Investigating microbial community structure in soils by physiological, biochemical and molecular fingerprinting methods

Several biochemical and molecular methods are used to investigate the microbial diversity and changes in microbial community structure in rhizospheres and bulk soils resulting from changes in management. We have compared the effects of plants on the microbial community, using several methods, in three different types of soils. Pots containing soil from three contrasting sites were planted with Lolium perenne (rye grass). Physiological (Biolog), biochemical (PLFA) and molecular (DGGE and TRFLP) fingerprinting methods were employed to study the change in soil microbial communities caused by the growth of rye grass. Different methods of DNA extraction and nested PCR on TRFLP profiles were examined to investigate whether they gave different views of community structure. Molecular methods were used for both fungal and bacterial diversity. Principal component analysis of Biolog data suggested a significant effect of the plants on the microbial community structure. We found significant effects of both soil type and plants on microbial communities in PLFA data. Data from TRFLP of soil bacterial communities showed large effects of soil type and smaller but significant effects of plants. Effects of plant growth on soil fungal communities were measured by TRFLP and DGGE. Multiple Procrustes analysis suggested that both methods gave similar results, with only soil types having a significant effect on fungal communities. However, TRFLP was more discriminatory as it generated more ribotype fragments for each sample than the number of bands detected by DGGE. Neither methods of DNA extraction nor the nested PCR had any effect on the evaluation of soil microbial community structure. In conclusion, the different methods of microbial fingerprinting gave qualitatively similar results when samples were processed consistently and compatible statistical methods used. However, the molecular methods were more discriminatory than the physiological and biochemical approaches. We believe results obtained from this experiment will have a major impact on soil microbial ecology in general and rhizosphere–microbial interaction studies in particular, as we showed that the different fingerprinting methods for microbial communities gave qualitatively similar results.     

Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition

The relative importance of specific plant properties versus soil characteristics in shaping the bacterial community structure of the rhizosphere is a topic of considerable debate. Here, we report the results of a study on the bacterial composition of the rhizosphere of the wild plant Carex arenaria (sand sedge) growing at 10 natural sites in The Netherlands. The soil properties of the sandy soils at these sites were highly disparate, most notably in pH, chloride and organic matter content. Rhizosphere and bulk soil bacterial communities were examined by culture-independent means, namely, 16S rDNA-directed PCR-DGGE profiling. Large differences were observed between the bacterial communities of the different sites for both bulk and rhizosphere soil. Cluster analysis of bacterial profiles revealed that the rhizosphere community of each site was generally more closely related to the bulk soil community of that site rather than to rhizosphere communities of other sites. Hence, bacterial community structure within the rhizosphere of C. arenaria appeared to be determined to a large extent by the bulk soil community composition. This conclusion was supported by a reciprocal planting experiment, where C. arenaria shoots of different sites yielded highly similar rhizosphere communities when planted in the same soil.     

Determination of the impact of continuous defoliation of Lolium perenne and Trifolium repens on bacterial and fungal community structure in rhizosphere soil

To determine the effects of defoliation on microbial community structure, rhizosphere soil samples were taken pre-, and post-defoliation from the root tip and mature root regions of Trifolium repens L. and Lolium perenne L. Microbial DNA isolated from samples was used to generate polymerase chain reaction–denaturing gradient gel electrophoresis molecular profiles of bacterial and fungal communities. Bacterial plate counts were also obtained. Neither plant species nor defoliation affected the bacterial and fungal community structures in both the root tip and mature root regions, but there were significant differences in the bacterial and fungal community profiles between the two root regions for each plant. Prior to defoliation, there was no difference between plants for bacterial plate counts of soils from the root tip regions; however, counts were greater in the mature root region of L. perenne than T. repens. Bacterial plate counts for T. repens were higher in the root tip than the mature root region. After defoliation, there was no effect of plant type, position along the root or defoliation status on bacterial plate counts, although there were significant increases in bacterial plate counts with time. The results indicate that a general effect existed during maturation in the root regions of each plant, which had a greater impact on microbial community structure than either plant type or the effect of defoliation. In addition there were no generic consequences with regard to microbial populations in the rhizosphere as a response to plant defoliation.     

