The effects of arbuscular mycorrhizal fungi (AMF) and Rhizophagus irregularis on soil microorganisms assessed by metatranscriptomics and metaproteomics

Arbuscular mycorrhizal fungi (AMF) form symbioses with approximately 80% of plant species and potentially benefit their hosts (e.g. nutrient acquisition) and the soil environment (e.g. soil aggregation). AMF also affect soil microbiota and soil multifunctionality. We manipulated AMF presence (via inoculation of non-sterile soil with Rhizophagus irregularis and using a hyphal compartment design) and used RNA-seq and metaproteomics to assess AMF roles in soil. The results indicated that AMF drove an active soil microbial community expressing transcripts and proteins related to nine metabolic functions, including the metabolism of C and N. We suggest two possible mechanisms: 1) the AMF hyphae produce exudates that select a beneficial community, or, 2) the hyphae compete with other soil microbes for available nutrients and consequently induce the community to mineralize nutrients from soil organic matter. We also identified candidate proteins that are potentially related to soil aggregation, such as Lpt and HSP60. Our results bridge microbial ecology and ecosystem functioning. We show that the AMF hyphosphere contains an active community related to soil respiration and nutrient cycling, thus potentially improving nutrient mineralization from soil organic matter and nutrient supply to the plants

Legacy effect of microplastics on plant–soil feedbacks

Microplastics affect plants and soil biota and the processes they drive. However, the legacy effect of microplastics on plant–soil feedbacks is still unknown. To address this, we used soil conditioned from a previous experiment, where Daucus carota grew with 12 different microplastic types (conditioning phase). Here, we extracted soil inoculum from those 12 soils and grew during 4 weeks a native D. carota and a range-expanding plant species Calamagrostis epigejos in soils amended with this inoculum (feedback phase). At harvest, plant biomass and root morphological traits were measured. Films led to positive feedback on shoot mass (higher mass with inoculum from soil conditioned with microplastics than with inoculum from control soil). Films may decrease soil water content in the conditioning phase, potentially reducing the abundance of harmful soil biota, which, with films also promoting mutualist abundance, microbial activity and carbon mineralization, would positively affect plant growth in the feedback phase. Foams and fragments caused positive feedback on shoot mass likely via positive effects on soil aeration in the conditioning phase, which could have increased mutualistic biota and soil enzymatic activity, promoting plant growth. By contrast, fibers caused negative feedback on root mass as this microplastic may have increased soil water content in the conditioning phase, promoting the abundance of soil pathogens with negative consequences for root mass. Microplastics had a legacy effect on root traits: D. carota had thicker roots probably for promoting mycorrhizal associations, while C. epigejos had reduced root diameter probably for diminishing pathogenic infection. Microplastic legacy on soil can be positive or negative depending on the plant species identity and may affect plant biomass primarily via root traits. This legacy may contribute to the competitive success of range-expanding species via positive effects on root mass (foams) and on shoot mass (PET films). Overall, microplastics depending on their shape and polymer type, affect plant–soil feedbacks

Extinction risk of soil biota

No species lives on earth forever. Knowing when and why species go extinct is crucial for a complete understanding of the consequences of anthropogenic activity, and its impact on ecosystem functioning. Even though soil biota play a key role in maintaining the functioning of ecosystems, the vast majority of existing studies focus on aboveground organisms. Many questions about the fate of belowground organisms remain open, so the combined effort of theorists and applied ecologists is needed in the ongoing development of soil extinction ecology

Microplastics of different shapes increase seed germination synchrony while only films and fibers affect seed germination velocity

Microplastics enter the soil in a variety of shapes and polymer types altering soil properties with known consequences for plant growth. However, the effects of a range of different microplastic shapes and types on seed germination are mostly unknown. Here, we established a glasshouse experiment that included 12 microplastic types representing different shapes (fibers, films, foams and fragments) and polymers, and mixed each of them with soil at a concentration of 0.4% (w/w). Fifty seeds of Daucus carota were sown and monitored for 49 days to evaluate different germination parameters. Our results showed that microplastic films and fibers decrease seed germination velocity as they may affect soil water status, likely interfering with different phases of seed germination: Seeds may imbibe toxic microplastic leachates, and be affected by a physical blockage; testa rupturing may be delayed as this also depends on water uptake. Microplastic toxic leachates may affect activity of enzymes key for seed germination, and delay embryo growth and radicle emergence. Microplastics, irrespective of their shape and polymer type, increase synchrony of seed germination, which might be linked with microplastics exerting a mild stress on seeds. The final percentage of germination was not affected by microplastics in soil, implying that microplastics did not affect seed viability. Our results showed that microplastics affect seed germination mainly as a function of their shape

