Soil microcosm
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BACKGROUND: Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the microorganisms. RESULTS: A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen (Armillaria mellea) and its biocontrol agent (Trichoderma atroviride) for 24 h under controlled conditions. More than 46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and neutral adaptation processes were activated in response to competitive (T. atroviride) or non-competitive (A. mellea) microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil microcosm in the presence of both A. mellea and T. atroviride. Biocontrol processes of T. atroviride were already activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem, and they were not further enhanced by the introduction of A. mellea. CONCLUSIONS: This work represents an additional step towards understanding molecular interactions between plant pathogens and biocontrol agents within a soil ecosystem. Global transcriptional analysis of the simplified soil microcosm revealed complex metabolic adaptation in the soil environment and specific responses to antagonistic or neutral intruders.
- MeSH
- anotace sekvence MeSH
- ekosystém * MeSH
- exprese genu MeSH
- interakce hostitele a patogenu genetika MeSH
- kořeny rostlin genetika mikrobiologie MeSH
- metagenom MeSH
- metagenomika metody MeSH
- půdní mikrobiologie * MeSH
- shluková analýza MeSH
- stanovení celkové genové exprese MeSH
- transkriptom * MeSH
- výpočetní biologie metody MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
In all terrestrial ecosystems, testate amoebae (TA) encounter fungi. There are strong indications that both groups engage in multiple interactions, including mycophagy and decomposition of TA shells, processes which might be fundamental in nutrient cycling in certain ecosystems. Here, we present the results of an experiment focusing on interactions between TA and saprotrophic microfungi colonizing Scots pine (Pinus sylvestris L.) litter needles. The needles were collected from a temperate pine forest and cultivated in damp chambers. Over a few weeks, melanized mycelium of Anavirga laxa Sutton started to grow out of some needles; simultaneously, the common forest-soil TA Phryganella acropodia (Hertwig and Lesser) Hopkinson reproduced and spread around the mycelium. We investigated whether a potential relationship between TA and saprotrophic microfungi exists by comparing the composition of TA communities on and around the needles and testing the spatial relationship between the A. laxa mycelium and P. acropodia shells in the experimental microcosm. Additionally, we asked whether P. acropodia utilized the A. laxa mycelium as a nutrient source and screened whether P. acropodia shells were colonized by the microfungi inhabiting the experimental microcosm. Our results indicate that saprotrophic microfungi may affect the composition of TA communities and their mycelium may affect distribution of TA individuals in pine litter. Our observations suggest that P. acropodia did not graze directly on A. laxa mycelium, but rather fed on its exudates or bacteria associated with the exudates. The fungus Pochonia bulbillosa (Gams & Malla) Zare & Gams was often found parasitising encysted shells or decomposing already dead individuals of P. acropodia. TA and pine litter microfungi engage in various direct and indirect interactions which are still poorly understood and deserve further investigation. Their elucidation will improve our knowledge on fundamental processes influencing coexistence of soil microflora and microfauna.
Sequestration of arsenic to biogenic sulfide minerals is known from As-contaminated anoxic environments. Despite numerous successful laboratory experiments, the process remains difficult to predict in moderate arsenic conditions. We performed microcosm experiments using naturally contaminated groundwater (containing ca. 6 mg/L As) and natural organic matter (NOM) particles both collected from wetland soil. Macroscopic realgar precipitates, occasionally accompanied by bonazziite, a FeS phase, elementary S, calcite, and whewellite, appeared after 4 to 18 months. Realgar only precipitated in microcosms moderately poisoned by azide or antibiotics and those in which oxidation of hydrogen sulfide to sulfur took place. The biomineralization process was not affected by the presence of additional carbon sources or the diversity, community structure, and functional composition of the microbial community. Hydrogen sulfide concentration was greater in the realgar-free microcosms, suggesting that arsenic thiolation prevented precipitation of realgar. We compared our data to available microbial community data from soils with different rates of realgar precipitation, and found that the communities from realgar-encrusted NOM particles usually showed limited sulfate reduction and the presence of fermentative metabolisms, whereas communities from realgar-free NOM particles were strongly dominated by sulfate reducers. We argue that the limited sulfate supply and intensive fermentation amplify reducing conditions, which make arsenic sulfide precipitation plausible in high-sulfate, low-arsenic groundwaters.
