Changes in Mycobacterium spp. population structure and pyrene mineralization in polycyclic aromatic hydrocarbon-amended soils

The effect of pyrene and phenanthrene contamination on soil Mycobacterium spp. community structure was examined using PCR-amplification of 16S rRNA genes with primers specific for the fast-growing group of Mycobacterium spp. and separation of phylotypes by temperature gradient gel electrophoresis (TGGE). The degradative potential of the soil microbial community was measured over time by mineralization of ¹⁴C-pyrene added to the contaminated soils. PCR-TGGE profiles, in combination with band sequencing and phylogenetic analysis of the prominent phylotypes, indicated shifts in the Mycobacterium spp. community during incubation. Reductions in species diversity and enrichments of specific populations were observed in all pyrene- and phenanthrene-treated soils, in contrast to the relatively stable control soil profiles. Mineralization studies indicated the shortest acclimation periods and the highest initial rates of pyrene degradation occurred in soils pre-exposed to phenanthrene, or a mixture of phenanthrene and pyrene, for 14 weeks. Pre-exposure of soil microorganisms to a single dose of pyrene for the same length of time also decreased the acclimation period for the degradation of pyrene. Monthly application of either pyrene or phenanthrene to soils, however, resulted in an increase in pyrene degradative potential 6 weeks after the first pre-exposure, but a decrease in degradative potential 14 weeks after the first pre-exposure. Similar PCR-TGGE profiles were obtained from soils with comparable pyrene mineralization curves or degradative potentials.     

Long-term soil feedback on plant N allocation in defoliated grassland miniecosystems

Defoliation of plants is known to have effects on soil organisms and nutrient availability in grassland communities, but few studies have examined whether changes in soil attributes can further feed back to plant growth and plant nutrient content. To examine defoliation-induced soil feedbacks, we established replicated miniecosystems with a grass Phleum pratense, defoliated half of the systems, collected soil from both defoliated and non-defoliated systems and planted new seedlings into each soil. The two soils did not differ in promoting shoot and root growth. However, seedlings that grew in the soil collected from defoliated systems had higher shoot N content, allocated relatively more N to shoots and had lower root N concentration than those growing in the soil collected from non-defoliated systems. Our study provides novel evidence that defoliation can generate long-lasting changes in grassland soil that in turn can affect plant N allocation.     

Long-term effects of mineral fertilizers on soil microorganisms – A review

Increasing nutrient inputs into terrestrial ecosystems affect not only plant communities but also associated soil microbial communities. Studies carried out in predominantly unmanaged ecosystems have found that increasing nitrogen (N) inputs generally decrease soil microbial biomass; less is known about long-term impacts in managed systems such as agroecosystems. The objective of this paper was to analyze the responses of soil microorganisms to mineral fertilizer using data from long-term fertilization trials in cropping systems. A meta-analysis based on 107 datasets from 64 long-term trials from around the world revealed that mineral fertilizer application led to a 15.1% increase in the microbial biomass (C_mic) above levels in unfertilized control treatments. Mineral fertilization also increased soil organic carbon (C_org) content and our results suggest that C_org is a major factor contributing to the overall increase in C_mic with mineral fertilization. The magnitude of the effect of fertilization on C_mic was pH dependent. While fertilization tended to reduce C_mic in soils with a pH below 5 in the fertilized treatment, it had a significantly positive effect at higher soil pH values. Duration of the trial also affected the response of C_mic to fertilization, with increases in C_mic most pronounced in studies with a duration of at least 20 years. The input of N per se does not seem to negatively affect C_mic in cropping systems. The application of urea and ammonia fertilizers, however, can temporarily increase pH, osmotic potential and ammonia concentrations to levels inhibitory to microbial communities. Even though impacts of fertilizers are spatially limited, they may strongly affect soil microbial biomass and community composition in the short term. Long-term repeated mineral N applications may alter microbial community composition even when pH changes are small. How specific microbial groups respond to repeated applications of mineral fertilizers, however, varies considerably and seems to depend on environmental and crop management related factors.     

