RESUMO
Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.
Assuntos
Micobioma , Árvores , Árvores/microbiologia , Fungos , Folhas de Planta/microbiologiaRESUMO
Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and 15N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N2 fixation. The latter were governed by the genus Sphingomonas, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and 15N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.
Assuntos
Microbiota , Picea , Bactérias , Florestas , Fungos , Picea/microbiologia , Madeira/microbiologiaRESUMO
Even though it is widely acknowledged that litter decomposition can be impacted by climate change, the functional roles of microbes involved in the decomposition and their answer to climate change are less understood. This study used a field experimental facility settled in Central Germany to analyze the effects of ambient vs. future climate that is expected in 50-80 years on mass loss and physicochemical parameters of wheat litter in agricultural cropland at the early phase of litter decomposition process. Additionally, the effects of climate change were assessed on microbial richness, community compositions, interactions, and their functions (production of extracellular enzymes), as well as litter physicochemical factors shaping their colonization. The initial physicochemical properties of wheat litter did not change between both climate conditions; however, future climate significantly accelerated litter mass loss as compared with ambient one. Using MiSeq Illumina sequencing, we found that future climate significantly increased fungal richness and altered fungal communities over time, while bacterial communities were more resistant in wheat residues. Changes on fungal richness and/or community composition corresponded to different physicochemical factors of litter under ambient (Ca2+, and pH) and future (C/N, N, P, K+, Ca2+, pH, and moisture) climate conditions. Moreover, highly correlative interactions between richness of bacteria and fungi were detected under future climate. Furthermore, the co-occurrence networks patterns among dominant microorganisms inhabiting wheat residues were strongly distinct between future and ambient climates. Activities of microbial ß-glucosidase and N-acetylglucosaminidase in wheat litter were increased over time. Such increased enzymatic activities were coupled with a significant positive correlation between microbial (both bacteria and fungi) richness and community compositions with these two enzymatic activities only under future climate. Overall, we provide evidence that future climate significantly impacted the early phase of wheat litter decomposition through direct effects on fungal communities and through indirect effects on microbial interactions as well as corresponding enzyme production.
Assuntos
Microbiota , Triticum , Bactérias/genética , Ecossistema , Fungos/genética , Folhas de Planta/microbiologiaRESUMO
Decomposition by microorganisms of plastics in soils is almost unexplored despite the fact that the majority of plastics released into the environment end up in soils. Here, we investigate the decomposition process and microbiome of one of the most promising biobased and biodegradable plastics, poly(butylene succinate-co-adipate) (PBSA), under field soil conditions under both ambient and future predicted climates (for the time between 2070 and 2100). We show that the gravimetric and molar mass of PBSA is already largely reduced (28-33%) after 328 days under both climates. We provide novel information on the PBSA microbiome encompassing the three domains of life: Archaea, Bacteria, and Eukarya (fungi). We show that PBSA begins to decompose after the increase in relative abundances of aquatic fungi (Tetracladium spp.) and nitrogen-fixing bacteria. The PBSA microbiome is distinct from that of surrounding soils, suggesting that PBSA serves as a new ecological habitat. We conclude that the microbial decomposition process of PBSA in soil is more complex than previously thought by involving interkingdom relationships, especially between bacteria and fungi.
Assuntos
Ascomicetos , Plásticos Biodegradáveis , Microbiota , Biodegradação Ambiental , Solo , Microbiologia do SoloRESUMO
Expanding the use of environmentally friendly materials to protect the environment is one of the key factors in maintaining a sustainable ecological balance. Poly(butylene succinate-co-adipate) (PBSA) is considered among the most promising bio-based and biodegradable plastics for the future with a high number of applications in soil and agriculture. Therefore, the decomposition process of PBSA and its consequences for the carbon stored in soil require careful monitoring. For the first time, the stable isotope technique was applied in the current study to partitioning plastic- and soil-originated C in the CO2 released during 80 days of PBSA decomposition in a Haplic Chernozem soil as dependent on nitrogen availability. The decomposition of the plastic was accompanied by the C loss from soil organic matter (SOM) through priming, which in turn was dependent on added N. Nitrogen facilitated PBSA decomposition and reduced the priming effect during the first 6 weeks of the experiment. During the 80 days of plastic decomposition, 30% and 49% of the released CO2 were PBSA-derived, while the amount of SOM-derived CO2 exceeded the corresponding controls by 100.2 and 132.3% in PBSA-amended soil without and with N fertilization, respectively. Finally, only 4.1% and 5.4% of the PBSA added into the soil was mineralized to CO2, in the treatments without and with N amendment, respectively.
