remain poorly understood, particularly in P-deficient forests in tropical and subtropical regions.
Method: Soil samples of 0–10 cm were collected from the plots after 9 years of thinning and understory removal (UR) in Pinus massoniana plantations in subtropical China. Soil physicochemical properties, microbial biomass and community composition, and Hedley P fractions were measured to assess the underlying mechanisms for the dynamics of soil P fractions.
Results: Compared to undisturbed plots, total soil inorganic P (Pi; + 24%) within the dominant species thinning (DST) plots showed a significant increase, which was associated with the accrual in resin-Pi (+ 30%), NaHCO₃-Pi (+ 21%), and C.CHl-Pi (+ 45%). These Pi fractions were primarily correlated with increased relative abundance of Ascomycota, Rozellomycota, and Proteobacteria. Conversely, post-management (thinning and UR) assessments revealed no significant changes in total P, total organic P (Po), and residual P. The observed decrease in total Po (– 9%) in DST plots was linked to reductions in NaHO-Po (– 7%) and C.CHl-Po (– 24%). Notably, these Po fractions were negatively affected by the relative abundance of Glomeromycota. Furthermore, variations in soil fungal and bacterial community structures accounted for 44.3% and 26.3% of the variances in soil Pi fractions, respectively, similarly explaining 20.4% and 33.3% for soil Po fractions, respectively.
Conclusions: These results indicate that P availability following forest management interventions within subtropical pine plantations is intricately connected to microbial community composition that enhances the transformation from Po into Pi forms.

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

With their various feeding types, soil nematodes play a crucial role in the soil food web. Here, we investigated if and how soil nematodes responded to a long-term irrigation in a drought-prone Scots pine (Pinus sylvestris) forest in southern Switzerland, applied to study whether greater soil water availability would improve tree health and reduce tree mortality. After 14 years of irrigation, tree vitality and soil development had improved significantly. However, morphological observations of the soil nematodes revealed a decrease in their total number in the irrigated plots. Overall, the irrigated plots had a lower nematode richness compared with the dry control plots, but the Shannon index did not differ between the two treatments. In addition, the nematode community shifted significantly as a result of the irrigation. Soil physical parameters, such as sand and silt contents and bulk density, were significantly positively correlated with the nematode community in the irrigation treatment. According to a DNA marker sequence analysis, a total of 43 genera of nematodes were assigned. Predatory nematodes were significantly less abundant in the irrigated plots than in the dry control plots, as the average number decreased to 74 in the irrigated plots compared to 3579 in the dry control plots, while non-predators were not significantly affected. A differential abundance analysis revealed that the genera Tripyla and Anatonchus were the predators that declined the most. Overall, marker sequence analysis of forest soil nematodes appears to be a suitable tool for assessing changes in nematode communities and taxa. The disappearance of predatory nematodes under irrigation, however, can perhaps only be explained if other predatory animal groups, such as predatory mites or millipedes, are also analyzed at the same time.

In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.