Differential responses of total and active soil microbial communities to long-term experimental N deposition

The relationship between total and metabolically active soil microbial communities can provide insight into how these communities are impacted by environmental change, which may impact the flow of energy and cycling of nutrients in the future. For example, the anthropogenic release of biologically available N has dramatically increased over the last 150 years, which can alter the processes controlling C storage in terrestrial ecosystems. In a northern hardwood forest ecosystem located in Michigan, USA, nearly 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. A microbial mechanism underlies this response, as compositional changes in the soil microbial community have been concomitantly documented with these biogeochemical changes. Here, we co-extracted DNA and RNA from decaying leaf litter to determine if experimental atmospheric N deposition has lowered the diversity and altered the composition of the whole communities of bacteria and fungi (i.e., DNA-based) and well as its active members (i.e., RNA-based). In our experiment, experimental N deposition did not affect the composition, diversity, or richness of the total forest floor fungal community, but did lower the diversity (−8%), as well as altered the composition of the active fungal community. In contrast, neither the total nor active forest floor bacterial community was significantly affected by experimental N deposition. Our results suggest that future rates of atmospheric N deposition can fundamentally alter the organization of the saprotrophic soil fungal community, key mediators of C cycling in terrestrial environments.     

亚马逊黑土及其黑碳颗粒中的真菌丰度和多样性互不相同

Amazonian Dark Earth (ADE) is a highly fertile soil of anthropogenic origin characterized by high levels of charred black carbon (BC).It is considered a model of fertility;however,knowledge on the fungal community structure and diversity inhabiting ADE and its BC particles is scarce.Fungal community structure and diversity of ADE and its BC from four sites under different land uses (three agricultural systems and a secondary pristine forest) in the Brazilian Central Amazon were evaluated by 18S rRNA gene pyrosequencing.Fungal communities in ADE and BC were dissimilar and showed differential abundances of fungal operational taxonomic units (OTUs).Estimated fungal species richness (abundance-based coverage estimate and Chao-1 index) and diversity estimators (Shannon and Simpson's reciprocal indices) were higher in ADE than in BC in all agricultural areas.No differences were observed in those parameters in ADE and BC samples from the secondary forest.Pezizomycotina fungi and OTUs assigned to Cordyceps confragosa,Acremonium vitellinum,Camarops microspora,and Hirsutella rhossiliensis were more abundant in BC particles than in ADE.These findings represent a breakthrough in our understanding of fungal communities in BC particles from ADE,and will be valuable in future studies considering biochar application in soil.     

Influence of drought and litter age on Collembola communities

A field experiment was carried out to study the impact of drought and litter quality on the structure and performance of collembolan communities. The hypothesis was tested that changes in substrate humidity and resource quality significantly influence decomposition processes via alterations in soil faunal community structure. Litterbags (1000 μm mesh size) containing either freshly fallen or aged spruce litter were placed on the floor of a German spruce forest for one year. The bags were exposed to either ambient conditions (control) or drought (covered with roofs). Drought-induced changes in biological parameters were associated with a strong reduction in decomposition rates. Moreover, drought stress decreased Collembola abundance and species richness. The influence of drought on some microbiological parameters strongly depended on the litter age. A comparison of the two litter treatments revealed major effects of litter age on microbiological and physico-chemical parameters, but no effects on Collembola abundance and species richness. A detailed analysis of the collembolan community structure showed that certain species are highly adapted to specific characteristics of the substrate and thus rapidly respond to changes in microhabitat conditions.     

Spruce forest conversion to a mixed beech-coniferous stand modifies oribatid community structure

We investigated oribatid mite community diversity and structure in the managed conversion of coniferous stands into semi-natural montane forests that are composed of a small-scale mosaic formed by different age classes of silver fir, Norway spruce and European beech in the southern Black Forest area, South-Western Germany, using the space-for-time substitution method. The core hypothesis was that changing tree composition and management practice will affect functional structure and diversity of oribatid mite community through changing substrate quality and litter diversity. Three forest districts were selected within the research region. Four stand types representing the major stages of forest conversion were selected within each forest district: (i) even-aged spruce monocultures, (ii) species enrichment stage, (iii) forest stand structuring stage, at which fur and beech and other deciduous trees penetrate the upper storey of the forest and (iv) a diverse continuous cover forest respectively. Oribatid mite abundance, species richness and composition, biomass, ecomorphs and feeding groups relative abundance were determined. An overall increase in species richness moving from the spruce monoculture to a continuous cover forest was detected. However, the herbivorous and litter-dwelling mites were most sensitive to forest conversion demonstrating significant differences in abundance between conversion stages. Almost all changes in the oribatid community were associated with the properties of the changing litter layer. Abundance of soil-dwelling mites remained very stable what is in contradiction with the response of the other soil fauna groups found at the same sites. Overall oribatid community seemed to be more dependent on total microbial biomass than fungi. However, observed effects were overshadowed by considerable district-induced differences.     