Microbial community composition and functioning in the rhizosphere of three Banksia species in native woodland in Western Australia

Annual plant species differ in their rhizosphere microbial community composition. However, rhizosphere communities are often investigated under controlled conditions, and it is unclear if perennial plants growing in the field also have rhizosphere communities that are specific to a particular plant species. The aim of our study was to determine the bacterial community composition of three species of Banksia (B. attenuata R. Brown, B. ilicifolia R. Brown and B. menziesii R. Brown) growing in close proximity in a native woodland in Western Australia and to relate community structure to function. All three species are small trees that produce cluster roots in the field following winter rains. Cluster roots and rhizosphere soil were sampled in early spring (August 2001) and again four weeks later (September 2001). Many new cluster roots were formed in the period between the August and the September sampling. Rhizosphere soil pH, percent soil moisture and C and N content did not differ significantly among species or sampling times. However, the bacterial community composition on the cluster roots and in the rhizosphere soil, studied by denaturing gradient gel electrophoresis (DGGE), differed among the three species, with cluster root age class (young or mature to senescing) and also between sampling times. These changes in community composition were accompanied by changes in the activity of some of the enzymes studied. The activities of β-glucosidase and protease increased over time. The three species differed in asparaginase activity, but not in the activity of acid and alkaline phosphatase in the rhizosphere. These results suggest a relationship between the changes in composition and function of bacterial communities.     

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.     

Impact of fresh root material and mature crop residues of oilseed rape (Brassica napus) on microbial communities associated with subsequent oilseed rape

Glasshouse bioassays were conducted to assess the impact of different inputs of oilseed rape plant material on soil and rhizosphere microbial diversity associated with subsequently grown oilseed rape (Brassica napus) plants. The first bioassay focussed on the effect of oilseed rape rhizodeposits and fresh detached root material on microbial communities, in a rapid-cycling experiment in which oilseed rape plants were grown successively in pots of field soil for 4 weeks at a time, with six cycles of repeated vegetative planting in the same pot. Molecular analyses of the microbial communities after each cycle showed that the obligate parasite Olpidium brassicae infected the roots of oilseed rape within 4 weeks after the first planting (irrespective of the influence of rhizodeposits alone or in the presence of fresh detached root material), and consistently dominated the rhizosphere fungal community, ranging in relative abundance from 43 to 88 % when oilseed rape was grown more than once in the same soil. Fresh detached root material also led to a reduction in diversity within the soil fungal community, due to the increased relative abundance of O. brassicae. In addition, rhizosphere bacterial communities were found to have a reduced diversity over time when fresh root material was retained in the soil. In the second glasshouse experiment, the effect of incorporating mature, field-derived oilseed rape crop residues (shoots and root material) on microbial communities associated with subsequently grown oilseed rape was investigated. As before, molecular analyses revealed that O. brassicae dominated the rhizosphere fungal community, despite not being prevalent in either the residue material or soil fungal communities.     

Long-term plant growth legacies overwhelm short-term plant growth effects on soil microbial community structure

Plant-soil feedbacks are gaining attention for their ability to determine plant community development. Plant-soil feedback models and research assume that plant-soil interactions occur within days to weeks, yet, little is known about how quickly and to what extent plants change soil community composition. We grew a dominant native plant (Pseudoroegneria spicata) and a dominant non-native plant (Centaurea diffusa) separately in both native- and non-native-cultivated field soils to test if these species could overcome soil legacies and create new soil communities in the short-term. Soil community composition before and after plant growth was assessed in bulk and rhizosphere soils using phospholipid fatty acid analyses. Nematode abundance and mycorrhizal colonization were also measured following plant growth. Field-collected, native-cultivated soils showed greater bacterial, Gram (−), fungal, and arbuscular mycorrhizal PLFA abundance and greater PLFA diversity than field-collected, non-native-cultivated soils. Both plant species grew larger in native- than non-native-cultivated soils, but neither plant affected microbial composition in the bulk or rhizosphere soils after two months. Plants also failed to change nematode abundance or mycorrhizal colonization. Plants, therefore, appear able to create microbial legacies that affect subsequent plant growth, but contrary to common assumptions, the species in this study are likely to require years to create these legacies. Our results are consistent with other studies that demonstrate long-term legacies in soil microbial communities and suggest that the development of plant-soil feedbacks should be viewed in this longer-term context.     

