A comparison of soil food webs beneath C<Subscript>3</Subscript>- and C<Subscript>4</Subscript>-dominated grasslands

Soil food webs influence organic matter mineralization and plant nutrient availability, but the potential for plants to capitalize on these processes by altering soil food webs has received little attention. We compared soil food webs beneath C₃- and C₄-grass plantings by measuring bacterial and fungal biomass and protozoan and nematode abundance repeatedly over 2 years. We tested published expectations that C₃ detritus and root chemistry (low lignin/N) favor bacterial-based food webs and root-feeding nematodes, whereas C₄ detritus (high lignin/N) and greater production favor fungal decomposers and predatory nematodes. We also hypothesized that seasonal differences in plant growth between the two grassland types would generate season-specific differences in soil food webs. In contrast to our expectations, bacterial biomass and ciliate abundance were greater beneath C₄ grasses, and we found no differences in fungi, amoebae, flagellates, or nematodes. Soil food webs varied significantly among sample dates, but differences were unrelated to aboveground plant growth. Our findings, in combination with previous work, suggest that preexisting soil properties moderate the effect of plant inputs on soil food webs. We hypothesize that high levels of soil organic matter provide a stable environment and energy source for soil organisms and thus buffer soil food webs from short-term dynamics of plant communities.     

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

Background, aim, and scope  Fertilization is an important agricultural practice for increasing crop yields. In order to maintain the soil sustainability, it is important to monitor the effects of fertilizer applications on the shifts of soil microorganisms, which control the cycling of many nutrients in the soil. Here, culture-dependent and culture-independent approaches were used to analyze the soil bacterial and fungal quantities and community structure under seven fertilization treatments, including Control, Manure, Return (harvested peanut straw was returned to the plot), and chemical fertilizers of NPK, NP, NK, and PK. The objective of this study was to examine the effects on soil microbial composition and diversity of long-term organic and chemical fertilizer regimes in a Chinese upland red soil. Materials and methods  Soil samples were collected from a long-term experiment station at Yingtan (28°15′N, 116°55′E), Jiangxi Province of China. The soil samples (0–20 cm) from four individual plots per treatment were collected. The total numbers of culturable bacteria and fungi were determined as colony forming units (CFUs) and selected colonies were identified on agar plates by dilution plate methods. Moreover, soil DNAs were extracted and bacterial 16S rRNA genes and fungal 18S rRNA genes were polymerase chain reaction amplified, and then analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. Results  The organic fertilizers, especially manure, induced the least culturable bacterial CFUs, but the highest bacterial diversity ascertained by DGGE banding patterns. Chemical fertilizers, on the other hand, had less effect on the bacterial composition and diversity, with the NK treatment having the lowest CFUs. For the fungal community, the manure treatment had the largest CFUs but much fewer DGGE bands, also with the NK treatment having the lowest CFUs. The conventional identification of representative bacterial and fungal genera showed that long-term fertilization treatments resulted in differences in soil microbial composition and diversity. In particular, 42.4% of the identified bacterial isolates were classified into members of Arthrobacter. For fungi, Aspergillus, Penicillium, and Mucor were the most prevalent three genera, which accounted for 46.6% of the total identified fungi. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Discussion  It was evident that more representative fungal genera appeared in organic treatments than other treatments, indicating that culturable fungi were more sensitive to organic than to chemical fertilizers. A very notable finding was that fungal CFUs appeared maximal in organic manure treatments. This was quite different from the bacterial CFUs in the manure, indicating that bacteria and fungi responded differently to the fertilization. Similar to bacteria, the minimum fungal CFUs were also observed in the NK treatment. This result provided evidence that phosphorus could be a key factor for microorganisms in the soil. Thus, despite the fact that culture-dependent techniques are not ideal for studies of the composition of natural microbial communities when used alone, they provide one of the more useful means of understanding the growth habit, development, and potential function of microorganisms from soil habitats. A combination of culture-dependent and culture-independent approaches is likely to reveal more complete information regarding the composition of soil microbial communities. Conclusions  Long-term fertilization had great effects on the soil bacterial and fungal communities. Organic fertilizer applications induced the least culturable bacterial CFUs but the highest bacterial diversity, while chemical fertilizer applications had less impact on soil bacterial community. The largest fungal CFUs were obtained, but much lower diversity was detected in the manure treatment. The lowest bacterial and also fungal CFUs were observed in the NK treatment. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Phosphorus fertilizer could be considered as a key factor to control the microbial CFUs and diversity in this Chinese upland red soil. Recommendations and perspectives  Soil fungi seem to be a more sensitive indicator of soil fertility than soil bacteria. Since the major limitation of molecular methods in soil microbial studies is the lack of discrimination between the living and dead, or active and dormant microorganisms, both culture-dependent and culture-independent methods should be used to appropriately characterize soil microbial diversity.     

Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

Soil microbial communities in dryland ecosystems play important roles as root associates of the widely spaced plants and as the dominant members of biological soil crusts (biocrusts) colonizing the plant interspaces. We employed rRNA gene sequencing (bacterial 16S/fungal large subunit) and shotgun metagenomic sequencing to compare the microbial communities inhabiting the root zones of the dominant shrub, Larrea tridentata (creosote bush), and the interspace biocrusts in a Mojave desert shrubland within the Nevada Free Air CO₂ Enrichment (FACE) experiment. Most of the numerically abundant bacteria and fungi were present in both the biocrusts and root zones, although the proportional abundance of those members differed significantly between habitats. Biocrust bacteria were predominantly Cyanobacteria while root zones harbored significantly more Actinobacteria and Proteobacteria. Pezizomycetes fungi dominated the biocrusts while Dothideomycetes were highest in root zones. Functional gene abundances in metagenome sequence datasets reflected the taxonomic differences noted in the 16S rRNA datasets. For example, functional categories related to photosynthesis, circadian clock proteins, and heterocyst-associated genes were enriched in the biocrusts, where populations of Cyanobacteria were larger. Genes related to potassium metabolism were also more abundant in the biocrusts, suggesting differences in nutrient cycling between biocrusts and root zones. Finally, ten years of elevated atmospheric CO₂ did not result in large shifts in taxonomic composition of the bacterial or fungal communities or the functional gene inventories in the shotgun metagenomes.     

Succession of plant and soil microbial communities with restoration of abandoned land in the Loess Plateau, China

Purpose

There have been a number of studies on the succession of vegetation; however, the succession of soil microbes and the collaborative relationships between microbes and vegetation during land restoration remain poorly understood. The objectives of this study were to characterize soil microbial succession and to explore the collaborative mechanisms between microbes and vegetation during the restoration of abandoned land through quantitative ecology methods.

Materials and methods

The present research was carried out in the succession of a 5-year abandoned land and its conversion to Hippophae rhamnoides shrubs, Larix principis-rupprechtii plantation, and a naturally regenerated forest (mixed forest). Soil bacterial, archaeal and fungal characteristics were tested by real-time quantitative PCR assays and terminal restriction fragment length polymorphism. The richness, diversity, and evenness indices were employed to analyze plant and microbial communities’ structure. The stability of plant and microbial communities was tested using Spearman’s rank correlation. The relationships between the regeneration scenarios and environmental factors were determined through canonical correspondence analysis.

Results and discussion

The aboveground biomass was significantly different among the sites. Soil bacterial, archaeal, and fungal rRNA gene abundances did not increase significantly with increasing soil organic carbon content. There were higher correlation coefficients between plant and total microbial communities on the richness, diversity, and evenness indices and ratios of positive to negative association compared to ones between plant and individual bacteria, archaea, and fungi. Soil bulk density, clay, pH, and litter were the primary significant environmental factors affecting the structure of plant and microbial communities. The positive relationships between plant and soil bacteria, fungi, and total microbe communities, as well as the negative relationships between plant and archaea, were demonstrated.

Conclusions

The results suggested that plants promote the growth of soil bacteria and fungi during the process of community succession on a small scale; however, plants inhibit the growth of soil archaea.     

