Grapevine decline is associated with difference in soil microbial composition and activity

Grapevine decline is a top concern in viticulture worldwide and is often associated with many biotic and abiotic factors. Grape trunk diseases and viruses are some of the most frequently identified causes of vine dieback. However, a decline is sometimes observed when no mineral deficiency or excess, or pathogenic causes can be identified. Soil enzymatic and microbial activities are relevant bio-indicators since they are known to influence vine health. Grapevine associated microbiota, linked to vine fitness, is known to be influenced by soil microbiota coming from the microbial pool inhabiting the vineyard. This work describes the microbial diversity and activity of four different vineyard plots of the Bordeaux region, selected due to the presence of localised declining areas unexplained yet by disease symptoms. Soils were sampled in declining areas and areas within the same plot showing no decline symptoms, during autumn and spring periods. Significant differences in enzymatic activities, microbial biomass and activity were found among soils even if those soils presented quite similar physicochemical characteristics that could not explain these observed declines. The results of enzymatic assays distinguished patterns in autumn and spring periods with an overall greater enzymatic activity in soils from non-declining areas. This work suggests that soils displaying decline symptoms present a dysbiosis in functionality and diversity which is linked to vine health.

Effects of Glucosinolate-Derived Isothiocyanates on Fungi: A Comprehensive Review on Direct Effects, Mechanisms, Structure-Activity Relationship Data and Possible Agricultural Applications

Plants heavily rely on chemical defense systems against a variety of stressors. The glucosinolates in the Brassicaceae and some allies are the core molecules of one of the most researched such pathways. These natural products are enzymatically converted into isothiocyanates (ITCs) and occasionally other defensive volatile organic constituents (VOCs) upon fungal challenge or tissue disruption to protect the host against the stressor. The current review provides a comprehensive insight on the effects of the isothiocyanates on fungi, including, but not limited to mycorrhizal fungi and pathogens of Brassicaceae. In the review, our current knowledge on the following topics are summarized: direct antifungal activity and the proposed mechanisms of antifungal action, QSAR (quantitative structure-activity relationships), synergistic activity of ITCs with other agents, effects of ITCs on soil microbial composition and allelopathic activity. A detailed insight into the possible applications is also provided: the literature of biofumigation studies, inhibition of post-harvest pathogenesis and protection of various products including grains and fruits is also reviewed herein.

Positive Effects of Crop Diversity on Productivity Driven by Changes in Soil Microbial Composition

Intensive agriculture has major negative impacts on ecosystem diversity and functioning, including that of soils. The associated reduction of soil biodiversity and essential soil functions, such as nutrient cycling, can restrict plant growth and crop yield. By increasing plant diversity in agricultural systems, intercropping could be a promising way to foster soil microbial diversity and functioning. However, plant–microbe interactions and the extent to which they influence crop yield under field conditions are still poorly understood. In this study, we performed an extensive intercropping experiment using eight crop species and 40 different crop mixtures to investigate how crop diversity affects soil microbial diversity and activity, and whether these changes subsequently affect crop yield. Experiments were carried out in mesocosms under natural conditions in Switzerland and in Spain, two countries with drastically different soils and climate, and our crop communities included either one, two or four species. We sampled and sequenced soil microbial DNA to assess soil microbial diversity, and measured soil basal respiration as a proxy for soil activity. Results indicate that in Switzerland, increasing crop diversity led to shifts in soil microbial community composition, and in particular to an increase of several plant-growth promoting microbes, such as members of the bacterial phylum Actinobacteria. These shifts in community composition subsequently led to a 15 and 35% increase in crop yield in 2 and 4-species mixtures, respectively. This suggests that the positive effects of crop diversity on crop productivity can partially be explained by changes in soil microbial composition. However, the effects of crop diversity on soil microbes were relatively small compared to the effects of abiotic factors such as fertilization (three times larger) or soil moisture (three times larger). Furthermore, these processes were context-dependent: in Spain, where resources were limited, soil microbial communities did not respond to crop diversity, and their effect on crop yield was less strong. This research highlights the potential beneficial role of soil microbial communities in intercropping systems, while also reflecting on the relative importance of crop diversity compared to abiotic drivers of microbiomes and emphasizing the context-dependence of crop–microbe relationships.

