There is increasing evidence that the soil microbial community produces a suite of volatile organic compounds that suppress plant pathogens. However, it remains unknown which soil properties and ...management practices influence volatile-mediated pathogen suppression. The aim of this study was to relate soil properties to growth suppression of three plant pathogens by soil volatiles. We measured the effect of volatiles emitted from a broad range of agricultural soils on the in vitro growth of the plant pathogenic fungi Rhizoctonia solani and Fusarium oxysporum, and the oomycete Pythium intermedium. Growth suppression of pathogens by soil volatiles could be linked to various soil properties, and some aspects of microbial community composition and field history, using multiple linear regression. Volatile-mediated suppression of mycelial development occurred for each pathogen type, but the magnitude of inhibition differed among soils as well as pathogens. On average R. solani and P. ultimum appeared more sensitive to volatile suppression than F. oxysporum. Suppression of R. solani by volatiles was positively correlated with organic matter content, microbial biomass and proportion of litter saprotrophs in the microbial community, but negatively correlated with pH, microbial diversity (Shannon), and the proportion of Acidobacteria in the community. R. solani, F. oxysporum, and P. intermedium suppression by volatiles was affected by various management practices occurring in the soil's field history, such as reduced tillage, the presence of certain crops in the crop rotation, and the application of solid manure. P. intermedium suppression was also negatively correlated with soil sulphur content. This study identifies pathogen-specific drivers of growth-suppressive volatiles, a critical step in integrating soil volatiles into prediction and management of soil-borne plant diseases.
•Volatiles from 50 soils suppressed growth of three pathogens in 91% of pairings.•Rhizoctonia solani suppression was most related to soil organic matter content.•Fusarium oxysporum and Pythium intermedium suppression was driven by field management.•Microbial community attributes only explained a small proportion of suppression.•Results suggest natural suppression by volatiles can be promoted via management.
The contribution of low‐abundance microbial species to soil ecosystems is easily overlooked because there is considerable overlap between metabolic abilities (functional redundancy) of dominant and ...subordinate microbial species. Here we studied how loss of less abundant soil bacteria affected the production of antifungal volatiles, an important factor in the natural control of soil‐borne pathogenic fungi. We provide novel empirical evidence that the loss of soil bacterial species leads to a decline in the production of volatiles that suppress root pathogens. By using dilution‐to‐extinction for seven different soils we created bacterial communities with a decreasing number of species and grew them under carbon‐limited conditions. Communities with high bacterial species richness produced volatiles that strongly reduced the hyphal growth of the pathogen Fusarium oxysporum. For most soil origins loss of bacterial species resulted in loss of antifungal volatile production. Analysis of the volatiles revealed that several known antifungal compounds were only produced in the more diverse bacterial communities. Our results suggest that less abundant bacterial species play an important role in antifungal volatile production by soil bacterial communities and, consequently, in the natural suppression of soil‐borne pathogens.
•An inventory of the pool of plant pathogenic fungi in 42 agricultural soils is made.•The reservoir of plant pathogenic propagules in soil is driven by the biotic and abiotic environment.•The pools ...of root- and shoot-infecting pathogens are influenced by different environmental factors.•Pathogen traits like dispersal may determine differences in occurrence.
Soil-borne pathogens cause great crop losses in agriculture. Because of their resilience in the soil, these pathogens persist in a population reservoir, causing future outbreaks of crop diseases. Management focus is usually on the most common pathogens occurring, but it is likely that a mixed population of pathogens together affect crops. Next generation sequencing of DNA from environmental samples can provide information on the presence of potential pathogens. The aim of this study was to obtain insight into the factors that drive the composition of potential plant pathogen populations in agricultural soils. To this end, the alpha and beta diversity of fungal OTUs that were assigned as potential plant pathogens for 42 agricultural soils were assessed. The presented study is the first inventory of the pool of pathogens and its correlating factors. The results of this inventory indicate that the composition of pathogens in soil is driven by pH, soil type, crop history, litter saprotrophic fungi and spatial patterns. The major driving factors differed between potential root- and shoot-infecting fungi, suggesting interactions among environmental factors and pathogen traits like reproduction, survival and dispersal. This information is important to understand risks for disease outbreaks and to recommend management strategies to prevent such outbreaks.
Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible ...hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates.
There is increasing evidence showing that microbes can influence plant-insect interactions. In addition, various studies have shown that aboveground pathogens can alter the interactions between ...plants and insects. However, little is known about the role of soil-borne pathogens in plant-insect interactions. It is also not known how environmental conditions, that steer the performance of soil-borne pathogens, might influence these microbe-plant-insect interactions. Here, we studied effects of the soil-borne pathogen Rhizoctonia solani on aphids (Sitobion avenae) using wheat (Triticum aestivum) as a host. In a greenhouse experiment, we tested how different levels of soil organic matter (SOM) and fertilizer addition influence the interactions between plants and aphids. To examine the influence of the existing soil microbiome on the pathogen effects, we used both unsterilized field soil and sterilized field soil. In unsterilized soil with low SOM content, R. solani addition had a negative effect on aphid biomass, whereas it enhanced aphid biomass in soil with high SOM content. In sterilized soil, however, aphid biomass was enhanced by R. solani addition and by high SOM content. Plant biomass was enhanced by fertilizer addition, but only when SOM content was low, or in the absence of R. solani. We conclude that belowground pathogens influence aphid performance and that the effect of soil pathogens on aphids can be more positive in the absence of a soil microbiome. This implies that experiments studying the effect of pathogens under sterile conditions might not represent realistic interactions. Moreover, pathogen-plant-aphid interactions can be more positive for aphids under high SOM conditions. We recommend that soil conditions should be taken into account in the study of microbe-plant-insect interactions.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In three dairy grasslands on peat, minerals were added to manipulate the soil Ca:Mg ratio with or without effect on pH. The responses of soil properties and grass N yield were measured. CaCO
3
...application led to higher soil Ca:Mg ratio and pH
KCl
compared to the untreated control, decreased N
total
and C
total
, and increased P availability. Grass N yield increased in the first year by only 6% of the reduction in soil N
total
, but not in the second year. A higher pH increased SOM decomposition, especially in soils with high P availability. MgCO
3
reduced the Ca:Mg ratio, had little influence on soil parameters and no effect on grass N yield. In contrast, CaSO
4
and MgSO
4
did not influence pH
KCl
but reduced grass N yield in most cases. Results suggest stabilisation of organic matter by Ca binding in treatments with added Ca. We conclude that grass N yield was not linked with changes in Ca:Mg ratio but with soil pH. The pH effects on SOM decomposition depended on P availability and Ca binding. Hence, to avoid potentially large soil losses of C and N, the current agricultural advice on pH management in peat grasslands should be better adapted to local edaphic characteristics.
There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of ...suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the suggested importance of microbial VOCs in the natural buffer of soils against diseases caused by soil-borne pathogens.
The intestinal helminth parasite,
Heligmosomoides polygyrus bakeri offers a tractable experimental model for human hookworm infections such as
Ancylostoma duodenale and veterinary parasites such as
...Haemonchus contortus. Parasite excretory–secretory (ES) products represent the major focus for immunological and biochemical analyses, and contain immunomodulatory molecules responsible for nematode immune evasion. In a proteomic analysis of adult
H. polygyrus secretions (termed HES) matched to an extensive transcriptomic dataset, we identified 374 HES proteins by LC–MS/MS, which were distinct from those in somatic extract HEx, comprising 446 identified proteins, confirming selective export of ES proteins. The predominant secreted protein families were proteases (astacins and other metalloproteases, aspartic, cysteine and serine-type proteases), lysozymes, apyrases and acetylcholinesterases. The most abundant products were members of the highly divergent venom allergen-like (VAL) family, related to
Ancylostoma secreted protein (ASP); 25 homologues were identified, with VAL-1 and -2 also shown to be associated with the parasite surface. The dominance of VAL proteins is similar to profiles reported for
Ancylostoma and
Haemonchus ES products. Overall, this study shows that the secretions of
H. polygyrus closely parallel those of clinically important GI nematodes, confirming the value of this parasite as a model of helminth infection.