RESUMO
Although microbial decomposition of plant litter plays a crucial role in nutrient cycling and soil fertility, we know less about likely links of specific microbial traits and decomposition, especially in relation to climate change. We study here wheat straw decomposition under ambient and manipulated conditions simulating a future climate scenario (next 80 years) in agroecosystems, including decay rates, macronutrient dynamics, enzyme activity, and microbial communities. We show that future climate will accelerate straw decay rates only during the early phase of the decomposition process. Additionally, the projected climate change will increase the relative abundance of saprotrophic fungi in decomposing wheat straw. Moreover, the impact of future climate on microbial community assembly and molecular ecological networks of both bacteria and fungi will strongly depend on the decomposition phase. During the early phase of straw decomposition, stochastic processes dominated microbial assembly under ambient climate conditions, whereas deterministic processes highly dominated bacterial and fungal communities under simulated future climate conditions. In the later decomposition phase, similar assembly processes shaped the microbial communities under both climate scenarios. Furthermore, over the early phases of decomposition, simulated future climate enhanced the complexity of microbial interaction networks. We concluded that the impact of future climate on straw decay rate and associated microbial traits like assembly processes and inter-community interactions is restricted to the early phase of decomposition.
Assuntos
Microbiota , Triticum , Bactérias/genética , Solo , Fungos/genética , Microbiologia do Solo , EcossistemaRESUMO
Poly(butylene succinate-co-adipate) (PBSA) degradation and its plastisphere microbiome in cropland soils have been studied; however, such knowledge is limited in the case of forest ecosystems. In this context, we investigated: i) the impact of forest types (conifer and broadleaved forests) on the plastisphere microbiome and its community assembly, ii) their link to PBSA degradation, and iii) the identities of potential microbial keystone taxa. We determined that forest type significantly affected microbial richness (F = 5.26-9.88, P = 0.034 to 0.006) and fungal community composition (R2 = 0.38, P = 0.001) of the plastisphere microbiome, whereas its effects on microbial abundance and bacterial community composition were not significant. The bacterial community was governed by stochastic processes (mainly homogenizing dispersal), whereas the fungal community was driven by both stochastic and deterministic processes (drift and homogeneous selection). The highest molar mass loss was found for PBSA degraded under Pinus sylvestris (26.6 ± 2.6 to 33.9 ± 1.8 % (mean ± SE) at 200 and 400 days, respectively), and the lowest molar mass loss was found under Picea abies (12.0 ± 1.6 to 16.0 ± 0.5 % (mean ± SE) at 200 and 400 days, respectively). Important fungal PBSA decomposers (Tetracladium) and atmospheric dinitrogen (N2)-fixing bacteria (symbiotic: Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Methylobacterium and non-symbiotic: Mycobacterium) were identified as potential keystone taxa. The present study is among the first to determine the plastisphere microbiome and its community assembly processes associated with PBSA in forest ecosystems. We detected consistent biological patterns in the forest and cropland ecosystems, indicating a potential mechanistic interaction between N2-fixing bacteria and Tetracladium during PBSA biodegradation.