Positive effects of crop diversity on productivity driven by changes in soil microbial composition

SummaryIntensive agriculture has major negative impacts on ecosystem diversity and functioning, including that of soils. The associated reduction of soil biodiversity and essential soil functions, such as nutrient cycling, can restrict plant growth and crop yield. By increasing plant diversity in agricultural systems, intercropping could be a promising way to foster soil microbial diversity and functioning. However, plant–microbe interactions and the extent to which they influence crop yield under field conditions are still poorly understood. In this study, we performed an extensive intercropping experiment using eight crop species and 40 different crop mixtures to investigate how crop diversity affects soil microbial diversity and functions, and whether these changes subsequently affect crop yield. Experiments were carried out in mesocosms under natural conditions in Switzerland and in Spain, two countries with drastically different soils and climate, and our crop communities included either one, two or four species. We sampled and sequenced soil microbial DNA to assess soil microbial diversity, and measured soil basal respiration as a proxy for soil activity. Results indicate that in Switzerland, increasing crop diversity led to shifts in soil microbial community composition, and in particular to an increase of several plant-growth promoting microbes, such as members of the bacterial phylum Actinobacteria. These shifts in community composition subsequently led to a 15 and 35% increase in crop yield in 2 and 4-species mixtures, respectively. This suggests that the positive effects of crop diversity on crop productivity can partially be explained by changes in soil microbial composition. However, the effects of crop diversity on soil microbes were relatively small compared to the effects of abiotic factors such as fertilization (3 times larger) or soil moisture (3 times larger). Furthermore, these processes were context-dependent: in Spain, where soil resources were limited, soil microbial communities did not respond to crop diversity, and their effect on crop yield was less strong. This research highlights the potential beneficial role of soil microbial communities in intercropping systems, while also reflecting on the relative importance of crop diversity compared to abiotic drivers of microbiomes, thereby emphasizing the context-dependence of crop–microbe relationships.

Bark decomposition in white oak soil outperforms eastern hemlock soil, while bark type leads to consistent changes in soil microbial composition

Bark decomposition is an underexamined component of soil carbon cycling and soil community assembly. Numerous studies have shown faster decomposition of leaf litter in “home” environments (i.e. within soil adjacent to the plant that produced the leaves), suggesting potential legacy effects from previous deposition of similar litter. This is expected to occur through, in part, accumulation of microorganisms that metabolize substrates the litter provides. Whether a similar “home-field advantage” (HFA) exists for bark decomposition is unknown, but this dynamic may differ because annual bark deposits to soil are minimal relative to leaf deposits. We hypothesized that (1) as with leaf litter, bark will be better decomposed near to the tree from which it was collected, and (2) that decomposing bark can initiate change in soil microbial composition. To test these hypotheses, we used a full factorial design that included two bark types (collected from eastern hemlock, Tsuga canadensis, and white oak, Quercus alba) and two soil types (‘home’ and ‘away’) within a temperate mixed hardwood forest at the Shale Hills Catchment in central Pennsylvania, USA. Bark was excised from 25 replicates of each tree type, buried in either home or away soil, and incubated belowground from July 2017 to June 2018. Decomposition was assessed through proportionate mass loss over time, while microbial composition in the bark and adjacent soil was assessed through high-throughput sequencing of 16S rRNA gene and fungal ITS fragments. Overall, bark degraded faster in white oak soils, and there was also an effect of bark type on decomposition. Although white oak bark decomposed more quickly in its home environment, this could be due to either soil conditioning or inherent differences in the soils in which each species grows. Soil microbial assemblages also sorted according to bark type rather than soil type, suggesting that bark strongly influences the composition of nearby microorganisms during decomposition. Our results suggest that both bark type and soil type are important factors during bark decomposition, but our findings suggest no clear evidence for HFA.

Soil microbial composition varies in response to coffee agroecosystem management

ABSTRACT Soil microbes are essential to the continued productivity of sustainably managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability and coffee productivity have been demonstrated, but the effects of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, the soil fungal and bacterial communities, soil chemistry, and canopy composition were surveyed in a Nicaraguan coffee cooperative, across 19 individual farms. Amplicon sequencing analyses showed that management (organic or conventional), stand age and previous land use affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, these results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e. an agricultural plot's previous land use) and short-term press disturbance (i.e. farm age).

Soil microbial composition varies in response to coffee agroecosystem management

ABSTRACTSoil microbes are essential to the continued productivity of sustainably-managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability, and coffee productivity have been demonstrated, but the effect of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, we surveyed the soil fungal and bacterial communities, as well as soil chemistry and canopy composition in a Nicaraguan coffee cooperative, across 19 individual farms. Using amplicon sequencing, we found that management (organic or conventional), stand age, and previous land use strongly affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, our results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e., an agricultural plot’s previous land use) and short-term press disturbance (i.e., farm age).One-sentence-summaryThe composition of soil fungal and bacteria communities in shade coffee plantations depend on the combination of the farm’s management type, its previous land use, and the coffee plants’ stand age, but are differently influenced by each.