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► We identify 374 proteins secreted by adult worms of the model nematode parasite Heligmosomoides polygyrus. ► Multiple proteases, lysozymes, apyrases and acetylcholinesterase were identified. ► The dominant gene family in the secretome are members of the venom allergen-like (VAL) family of no known function. ► The secretion of VAL proteins and enzymes is also found in secretomes of major human and veterinary nematodes. ► Up to 90 novel gene products were found to be secreted, all bearing signal peptides, by the adult parasites.
Organic farming is increasingly promoted as a means to reduce the environmental impact of artificial fertilizers, pesticides, herbicides, and antibiotics in conventional dairy systems. These factors ...potentially affect the microbial communities of the production stages (soil, silage, dung, and milk) of the entire farm cycle. However, understanding whether the microbiota representative of different production stages reflects different agricultural practices – such as conventional versus organic farming – is unknown. Furthermore, the translocation of the microbial community across production stages is scarcely studied. We sequenced the microbial communities of soil, silage, dung, and milk samples from organic and conventional dairy farms in the Netherlands. We found that community structure of soil fungi and bacteria significantly differed among soil types, but not between organic versus conventional farming systems. The microbial communities of silage also did not differ among conventional and organic systems. Nevertheless, the dung microbiota of cows and the fungal communities in the milk were significantly structured by agricultural practice. We conclude that, while the production stages of dairy farms seem to be disconnected in terms of microbial transfer, certain practices specific for each agricultural system, such as the content of diet and the use of antibiotics, are potential drivers of shifts in the cow’s microbiota, including the milk produced. This may reflect differences in farm animal health and quality of dairy products depending on farming practices.
There is a global pattern of a decline in insect abundance and diversity. The presence of residues of pesticides in animal feed and fly treatments results in polluted animal dung, which may hamper ...the survival of insects feeding and breeding in and on dung. To study the route from pesticide contamination in the feed and the dung to insect survival in dung pats, two experiments were performed. In Experiment 1, the feed and dung of dairy cows were collected on eight Dutch dairy farms (six conventional, two organic). All the feeds in the ration as well as the dung were analysed for the presence of pesticides. In Experiment 2, dung was collected from a herd of dairy cows and was spiked with four concentrations of deltamethrin. In both experiments, a field experiment was implemented with artificial dung pats of 2 kg of fresh dung. The dung pats were retrieved after 7 and 14 days (Experiment 1), or 7, 14, 21, and 35 days (Experiment 2), and invertebrates in the dung were counted. A total of 70 pesticides were detected in the different types of feed of the eight farms. The concentration of pesticides in the dung was on average 423 µg kg−1 DM (range of 112–1980 µg kg−1 DM). In Experiment 1, the number of Coleoptera present in dung was negatively correlated with the pesticide concentration, and more Coleoptera were present in the dung of organic farms (23.7 on organic farms vs. 11.4 Coleoptera on conventional farms, per 500 g freshly deposited dung). In Experiment 2, the dung which was not spiked with deltamethrin contained more than twice as many Coleoptera larvae and adults (5.6 Coleoptera per 500 g freshly deposited dung on treatment without deltamethrin vs. 2.2 with highest concentration of deltamethrin). We conclude that pesticides are widely present in feed for dairy cows and that a number of these pesticides are transferred to dung. The pesticides have a negative effect on the number of Coleoptera and as a consequence may also affect ecosystem services such as the disappearance of dung pats and the presence of insects in dung pats as feed for farm birds or bats.
•Pesticides are widely present in feeds for dairy cows.•Up to 50 different pesticides are present in the ration.•A number of the pesticides in feeds are transferred to dung.•Pesticides in dung have a negative effect on the number of Coleoptera.
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