Assuntos
Plásticos Biodegradáveis , Microbiota , Árvores , Solo , Florestas , Bactérias/metabolismo , Adipatos/metabolismo , Succinatos/metabolismo , Microbiologia do SoloRESUMO
Background: Tree mycorrhizal types (arbuscular mycorrhizal fungi and ectomycorrhizal fungi) alter nutrient use traits and leaf physicochemical properties and, thus, affect leaf litter decomposition. However, little is known about how different tree mycorrhizal species affect the microbial diversity, community composition, function, and community assembly processes that govern leaf litter-dwelling microbes during leaf litter decomposition. Methods: In this study, we investigated the microbial diversity, community dynamics, and community assembly processes of nine temperate tree species using high-resolution molecular technique (Illumina sequencing), including broadleaved arbuscular mycorrhizal, broadleaved ectomycorrhizal, and coniferous ectomycorrhizal tree types, during leaf litter decomposition. Results and discussion: The leaves and needles of different tree mycorrhizal types significantly affected the microbial richness and community composition during leaf litter decomposition. Leaf litter mass loss was related to higher sequence reads of a few bacterial functional groups, particularly N-fixing bacteria. Furthermore, a link between bacterial and fungal community composition and hydrolytic and/or oxidative enzyme activity was found. The microbial communities in the leaf litter of different tree mycorrhizal types were governed by different proportions of determinism and stochasticity, which changed throughout litter decomposition. Specifically, determinism (mainly variable selection) controlling bacterial community composition increased over time. In contrast, stochasticity (mainly ecological drift) increasingly governed fungal community composition. Finally, the co-occurrence network analysis showed greater competition between bacteria and fungi in the early stages of litter decomposition and revealed a contrasting pattern between mycorrhizal types. Conclusion: Overall, we conclude that tree mycorrhizal types influence leaf litter quality, which affects microbial richness and community composition, and thus, leaf litter decomposition.
RESUMO
Biobased and biodegradable plastics have been intensively used in agriculture as mulching films. They provide a distinctive habitat for soil microbes, yet much less is known about the community assembly and interactions of plastisphere microbiota in soils under future climate change. For the first time, we explored the relative importance of ecological processes and the co-occurrence networks of plastic-associated microbes under ambient and future climates. The drift primarily dominated the community assembly of bacteria and fungi after 180D and 328D incubation in both climate regimes. The neutral community model prediction indicated that the migration rate of the plastisphere community in the later decay phase was lower than that in the early decay phase, contributing to the generation of the specific niches. Furthermore, future climate promoted the complexity and modularity of plastic-associated microbial networks: more competition and cooperation were observed in bacteria (or inter-kingdom) and fungi under future climate conditions, respectively. Overall, our findings strengthened the understanding of ecological processes and interplay of plastisphere microbiota during plastic biodegradation in soils under ambient and future climate regimes.
Assuntos
Mudança Climática , Microbiota , Bactérias , Fungos , Consórcios Microbianos , Plásticos , Solo , Microbiologia do SoloRESUMO
Bio-based and biodegradable plastic mulching films have been proposed to replace the non-biodegradable plastic mulch films to solve plastic pollution problems in agricultural soils. However, the impact of bio-based and biodegradable plastics on plant and human health remains largely unexplored. Here, we aimed to assess the risk under field conditions of a bio-based and biodegradable poly(butylene succinate-co-adipate; PBSA), a widely used mulching film as carrier of potential pathogenic microorganisms (bacteria and fungi) at ambient and future climate conditions. Overall, we affiliated 64 fungal and 11 bacterial operational taxonomic units (OTUs) as pathogens by using Next-Generation Sequencing approach. Our results revealed that PBSA hosted at least 53 plant pathogens, of which 51 were classified as fungi, while the other two were bacteria. Most fungal plant pathogens were able to withstand the anticipated future climate changes. We detected 13 fungal and eight bacterial OTUs, which were classified as opportunistic human pathogens. Only one bacterial OTU (Enterococcus faecium) was assigned to a human pathogen. While future climate conditions only significantly impacted on the presence and frequency of detection of few pathogens, incubation time was found to significantly impacted on nine pathogens. This result demonstrates the temporal dynamics of pathogens associated with PBSA. The threats to plant and human health were discussed. We emphasize that the risks to human health are relatively low because we mainly found opportunistic pathogens associated with PBSA and the amount are comparable to the plant debris. However, the risks to plant health may be considered as moderate because many plant pathogens were discovered and/or enriched in PBSA. Furthermore, in soil environments, the pathogenic risk of plastic is highly depending on the surrounding soil pathobiome where plastic is being decomposed.
