Nonlegumes, legumes, and root nodules harbor different arbuscular mycorrhizal fungal communities

Legumes are an important plant functional group since they can form a tripartite symbiosis with nitrogen-fixing Rhizobium bacteria and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). However, not much is known about AMF community composition in legumes and their root nodules. In this study, we analyzed the AMF community composition in the roots of three nonlegumes and in the roots and root nodules of three legumes growing in a natural dune grassland. We amplified a portion of the small-subunit ribosomal DNA and analyzed it by using restriction fragment length polymorphism and direct sequencing. We found differences in AMF communities between legumes and nonlegumes and between legume roots and root nodules. Different plant species also contained different AMF communities, with different AMF diversity. One AMF sequence type was much more abundant in legumes than in nonlegumes (39 and 13%, respectively). Root nodules contained characteristic AMF communities that were different from those in legume roots, even though the communities were similar in nodules from different legume species. One AMF sequence type was found almost exclusively in root nodules. Legumes and root nodules have relatively high nitrogen concentrations and high phosphorus demands. Accordingly, the presence of legume- and nodule-related AMF can be explained by the specific nutritional requirements of legumes or by host-specific interactions among legumes, root nodules, and AMF. In summary, we found that AMF communities vary between plant functional groups (legumes and nonlegumes), between plant species, and between parts of a root system (roots and root nodules).     

Soil nitrogen transformations and nitrate utilization by Deschampsia flexuosa (L.) Trin. at two contrasting heathland sites

Two Dutch heathland sites Hoorneboeg (HB) and Ede, dominated by Deschampsia flexuosa and differing in nitrate production, were sampled for an entire growing season. A large number of soil and plant parameters were monitored in an attempt to assess the contribution of nitrate in the N supply and its assimilation by Deschampsia.Average NO₃ ^– and NH₄ ⁺ concentrations (mg kg^–1) in the top 10-cm depth were 0.03 and 2.2, respectively, for HB, and 2.1 and 6.7, respectively, for Ede. Laboratory incubations of intact cores and experiments with FH-layer suspensions showed significantly higher mineralization and nitrification rates for the Ede site during most of the season. Nitrification was largely controlled by the rate of net N-mineralization, which in turn was highly affected by soil moisture. Nitrate production was virtually zero at HB and accounted for 25% of the net N-mineralization at Ede.Shoot chemical composition showed no essential differences for the two sites, but mean in vivo (current) foliar NRA was almost 2-fold higher at Ede than at HB, indicating some utilization of nitrate at the former location. At the HB site with essentially no nitrate production, however, enzyme activities were clearly higher than basal constitutive levels in NH₄ ⁺-fed plants. Apparently, shoot NRA at the HB site became positively affected by factors other than nitrate availability and/or showed disproportional increases in response to atmospheric nitrate inputs. Root NRA displayed the same low basal level at the two sites. Nitrate fertilization (100 kg N ha^–1) yielded maximally induced foliar NRAs similar to levels found in hydroponic nitrate plants. Although no accumulation of free NO₃ ^– was observed in shoots from fertilized plots, increases in foliar concentrations of both organic N and carboxylates clearly indicated nitrate assimilation. Root NRA showed no response to nitrate addition.It is concluded that current NRA measurements in Deschampsia at heathland sites are of limited value only, especially when interpreted in isolation. A combined approach, using concurrently conducted soil and plant analyses, will allow the extent of nitrate utilization in the field to be best characterized.Publication 2013 of the Netherlands Institute of Ecology.FAX no corresponding author: +31 8306 23227     

Glutamine synthetase isoforms in Trientalis europaea: a biochemical and molecular approach

Ion-exchange chromatography of extracts from Trientalis europaea L. leaf tissue have been shown to contain two distinct isoforms of glutamine synthetase (GS). However, analysis by Western blotting has shown that the first peak to elute contains a mixture of large and small GS subunits, whilst the second peak is comprised entirely of a smaller subunit. This is contrary to the widespread assumptions concerning plant GS biochemistry. Isolation of intact chloroplasts and subsequent extraction of GS, followed by ion-exchange chromatography, has shown that the first peak to elute contains a large subunit, and the second chloroplastic peak is composed entirely of the small subunit. This smaller subunit may be present due to it being encoded by a separate chloroplastic GS gene, or it may be present as a product of post-translational modification. DNA sequencing has been used to try and determine which of these may be occurring. The three partial DNA sequences (505 nucleotides) we have obtained from T. europaea have been compared with 64 other sequences available on the NCBI database, which have mainly been obtained from crop species. Neighbour joining and parsimony analysis (1000 bootstrap) has shown support (_∼30%) for the separation of plant GS from all other phyla. Within the plant phylum, there is total support for the separation of chloroplastic and cytosolic GS (100%), whilst the cytosolic sequences divide further into monocot and dicot species (77% support by NJ). Further subgroups of plants from the same families is also suggested. This is consistent with previous work containing fewer, but longer (_∼1000 nucleotides) GS sequences. The addition of GS sequences obtained from wild plant species, such as T. europaea, to the large amount of information already available on the database, will permit a better understanding of the evolution of this important enzyme. This revised version was published online in June 2006 with corrections to the Cover Date.     