黄土高原油松根际土壤酶活性及真菌群落多样性研究——以黄龙山林场为例

为了解黄土高原油松林根际土壤酶活性和真菌群落多样性,本研究分析了陕西黄龙县不同样区油松根际土壤脲酶、碱性磷酸酶、多酚氧化酶和过氧化氢酶活性,并采用巢式PCR-变性梯度凝胶电泳(PCR-DGGE)技术研究了油松根际土壤中真菌群落多样性。结果表明,该地区油松根际真菌群落相似性较高,但受坡向、海拔、土壤水分及人类扰动等诸多因素的影响,不同样区的真菌群落多样性和土壤酶活性存在差异。油松根际各土壤酶活性均表现出坡顶样地高于坡底样地,阴面样地高于阳面样地,林区路旁样地由于采样环境不同于林中样地,酶活性介于其他样地之间;丰富度(S)、Shannon-Wiener指数(H)、Simpson指数(D)、均匀度指数(EH)分析表明,该区域油松根际土壤真菌群落多样性分布特征与酶活性分布特征相一致。相关性分析表明,除过氧化氢酶外,其余酶活性之间、以及与真菌多样性均呈显著正相关(p0.05);土壤含水量与真菌多样性和土壤酶活性除多酚氧化酶外均呈显著正相关(p0.05);而土壤p H与各种酶活性之间均未达显著相关水平(p0.05)。土壤含水量是影响该地区真菌群落多样性与土壤酶活性主要因素之一。     

Plant nitrogen uptake drives rhizosphere bacterial community assembly during plant growth

When plants establish in novel environments, they can modify soil microbial community structure and functional properties in ways that enhance their own success. Although soil microbial communities are influenced by abiotic environmental variability, rhizosphere microbial communities may also be affected by plant activities such as nutrient uptake during the growing season. We predicted that during the growing season, plant N uptake would explain much of the variation in rhizosphere microbial community assembly and functional traits. We grew the invasive C₃ grass Bromus tectorum and three commonly co-occurring native C₃ grasses in a controlled greenhouse environment, and examined rhizosphere bacterial community structural and functional characteristics at three different plant growth stages. We found that soil N availability and plant tissue N levels strongly correlated with shifts in rhizosphere bacterial community structure. It also appeared that the rapid drawdown of soil nutrients in the rhizosphere during the plant growing season triggered a selection event whereby only those microbes able to tolerate the changing nutrient conditions were able to persist. Plant N uptake rates inversely corresponded to microbial biomass N levels during periods of peak plant growth. Mechanisms which enable plants to influence rhizosphere bacterial community structure and function are likely to affect their competitive ability and fitness. Our study suggests that plants can alter their rhizosphere microbiomes through influencing nutrient availability. The ways in which plants establish their rhizosphere bacterial communities may now be viewed as a selection trait related to intrinsic plant species nutrient demands.     

Development of microbial community during primary succession in areas degraded by mining activities

Together with plants, soil microbial communities play an essential role in the development of stable ecosystems on degraded lands, such as postmining spoil heaps. Our study addressed concurrent development of the vegetation and soil fungal and bacterial communities in the course of primary succession in a brown coal mine spoil deposit area in the Czech Republic across a chronosequence spanning 54 years. During succession, the plant communities changed from sparse plants over grassland and shrubland into a forest, becoming substantially more diverse with time. Microbial biomass increased until the 21st year of ecosystem development and later decreased. Although there was a close association between fungi and vegetation, with fungi mirroring the differences in plant community assemblages, the development of the bacterial community was different. The early succession community in the barren nonvegetated soil largely differed from that in the older sites, especially in its high abundance of autotrophic and free‐living N₂‐fixing bacteria. Later in succession, bacterial community changes were minor and reflected the chemical parameters of the soil, including pH, which also showed a minor change with time. Our results show that complex forest ecosystems developed over 54 years on the originally barren soil of the temperate zone and indicate an important role of bacteria in the initial stage of soil development. Although the arrival of vegetation affects substantially fungal as well as bacterial communities, it is mainly fungi that respond to the ongoing development of vegetation.     