RESUMO
The incomplete degradation of bio-based and biodegradable plastics (BBPs) in soils causes multiple threats to soil quality, human health, and food security. Plastic residuals can interact with soil microbial communities. We aimed to link the structure and enzyme-mediated functional traits of a microbial community composition that were present during poly (butylene succinate-co-butylene adipate (PBSA) decomposition in soil with (PSN) and without (PS) the addition of nitrogen fertilizer ((NH4)2SO4). We identified bacterial (Achromobacter, Luteimonas, Rhodanobacter, and Lysobacter) and fungal (Fusarium, Chaetomium, Clonostachys, Fusicolla, and Acremonium) taxa that were linked to the activities of ß-glucosidase, chitinase, phosphatase, and lipase in plastic-amended soils. Fungal biomass increased by 1.7 and 4 times in PS and PSN treatment, respectively, as compared to non-plastic amended soil. PBSA significantly changed the relationships between soil properties (C: N ratio, TN, and pH) and microbial community structure; however, the relationships between fungal biomass and soil enzyme activities remained constant. PBSA significantly altered the relationship between fungal biomass and acid phosphatase. We demonstrated that although the soil functions related to nutrient cycling were not negatively affected in PSN treatment, potential negative effects are reasoned by the enrichment of plant pathogens. We concluded that in comparison to fungi, the bacteria demonstrated a broader functional spectrum in the BBP degradation process.
RESUMO
Despite the abundance of observations of foliar pathogens, our knowledge is severely lacking regarding how the potential fungal pathobiome is structured and which processes determine community assembly. In this study, we addressed these questions by analysing the potential fungal pathobiome associated with the senescing leaves and needles of 12 temperate tree species. We compared fungal plant pathogen load in the senescing leaves/needles and demonstrated that healthy-looking leaves/needles are inhabited by diverse and distinct fungal plant pathogens. We detected 400 fungal plant pathogenic ASVs belonging to 130 genera. The fungal plant pathogenic generalist, Mycosphaerella, was found to be the potential most significant contributor to foliar disease in seedlings. The analyses of assembly process and co-occurrence network showed that the fungal plant pathogenic communities in different tree types are mainly determined by stochastic processes. However, the homogenising dispersal highly contributes in broadleaf trees, whereas ecological drift plays an important role in coniferious trees. The deterministic assembly processes (dominated by variable selection) contributed more in broadleaf trees as compared to coniferous trees. We found that pH and P level significantly corresponded with fungal plant pathogenic community compositions in both tree types. Our study provides the first insight and mechanistic understanding into the community assembly, networks, and complete taxonomy of the foliar fungal pathobiome in senescing leaves and needles.
RESUMO
Currently, lichen surveys are generally based on the examination of fruiting bodies. Lichens in the mycelial stage, in spores, or awaiting conditions for fruiting body formation are usually overlooked, even though they are important for maintaining biodiversity and ecosystem functions. This study aimed to explore the lichenized fungal community composition and richness associated with leaves and needles of 12 temperate tree species using Illumina MiSeq-based amplicon sequencing of the internal transcribed spacer (ITS) 2 region. Picea abies harbored the highest richness and number of lichenized fungal species. We found that the lichenized fungus Physcia adscendens dominated the leaves and needles of the most temperate tree species. Eleven lichenized fungal species detected in this study were recorded for the first time on leaves and needles. In addition, we identified Athallia cerinella, Fellhanera bouteillei, and Melanohalea exasperata that are on the German national red lists. Lichenized fungal richness was higher in conifer compared to broadleaf trees. Overall, tree species (within coniferous trees) and tree types (broadleaved vs. coniferous trees) harbored significantly different lichenized fungal community compositions pointing out the importance of host species. Diversity and community composition patterns of lichenized fungi were correlated mainly with tree species. Our study demonstrates that the diversity of foliicolous lichens associated with leaves and needles of 12 temperate tree species can be appropriately analyzed and functionally assigned using the ITS-based high-throughput sequencing. We highlighted the importance of conifers for maintaining the biodiversity of foliicolous lichens. Based on the discovery of many red list lichens, our methodological approach and results are important contributions to subsequent actions in the bio-conversation approaches.