- MeSH
- arsenikové přípravky analýza MeSH
- biomineralizace * MeSH
- chemické látky znečišťující vodu analýza MeSH
- huminové látky analýza MeSH
- mikrobiota * MeSH
- mokřady MeSH
- oxidace-redukce MeSH
- podzemní voda chemie mikrobiologie MeSH
- půda chemie MeSH
- sírany chemie MeSH
- sulfidy analýza MeSH
- teoretické modely MeSH
- Publikační typ
- časopisecké články MeSH
Plant-soil feedback (PSF) effects are studied as plant growth responses to soil previously conditioned by another plant. These studies usually exclude effects of soil fauna, such as nematodes, soil arthropods, and earthworms, although these organisms are known to influence plant performance. Here, we aimed to explore effects of a model microarthropod community on PSFs. We performed a PSF experiment in microcosms with two plant species, Phleum pratense and Poa pratensis. We added a model microarthropod community consisting of three fungivorous springtail species (Proisotoma minuta, Folsomia candida, and Sinella curviseta) and a predatory mite (Hypoaspis aculeifer) to half of the microcosms. We measured seedling establishment and plant biomass, nematode and microbial community composition, microbial biomass, and mycorrhizal colonization of roots. Microarthropods caused changes in the composition of nematode and microbial communities. Their effect was particularly strong in Phleum plants where they altered the composition of bacterial communities. Microarthropods also generally influenced plant performance, and their effects depended on previous soil conditioning and the identity of plant species. Microarthropods did not affect soil microbial biomass and mycorrhizal colonization of roots. We conclude that the role of soil microarthropods should be considered in future PSF experiments, especially as their effects are plant species-specific.
- MeSH
- biomasa MeSH
- členovci klasifikace fyziologie MeSH
- druhová specificita MeSH
- ekosystém MeSH
- feedback psychologický fyziologie MeSH
- hlístice fyziologie MeSH
- kořeny rostlin mikrobiologie parazitologie fyziologie MeSH
- mykorhiza fyziologie MeSH
- Oligochaeta fyziologie MeSH
- Phleum mikrobiologie parazitologie fyziologie MeSH
- Poa mikrobiologie parazitologie fyziologie MeSH
- půda parazitologie MeSH
- půdní mikrobiologie * MeSH
- roztoči fyziologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: The importance of soil biota in the composition of mature plant communities is commonly acknowledged. In contrast, the role of soil biota in the early establishment of new plant communities and their relative importance for soil abiotic conditions are still poorly understood. AIMS AND METHODS: The aim of this study was to understand the effects of soil origin and soil fungal communities on the composition of a newly established dry grassland plant community. We used soil from two different origins (dry grassland and abandoned field) with different pH and nutrient and mineral content. Grassland microcosms were established by sowing seeds of 54 species of dry grassland plants into the studied soils. To suppress soil fungi, half of the pots were regularly treated with fungicide. In this way, we studied the independent and combined effects of soil origin and soil community on the establishment of dry grassland communities. KEY RESULTS: The effect of suppressing the soil fungal community on the richness and composition of the plant communities was much stronger than the effect of soil origin. Contrary to our expectations, the effects of these two factors were largely additive, indicating the same degree of importance of soil fungal communities in the establishment of species-rich plant communities in the soils from both origins. The negative effect of suppressing soil fungi on species richness, however, occurred later in the soil from the abandoned field than in the soil from the grassland. This result likely occurred because the negative effects of the suppression of fungi in the field soil were caused mainly by changes in plant community composition and increased competition. In contrast, in the grassland soil, the absence of soil fungi was limiting for plants already at the early stages of their establishment, i.e., in the phases of germination and early recruitment. While fungicide affects not only arbuscular mycorrhizal fungi but also other biota, our data indicate that changes in the AMF communities are the most likely drivers of the observed changes. The effects of other soil biota, however, cannot be fully excluded. CONCLUSIONS: These results suggest that the availability of soil fungi may not be the most important limiting factor for the establishment of grassland species in abandoned fields if we manage to reduce the intensity of competition at these sites e.g., by mowing or grazing.