Grassland management influences spatial patterns of soil microbial communities

Soil micro-organisms play a vital role in grassland ecosystem functioning but little is known about the effects of grassland management on spatial patterns of soil microbial communities. We compared plant species composition with terminal restriction fragment length polymorphism (T-RFLP) fingerprints of soil bacterial and fungal communities in unimproved, restored and improved wet grasslands. We assessed community composition of soil micro-organisms at distances ranging from 0.01 m to 100 m and determined taxa–area relationships from field- to landscape level. We show that land management type influenced bacterial but not fungal community composition. However, extensive grassland management to restore aboveground diversity affected spatial patterns of soil fungi. We found distinct distance–decay and small-scale aggregation of fungal populations in extensively managed grasslands restored from former arable use. There were no clear spatial patterns in bacterial communities at the field-scale. However, at the landscape level there was a moderate increase in bacterial taxa and a strong increase in fungal taxa with the number of sites sampled. Our results suggest that grassland management affects soil microbial communities at multiple scales; the observed small-scale variation may facilitate plant species coexistence and should be taken into account in field studies of soil microbial communities.     

Abundance and composition response of wheat field soil bacterial and fungal communities to elevated CO<Subscript>2</Subscript> and increased air temperature

The abundance and diversity of soil bacterial and fungal communities in a wheat field under elevated atmospheric CO₂ concentrations and increased air temperatures were investigated using qPCR and pyrosequencing. Elevated CO₂ concentrations significantly increased the abundances of bacteria and fungi, and an increase of air temperatures significantly reduced fungal abundance. We found that Proteobacteria, Bacteroidetes, Chloroflexi, and Ascomycota were the most abundant bacterial and fungal phyla in the wheat field soil. Elevated CO₂ concentrations and increased air temperatures had no significant effect on the bacterial alpha diversity, whereas fungal richness was reduced under warming treatments. Moreover, we note that certain bacterial and fungal groups responded differentially to elevated CO₂ concentrations and increased air temperatures, and fungal species were highly sensitive to climatic changes.     

Influence of long-term fertilisation and crop rotation on changes in fungal and bacterial residues in a tropical rice-field soil

Amino sugars, as a microbial residue biomarker, are highly involved in microbial-mediated soil organic matter formation. However, accumulation of microbial biomass and responses of bacterial and fungal residues to the management practices are different and poorly characterized in rice soils. The objectives of this study were to evaluate the effects of mineral fertiliser (MIN), farmyard manure (FYM) and groundnut oil cake (GOC) on crop yield and co-accumulation of microbial residues and microbial biomass under rice-monoculture (RRR) and rice–legume–rice (RLR) systems. In the organic fertiliser treatments and RLR, rice grain yield and stocks of soil and microbial nutrients were significantly higher than those of the MIN treatment and RRR, respectively. The increased presence of saprotrophic fungi in the organic fertiliser treatments and RRR was indicated by significantly increased ergosterol/C_mic ratio and extractable sulphur. In both crop rotation systems, the long-term application of FYM and GOC led to increased bacterial residues as indicated by greater accumulation of muramic acid. In contrast, the higher fungal C/bacterial C ratio and lower ergosterol/C_mic ratio in the MIN treatment, is likely caused by a shift within the fungal community structure towards ergosterol-free arbuscular mycorrhizal fungi (AMF). The organic fertiliser treatments contributed 22 % more microbial residual C to soil organic C compared to the MIN treatment. Our results suggest that the negative relationship between the ratios ergosterol/C_mic and fungal C/bacterial C encourages studying responses of both saprotrophic fungi and AMF when assessing management effects on the soil microbial community.     

Effects of inoculation with ectomycorrhizal fungi on microbial biomass and bacterial functional diversity in the rhizosphere of Pinus tabulaeformis seedlings

This study investigated the effects of inoculation with three individual ectomycorrhizal (ECM) fungal species on soil microbial biomass carbon and indigenous bacterial community functional diversity in the rhizosphere of Chinese pine (Pinus tabulaeformis Carr.) seedlings under field experimental conditions. The results showed that ECM fungal inoculation significantly increased the ectomycorrhizal colonization compared with non-inoculated seedlings. ECM fungal inoculations have higher soil microbial biomass carbon than that of control, ranging from 49.6 μg C g^?1 dry soil in control to 134.02 μg C g^?1 dry soil in treatment inoculated with Boletus luridus Schaeff ex Fr. Multivariate analyses (PCA) of BIOLOG data revealed that the application of ECM fungi significantly influenced bacterial functional diversity in the rhizosphere of P. tabulaeformis seedlings. The highest average well-color development (AWCD) and functional diversity indices were also observed in treatment inoculated with B. luridus. A wider range of sole carbon sources were utilized by the bacterial community in the rhizosphere of inoculated seedlings. The data gathered from this study provides important information for utilization of ECM fungi in forest restoration project in the Northwestern China. The present study will also significantly broaden our understanding of practical importance in the application of ECM fungal inoculum to promote soil microbial community diversity of soil.     