RESUMO
We discovered a biological mechanism supporting microbial degradation of bio-based poly(butylene succinate-co-adipate) (PBSA) plastic in soils under ambient and future climates. Here, we show that nitrogen-fixing bacteria facilitate the microbial degradation of PBSA by enhancing fungal abundance, accelerating plastic-degrading enzyme activities, and shaping/interacting with plastic-degrading fungal communities.
Assuntos
Plásticos Biodegradáveis , Bactérias Fixadoras de Nitrogênio , Plásticos Biodegradáveis/metabolismo , Biodegradação Ambiental , Fungos/metabolismo , Bactérias Fixadoras de Nitrogênio/metabolismo , SoloRESUMO
INTRODUCTION: Specific microbial communities are associated to host plants, influencing their phenotype and fitness.Despite the rising interest in plant microbiome, the role of microbial communities associated with perennial fruit plants remains overlooked. OBJECTIVES: This work provides the first comprehensive descriptionof the taxonomical and functional bacterial and fungal microbiota of below- and above-ground organsof three commercially important strawberry genotypes under cultural conditions. METHODS: Strawberry-associatedfungal and bacterial microbiomes were characterised by Next-Generation Sequencing and the potential functions expressed by the bacterial microbiome were analysed by both in silico and in vitro characterisation of plant growth-promoting abilities of native bacteria. Additionally, the association between the strawberry microbiome, plant disease tolerance, plant mineral nutrient content, and fruit quality was investigated. RESULTS: Results showed that thestrawberry core microbiome included 24 bacteria and 15 fungal operational taxonomicunits (OTUs).However, plant organ and genotype had a significant role in determining the taxonomical and functional composition of microbial communities. Interestingly, the cultivar with the highesttolerance against powdery mildew and leaf spot and the highest fruit productivity was the only one able to ubiquitously recruit the beneficial bacterium, Pseudomonasfluorescens, and to establish a mutualistic symbiosis with the arbuscular mycorrhizaRhizophagus irregularis. CONCLUSION: This work sheds light on the interaction of cultivated strawberry genotypes with a variety of microbes and highlights the importance of their applications to increase the sustainability of fruit crop production.
Assuntos
Fragaria , Microbiota , Fragaria/microbiologia , Bactérias/genética , Genótipo , SimbioseRESUMO
Drought events weaken trees and make them vulnerable to attacks by diverse plant pathogens. Here, we propose a molecular method for fast screening of microorganisms associated with European beech decline after an extreme drought period (2018) in a forest of Thuringia, Germany. We used Illumina sequencing with a recent bioinformatics approach based on DADA2 to identify archaeal, bacterial, and fungal ASVs (amplicon sequence variants) based on bacterial and archaeal 16S and fungal ITS genes. We show that symptomatic beech trees are associated with both bacterial and fungal plant pathogens. Although the plant pathogen sequences were detected in both discolored and non-discolored wood areas, they were highly enriched in the discolored wood areas. We show that almost each individual tree was associated with a different combination of pathogens. Cytospora spp. and Neonectria coccinea were among the most frequently detected fungal pathogens, whereas Erwinia spp. and Pseudomonas spp. were the dominant bacterial plant pathogens. We demonstrate that bacterial plant pathogens may be of major importance in beech decline.