- MeSH
- mikrobiální společenstva fyziologie MeSH
- mykorhiza fyziologie MeSH
- pastviny * MeSH
- půdní mikrobiologie * MeSH
- Publikační typ
- časopisecké články MeSH
The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites have a strong effect on the bacterial community structure, activity, and associated degradative ability.
- MeSH
- Bacteria klasifikace genetika izolace a purifikace metabolismus MeSH
- biodegradace MeSH
- látky znečišťující půdu metabolismus MeSH
- polychlorované bifenyly metabolismus MeSH
- půda chemie MeSH
- půdní mikrobiologie MeSH
- rostliny metabolismus mikrobiologie MeSH
- sekundární metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The objective of this study is to characterize changes in the fate, behaviour and bioavailability of four conazole fungicides - CFs (prochloraz - PRO, tebuconazole - TEB, epoxiconazole - EPO, flusilazole - FLU) in 12 diverse agricultural soils in complex microcosm systems consisting of agriculturally-used fluvisols, plants (Lactuca sativa), earthworms (Eisenia fetida) and passive samplers (SPME, Empore™ discs, silicone rubber). Due to great variability of the data and other methodological problems, the in-matrix passive samplers failed to be indicators of pore-water concentration and (bio)availability/(bio)accessibility of CFs. A dissipation of all CFs followed the first order kinetics (usually after initial lag phase) with large span of resulting half-lives (7-670 d) depending on soils and compounds. In many soils, the model revealed the ending plateau, which indicates the non-degradable or slowly-degradable residues. The half-lives and the residues were generally higher for EPO and FLU, than for PRO and TEB. Greater but slower total dissipation of CFs was observed in soils with higher percentage of organic matter. Earthworm concentrations were highest at first sampling time (14 days) and considerably decreased afterwards often resulting in PRO concentration below LOQ. Earthworm uptake was influenced by amount of organic matter and soil texture. Accumulation to lettuce roots was generally higher than to leaves and differed greatly among CFs. Concentration shoot to root ratios were generally the lowest for FLU (0.04) and highest for TEB (0.37). PRO was not detected in lettuce leaves during experiment. The study brings new results on fate and bioavailability of CFs in soils.
Bacterial genes responsible for resistance to antibiotic agents (ARG) are spread from livestock to soil through application of manure, threatening environmental and human health. We investigated the mechanisms of ARG dissemination and persistence to disentangle i) the influence of nutrients and microorganisms on the soil tetracycline (TET) resistome, and ii) the role of indigenous soil microbiota in preventing ARG spread. We analysed short-term (7 days) and persistent (84 days) effects of manure on the resistome of three antibiotic-free pasture soils. Four microcosm treatments were evaluated: control, mineral nutrient fertilization, and deposition of a layer of fresh manure onto soil or γ-irradiated soil. We quantified five TET-resistance genes, isolated 135 TET-resistant bacteria and sequenced both culturable TET-resistant and whole bacterial communities. Manure amendments, but not nutrient addition, increased the abundance of TET-r genes such as tet(Y). Such changes persisted with time, in contrast with the TET-resistant bacterial composition, which partially recovered after manure amendments. Manured γ-irradiated soils showed significantly lower nutrient content and higher TET-r gene abundance than non-irradiated soils, suggesting that native soil bacteria are essential for the fertilization effect of manure on soil as well as control the dissemination of potentially risky TET-r genes.