Temporal variability in plant and soil nitrogen pools in a high-Arctic ecosystem

This study determined temporal variability in N pools, both aboveground and belowground, across two contrasting plant communities in high-Arctic Spitsbergen, Svalbard (78°N). We measured N pools in plant material, soil microbial biomass and soil organic matter in moist (Alopecurus borealis dominated) and dry (Dryas octopetala dominated) meadow communities at four times during the growing season. We found that plant, microbial and dissolved inorganic and organic N pools were subject to significant, but surprisingly low, temporal variation that was controlled primarily by changes in temperature and moisture availability over the short growing season. This temporal variability is much less than that experienced in other seasonally cold ecosystems such as alpine tundra where strong seasonal partitioning of N occurs between plant and soil microbial pools. While only a small proportion of the total ecosystem N, the microbial biomass represented the single largest of the dynamic N pools in both moist and dry meadow communities (3.4% and 4.6% of the total ecosystem N pool, respectively). This points to the importance of soil microbial community dynamics for N cycling in high-Arctic ecosystems. Microbial N was strongly and positively related to soil temperature in the dry meadow, but this relationship did not hold true in the wet meadow where other factors such as wetter soil conditions might constrain biological activity. Vascular live belowground plant parts represented the single largest plant N pool in both dry and moist meadow, constituting an average of 1.6% of the total N pool in both systems; this value did not vary across the growing season or between plant communities. Overall, our data illustrate a surprisingly low growing season variability in labile N pools in high-Arctic ecosystems, which we propose is controlled primarily by temperature and moisture.     

Influence of organic and mineral amendments on microbial soil properties and processes

Microbial diversity in soils is considered important for maintaining sustainability of agricultural production systems. However, the links between microbial diversity and ecosystem processes are not well understood. This study was designed to gain better understanding of the effects of short-term management practices on the microbial community and how changes in the microbial community affect key soil processes. The effects of different forms of nitrogen (N) on soil biology and N dynamics was determined in two soils with organic and conventional management histories that varied in soil microbial properties but had the same fertility. The soils were amended with equal amounts of N (100 kg ha⁻¹) in organic (lupin, Lupinus angustifolius L.) and mineral form (urea), respectively. Over a 91-day period, microbial biomass C and N, dehydrogenase enzyme activity, community structure of pseudomondas (sensu stricto), actinomycetes and α proteobacteria (by denaturing gradient gel electrophoresis (DGGE) following PCR amplification of 16S rDNA fragments) and N mineralisation were measured. Lupin amendment resulted in a two- to five-fold increase in microbial biomass and enzyme activity, while these parameters did not differ significantly between the urea and control treatments. The PCR–DGGE analysis showed that the addition of mineral and organic compounds had an influence on the microbial community composition in the short term (up to 10 days) but the effects were not sustained over the 91-day incubation period. Microbial community structure was strongly influenced by the presence or lack of substrate, while the type of amendment (organic or mineral) had an effect on microbial biomass size and activity. These findings show that the addition of green manures improved soil biology by increasing microbial biomass and activity irrespective of management history, that no direct relationship existed among microbial structure, enzyme activity and N mineralisation, and that microbial community structure (by PCR–DGGE) was more strongly influenced by inherent soil and environmental factors than by short-term management practices.     

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.     

Impact of low-molecular-weight organic acids on the availability of phenanthrene and pyrene in soil

The impact of low-molecular-weight organic acids (LMWOAs) on the availability of phenanthrene and pyrene was investigated using laboratory batch assays. Experiments were conducted with two types of soil with different organic contents. The LMWOAs used were citric and oxalic acid. A mild solvent extraction procedure and a sorption-desorption experiment were used to predict the availability of phenanthrene and pyrene. Results showed that the extractable amounts of phenanthrene and pyrene in both soil types increased with increased citric or oxalic acid concentration. Citric acid addition promoted phenanthrene and pyrene extraction to a greater degree than oxalic acid. Compared with freshly spiked soils, the extractable amounts of phenanthrene and pyrene with the addition of LMWOAs decreased significantly after 60 days of cultivation. Soils with higher values of soil organic carbon content (f_oc) showed decreased phenanthrene and pyrene availability after the addition of LMWOAs. The sorption and desorption results also demonstrated the enhanced availability of PAHs with LMWOA addition. Phenanthrene sorption could be described using a linear model, regardless of the addition of LMWOAs. The simulated distribution constants (K_d) for phenanthrene sorption decreased significantly with the addition of LMWOAs. In contrast, phenanthrene desorption clearly increased with the addition of LMWOAs. These results suggest that the availabilities of phenanthrene and pyrene can be increased with the addition of suitable LMWOAs.     