Juniperus virginiana encroachment into upland oak forests alters arbuscular mycorrhizal abundance and litter chemistry

Upland oak forests in the ecotone between the eastern deciduous forest and the southern Great Plains are threatened by encroachment of eastern redcedar (Juniperus virginiana) due to fire suppression. The rapid rate of encroachment caused concern about concomitant alterations of site characteristics including nutrient cycling and the soil microbial communities (SMC) that could lead to positive feedbacks reinforcing eastern redcedar encroachment. We studied eight upland oak forests across central and western Oklahoma with stands representing three levels of encroachment: oak-dominated, eastern redcedar-dominated, and an intermediate mixture of both species. We analyzed litter chemistry (carbon, lignin, and nitrogen), soil chemistry (soil organic matter, NH₄N, NO₃-N, PO₄, K, and pH), and profiled soil microbial communities using phospholipid fatty acid analysis (PLFA). Eastern redcedar encroachment was accompanied by reduced litter carbon along with higher levels of arbuscular mycorrhizal (AM) fungi while litter N was lower in mixed stands. However, we detected no change in soil chemistry. Our results indicate eastern redcedar encroachment in these upland oak forests reduced litter quality and altered the SMC through increases in AM fungi, a symbiont associated with eastern redcedar. These alterations may create positive soil–microbial feedbacks by reducing the fitness of the dominant oak species and facilitating rapid increase in eastern redcedar in this threatened, oak-dominated ecosystem.     

How distinct are arbuscular mycorrhizal fungal communities associating with grapevines?

Grapevines form associations with arbuscular mycorrhizal (AM) fungi. These root-dwelling fungi have the potential to contribute to crop vigor, productivity, pathogen protection, and nutrient content in grapes. In this study the arbuscular mycorrhizal fungal communities of grapevines and the surrounding interrow and native vegetation are compared. We found over 40 different taxa associating with both vines and interrow vegetation, but these communities differed based on host plant identity. These differences were apparent even after accounting for differences in soil chemical properties and differences in host plant diversity between vinerows and interrows, indicating that Vitis preferentially interacts with a subset of the viticultural fungal community. Since AM fungal communities play a major role in grapevine health, our results suggest that host identity and the diversity of AM fungal hosts in a vineyard can have strong effects on arbuscular mycorrhizal fungi community structure. In this paper, we used high throughput sequencing of the large subunit rDNA to analyze the diversity of AM fungi growing in a vineyard.     

Influence of repeated prescribed burning on incorporation of C from cellulose by forest soil fungi as determined by RNA stable isotope probing

Repeated prescribed burning is frequently used as a forest management tool and can influence soil microbial diversity and activity. Soil fungi play key roles in carbon and nutrient cycling processes and soil fungal community structure has been shown to alter with increasing burning frequency. Such changes are accompanied by changes to soil carbon and nitrogen pools, however, we know little regarding how repeated prescribed burning alters functional diversity in soil fungal communities. We amended soil with ¹³C-cellulose and used RNA stable isotope probing to investigate the effect of biennial repeated prescribed burning over a 34-year period on cellulolytic soil fungi. Results indicated that repeated burning altered fungal community structure. Moreover, fungal community structure and diversity in ¹²C and ¹³C fractions from the unburned soil were not significantly different from each other, while those from the biennial burned soils differed from each other. The data indicate that fewer active fungi in the biennially burned soil incorporated ¹³C from the labelled cellulose and that repeated prescribed burning had a significant impact on the diversity of an important functional group of soil fungi (cellulolytic fungi) that are key drivers of forest soil decomposition and carbon cycling processes.     