- MeSH
- antibakteriální látky farmakologie MeSH
- Bacteria účinky léků genetika MeSH
- bakteriální geny genetika MeSH
- hnůj mikrobiologie MeSH
- půdní mikrobiologie * MeSH
- rezistence na tetracyklin genetika MeSH
- skot MeSH
- tetracyklin farmakologie MeSH
- zvířata MeSH
- Check Tag
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Functional diversity covers diverse functional traits of microorganisms in an ecosystem. Thus, we hypothesized that it could play an important role in the isolation of nitrogen-fixing and phosphate-solubilizing bacteria. These bacteria have been considered as biofertilizer for sustainable agriculture development. Soils were collected from different sites of agricultural field and performed several microbiological tests in which we observed considerable differences in heterotrophic microbial abundance and microbial activities among the microcosms. Functional diversity depends on both microbial richness and evenness. Based on the results of metabolic fingerprinting of the carbon sources of BiOLOG-ECO plates, richness and evenness was measured by determining Shannon diversity index and Gini coefficient, respectively. The results showed significant differences in both microbial richness and evenness, suggesting considerable variation of functional diversity among the microcosms. Thereafter, nitrogen-fixing and phosphate-solubilizing bacteria were isolated on Burk's and Pikovskaya media, respectively. The results revealed considerable variation of both types of bacterial abundance among the microcosms. Microcosm (T2) showing the highest functional diversity houses the maximum numbers of nitrogen-fixing and phosphate-solubilizing bacteria. Similarly, the microcosm (T5) exhibiting the lowest functional diversity houses the minimum numbers of nitrogen-fixing and phosphate-solubilizing bacteria. Thus, a strong positive correlation was observed between functional diversity and both types of bacterial abundance among the soil samples. Higher richness and evenness lead to the development of increased functional diversity that facilitates to accommodate substantial numbers of nitrogen-fixing and phosphate-solubilizing bacteria in soil. Taken together, the results demonstrated that functional diversity plays an important role in the isolation of nitrogen-fixing and phosphate-solubilizing bacteria from soil.
Fertilizing soils with animal excrements from farms with common antibiotic use represents a risk of disseminating antibiotic resistance genes into the environment. In the case of tetracycline antibiotics, it is not clear, however, whether the presence of antibiotic residues further enhances the gene occurrence in manured soils. We established a microcosm experiment in which 3 farm soils that had no recent history of fertilization with animal excrements were amended on a weekly basis (9 times) with excrements from either an oxytetracycline-treated or an untreated cow. Throughout the study, the concentration of oxytetracycline in excrements from the treated cow was above 500 μg g(-1)dw, whereas no oxytetracycline was detected in excrements from the healthy cow. Both excrements contained tetracycline resistance (TC-r) genes tet(L), tet(M), tet(V), tet(Z), tet(Q) and tet(W). The excrements from the treated cow also contained the tet(B) gene, and a higher abundance of tet(Z), tet(Q) and tet(W). Three weeks after the last excrement addition, the individual TC-r genes differed in their persistence in soil: tet(Q) and tet(B) were not detectable while tet(L), tet(M), tet(Z) and tet(W) were found in all 3 soils. There were, however, no significant differences in the total number, nor in the abundance, of TC-r genes between soil samples amended with each excrement type. The oxytetracycline-rich and the oxytetracycline-free excrement therefore contributed equally to the increase of tetracycline resistome in soil. Our results indicate that other mechanisms than OTC-selection pressure may be involved in the maintenance of TC-r genes in manured soils.
- MeSH
- antibakteriální látky analýza MeSH
- bakteriální geny MeSH
- hnůj analýza mikrobiologie MeSH
- látky znečišťující půdu analýza MeSH
- oxytetracyklin analýza MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- rezistence na tetracyklin genetika MeSH
- skot MeSH
- zemědělství MeSH
- zvířata MeSH
- Check Tag
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