Evolutionary implications of microplastics for soil biota

This is the author accepted manuscript. The final version is available from CSIRO Publishing via the DOI in this recordMicroplastic pollution is increasingly considered to be a factor of global change: in addition to aquatic ecosystems, this persistent contaminant is also found in terrestrial systems and soils. Microplastics have been chiefly examined in soils in terms of the presence and potential effects on soil biota. Given the persistence and widespread distribution of microplastics, it is also important to consider potential evolutionary implications of the presence of microplastics in soil; we offer such a perspective for soil microbiota. We discuss the range of selection pressures likely to act upon soil microbes, highlight approaches for the study of evolutionary responses to microplastics, and present the obstacles to be overcome. Pondering the evolutionary consequences of microplastics in soils can yield new insights into the effects of this group of pollutants, including establishing ‘true’ baselines in soil ecology, and understanding future responses of soil microbial populations and communities.MR acknowledges support from the ERC Advanced Grant ‘Gradual Change’ (694368). UK received funding from the European Union's Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement no. 751699

Microplastics Reduce the Negative Effects of Litter-Derived Plant Secondary Metabolites on Nematodes in Soil

Microplastics and plant litter are ubiquitous in the soil environment, and both materials can influence soil properties and biota. Plant litter releases secondary metabolites (e.g., phenolic compounds) during the decomposition process, including chemical compounds active in plant defense. Effects of microplastics and plant litter on soil biota have been studied independently but we have limited information about the combined effects of both sources of chemicals. Here, we specifically focused on the interaction between plant litter and microplastics, as well as their potential effects on soil biota (i.e., nematodes). We used soils from a previous experiment that included three different types of microplastic fibers (MFs) and four different types of plant litter, which were incubated in the soil in all combinations of materials. After soil incubation (42 days) in the previous experiment, we here tested for effects on nematodes (Caenorhabditis elegans). Plant litter treatments negatively affected the reproduction of nematodes, but these effects were reduced when the soils were incubated along with MFs. We measured the phenolic concentrations in plant litter extracts in a kinetic experiment and found that phenolic concentrations significantly decreased with some of the MF additions. Our results suggest that microplastics can affect the potential effects of natural chemicals such as plant phenolic compounds. We urge future studies to consider this possibility as a key explanatory process underpinning effects of microplastic in the soil environment

Drought legacy effects on root morphological traits and plant biomass via soil biota feedback

1. Drought causes soil feedback effects on plant performance. However, how the linkages between conditioned soil biota and root traits contribute to explain plant–soil feedback (PSF) as a function of drought is unknown. 2. We utilized soil inoculum from a conditioning experiment where grassland species grew under well-watered and drought conditions, and their soil fungi were analyzed. Under well-watered conditions, we grew 21 grassland species with those inocula from either conspecific or heterospecific soils. At harvest, plant biomass and root traits were measured. 3. Negative PSF (higher biomass in heterospecific than in conspecific soils) was predominant, and favored in drought-conditioned soils. Previous drought affected the relationship between root traits and fungal groups. Specific root surface area (SRSA) was higher in heterospecific than in conspecific droughted soils and was linked to an increase in saprotroph richness. Overall, root diameter was higher in conspecific soils and was linked to mutualist and pathogen composition, whereas the decrease of root : shoot in heterospecific soils was linked to pathogenic fungi. 4. Drought legacy affects biomass and root morphological traits via conditioned soil biota, even after the drought conditions have disappeared. This provides new insights into the role that soil biota have modulating PSF responses to drought

Sodium demand of microorganisms in the phyllosphere and the organic layer of a tropical montane forest in south Ecuador