Effects of PAH-Contaminated Soil on Rhizosphere Microbial Communities

Bacterial associations with plant roots are thought to contribute to the success of phytoremediation. We tested the effect of addition of a polycyclic aromatic hydrocarbon contaminated soil on the structure of the rhizosphere microbial communities of wheat (Triticum aestivum), lettuce (Lactuca sativa var. Tango), zucchini (Cucurbita pepo spp. pepo var. Black Beauty), and pumpkin (C. pepo spp. pepo var. Howden) 16S rDNA terminal restriction fragment length polymorphism (T-RFLP) profiles of rhizosphere microbial communities from different soil/plant combinations were compared with a pairwise Pearson correlation coefficient. Rhizosphere microbial communities of zucchini and pumpkin grown in the media amended with highest degree of contaminated soil clustered separately, whereas communities of these plants grown in unamended or amended with lower concentrations of contaminated soil, grouped in a second cluster. Lettuce communities grouped similarly to cucurbits communities, whereas wheat communities did not display an obvious clustering. The variability of 16S rDNA T-RFLP profiles among the different plant/soil treatments were mostly due to the difference in relative abundance rather than presence/absence of T-RFLP fragments. Our results suggest that in highly contaminated soils, the rhizosphere microbial community structure is governed more by the degree of contamination rather than the plant host type.     

<Emphasis Type="Italic">p</Emphasis>-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions

Phenolics from root exudates or decaying residues are usually referred as autotoxins of several plant species. However, how phenolics affect soil microbial communities and their functional significances are poorly understood. Rhizosphere bacterial and fungal communities from cucumber (Cucumis sativus L.) seedlings treated with p-coumaric acid, an autotoxin of cucumber, were analyzed by high-throughput sequencing of 16S rRNA gene and internal transcribed spacer amplicons. Then, feedback effects of the rhizosphere biota on cucumber seedlings were evaluated by inoculating non-sterilized and sterilized rhizosphere soils to sterilized background soils. p-Coumaric acid decreased the bacterial diversity of rhizosphere but increased fungal diversity and altered the compositions of both the bacterial and fungal communities. p-Coumaric acid increased the relative abundances of microbial taxa with phenol-degrading capability (such as Chaetomium, Humicola, and Mortierella spp.) and microbial taxa which contained plant pathogens (such as Fusarium spp.). However, p-coumaric acid inhibited the relative abundances of Lysobacter, Haliangium, and Gymnoascus spp., whose species can have pathogen-antagonistic and/or plant-growth-promoting effects. The positive effect of cucumber rhizosphere microbiota on cucumber seedling growth was reduced by p-coumaric acid. Overall, our results showed that, besides its direct phytotoxicity, p-coumaric acid can inhibit cucumber seedling growth through generating negative plant-soil microbial interactions.     

Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars

The progenitor of maize is Balsas teosinte (Zea mays subsp. parviglumis) which grows as a wild plant in the valley of the Balsas river in Mexico. Domestication, primarily targeting above-ground traits, has led to substantial changes in the plant's morphology and modern maize cultivars poorly resemble their wild ancestor. We examined the hypotheses that Balsas teosinte (accession PI 384071) has a) a different root system architecture and b) a structurally and functionally different rhizosphere microbial community than domesticated cultivars sweet corn (Zea mays subsp. mays accession PI 494083) and popping corn (Zea mays subsp. mays accession PI 542713). In a greenhouse experiment, five plants from each corn variety were grown in individual pots containing a Maury silt loam – perlite (2:1) mixture and grown to the V8 growth stage at which rhizosphere bacterial and fungal community structure was assessed using terminal restriction fragment length polymorphism and fatty acid methyl ester analysis. Functional characteristics of the rhizosphere were assayed by examining the potential activity of seven extracellular enzymes involved in carbon, nitrogen and phosphorus cycling. Root system architecture was characterized by root scans of sand grown plants at the V5 growth stage. Compared to the control the sweet corn rhizosphere had different bacterial and fungal community structure, decreased fungal diversity and increased bacterial abundance. Teosinte caused a significant change in the rhizosphere bacterial and fungal community structure and increased bacterial abundance, but no significant decrease in bacterial or fungal diversity where the former was found to be significantly greater than in the sweet corn rhizosphere. Popping corn did not trigger significant changes in the bacterial or fungal diversity and bacterial abundance in the soil. The individual popping corn plants changed the bacterial and fungal communities in different directions and the overall effect on community structure was significant, but small. Of the enzymes analyzed, potential N-acetylglucosaminidase (NAG) activity was found to contributed most to the differentiation of teosinte rhizosphere samples from the other corn varieties. The teosinte root system had proportionally more very fine (diameter < 0.03 mm) roots than popping corn and sweet corn and it developed the highest root to shoot dry weight ratio, followed by popping corn. Sweet corn had significantly lower average root diameter than popping corn and teosinte and grew proportionally the least below-ground dry mass. The results allude to functional and structural differences in the rhizosphere microbial communities of the corn varieties that, with additional research, could lead to useful discoveries on how corn domestication has altered rhizosphere processes and how plant genotype influences nutrient cycling.     

Relationships between microbial indices in roots and silt loam soils forming a gradient in soil organic matter

Perennial rye grass (Lolium perenne) was grown in a greenhouse pot experiment on seven soils to answer the question whether the microbial colonisation of roots is related to existing differences in soil microbial indices. The soils were similar in texture, but differed considerably in soil organic matter, microbial biomass, and microbial community structure. Ergosterol and fungal glucosamine were significantly interrelated in the root material. This ergosterol was also significantly correlated with the average ergosterol content of bulk and rhizosphere soil. In addition, the sum of fungal C and bacterial C in the root material revealed a significant linear relationship with microbial biomass C in soil. The colonisation of roots with microorganisms increased apparently with an increase in soil microbial biomass. In the root material, microbial tissue consisted of 77% fungi and 23% bacteria. In soil, the fungal dominance was slightly, but significantly lower, with 70% fungi and 30% bacteria. Fungal glucosamine in the root material was significantly correlated with that in soil (r=0.65). This indicates a close relationship between the composition of dead microbial remains in soil and the living fraction in soil and root material for unknown reasons.     

Soil structural responses to alterations in soil microbiota induced by the dilution method and mycorrhizal fungal inoculation

This investigation examines the effect of manipulating soil microbial community composition and species richness on the development of soil structure over a seven month period in planted (with or without mycorrhizal fungi) and in unplanted macrocosms. The dilution method effectively resulted in soil communities with consistently contrasting levels of species (TRF) richness. In particular, the 10^?6 dilution of field soil resulted in less rich communities in bare unplanted soil than did the 10^?1 soil dilution. However, this was not the case in planted soils where root activity was a powerful influence on species richness. After seven months, principal components analysis (PCA) separated bacterial community composition primarily on planting regime; planted mycorrhizal, planted non-mycorrhizal and bare soil treatments all contained different bacterial community compositions. A consistent finding in planted and unplanted soils was that aggregate stability was positively correlated with small pore sizes. Mycorrhizal colonisation decreased plant biomass and also resulted in reduced soil bacterial species richness, lower percentage organic matter and smaller pore sizes relative to planted but non-mycorrhizal soils. However, soil aggregate stability and water repellency were increased in these (mycorrhizal) soils probably due to AMF hyphal activities including enmeshment and/or glomalin production. In contrast, bacterial TRF richness was positively correlated with aggregate stability in the bare and non-mycorrhizal planted soils. Soil organic carbon was an important factor in all treatments, but in the bare soil where there was no additional input of labile C from roots, the percentage C could be directly related to fungal TRF richness. The less species rich bare soil contained more organic C than the more species rich bare soil. This suggests a degree of redundancy with regard to mineralisation of organic matter when additional, more utilisable C sources are unavailable. Understanding the effects of microbial diversity on functional parameters is important for advancing sustainable soil management techniques, but it is clear that soil is a dynamic ecosystem.     

Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities

We studied the microbial communities in maize (Zea mays) rhizosphere to determine the extent to which their structure, biomass, activity and growth were influenced by plant genotype (su1 and sh2 genes) and the addition of standard and high doses of different types of fertilizer (inorganic, raw manure and vermicompost). For this purpose, we sampled the rhizosphere of maize plants at harvest, and analyzed the microbial community structure (PLFA analysis) and activity (basal respiration and bacterial and fungal growth rates). Discriminant analysis clearly differentiated rhizosphere microbial communities in relation to plant genotype. Although microorganisms clearly responded to dose of fertilization, the three fertilizers also contributed to differentiate rhizosphere microbial communities. Moreover, larger plants did not promoted higher biomass or microbial growth rates suggesting complex interactions between plants and fertilizers, probably as a result of the different performance of plant genotypes within fertilizer treatments, i.e. differences in the quality and/or composition of root exudates.     

Impact of 12-year field treatments with organic and inorganic fertilizers on crop productivity and mycorrhizal community structure

The effect of manure and mineral fertilization on the arbuscular mycorrhizal (AM) fungal community structure of sunflower (Helianthus annuus L.) plants was studied. Soils were collected from a field experiment treated for 12 years with equivalent nitrogen (N) doses of inorganic N, dairy manure slurry, or without N fertilization. Fresh roots of tall fescue (Festuca arundinacea Schreb.) grass collected from the field plots without N fertilization and unfumigated field soils were used as native microbial inoculum sources. Sunflower plants were sown in pots containing these soils, and three different means of manipulating the microbial community were set: unfumigated soil with fresh grass roots, fumigated soil with fresh grass roots, or fumigated soil with sterilized grass roots. Assessing the implications with respect to plant productivity and mycorrhizal community structure was investigated. Twelve AM fungal OTUs were identified from root or soil samples as different taxa of Acaulospora, Claroideoglomus, Funneliformis, Rhizophagus, and uncultured Glomus, using PCR-DGGE and sequencing of an 18S rRNA gene fragment. Sunflower plants grown in manure-fertilized soils had a distinct AMF community structure from plants either fertilized with mineral N or unfertilized, with an abundance of Rhizophagus intraradices-like (B2). The results also showed that AM inoculation increased P and N contents in inorganic N-fertilized or unfertilized plants, but not in manure-fertilized plants.     

Characterization of rhizosphere microbial community structure in five similar grass species using FAME and BIOLOG analyses

Accelerated biodegradation of organic contaminants in planted soil is frequently reported yet our current understanding of plant–microbe interactions does not allow us to predict which plant species can encourage the development of rhizosphere communities with enhanced degradation capacity. In a companion study, five grass species (Sudan grass, ryegrass, tall fescue, crested wheatgrass, and switch grass) were grown in a Matapeake silt loam soil to study the degradation of atrazine and phenanthrene by rhizosphere microorganisms (see Fang et al., 2000, this vol., Fang, C., Radosevich, M., Fuhrmann, J. J., 2000. Atrizine and phenanthrene degradation in grass rhizosphere soil. Soil Biology & Biochemistry, in press). In the present paper substrate utilization patterns (BIOLOG^®), and fatty acid methyl ester (FAME) profiles of the same rhizosphere microbial communities were determined. Both FAME and BIOLOG^® analyses detected changes in soil microbial community structure among treatments. However, community structure did not directly correlate to either ATR or PHE degradation rates.     