Insights into the effects of serpentine soil conditions on the community composition of fungal symbionts in the roots of Onosma echioides

In this study, we investigated the impact of the extreme edaphic conditions of serpentine soils on the community structure of fungal symbionts in the roots of the perennial herb Onosma echioides (Boraginaceae). Sixteen root systems of O. echioides were obtained from two serpentine and two non-serpentine sites in the region of Tuscany (Italy) and the associated fungal communities were characterized by 454 pyrosequencing of fungal internal transcribed spacer 1 (ITS1) amplicon libraries. Clustering analysis of 173,639 sequence reads yielded a total of 699 non-singleton operational taxonomic units (OTUs), with the number of non-singleton OTUs per fungal community varying between 65 and 225. The richness of the fungal communities did not appear to be affected by the edaphic conditions of serpentine soils but the compositions of the serpentine and non-serpentine communities differed significantly, even though community structures were mainly influenced by strong spatial effects at low-to-medium distance scales. Whereas non-serpentine communities were dominated, at least in terms of sequence read abundance, by OTUs assigned to the genera Rhizophagus and Glomus (Glomeromycota), serpentine communities were dominated by OTUs assigned to the genera Ceratobasidium and Coprinellus (Basidiomycota). The functional roles of these basidiomycetous species in the roots of serpentine O. echioides specimens are, however, unclear and although their presence may affect the serpentine tolerance of the host plant, they may also be opportunistic symbionts that benefited from the reduced abundance of arbuscular mycorrhizal fungi to colonize the roots of O. echioides in serpentine environments.     

Nitrogen and water addition regulate soil fungal diversity and co-occurrence networks

Purpose

A field experiment was conducted to assess the role of nitrogen (N) and water addition in shaping soil fungal communities and co-occurrence networks in temperate grassland, northern China.

Materials and methods

We measured soil fungal and plant community compositions, and also soil properties including available N, phosphorus, potassium concentrations, soil pH, and soil moisture. Soil fungal co-occurrence networks were constructed using a random matrix theory–based network inference approach.

Results and discussion

Plant species richness was decreased by N addition but increased by water addition, whereas fungal richness was decreased by N addition. The fungal community composition was significantly changed by both N addition and water addition. Soil fungal α diversity and β diversity were explained by a combination of variations in plant species richness and plant functional composition, and also by changes in soil pH via the soil acidification pathway induced by N and water addition. The fungal co-occurrence networks were more complex and clustered under water addition than that in ambient precipitation.

Conclusions

Our results suggested that plant functional composition, plant species richness, and soil acidification should be incorporated into ecosystem models for predicting soil fungal communities under future climate changes in terrestrial ecosystems.

     

Differential effect of arbuscular mycorrhizal fungal communities from ecosystems along management gradient on the growth of forest understorey plant species

Arbuscular mycorrhizal fungi (AMF) are important functional components of ecosystems. Although there is accumulating knowledge about AMF diversity in different ecosystems, the effect of forest management on diversity and functional characteristics of AMF communities has not been addressed. Here, we used soil inoculum representing three different AM fungal communities (from a young forest stand, an old forest stand and an arable field) in a greenhouse experiment to investigate their effect on the growth of three plant species with contrasting local distributions - Geum rivale, Trifolium pratense and Hypericum maculatum. AM fungal communities in plant roots were analysed using the terminal restriction fragment length polymorphism (T-RFLP) method. The effect of natural AMF communities from the old and young forest on the growth of studied plant species was similar. However, the AMF community from the contrasting arable ecosystems increased H. maculatum root and shoot biomass compared with forest inocula and T. pratense root biomass compared to sterile control. According to ordination analysis AMF inocula from old and young forest resulted in similar root AMF communities whilst plants grown with AM fungi from arable field hosted a different AMF community from those grown with old forest inocula. AMF richness in plant roots was not related to the origin of AMF inoculum. G. rivale hosted a significantly different AM fungal community to that of T. pratense and H. maculatum. We conclude that although the composition of AM fungal communities in intensively managed stands differed from that of old stands, the ecosystem can still offer the ‘symbiotic service’ necessary for the restoration of a characteristic old growth understorey plant community.     