Recent studies raise the hypothesis that Na shortage restricts decomposition and affects the carbon cycle in tropical forests. When Na concentrations in soils are low and the stands are far off-coast, they do not receive substantial Na inputs from the atmosphere. Since terrestrial plants have low concentrations of Na, which is not considered as an essential element, the demand of soil fauna may not be covered. Yet, in contrast to animals, little is known of Na demands of fungi and phyllosphere microorganisms. We present results from a study on Na limitation in a montane forest ecosystem in South Ecuador, which is located on the eastern cordillera of the Andes. We tested the hypotheses that (1) the study area is characterized by low Na concentrations because of low deposition rates with incident precipitation (wind directions mainly from the Amazonian Basin), (2) decomposition processes are limited by fauna and fungal Na restrictions and (3) Na is retained in the canopy because of Na limitation of microorganisms in phyllosphere. Since 1998, we measure Na fluxes in rainfall, throughfall, stemflow, litter leachate, litterfall and organic layer in a microcatchment under an undisturbed lower montane rainforest. Results reveal comparatively low Na concentrations in the ecosystem and similar Na concentrations in throughfall and stemflow. Since Na fluxes are lower with throughfall than with incident rainfall, we conclude that Na is retained in the canopy. To explore the role of the phyllosphere in Na retention we sampled leaves covered by phyllosphere microorganisms and leaves without phyllosphere cover from several tree species, which were sprayed with a NaCl solution containing 0.5 mg L-1 Na, corresponding to the Na concentration in incident rainfall in our study area. Additionally, responses of litter decomposition to Na additions and the involved interaction of soil fungi and fauna were tested in a litterbag experiment at two sites (1000 and 2000 m a.s.l.). Results revealed enhanced decomposition rates following Na additions, though only in the presence of soil fauna. These results might have future ecosystem implications, since our time series showed that total Na deposition decreased within the past 15 years from ca. 40 kg ha-1 a-1 to 10 kg ha-1 a-1, suggesting a potential role of Na in regulating ecosystem processes

Photodegradation modifies microplastic effects on soil properties and plant performance

1. Microplastics (MPs) in soil affect plant–soil systems depending on their shape and polymer type. However, previous research has not yet considered the effects of degraded plastics, which are the plastic materials actually present in the environment. 2. We selected eight MPs representing different shapes (fibres, films and foams) and polymer types, and exposed them to UV-C degradation. Each MP was mixed with soil at a concentration of 0.4% (w/w). The phytometer Daucus carota grew in each pot. At harvest, soil properties and plant biomass were measured. 3. Photodegradation altered MP physical and chemical properties, impacting plant–soil systems. MP degradation effects on plant and soil were observed with fibres and foams, but there were negligible effects with films. The latter could be explained by the polymer structure of films and manufacturer's additives, potentially delaying their degradation. 4. Degraded fibres increased soil respiration more than their non-degraded counterparts, as photodegradation increased the positive effects of fibres on soil water retention. The emergence of oxygenated groups during degradation may have increased the hydrophilicity of fibres, enhancing their ability to retain water. Degraded foams increased soil respiration, which could be related to the possible leaching of organic substances with lower partition coefficients, which may promote soil microbial activity. 5. In contrast, degraded foams decreased soil aggregation, likely as degradation produced larger holes increasing their permeability. Also, the increase in hydrophilic molecules could have decreased soil particle cohesiveness. Degraded fibres and foams increased shoot and root mass as a result of MP effects on soil properties. Photodegraded MPs affected root traits, which could be linked to MP effects on soil water status and plant coping strategies. 6. Synthesis and applications. Photodegradation can intensify the effects that microplastics (MPs) have on plant–soil systems, which would have frequently been underestimated had we only worked with pristine MPs. Plastic companies, agricultural practitioners and researchers should consider that plastics are being degraded as they enter the soil. Policies should promote practices to minimize MP accumulation in soils and ensure their proper disposal

Indigenous Arbuscular Mycorrhizal Fungal Assemblages Protect Grassland Host Plants from Pathogens

Plant roots can establish associations with neutral, beneficial and pathogenic groups of soil organisms. Although it has been recognized from the study of individual isolates that these associations are individually important for plant growth, little is known about interactions of whole assemblages of beneficial and pathogenic microorganisms associating with plants