Microbial function in adjacent subtropical forest and agricultural soil

Soil microbial communities and their activities are altered by land use change; however impacts and extent of these alterations are often unclear. We investigated the functional responses of soil microbes in agricultural soil under sugarcane and corresponding native soil under Eucalyptus forest to additions of contrasting plant litter derived from soybean, sugarcane and Eucalyptus in a microcosm system, using a suite of complimentary techniques including enzyme assays and community level physiological profiles (CLPP). Initially agricultural soil had 50% less microbial biomass and lower enzyme activities than forest soil, but significantly higher nitrification rates. In response to litter addition, microbial biomass increased up to 11-fold in agricultural soil, but only 1.8-fold in forest soil, suggesting a prevalence of rapidly proliferating ‘r’ and slower growing ‘K’ strategists in the respective soils. Litter-driven change in microbial biomass and activities were short lived, largely returning to pre-litter addition levels by day 150. Decomposition rates of sugarcane and soybean litter as estimated via CO₂ production were lower in agricultural than in forest soil, but decomposition of more recalcitrant Eucalyptus litter was similar in both soils, contradicting the notion that microbial communities specialise in decomposing litter of the dominant local plant species. Enzyme activities and community level physiological profiles (CLPP) were closely correlated to microbial biomass and overall CO₂ production in the agricultural soil but not the forest soil, suggesting contrasting relationships between microbial population dynamics and activity in the two soils. Activities of enzymes that break down complex biopolymers, such as protease, cellulase and phenol oxidase were similar or higher in the agricultural soil, which suggests that the production of extracellular biopolymer-degrading enzymes was not a factor limiting litter decomposition. Enzyme and CLPP analyses produced contrasting profiles of microbial activity in the two soils; however the combination of both analyses offers additional insights into the changes in microbial function and community dynamics that occur after conversion of forest to agricultural land.     

Benefactor and allelopathic shrub species have different effects on the soil microbial community along an environmental severity gradient

Patches where shrubs have either positive or negative effects on their understory plant community are common in arid ecosystems. The intensity and balance of these effects change along environmental severity gradients but, despite the major role of soil microbes in plant interactions, little is known about the differences among soil microbial communities under these species and their possible influence on such contrasting shrub effects. We hypothesized that microbial communities associated to benefactor and allelopathic shrubs would differ among them and that differences would increase with environmental severity. To test these hypotheses we characterized soil microbial biomass, activity and community composition under a benefactor shrub species, Retama sphaerocarpa, an allelopathic shrub species, Thymus hyemalis, and in bare soil among plants (gaps) at three sites along an environmental severity gradient. Shrubs promoted an increase in soil bacterial diversity, being bacterial communities associated to benefactor shrubs, allelopathic shrubs and gaps different in composition. Microbial enzymatic activity and biomass increased under shrubs and under more mesic conditions; nonetheless, they were highest under benefactor shrubs at the most arid site and under allelopathic shrubs at the less severe site. Compared to gaps, the presence of shrubs induced changes in microbial activity and community composition that were larger at the most severe site than at the less severe site. Along the gradient, benefactor shrubs enhanced the abundance of bacterial groups involved in organic matter decomposition and N fixation as well as plant pathogens, which could contribute to Retama's outstanding positive effects on understory plant biomass and diversity. Plant patches mitigate the effects of extreme conditions on associated plant and soil microbial communities and promote soil biodiversity and ecosystem functioning in arid ecosystems, with shrubs actively selecting for specific microbial groups in their understory.     

Eucalyptus grandis and Acacia mangium in monoculture and intercropped plantations: Evolution of soil and litter microbial and chemical attributes during early stages of plant development