Herbivory and ramet performance in the clonal herb Trientalis europaea L.

1 The intensity of leaf damage caused by invertebrate herbivores and grazing by vertebrates and their effects on clonal growth, survival and reproduction were examined in a population of the forest herb Trientalis europaea during 4 years.
2 Levels of herbivory were low and varied between years in the studied population. Larger ramets were exposed to a greater risk of both grazing and leaf defoliation. Ramets that suffered leaf damage in 1 year experienced an increased probability of leaf damage in succeeding years. The probability of suffering herbivore attack was independent among the ramets belonging to the same clonal fragment, suggesting that clonal propagation might operate as a risk-spreading strategy in this species.
3 Leaf damage did not affect any measure of plant performance, probably due to the low amounts of leaf area removed by invertebrate herbivores. In contrast, vertebrate grazing affected all phases of the pseudo-annual life cycle of T. europaea . Grazing prevented flowering and fruiting, increased ramet mortality during summer and decreased tuber production. Furthermore, grazed ramets produced shorter stolons and smaller tubers, which in turn had a lower winter survival and produced smaller ramets in the following growing season. The large impact of grazing was due to the consumption of the whole of the single shoot of ramets of T. europaea . Although regrowth was possible, secondary shoots were significantly smaller and assimilation was delayed.
4 Tubers originating from grazed ramets were placed shallower than tubers from ungrazed ramets. This could be due to an alteration in the growth pattern of stolons of the grazed ramets.     

烟草根部内生真菌群落结构和功能特征

烟草内生真菌是烟田生态系统的重要组成,根系是烟草内生真菌重要来源途径。本研究通过高通量测序技术分析了5个品种的烟草根部内生真菌群落结构及功能特征。结果表明,烟草根部内生真菌群落多样性较低;粪壳菌纲Sordariomycetes、座囊菌纲Dothideomycetes、散囊菌纲Eurotiomycetes、伞菌纲Agaricomycetes及锤舌菌纲Leotiomycetes为主要菌群,肉座菌目Hypocreales、煤炱目Capnodiales和散囊菌目Eurotiales为优势真菌目,丛赤壳科Nectriaceae、小戴维霉科Davidiellaceae和发菌科Trichocomaceae为优势真菌科,未定义腐生菌和动物病原菌是主要的生态功能群,但不同品种之间的真菌群落组成和生态功能分布差异显著。本研究为进一步挖掘利用烟草内生真菌资源,阐明烟草内生真菌的生态功能提供了参考。     

Ectomycorrhizal root tips harbor distinctive fungal associates along a soil nitrogen gradient

A diverse range of fungi associate with ectomycorrhizal (EcM) root tips, however, their identity and the biotic and abiotic filters structuring these communities remain unknown. We employed a metabarcoding approach to characterize fungal communities associating with the EcM root tips of Quercus rubra along a natural soil nitrogen gradient. EcM communities and ectomycorrhizal associated fungi (EcAF) were tightly linked across the breadth of the soil gradient. Notably, EcAF communities were primarily shaped by the morphological attributes of EcM communities, particularly the relative abundance of EcM taxa forming rhizomorphic hyphae. Edaphic properties (soil C:N and net N mineralization) exerted minimal influence, suggesting a strong role of biotic interactions in EcAF community assembly. The presence of plants forming ericoid mycorrhizal associations also shapes the prevalence of ericoid mycorrhizal fungi associating with EcM root tips. Overall, EcAF communities were dominated by helotialean fungi, ericoid mycorrhizal fungi, dark septate endophytes, and the white-rot fungi Mycena.     

Groundcover management changes grapevine root fungal communities and plant-soil feedback

Plant and Soil - The objective of this study was to determine if vineyard groundcover management can mitigate negative plant-soil feedback caused by soil borne pathogens through changes in root...     