RESUMO
Little is known about microbial communities of aquatic plants despite their crucial ecosystem function in aquatic ecosystems. Here, we analyzed the microbiota of an aquatic rheophyte, Hanseniella heterophylla, growing at three areas differing in their degree of anthropogenic disturbance in Thailand employing a metabarcoding approach. Our results show that diverse taxonomic and functional groups of microbes colonize H. heterophylla. Proteobacteria, Actinobacteria, Dothideomycetes, and Sordariomycetes form the backbone of the microbiota. Surprisingly, the beneficial microbes reported from plant microbiomes in terrestrial habitats, such as N-fixing bacteria and ectomycorrhizal fungi, were also frequently detected. We showed that biofilms for attachment of H. heterophylla plants to rocks may associate with diverse cyanobacteria (distributed in eight families, including Chroococcidiopsaceae, Coleofasciculaceae, Leptolyngbyaceae, Microcystaceae, Nostocaceae, Phormidiaceae, Synechococcaceae, and Xenococcaceae) and other rock biofilm-forming bacteria (mainly Acinetobacter, Pseudomonas, and Flavobacterium). We found distinct community compositions of both bacteria and fungi at high and low anthropogenic disturbance levels regardless of the study areas. In the highly disturbed area, we found strong enrichment of Gammaproteobacteria and Tremellomycetes coupled with significant decline of total bacterial OTU richness. Bacteria involved with sulfamethoxazole (antibiotic) degradation and human pathogenic fungi (Candida, Cryptococcus, Trichosporon, and Rhodotorula) were exclusively detected as indicator microorganisms in H. heterophylla microbiota growing in a highly disturbed area, which can pose a major threat to human health. We conclude that aquatic plant microbiota are sensitive to anthropogenic disturbance. Our results also unravel the potential use of this plant as biological indicators in remediation or treatment of such disturbed ecosystems.
RESUMO
The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50-70 years in comparison with the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonizing each plant compartment were predicted using FUNGuild, FAPROTAX, and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonized by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilization (nitrogen fixation, phosphorus solubilization, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion but also to ecosystem sustainability.
Assuntos
Aclimatação/genética , Bactérias/genética , Mudança Climática , Fungos/genética , Trifolium/crescimento & desenvolvimento , Trifolium/microbiologia , Bactérias/classificação , Fungos/classificação , Alemanha , Ácidos Indolacéticos/metabolismo , Microbiota/genética , Micobioma/genética , Fixação de Nitrogênio/fisiologia , Fósforo/metabolismo , Raízes de Plantas/microbiologia , Rizosfera , Sideróforos/biossíntese , Microbiologia do SoloRESUMO
The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (ß-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.
RESUMO
Returning wheat residues to the soil is a common practice in modern agricultural systems and is considered to be a sustainable practice. However, the negative contribution of these residues in the form of "residue-borne pathogens" is recognized. Here, we aimed to investigate the structure and ecological functions of fungal communities colonizing wheat residues during the early phase of decomposition in a conventional farming system. The experiment was conducted under both ambient conditions and a future climate scenario expected in 50-70 years from now. Using MiSeq Illumina sequencing of the fungal internal transcribed spacer 2 (ITS2), we found that plant pathogenic fungi dominated (~87% of the total sequences) within the wheat residue mycobiome. Destructive wheat fungal pathogens such as Fusarium graminearum, Fusarium tricinctum, and Zymoseptoria tritci were detected under ambient and future climates. Moreover, future climate enhanced the appearance of new plant pathogenic fungi in the plant residues. Our results based on the bromodeoxyuridine (BrdU) immunocapture technique demonstrated that almost all detected pathogens are active at the early stage of decomposition under both climate scenarios. In addition, future climate significantly changed both the richness patterns and the community dynamics of the total, plant pathogenic and saprotrophic fungi in wheat residues as compared with the current ambient climate. We conclude that the return of wheat residues can increase the pathogen load, and therefore have negative consequences for wheat production in the future.