Soil microorganisms and microbial processes are influenced by the quality and quantity of plant waste entering the soil, by its seasonal and spatial distribution, by the ratio of above- to below-ground inputs, and by changes in nutrient inputs. Soil management strategies sometimes promote mixed-species plantations to mitigate the loss of soil nutrients and improve biogeochemical cycling. The objective of this study was to explore changes in microbiological and chemical attributes of soils and litter in the early stages of the second rotation of mixed and pure plantations of Eucalyptus grandis and Acacia mangium, and to look for correlations between attributes. Soil samples at 0–10 cm depth were collected two, seven, 14, and 20 months after planting in the following treatments: monocultures of A. mangium and E. grandis, a monoculture of E. grandis with N-fertilizer, and an intercropped plantation with E. grandis and A. mangium. Microbial soil attributes varied dramatically between treatments 20 months after planting. Total C, N and P contents in litter showed the strongest correlations with microbial biomass C and N (C_mic and N_mic), microbial respiration, and dehydrogenase activity in all sampling periods. Lower C/N and C/P ratios in litter and lower C/N and C_mic/tC ratios in soils after 20 months in the intercropped plantation illustrated the system's capacity for supplying inputs of high-quality organic matter rich in N and P, but this did not result in higher contents of these elements or greater microbial activity in soils. An implication of this finding is that, at least in the initial growth phase of these plantations, chemical attributes of the litter and variation in those attributes govern microbial processes and, consequently, are mostly responsible for plant development. Canonical discriminant analysis revealed changes in the microbiological and chemical attributes of soil in the intercropped plantation due to the plants growth and the leaf litter accumulation. Twenty months after planting, the different plantations could be discriminated by differences in litter chemistry (C, N, and P), total soil C, N_mic, and dehydrogenase activity, which were very similar in intercropped plantations and E. grandis with N-fertilizer. These results from the early stages of plantation development are important for understanding the dynamics of soil attributes in these systems, and especially in intercropped plantations. In intercropped areas the cumulative effect of microbial attributes reflects a more sustainable system. Long-term studies are needed to identify patterns that develop after 20 months, during the growth period of these plantations.     

Pasture and forest soil microbial communities show distinct patterns in their catabolic respiration responses at a landscape scale

Catabolic responses to specific substrates can be used to differentiate soil microbial communities. We hypothesized that the catabolic respiration responses of microbial communities from pastures would differ from those of forest soils, and that the differences would be consistent at a landscape scale, due to inherent differences in litter quality and management regimes. We analysed respiration responses to 25 different substrates of 20 pasture soils (dominated by rye grass and white clover) and 20 forest soils (indigenous forest species or the plantation species Pinus radiata) over a wide geographical range in New Zealand.Within each pasture or forest category, the catabolic responses showed a similar pattern, suggesting similarities in functional catabolic capability and microbial community Indigenous forests and pine forests microbial communities did not differ in their responses. Pasture soil communities had significantly higher relative responses to carbohydrate and amino-acid substrates and significantly lower relative response to carboxylic acid substrates, than microbial communities from forest soils. Forest soils had relatively greater responses to carboxylic acids as a group, as well as citric acid, α-ketobutyric acid, α-ketoglutaric acid, and α-ketovaleric acid, than did the pasture soils. A subset of 6 substrates was equally as effective at differentiating the microbial catabolic response of pasture soils from forest soils as the entire set of 25 substrates. The results demonstrated distinct differences in the respiration responses of the soil microbial communities of pastures and forests, but showed strong similarities within each vegetation class, despite the wide geographical spread, different soils and plant species.     

Rhizosphere microbial community and Zn uptake by willow (Salix purpurea L.) depend on soil sulfur concentrations in metalliferous peat soils

On numerous occasions, rhizosphere microbial activities have been identified as a key factor in metal phytoavailability to various plant species and in phytoremediation of metal-contaminated sites. For soil bioremediation efforts in heavy metal contaminated areas, microbes adapted to higher concentrations of heavy metals are required. This study was a field survey undertaken to examine rhizosphere microbial communities and biogeochemistry of soils associated with Zn accumulation by indigenous willows (Salix purpurea L.) in the naturally metalliferous peat soils located near Elba, NY. Soil and willow leaf samples were collected from seven points, at intervals 18 m apart along a willow hedgerow, on four different dates during the growing season. Soil bacterial community composition was characterized by terminal restriction fragment length polymorphism (T-RFLP) analysis and a 16S clone library was created from the rhizosphere of willows and soils containing the highest concentrations of Zn. Bacterial community composition was correlated with soil sulfate, but not with soil pH. The clone library revealed comparable phylogenetic associations to those found in other heavy metal-contaminated soils, and was dominated by affiliations within the phyla Acidobacteria (32%), and Proteobacteria (37%), and the remaining clones were associated with a wide array of phyla including Actinobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Bacteriodetes, and Cyanobacteria. Diverse microbial populations were present in both rhizosphere and bulk soils of these naturally metalliferous peat soils with community composition highly correlated to the soil sulfate cycle throughout the growing season indicative of a sulfur-oxidizing rhizosphere microbial community. Results confirm the importance of soil characterization for informing bioremediation efforts in heavy metal contaminated areas and the reciprocity that microbial communities uniquely adapted to specific conditions and heavy metals may have on an ecosystem.     