十种湿生植物根际真菌群落参数和土壤肥力的比较

【目的】利用人工湿地是目前我国进行点源污水处理的一项重要技术,人工湿地的湿生植物及其根际微生物对污水处理有重要影响。目前人们普遍关注的是湿生植物根际细菌的群落结构和功能,而对根际真菌群落结构的信息较少。本文主要研究10种湿生植物根际的土壤肥力、真菌数量、生物量和真菌的碳代谢,目的在于筛选出根际土壤真菌生物量和活性均较大的植物种类,为今后人工湿地的建设提供参考依据。【方法】采用"向后抛石法"随机选取采样点,收集10种湿生植物根际土壤。采用常规方法测定土壤有机碳、全氮和全磷含量;真菌数量采用稀释平板法,真菌生物量(麦角固醇含量)采用高效液相色谱法(HPLC)测定;真菌碳代谢指纹采用FF板进行分析。【结果】银边石菖蒲、花叶香蒲和黄菖蒲根际土壤分别有较高的有机碳、全氮和全磷含量(P0.05)。黄菖蒲根际土壤真菌数量和生物量最大(P0.05)。相关分析表明,土壤全磷与真菌数量和生物量有极显著的正相关关系(P0.05),是制约土壤真菌分布的重要因素。碳代谢指纹分析表明,水生美人蕉土壤真菌对95种碳源的平均利用活性以及对6种碳源群的利用强度均大于其它植物,土壤全氮显著地影响了真菌群落对碳水化合物的利用(P0.05)。【结论】10种湿生植物根际土壤肥力和真菌群落有显著性差异,因而土壤肥力和真菌群落可以作为筛选人工湿地植物的重要依据,但这一结论还有待从分子生物学的角度进一步验证。     

Effects of two grass species on the composition of soil fungal communities

Many studies have shown effects of plants species on fungal communities, but these are often confounded with soil effects. Thus, the specific role of plant species in structuring rhizospheric and soil fungal communities is poorly described. Our study used microcosms in which plants were grown under artificial conditions to bridge this gap. Two perennial grasses dominating subalpine grasslands, Festuca paniculata and Dactylis glomerata, were grown at two levels of fertilization on standard soil. Fungal communities were determined by 454 pyrosequencing of the internal transcribed spacer 1 region. Among the fungal communities characterized by the primers used, original communities were associated to each plant species and also diverged between rhizosphere and bulk soils within each plant species, though there were no significant fertilization effects. Differences regarded global composition of the fungal communities and abundant molecular operational taxonomic units (MOTUs). Both plant species and location effects were reflected more in the abundance than in the composition of MOTUs. The observed differences in fungal communities coincide with differing strategies of plant root growth, with D. glomerata having greater root mass, length, and area than F. paniculata. Our study, by dissociating soil effects from plant effects, demonstrated that plant species exert a key control on soil fungi. We suggest that such effects may be linked to inter-specific differences in root traits and their consequences on nitrogen uptake.     

Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield

Plants directly interact with the soil microbial community through litter inputs and root exudates, and these interactions may be particularly important in nutrient poor soils that typically characterize early ecosystem development. However, little is known regarding how plant–microbe interactions may actually drive ecosystem processes in early succession, a perspective this study helps to define. We investigated how soil microbial communities develop and interact with the establishment of the first plants in the recently exposed soils of the Mendenhall Glacier forefield near Juneau, AK, USA. We sampled soils from under two different plant species (alder, Alnus sinuata and spruce, Picea sitchensis) and from unvegetated areas; all samples were collected along a single soil transect that had been exposed for 6 years. The presence or absence of vegetation as well as the type of plant (i.e., alder vs. spruce) structured the soil microbial community. Furthermore, asymbiotic nitrogen (N) fixation rates, which were greater in vegetated soils, correlated with differences in bacterial community composition. Although soil microbial community composition varied with vegetation type, soil nutrient and carbon (C) pools did not correlate with bacterial community composition. Moreover, pH did not significantly vary by vegetation type, yet it was the only soil parameter that correlated with bacterial community composition. Vegetation type explained more of the variation in bacterial community composition than pH, suggesting that plant acidification of soils only partly explains the observed shifts in bacterial communities. Plant specific differences in bacterial community structure may also relate to the chemical composition of litter and root exudates. Our research reveals differences in the bacterial community composition of vegetated soils, and how such differences may promote shifts in fundamental biogeochemical processes, such as rates of asymbiotic N fixation, in early stages of primary succession where low N availability may limit bacterial and plant growth and thus constrain ecosystem development. As such, this suggests that plant–soil microbe interactions in themselves may drive processes that shape the trajectory of primary succession.     