Response of the soil fungal community to multi-factor environmental changes in a temperate forest

Both environmental and climatic changes are known to influence soil microbial biomes in terrestrial ecosystems. However, there are limited data defining the interactive effects of multi-factor environmental disturbances, including N-deposition, precipitation, and air temperature, on soil fungal communities in temperate forests. A 3-year outdoor pot experiment was conducted to examine the temporal shifts of soil fungal communities in a temperate forest following N-addition, precipitation and air temperature changes. The shifts in the structure and composition of soil fungal communities were characterized by denaturing gradient gel electrophoresis and DNA sequencing. N-addition regimen induced significant alterations in the composition of soil fungal communities, and this effect was different at both higher and lower altitudes. The response of the soil fungal community to N-addition was much stronger in precipitation-reduced soils compared to soils experiencing enhanced precipitation. The combined treatment of N-addition and reduced precipitation caused more pronounced changes in the lower altitude versus those in the higher one. Certain fungal species in the subphylum Pezizomycotina and Saccharomycotina distinctively responded to N fertilization and soil water control at both altitudes. Redundancy discrimination analysis showed that changes in environmental factors and soil physicochemical properties explained 43.7% of the total variability in the soil fungal community at this forest ecosystem. Variations in the soil fungal community were significantly related to the altitude, soil temperature, total soil N content (TN) and pH value (P < 0.05). We present evidence for the interactive effects of N-addition, water manipulation and air temperature to reshape soil fungal communities in the temperate forest. Our data could provide new insights into predicting the response of soil micro-ecosystem to climatic changes.     

Humus structure during a spruce forest rotation: quantitative changes and relationship to soil biota

Temporal dynamics of edaphic communities affect numerous processes in forests and also strongly influence the soil's organic matter status. We have linked long-term changes in the formation of organic matter (using humus micromorphological analyses) to changes in the soil's community structure during a spruce forest cycle on acid soil. The study was carried out at four sites of different age-classes in the Tharandter forest, Germany. The composition of the deeper humus layers (OH, A) was stable. Herbaceous litter, recent spruce litter, fragmented spruce litter, decomposed litter and faeces and fungi, which contributed to the organic layer (OL and OH horizon), significantly changed during the forestry cycle, especially with the shift from the early stage to intermediate stages. Parallel changes of the faunal assemblage of the soil showed quantitative relations between major stages of the forest development, humus dynamics and soil community composition. The herbaceous litter was correlated with surface-dwelling Collembola and microbial properties with faeces and fungi. Our results suggest that the long-term stability of deep organic layers provides a refuge for decomposers and detritivores that allows a rapid response to both adverse and favourable conditions, taking place in OL and OF layers. Furthermore, the opening of the canopy in mature stands allows the decomposers to adapt to changes in resource input long before the collapse of the forest.     

The Collembola community of pure and mixed stands of beech (Fagus sylvatica) and spruce (Picea abies) of different age

The idea of establishing mixed forests that are better adapted to site conditions than spruce monocultures has attracted increasing attention of forest owners and governmental institutions over the last decades. Currently, beech is being replanted and an increasing proportion of German forests are mixed stands. Focusing on the reaction of the soil fauna to forest conversion, this study investigates the response of the Collembola community to replacement of beech by spruce or by mixed stands of beech and spruce. Stands of different age were investigated in a factorial design with the factors stand type (beech, spruce and mixed stands) and stand age (30 and 120 years). Collembola communities did not differ strongly between stand types and stand age and were dominated by Folsomia quadrioculata and Mesaphorura species (e.g. Mesaphorura macrochaeta). Moreover, neither total abundance of Collembola nor densities of the fungal feeding euedaphic Onychiurinae and Tullbergiinae significantly responded to stand type and stand age. The density of the epedaphic and partly herbivorous groups Symphypleona/Neelipleona and Entomobryidae in the 120-year-old stands significantly exceeded that in the 30-year-old stands; presumably, this was due to the well developed herb layer in the 120-year-old stands with more open canopies. Canonical correspondence analysis (CCA) of the Collembola community of the L/F horizon also indicated that most of the epigeic species were associated with the 120-year-old stands. Moreover, the diversity of Collembola significantly increased with forest age which likely reflects increased amount and diversity of food resources in the 120-year-old stands. The density of the hygrophilous species Fo. quadrioculata was significantly higher in the spruce than in the beech stands; probably this was due to the higher water content in litter of the spruce stands. Moreover, the results of the CCAs indicated that soil pH is an important structuring force for the Collembola communities. Overall, the results suggest that stand type and forest age impact Collembola communities, presumably via changes in the amount and quality of food resources, such as living plant and herb litter materials. The pronounced changes which occurred with forest age likely were related to the development of more dense and diverse herb layer in mature forests which provides additional food resources in particular for epedaphic species. On the other hand, dominant species/functional groups of Collembola, such as hemiedaphic species, appear to depend predominantly on abiotic factors, most importantly soil pH and soil water content.