Response of microbial diversity to C:N:P stoichiometry in fine root and microbial biomass following afforestation

Soil samples were collected in June and October from areas with three land-use types, i.e., Robinia pseudoacacia L. (RP), Caragana korshinskii Kom. (CK), and abandoned land (AL), of which the former two were afforested areas, whereas the latter was not. These areas were converted from similar farmlands 40 years prior. Illumina sequencing of 16S rRNA gene and fungal ITS gene was used to analyze soil bacterial and fungal diversity. Additionally, plant communities, soil properties, fine root biomass, and C, N, and P levels in fine root and microbial biomass were estimated. Compared to AL, the C:N:P stoichiometry in fine root and microbial biomass in the afforested lands was synchronously changed, especially the N:P ratio. Soil microbial diversities were affected by afforestation and were more related to N:P ratio than C:P and C:N ratios. Moreover, Alpha-proteobacteria, Gamma-proteobacteria, and Bacteroidetes were significantly more abundant in afforested soils than in the AL soil, and the abundances of Actinobacteria, Chloroflexi, Cyanobacteria, and Nitrospirae ranked as AL > RP or CK. For fungal taxa, Ascomycota abundance responded positively to afforestation, whereas Basidiomycota abundance responded negatively. Changes of soil microbial taxa were significantly correlated with the N:P ratio in fine root and microbial biomass, which explained 54.1 and 55% of the total variation in bacterial and fungal taxa, respectively. Thus, our results provide evidence that compositions of soil microbial communities are linked to the N:P ratio in the plant-soil system.     

RHIZOSPHERE MICROBIAL POPULATIONS IN CONTAMINATED SOILS

Rhizosphere microbial populations may increase bioremediation of soil contaminated with organic chemicals. A growth chamber study was conducted to evaluate rhizosphere microbial populations in contaminated and non-contaminated soil. Alfalfa (Medicago sativa L.) and alpine bluegrass (Poa alpina L.) were grown in soil containing a mixture of organic chemicals for 14 weeks. The equal millimolar mixture of hexadecane, (2,2-dimethylpropyl)benzene, cis-decahydronaphthalene (decalin), benzoic acid, phenanthrene, and pyrene was added at levels of 0 and 2000 mg/kg. Organic chemical degrader (OCD) populations were assessed by a Most-Probable-Number technique, and bacteria and fungi were enumerated by plate count methods. Different methods for expressing OCD rhizosphere populations were investigated to determine the effect it had on interpretation of the results. At 9 weeks, the OCD numbers were significantly higher in rhizosphere and contaminated soils than in bulk and non-contaminated soils, respectively. Alfalfa rhizosphere OCD levels were 4 × 10⁷/g for contaminated and 6 × 10⁶/g for non-contaminated soils. Bluegrass rhizosphere OCD levels were 1 × 10⁷/g and 1 × 10⁶/g in contaminated and non-contaminated soils, respectively. Selective enrichment of OCD populations was observed in contaminated rhizosphere soil. Higher numbers of OCD in contaminated rhizospheres suggest potential stimulation of bioremediation around plant roots.     

Enrichment of functional microbes and genes during pyrene degradation in two different soils

Purpose

Stimulating microbial degradation is a promising strategy for the remediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs). To better understand the functional microbial populations and processes involved in pyrene biodegradation in situ, the dynamics of pyrene degradation and functional microbial abundance were monitored during pyrene incubation in soils. We hope our findings will provide new insights into in situ pyrene biodegradation in soils and help to identify functional microbes from soils.

Materials and methods

Pyrene (60 mg kg^?1) was incubated with two different soils, one is lower PAH-containing agricultural soil (LS), and the other is higher PAH-containing industrial soil (HS). During incubation, triplicate samples were collected on days 0, 3, 7, 14, and 35. Pyrene in soil samples was analyzed using an Agilent gas chromatograph (7890A) equipped with a mass-selective detector (model 5897). DNA in soils was extracted with a FastDNA Spin kit for soil (Bio101, USA). The abundance of functional microbes and genes was monitored by a Taqman or SYBR Green based real-time PCR quantification using an iCycler iQ5 themocycler (Bio-Rad, USA). The diversity of PAH-RHDα GP genes was evaluated by constructing clone libraries and sequencing.

