Aims In order to counteract the enduring decreases in the quality of agricultural land, mechanistic studies for a more sustainable agricultural crop production were performed. They aimed to assess the effects of organic amendments in combination with mineral fertilizer on soil-rhizosphere microbiota and their influence on soil health and plant performance. Methods In a short-term greenhouse experiment, the effects of pelletized spent mushroom substrate, with different combinations of biochar and mineral fertilizer, on agricultural soil and performance of Hordeum vulgare L were scrutinized. To evaluate improved soil quality, different soil biological and chemical properties, microbial activity, bacterial diversity and plant performance were assessed. Results Plant performance increased across all fertilizer combinations. Bacterial β-diversity changed from the initial to the final sampling, pointing at a strong influence of plant development on the rhizosphere with increasing abundances of Acidobacteria and decreasing abundances of Actinobacteria, Chloroflexi, and Bacteroidetes. Microbial activity (FDA), potential enzyme activity and metabolic diversity of the microbial community (BIOLOG) were not affected by the amendments, whereas bacterial community structure changed on family level, indicating functional redundancy. Treatments containing biochar and the highest amount of mineral fertilizer (B_MF140) caused the strongest changes, which were most pronounced for the families Xanthobacteraceae, Mycobacteriaceae, and Haliangiaceae. Conclusion Applying organic amendments improved plant performance and maintained soil health, contributing to more sustainable crop production. Nevertheless, long-term field studies are recommended to verify the findings of this short-term experiment.

Early childhood exposure to a farming environment has been found to be protective against asthma and other atopic disorders. Here, we report the complete genome sequence of Lactococcus lactis subsp. lactis G121, which was isolated from the kitchen of a farm in Bavaria (Germany) and is recognized for its allergy-protective properties. It could be assembled into one circular chromosome, three circular plasmids, and one linear plasmid.

Agroforestry is a land-use system that combines arable and/or livestock management with tree cultivation, which has been shown to provide a wide range of socio-economic and ecological benefits. It is considered a promising strategy for enhancing resilience of agricultural systems that must remain productive despite increasing environmental and societal pressures. However, agroforestry systems pose a number of challenges for experimental research and scientific hypothesis testing because of their inherent spatiotemporal complexity. We reviewed current approaches to data analysis and sampling strategies of bio-physico-chemical indicators, including crop yield, in European temperate agroforestry systems to examine the existing statistical methods used in agroforestry experiments. We found multilevel models, which are commonly employed in ecology, to be underused and under-described in agroforestry system analysis. This Short Communication together with a companion R script are designed to act as an introduction to multilevel models and to promote their use in agroforestry research.

In natural farming rice paddies, intertillage (tillage between rows, during rice growth period) is often performed mainly to remove weeds without the use of chemicals. Also, the intertillage disturbs soil surfaces, potentially impacting the characteristics of soil microbial communities, such as their diversity and abundance. Natural farming systems aim to maintain biodiversity, but it remains unclear whether the intertillage impacts soil microbes in rice paddies. Thus, this study aimed to understand to what extent “five times intertillage” treatment (5T) influences soil bacterial abundance and community structures compared with no tillage (NT), under a natural farming rice paddy system. Soils were sampled at rice proximity, soil surface, and 10 cm depth in a natural farming rice paddy, during the early to late vegetative phase (June to July), in Hokkaido, Japan. The 16S rRNA community structures and abundance were analyzed by next generation sequencing (NGS) and quantitative PCR, respectively. We observed that NT had significantly higher bacterial abundances at the soil surface than 5T. However, there were no clear differences between 5T and NT, regarding the bacterial community structures, including their diversity indices. Instead, the sampling timings markedly impacted the bacterial community structures for the rice proximity and soil surface, showing increasing diversity indices at the late vegetative stage, compared to the early vegetative stage, suggesting the interaction between the crop growth and bacterial communities. In this study, we did not observe the significant difference between the rice yield from NT (2.3 ± 0.7 t·ha−1) and 5T plots (2.7 ± 0.9 t·ha−1); however, the 5T might have negatively impacted soil bacterial abundances but not the community structure of the bacteria.