Fire severity shapes plant colonization effects on bacterial community structure,microbial biomass,and soil enzyme activity in secondary succession of a burned forest

The increasing frequency and severity of wildfires has led to growing attention to the effects of fire disturbance on soil microbial communities and biogeochemical cycling. While many studies have examined fire impacts on plant communities, and a growing body of research is detailing the effects of fire on soil microbial communities, little attention has been paid to the interaction between plant recolonization and shifts in soil properties and microbial community structure and function. In this study, we examined the effect of a common post-fire colonizer plant species, Corydalis aurea, on soil chemistry, microbial biomass, soil enzyme activity and bacterial community structure one year after a major forest wildfire in Colorado, USA, in severely burned and lightly burned soils. Consistent with past research, we find significant differences in soil edaphic and biotic properties between severe and light burn soils. Further, our work suggests an important interaction between fire severity and plant effects by demonstrating that the recolonization of soils by C. aurea plants only has a significant effect on soil bacterial communities and biogeochemistry in severely burned soils, resulting in increases in percent nitrogen, extractable organic carbon, microbial biomass, β-glucosidase enzyme activity and shifts in bacterial community diversity. This work propounds the important role of plant colonization in succession by demonstrating a clear connection between plant colonization and bacterial community structure as well as the cycling of carbon in a post-fire landscape. This study conveys how the strength of plant–microbe interactions in secondary succession may shift based on an abiotic context, where plant effects are accentuated in harsher abiotic conditions of severe burn soils, with implications for bacterial community structure and enzyme activity.     

In situ dynamics of soil fungal communities under different genotypes of potato, including a genetically modified cultivar

Fungi are key to the functioning of soil ecosystems, and exhibit a range of interactions with plants. Given their close associations with plants, and importance in ecosystem functioning, soil-borne fungi have been proposed as potential biological indicators of disturbance and useful agents in monitoring strategies, including those following the introduction of genetically modified (GM) crops. Here we report on the impact of potato crop varieties, including a cultivar that was genetically modified for its starch quality, on the community composition of the main phyla of fungi in soils, i.e. Ascomycota, Basidiomycota and Glomeromycota in rhizosphere and bulk soil. Samples were collected at two field sites before sowing, at three growth stages during crop development and after the harvest of the plants, and the effects of field site, plant growth stage and plant cultivar (genotype) on fungal community composition assessed using three phylum-specific T-RFLP profiling strategies and multivariate statistical analysis (NMDS ordinations with ANOSIM test). In addition, fungal biomass, arbuscular mycorrhizal colonization of roots and activities of extracellular fungal enzymes (laccases, Mn-peroxidases and cellulases) involved in degradation of lignocelluloses-rich organic matter were determined. Fungal community compositions, densities and activities were observed to differ significantly between the rhizosphere and bulk soil. The most important factors determining fungal community composition and functioning were plant growth stage for the rhizosphere communities and location and soil properties for the bulk soil communities. The basidiomycetes were the most numerous fungal group in the bulk soils and in the rhizosphere of young plants, with a shift toward greater ascomycete numbers in the rhizosphere at later growth stages. There were no detectable differences between the GM cultivar and its parental cultivar in terms of influence on fungal community structure of function. Fungal community structure and functioning of both GM- and parental cultivars fell within the range of other cultivars at most sampling moments.