Results and discussion

In both soils, more than 80 % of the added pyrene was degraded within 35 days. After 35-day incubation, there was a significant enrichment of Gram-positive bacteria harboring PAH-ring hydroxylation dioxygenase (PAH-RHD_α GP) genes, and the abundance of Mycobacterium increased significantly. In PAH-RHD_α GP clone libraries from two soils, Mycobacterium was detected, while most sequences were closely related to uncultured Gram-positive bacteria. In addition, two pyrene catabolic pathways might be involved in pyrene degradation, as pyrene dioxygenase genes, nidA and nidA3, were dramatically enriched during incubation. Moreover, the abundance and diversity of potential degraders in two soils showed significantly difference in responding to pyrene stress. This result indicates that soil condition can significantly affect functional microbial populations and biological process for pyrene biodegradation.

Conclusions

These results revealed that Mycobacterium as well as uncultured Gram-positive PAH-RHD_α genotypes may be the important group of pyrene degraders in soils, and two pyrene catabolic pathways, targeted by nidA and nidA3, might potentially contribute to in situ biodegradation of pyrene. This study characterized the response pattern of potential pyrene degraders to pyrene stress in two different soils, which would increase our understanding of the indigenous processes of pyrene biodegradation in soil environment.

     

The influence of <Emphasis Type="Italic">Aster x salignus</Emphasis> Willd. Invasion on the diversity of soil yeast communities

The annual dynamics of yeast communities were studied in the soddy-podzolic soil under the thickets of Aster x salignus Willd., one of the widespread invasive plant species in central Russia. Yeast groups in the soils under continuous aster thickets were found to differ greatly from the yeast communities in the soils under the adjacent indigenous meadow vegetation. In both biotopes the same species (Candida vartiovaarae, Candida sake, and Cryptococcus terreus) are dominants. However, in the soils under indigenous grasses, eurybiontic yeasts Rhodotorula mucilaginosa, which almost never occur in the soil under aster, are widespread. In the soil under aster, the shares of other typical epiphytic and pedobiontic yeast fungi (ascomycetic species Wickerhamomyces aniomalus, Barnettozyma californica and basidiomycetic species Cystofilobasidium macerans, Guehomyces pullulans) significantly increase. Thus, the invasion of Aster x salignus has a clear effect on soil yeast complexes reducing their taxonomic and ecological diversity.     

城郊土壤不透水表面有土壤机碳转化及其相关性质的研究

Installation of impervious surface in urban area prevents the exchange of material and energy between soil and other environmental counterparts, thereby resulting in negative effects on soil function and urban environment. Soil samples were collected at 0-20 cm depth in Nanjing City, China, in which seven sites were selected for urban open soils, and fourteen sites with similar parent material were selected for the impervious-covered soils, to examine the effect of impervious surface on soil properties and microbial activities, and to determine the most important soil properties associated with soil organic carbon （SOC） transformation in the urban soils covered by impervious surfaces. Soil organic carbon and water-soluble organic carbon （WSOC） concentrations, potential carbon （C） and nitrogen （N） mineralization rates, basal respiration, and physicochemical properties with respect to C transformation were measured. Installation of impervious surface severely affected soil physicochemical properties and microbial activities, e.g., it significantly decreased total N contents, potential C mineralization and basal respiration rate （P 〈 0.01）, while increased pH, clay and Olsen-P concentrations. Soil organic carbon in the sealed soils at 0-20 cm was 2.35 kg m-2, which was significantly lower than the value of 4.52 kg m-2 in the open soils （P 〈 0.05）. Canonical correlation analysis showed WSOC played a major role in determining SOC transformation in the impervious-covered soil, and it was highly correlated with total N content and potential C mineralization rate. These findings demonstrate that installation of impervious surface in urban area, which will result in decreases of SOC and total N concentrations and soil microbial activities, has certain negative consequences for soil fertility and long-term storage of SOC.     

