Testing contrast agents to improve micro computerized tomography (μCT) for spatial location of organic matter and biological material in soil

Soil carbon is essential for soil and ecosystem functioning. Its turnover and storage in soil are multifaceted processes that involve microbial activity in complex physical matrices. Biological litter, which include plants, animals, and microorganisms, is decomposed in soil stimulating soil biota (archaea, bacteria, fungi, protists, and animals) activity and yielding soil organic matter (SOM). Such decomposition processes are influenced by local physico-chemical characteristics including the spatial distribution of aggregates and pores. More refined analytical tools are needed to better understand these processes, especially considering the spatial 3D structure of soil matrices. Using synchrotron radiation (X-ray) micro computerized tomography (SR-μCT), we tested different contrast agents (staining methods) based on silver (Ag), eosin (Br based), and liquid and gaseous iodine (I) in order to spatially image biological material and SOM in soil samples. We also performed K-edge SR-μCT for the Ag and I2 treatments and conventional μCT for additional soil samples applying the I2 treatment. Our results indicated that I2 was the most efficient contrast method for SR-μCT imaging of soil samples. I2 qualitatively improved the images, but mainly, by using the K-edge SR-μCT, this method provided a powerful tool to determine the spatial location of SOM. We acknowledge that the use of SR-μCT is an expensive technique to study soil samples, which comes with bottlenecks in terms of access to facilities and measurement time. Nevertheless, we show that the I2 treatment improved soil images also using standard μCT. In conventional μCT the I2 treatment improved the visualization of biological material and consequently improved the qualitative analysis of fine plants roots and micro-fauna (Collembola). This improvement may have a positive implication in soil biology, by improving a non-destructive method to detect fungi (SR-μCT), soil fauna (conventional μCT) and roots in undisturbed soil samples. An unexpected finding was that the I2 treatment also stained the plastic sample containers (nylon and polyimide), indicating the potential for the I2 staining procedure to be applied for the detection of plastic pollution in soil samples

Fungal growth response to recurring heating events is modulated by species interactions

An increasing frequency of heat events can affect key organisms related to ecosystem functions. Soil saprobic fungi have important roles in carbon and nutrient cycling in soils, and they are clearly affected by heat events. When tested individually, saprobic soil fungi showed a variety of growth responses to a series of two heat events. However, in nature these fungi rarely grow alone. Coexistence theory predicts that diversity in the response to stressors can influence the outcome of species interactions and growth. This means that the co-cultivation of different fungi may affect their growth response to heat events. To test if recurring heat events affect fungal growth in small synthetic communities, we evaluated fungi previously known to respond to recurring heat events in experimental small communities composed of two and three species. For the fungi growing in pairs, surprisingly, most of the responses could not be predicted by how the isolates responded individually. In some cases, facilitation or increased competition were observed. For the three fungi growing together, results were also not predicted by the individual or pair responses. Both the heat events and the small communities influenced the growth of the fungi and growth properties emerged from the interactions among isolates and the heat stress. We show that not only do environmental conditions influence fungal interactions and growth rates, but also that the co-cultivation of different fungi affects fungal response to recurring heat events. These results indicate that more complex experimental designs are needed to better understand the effects of recurring heat events and climate change on soil fungi

Multi-Objective Big Data Optimization with jMetal and Spark

Big Data Optimization is the term used to refer to optimization problems which have to manage very large amounts of data. In this paper, we focus on the parallelization of metaheuristics with the Apache Spark cluster computing system for solving multi-objective Big Data Optimization problems. Our purpose is to study the influence of accessing data stored in the Hadoop File System (HDFS) in each evaluation step of a metaheuristic and to provide a software tool to solve these kinds of problems. This tool combines the jMetal multi-objective optimization framework with Apache Spark. We have carried out experiments to measure the performance of the proposed parallel infrastructure in an environment based on virtual machines in a local cluster comprising up to 100 cores. We obtained interesting results for computational e ort and propose guidelines to face multi-objective Big Data Optimization problems.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Root colonization by arbuscular mycorrhizal fungi is reduced in tomato plants sprayed with fungicides

Arbuscular mycorrhizal fungi (AMF) form symbioses with many agricultural crops and can improve plant biomass and health. The performance of the AM symbiosis is context dependent, for example, usually the inoculation of the AMF Rhizophagus irregularis benefits plant biomass, but benefits can be suppressed by high soil fertility levels. Nevertheless, the importance of many other agricultural management practices on AMF, such as fungicides application, is poorly understood. Also, pesticide regulations usually neglect a comprehensive safety testing of fungicides on AMF and lawmakers require empirical support to improve such laws. The objective of this study was to evaluate the effects of spraying fungicides on tomato plants and the subsequent root colonization of plants grown in natural soil containing AMF and inoculated with R. irregularis. We detected that the inoculation of R. irregularis increased the total root colonization of the control plants that did not receive fungicides and that spraying the plants with the fungicides Signum® and Topas® reduced total root colonization. The effect on specific AM fungal structures was variable according to the product. Signum® reduced the occurrence of arbuscules, while Topas® reduced the occurrence of AM hyphae in the colonized roots. Cuprozin® did not reduce total root colonization but reduced the occurrence of AM vesicles. Sampling time was also relevant. Effects were detected at 90 days, but not at 35 days. Our results show that fungicides safety should be evaluated for their effects on root colonization of crops in non-sterilized soils and at adequate sampling time

Multiple anthropogenic pressures eliminate the effects of soil microbial diversity on ecosystem functions in experimental microcosms

Biodiversity is crucial for the provision of ecosystem functions. However, ecosystems are now exposed to a rapidly growing number of anthropogenic pressures, and it remains unknown whether biodiversity can still promote ecosystem functions under multifaceted pressures. Here we investigated the effects of soil microbial diversity on soil functions and properties when faced with an increasing number of simultaneous global change factors in experimental microcosms. Higher soil microbial diversity had a positive effect on soil functions and properties when no or few (i.e., 1–4) global change factors were applied, but this positive effect was eliminated by the co-occurrence of numerous global change factors. This was attributable to the reduction of soil fungal abundance and the relative abundance of an ecological cluster of coexisting soil bacterial and fungal taxa. Our study indicates that reducing the number of anthropogenic pressures should be a goal in ecosystem management, in addition to biodiversity conservation