Canopy tree species and openness affect foliar endophytic fungal communities of understory seedlings

There is growing evidence demonstrating the diversity of foliar endophytic fungi and their ecological roles in the survival of tree seedlings. However, the factors that shape fungal communities in tree seedlings within natural forest ecosystems remain poorly understood. Here, we evaluated the composition of foliar endophytic fungi growing in current-year seedlings of Cornus controversa and Prunus grayana in a cool temperate deciduous forest through a seed-sowing experiment and fungal isolation. The composition of endophytic fungi was affected by canopy tree species, canopy openness, and time after germination. In total, 27 and 22 fungal taxa were isolated from C. controversa and P. grayana seedlings, respectively. The dominant fungal taxa in both seedling species were Colletotorichum spp., and their isolation frequencies were higher under C. controversa canopies than under P. grayana canopies; the frequencies also increased with time after germination. These results suggest that overstory tree species strongly influences the endophytic fungal communities of understory seedlings.     

Leaf growth in the fast-growing Holcus lanatus and the slow-growing Deschampsia flexuosa: tissue maturation

Inherent variation in the relative growth rate of grasses is negatively correlated with that in leaf mass per unit leaf area (LMA). To scrutinize this correlation, the LMA of two grass species was analysed. Changes in LMA and cell wall synthesis in leaf blades of the fast-growing grass Holcus lanatus and the slow-growing grass Deschampsia flexuosa were investigated above the elongation zone of the leaf blade. After the leaf had obtained its final length, in H. lantus final LMA values of 40-44 gm^-2 were obtained at full leaf length, whereas in D. flexuosa LMA values continued to rise to 110 gm^-2. During this period of tissue maturation the LMA value doubled in H. lanatus, whereas in D. flexuosa an increase of 30% was measured. Most of the cell walls could be hydrolysed with driselase, the residue was hydrolysed with sulphuric acid. Driselase hydrolysates were identical in sugar composition, whereas the sugars released by sulphuric acid treatment changed gradually in composition as the tissue matured. The major sites of cell wall deposition during cell maturation were the outer walls of epidermal cells, fibres adjacent to the epidermis and the mestome ring around the vascular bundles. Lignin deposition was restricted to the vascular bundles and lignin levels of the leaf blade did not exceed 0.9% of the total amount of cell wall polysaccharides. Lignin accumulation occurred mainly after the increase in LMA and is unlikely to affect measurably the growth of these leaves.     

Demography and modelling of clonal fragments in the pseudoannual plant shape Trientalis europaea L.

The clonal growth pattern and demography of clonal fragments (aggregation of ramets derived from a common parent ramet) in the pseudoannual plant Trientalis europaea were studied in field conditions from 1991 to 1993. During this period the population of clonal fragments declined, with a half-life of 7.4 years. Number and size of the clonal progeny and stolon length were positively related to the size of the mother ramet. Survival rates of ramets and tubers increased with size. The rate of clonal growth was low: after three years, about 70% of the clonal fragments had only one ramet. This suggests that the pseudoannual growth habit in T. europaea is more important as mechanism of perennation than of ramet multiplication.Field data were used in a simulation model of architecture and population dynamics of clonal fragments. About 10% of the clonal fragments survived to the end of the simulation (15 years) and the mean survival was 4.7 years. The model predicted a positive correlation between persistence of the clonal fragment and number of ramets produced. Sensitivity analysis showed that the production of a daughter ramet of at least the same size as the parent ramet was the most important pathway for the survival and the number of ramets of the clonal fragment, whereas the production of secondary ramets had a very small effect. This confirms the interpretation of the pseudoannual life-cycle as a mechanism of ramet replacement in this species. Sensitivity analysis also revealed that changes in survival probabilities of the smallest ramets had the largest impact on clonal fragment dynamics. This reflects the important role of the smallest size class of ramets as a source of new vegetative propagules, maintaining a hierarchy in the size structure of the population.     

The interaction between the clonal herb Trientalis europaea and the host specific smut fungus Urocystis trientalis

Summary The interaction between the clonal dicotyledonous herb Trientalis europaea and the systemic smut fungus Urocystis trientalis was investigated. By marking individual plants in the field and transplanting plants to the greenhouse, disease transmission and the effect of disease on survival and fecundity of plants were estimated. Field data showed that 50% of the diseased and none of the healthy plants died during summer. Surviving diseased plants produced significantly fewer winter buds than healthy plants (means ±S.E. 1.12±0.05 and 1.88±0.07, respectively). Seed capsule production was low overall and did not differ between diseased and healthy plants. Disease was not seed-transmitted and transmission from infected mother plants to daughter ramets was not total (means 33% and 46%, in two experiments). Disease transmission was also influenced by light conditions.     