Characterization of developing microbial communities in Mount St. Helens pyroclastic substrate

The 1980 eruption of Mount St. Helens created a unique opportunity to study microbial communities in a developing soil ecosystem containing little total carbon (C) or total nitrogen (N). We collected surface samples (0-5 cm) from areas near Mount St. Helens National Volcanic Monument 17 years after the eruption. The samples were from bare soil with no plant development, soil under living prairie lupine (Lupinus lepidus) and dead prairie lupine in the pyroclastic plain near Spirit Lake, Washington. We also collected soil from a nearby forested area. Phospholipid fatty acids (PLFAs) from pyroclastic materials were analyzed to determine changes in soil microbial composition. Total bacterial DNA was also extracted from the soils and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes and DNA sequence analysis of cloned 16S rRNA gene libraries were used to determine the influence of plants on microbial development. Both principal components analysis (PCA) of PLFA fingerprints and non-metric multidimensional scaling (NMS) of DGGE fingerprints distinguished the four soils. Lupine plants influenced the PLFA and DGGE fingerprints depending on the distance of the samples from the plant. DGGE and PLFA profiles from the forest soil were significantly different (P=0.001, based on Monte Carlo permutation test) from those of the bare soil and soil with live lupine. Bacterial clone libraries were constructed, and 800 clones were analyzed by amplified ribosomal DNA restriction analysis (ARDRA) and grouped into operational taxonomic units (OTUs). A total of 51, 77, 58, and 42 different OTUs were obtained from forest soil, soil with live and dead lupine, and bare soil, respectively. Phylogenetic analysis revealed that 62% of the 228 OTUs were classified as Proteobacteria, Actinobacteria, Acidobacterium, Verrucomicrobia, Bacteroides, Cyanobacteria, Planctomycetes, and candidate divisions TM7 and OP10. Members of Proteobacteria represented 29% of the OTUs. Thirty-eight percent of the OTUs could not be classified into known bacterial divisions. This study emphasized the role of prairie lupine in the establishment of pioneering microbial communities and the subsequent roles the biotic components played in improving the quality of pyroclastic soil.     

Microbial degradation of hydrolysable and condensed tannin polyphenol-protein complexes in soils from different land-use histories

Polyphenols are capable of binding to proteins and form polyphenol-protein complexes thus reducing the release of N from decomposing plant materials. The objective of this work was to test if under polyphenol-rich vegetations adapted microbial communities had developed capable of breaking down recalcitrant polyphenol-protein complexes. Soils used for this investigation were from different 10-year-old tropical agricultural systems (maize, sugarcane plots and Gliricidia sepium or Peltophorum dasyrrachis woodlots) and natural systems (secondary forest and Imperata cylindrica grassland). TA (tannic acid, hydrolysable tannin), QUE (quebracho, condensed tannin), BSA (bovine serum albumin, protein) or TA/BSA and QUE/BSA polyphenol-protein complexes were incubated at 28 °C in these soils. CO₂-C and ¹³C evolution were periodically monitored and mineral N release, microbial biomass N and phospholipid fatty acid (PLFA) profiles measured at the end.QUE was able to bind about 25% more protein than TA. In all systems the individual uncomplexed substrates were more easily degraded than the complexes. On average, net cumulative CO₂-C evolution from TA/BSA complexes was more than 5 times higher than from QUE/BSA complexes, indicating higher C availability and/or lower protection capability of TA compared to QUE. However, net N release was higher from QUE/BSA than from TA/BSA probably due to their higher protein-binding capacity and associated larger degradation of partly unprotected protein as suggested by ¹³C-CO₂ signatures. Microbial respiration patterns indicated that polyphenol complexes were initially degraded more quickly in the maize cropping system than in soils from under polyphenol-rich communities (Peltophorum and natural forest) but this pattern reversed with time. Long-term incubation of QUE/BSA complexes even caused a negative effect on microbial respiration in agricultural soils with low polyphenol contents (e.g. maize and sugarcane).Incubation of polyphenol complexes in soil depressed microbial biomass N in maize, sugarcane, Imperata and forest systems and led to reduced soil pH. However, microbial biomass was increased under the polyphenol-rich vegetation of Peltophorum. The PLFA group 18:2w6,9 was highly enhanced by condensed tannin-protein complexes additions as compared to control and hydrolysable polyphenol-protein complexes in soils with high polyphenol contents. Polyphenol complexes increased the fungi:bacteria ratio in systems with a high polyphenol content, particularly with condensed tannin complexes. The results indicated that systems with a high polyphenol content favoured development of fungal communities that are highly adaptable to phenol-rich soil conditions and high acidity, particularly with regards to the more recalcitrant condensed tannin-protein complexes.     

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.