Shifts in microbial diversity through land use intensity as drivers of carbon mineralization in soil

Land use practices alter the biomass and structure of soil microbial communities. However, the impact of land management intensity on soil microbial diversity (i.e. richness and evenness) and consequences for functioning is still poorly understood. Here, we addressed this question by coupling molecular characterization of microbial diversity with measurements of carbon (C) mineralization in soils obtained from three locations across Europe, each representing a gradient of land management intensity under different soil and environmental conditions. Bacterial and fungal diversity were characterized by high throughput sequencing of ribosomal genes. Carbon cycling activities (i.e., mineralization of autochthonous soil organic matter, mineralization of allochthonous plant residues) were measured by quantifying ¹²C- and ¹³C-CO₂ release after soils had been amended, or not, with ¹³C-labelled wheat residues. Variation partitioning analysis was used to rank biological and physicochemical soil parameters according to their relative contribution to these activities. Across all three locations, microbial diversity was greatest at intermediate levels of land use intensity, indicating that optimal management of soil microbial diversity might not be achieved under the least intensive agriculture. Microbial richness was the best predictor of the C-cycling activities, with bacterial and fungal richness explaining 32.2 and 17% of the intensity of autochthonous soil organic matter mineralization; and fungal richness explaining 77% of the intensity of wheat residues mineralization. Altogether, our results provide evidence that there is scope for improvement in soil management to enhance microbial biodiversity and optimize C transformations mediated by microbial communities in soil.     

Diversity of microorganisms from forest soils differently polluted with heavy metals

Large accumulation of heavy metals in organic layers of forest soils may adversely affect the structure and diversity of microbial communities. The objective of this study was to assess the influence of different soil chemical properties on structure and diversity of microbial communities in soils polluted with different levels of heavy metals. The soil samples were taken at ten sites located in the vicinity of the cities of Legnica and Olkusz, differently polluted with Cu, Zn and Pb. The samples were measured for pH and the contents of organic C (C_org), total N (N_t), total S (S_t) and total Zn, Cu and Pb. The measured gross microbial properties included microbial biomass (C_mic) and soil respiration (RESP). The structure of soil microbial communities was assessed using phospholipid fatty acid (PLFA) analysis and the structure of soil bacterial communities using pyrosequencing of 16S rRNA genes. To assess diversity of the bacterial communities the Chao1 index was calculated based on the pyrosequencing data. For C_mic and RESP the most important factors were N_t and C_org, respectively. The structure and diversity of soil microbial communities revealed by PLFA profiles and pyrosequencing depended mainly on soil pH. The effect of high heavy metal contents on soil microbial properties was weaker compared with other soil properties. High concentrations of heavy metals negatively affected RESP and the Chao1 diversity index. The heavy metal pollution altered the structure of microbial communities measured with PLFA analysis, but the effect of heavy metal pollution was not observed for the structure of soil bacteria measured by pyrosequencing. The obtained results indicate that the use of soil microbial properties to study heavy metal effects may be difficult due to confounding influences of other environmental factors. In large-scale studies local variability of soil properties may obscure the effect of heavy metals.     

Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils

A number of studies have reported species specific selection of microbial communities in the rhizosphere by plants. It is hypothesised that plants influence microbial community structure in the rhizosphere through rhizodeposition. We examined to what extent the structure of bacterial and fungal communities in the rhizosphere of grasses is determined by the plant species and different soil types. Three grass species were planted in soil from one site, to identify plant-specific influences on rhizosphere microbial communities. To quantify the soil-specific effects on rhizosphere microbial community structure, we planted one grass species (Lolium perenne L.) into soils from three contrasting sites. Rhizosphere, non-rhizosphere (bulk) and control (non-planted) soil samples were collected at regular intervals, to examine the temporal changes in soil microbial communities. Rhizosphere soil samples were collected from both root bases and root tips, to investigate root associated spatial influences. Both fungal and bacterial communities were analysed by terminal restriction fragment length polymorphism (TRFLP). Both bacterial and fungal communities were influenced by the plant growth but there was no evidence for plant species selection of the soil microbial communities in the rhizosphere of the different grass species. For both fungal and bacterial communities, the major determinant of community structure in rhizospheres was soil type. This observation was confirmed by cloning and sequencing analysis of bacterial communities. In control soils, bacterial composition was dominated by Firmicutes and Actinobacteria but in the rhizosphere samples, the majority of bacteria belonged to Proteobacteria and Acidobacteria. Bacterial community compositions of rhizosphere soils from different plants were similar, indicating only a weak influence of plant species on rhizosphere microbial community structure.     