抗感白粉病青稞的内生真菌群落差异分析

种子内生微生物组与种子的健康发育有着密切的关系。本研究收集对白粉病抗病和易感共11个品种的青稞种子,利用扩增子测序技术对内生真菌的群落、丰度和多样性进行研究。从不同品种的青稞种子中共鉴定4个门、17个纲、35个目、66个科、107个属的内生真菌,其中子囊菌门Ascomycota、担子菌门Basidiomycota和被孢菌门Mortierellomycota是优势菌门;链格孢属Alternaria、微座孢属Microdochium、亚隔孢壳属Didymella、镰刀菌属Fusarium和球腔菌属Mycosphaerella为优势菌属。根据生物信息学注释结果,在鉴定到的107个属中,抗病品种的青稞种子中特有的属有20个,感病品种的青稞种子中特有的属有50个;通过对两组样本的分析,发现感病品种中真菌物种多样性高于抗病品种。本研究通过扩增子测序技术初步确定了青稞抗、感白粉病两组样品中的真菌群落结构和优势菌群,为进一步研究青稞内携真菌与抗/感病的关系提供了基础,从内生菌的角度为青稞白粉病的防控提供新的策略。     

Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany

Fungi are an important component of microbial communities and are well known for their ability to decompose refractory, highly polymeric organic matter. In soils and aquatic systems, fungi play an important role in carbon processing, however, their diversity, community structure and function as well as ecological role, particularly in groundwater, are poorly studied. The aim of this study was to examine the fungal community composition, diversity and function in groundwater from 16 boreholes located in the vicinity of two lakes in NE Germany that are characterized by contrasting trophic status. The analysis of 28S rRNA gene sequences amplified from the groundwater revealed high fungal diversity and clear differences in community structure between the aquifers. Most sequences were assigned to Ascomycota and Basidiomycota, but members of Chytridiomycota, Cryptomycota, Zygomycota, Blastocladiomycota, Glomeromycota and Neocallimastigomycota were also detected. In addition, 27 species of fungi were successfully isolated from the groundwater samples and tested for their ability to decompose complex organic polymers – the predominant carbon source in the groundwater. Most isolates showed positive activities for at least one of the tested polymer types, with three strains, belonging to the genera Gibberella, Isaria and Cadophora, able to decompose all tested substrates. Our results highlight the high diversity of fungi in groundwater, and point to their important ecological role in breaking down highly polymeric organic matter in these isolated microbial habitats.     

Effects of litters with different concentrations of phenolics on the competition between Calluna vulgaris and Deschampsia flexuosa

We hypothesized that the outcome of competition between ericaceous plants and grasses is strongly affected by the concentrations of phenolics in the litter that they produce. To test the effect of phenolic-rich litter on soluble soil nitrogen concentrations, plant nitrogen uptake and inter-specific competition, we conducted a greenhouse experiment with the shrub Calluna vulgaris and the grass Deschampsia flexuosa and their leaf litters. Two litters of C. vulgaris were used, with equal nitrogen concentration but different (high and low) concentrations of total phenolics. The D. flexuosa leaf litter contained lower concentrations of phenolics, but higher concentrations of nitrogen than the C. vulgaris litters. The plants were grown in monocultures and in mixed cultures. Inorganic and dissolved organic nitrogen were measured monthly during the experiment. After four months, we measured above- and belowground biomass and the nutrient concentrations in above- and belowground plant parts. In monocultures, C. vulgaris produced more shoot and root biomass on its own litter than with no litter. Growth of Calluna was reduced on grass litter. D. flexuosa plants produced most biomass on their own litter type, whether in monocultures or in mixed cultures. Addition of Calluna litter stimulated the growth of D. flexuosa both in monoculture and in mixtures. The grass plants outcompeted Calluna both on shrub litter and on grass litter but not when grown without litter. The two C. vulgaris litter types that differed in their concentration of phenolics did not differ in their effects on the competition between the two species or on the production of inorganic and dissolved organic nitrogen. We conclude that the nitrogen content of the litter is more important as a plant feature driving competition between shrubs and grasses than the concentrations of phenolics.     

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities

Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near‐pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near‐pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near‐pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near‐pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near‐pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche‐based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β‐diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.     

Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities

Fungal communities play a key role in ecosystem functioning. However, only little is known about their composition in plant roots and the soil of biomass plantations. The goal of this study was to analyze fungal biodiversity in their belowground habitats and to gain information on the strategies by which ectomycorrhizal (ECM) fungi form colonies. In a 2-year-old plantation, fungal communities in the soil and roots of three different poplar genotypes (Populus × canescens, wildtype and two transgenic lines with suppressed cinnamyl alcohol dehydrogenase activity) were analyzed by 454 pyrosequencing targeting the rDNA internal transcribed spacer 1 (ITS) region. The results were compared with the dynamics of the root-associated ECM community studied by morphotyping/Sanger sequencing in two subsequent years. Fungal species and family richness in the soil were surprisingly high in this simple plantation ecosystem, with 5944 operational taxonomic units (OTUs) and 186 described fungal families. These findings indicate the importance that fungal species are already available for colonization of plant roots (2399 OTUs and 115 families). The transgenic modification of poplar plants had no influence on fungal root or soil communities. Fungal families and OTUs were more evenly distributed in the soil than in roots, probably as a result of soil plowing before the establishment of the plantation. Saprophytic, pathogenic, and endophytic fungi were the dominating groups in soil, whereas ECMs were dominant in roots (87%). Arbuscular mycorrhizal diversity was higher in soil than in roots. Species richness of the root-associated ECM community, which was low compared with ECM fungi detected by 454 analyses, increased after 1 year. This increase was mainly caused by ECM fungal species already traced in the preceding year in roots. This result supports the priority concept that ECMs present on roots have a competitive advantage over soil-localized ECM fungi.     

Resistance and resilience of root fungal communities to water limitation in a temperate agroecosystem

Understanding crop resilience to environmental stress is critical in predicting the consequences of global climate change for agricultural systems worldwide, but to date studies addressing crop resiliency have focused primarily on plant physiological and molecular responses. Arbuscular mycorrhizal fungi (AMF) form mutualisms with many crop species, and these relationships are key in mitigating the effects of abiotic stress in many agricultural systems. However, to date there is little research examining whether (1) fungal community structure in agroecosystems is resistant to changing environmental conditions, specifically water limitation and (2) resilience of fungal community structure is moderated by agricultural management systems, namely the integration of trees into cropping systems. Here, we address these uncertainties through a rainfall reduction field experiment that manipulated short‐term water availability in a soybean‐based (Glycine max L. Merr.) agroforest in Southern Ontario, Canada. We employed terminal restriction fragment length polymorphism analysis to determine the molecular diversity of both general fungal and AMF communities in soybean roots under no stress, stress (rainfall shelters added), and poststress (rainfall shelters removed). We found that general fungal and AMF communities sampled from soybean roots were resistant to rainfall reduction in a monoculture, but not in an agroforest. While AMF communities were unchanged after stress removal, general fungal communities were significantly different poststress in the agroforest, indicating a capacity for resiliency. Our study indicates that generalist fungi and AMF are responsive to changes in environmental conditions and that agroecosystem management plays a key role in the resistance and resilience of fungal communities to water limitation.     

Latent soil effects of grazing and ammonium deposition on Deschampsia flexuosa tillers inserted and grown in heather moorland soil

Upland heather moorlands support a range of increasingly rare and threatened biota, making them a priority habitat for conservation and restoration. Over-grazing and nitrogen deposition are two of the most important threats to maintaining these heather moorlands, yet there remains a paucity of research into their combined long-term effects. During the summer of 2008, we established an experiment within an existing research site at Pwllpeiran, mid-Wales. The original site, established in 1996, investigated long-term grazing and N deposition treatments (ammonium and nitrate) on heather moorland. Previous findings from the site, following a decade of treatment, suggested no significant, detectable impacts of treatments on soil C:N ratio and the foliar nitrogen of vegetation.The aim of our study was to investigate short- (2008) and long-term (1996–2008) N deposition treatment impacts, in combination with past grazing (1990–2007), on soil nutrient bioavailability. Soil cores were harvested and aboveground vegetation removed. Tillers of the grass Deschampsia flexuosa were planted into these cores which were then reciprocally transplanted back into the field experiment. The N deposition treatment was continued but grazing was excluded. D. flexuosa biomass changes were next assessed and leaf chemistry investigated using the metabolic fingerprinting method Fourier-transform infrared spectroscopy (FTIR) following three months of growth in the field (May–August 2008).Grazing treatment (on its own) had significant negative impacts on aboveground biomass and significant changes in plant chemistry were also revealed through the metabolic fingerprinting method Fourier transform infrared spectroscopy (FTIR). Short-term N deposition treatments during 2008 had no impacts on D. flexuosa growth or chemistry. There were also no detectable latent effects of long-term nitrate treatments on either growth or chemistry of D. flexuosa. However, plants grown in plots that had received long-term treatments of ammonium (NH₄⁺) had significantly lower poly-phenolic contents (revealed by FTIR) than plants grown in either nitrate (NO₃⁻) or control plots, suggesting detectable latent effects of N application in its reduced form. Further work needs to be undertaken to assess the relevance of residual soil nitrogen pools post N deposition and grazing.