水分含量对秸秆还田土壤碳矿化和微生物特性的影响

An 80-d incubation experiment was conducted to investigate straw decomposition,the priming effect and microbial characteristics in a non-fertilized soil(soil 1) and a long-term organic manure-fertilized soil(soil 2) with and without13 C-labeled maize straw amendment under different moisture levels. The soil 2 showed a markedly higher priming effect,microbial biomass C(Cmic),and β-glucosidase activity,and more abundant populations of bacteria and fungi than the soil 1. Also,soil CO2 emission,Cmic,β-glucosidase activity,and bacterial and fungal population sizes were substantially enhanced by straw amendment. In the presence of straw,the amount of straw mineralization and assimilation by microbes in the soil at 55% of water holding capacity(WHC) were significantly higher by 31% and 17%,respectively,compared to those at 25% of WHC. In contrast,β-glucosidase activity and fungal population size were both enhanced as the moisture content decreased. Cmicdecreased as straw availability decreased,which was mainly attributed to the reduction of straw-derived Cmic. Amended soils,except the amended soil 2 at 25% of WHC,had a more abundant fungal population as straw availability decreased,indicating that fungal decomposability of added straw was independent of straw availability. Non-metric multidimensional scaling analysis based on fungal denatured gradient gel electrophoresis band patterns showed that shifts in the fungal community structure occurred as water and straw availability varied. The results indirectly suggest that soil fungi are able to adjust their degradation activity to water and straw availability by regulating their community structure.     

Soil fungal and prokaryotic community structure exhibits differential short-term responses to timber harvest in the Pacific Northwest

Conventional clear-cut timber harvest is a widespread industrial practice across the Pacific Northwest;however,information regarding how these practices impact soil microbial community structure at the regional scale is limited.With evidence of consistent and substantial impact of harvest on soil microbial functional profiles across the region(despite a range of environmental conditions),the objective of this study was to determine the extent to which harvest also influences the structure of prokaryotic and fungal soil microbial communities,and how generalized these trends are throughout the geographic region.Paired soil samples were collected one year before and after harvest across nine second-growth Douglas-fir forests in the Pacific Northwest.Total community DNA was extracted from the soils,and high-throughput targeted gene sequencing of the 16 S r RNA gene for prokaryotes and the internal transcribed spacer(ITS)gene for fungi was performed.Alpha diversity was consistently and significantly higher after harvest;it was moderately so for fungal communities(+14.6%),but only marginally so for prokaryotic communities(+2.0%).Similarly,on average,a greater proportion of the variation in the community structure of fungi(20.1%)at each site was associated with forest harvest compared to that of prokaryotes(13.2%).Overall,the greatest influence of timber harvest on soil microbial communities appeared to be a relative depletion of ectomycorrhizal fungi,with a concomitant enrichment of saprotrophic fungi.Understanding the short-term responses of soil microbial communities across the region,particularly those of tree root-associated symbionts,may aid our understanding of the role soil microbial communities play in ecological succession.     

Degradation and humification of maize straw in soil microcosms inoculated with simple and complex microbial communities

Microbial communities are responsible for soil organic matter cycling and thus for maintaining soil fertility. A typical Orthic Luvisol was freed from organic carbon by thermal destruction at 600°C. Then the degradation and humification of ¹⁴C‐labelled maize straw by defined microbial communities was analysed. To study the role of microbial diversity on the humification of plant material, microcosms containing sterilized soil were inoculated with a natural microbial community or with microbial consortia consisting of bacterial and fungal soil isolates. Within 6 weeks, 41 ± 4% of applied ¹⁴C‐labelled maize straw was mineralized in the soil microcosms containing complex communities derived from a soil suspension, whilst the most efficient communities composed of soil isolates mineralized less than 35%. The humification products were analysed by solution state ¹³C‐NMR‐spectroscopy and gel permeation chromatography (GPC). The analyses of humic acids extracts by solution state ¹³C‐NMR‐spectroscopy revealed no difference in the development of typical chemical functional groups for humic substances during incubation. However, the increase in specific molecular size fractions of the extracted humic acids occurred only after inoculation with complex communities, but not with defined isolates. While it seems to be true that redundancy in soil microbial communities contributes to the resilience of soils, specific soil functions may no longer be performed if a microbial community is harshly affected in its diversity or growth conditions.