Impact of subterranean fungus-growing termites (Isoptera, Macrotermitiane) on chosen soil properties in a West African savanna

Fungus-growing termites (Isoptera, Macrotermitinae) play an important role in tropical ecosystems in modifying soil physical properties. Most of the literature regarding the impact of termites on soil properties refers to termite epigeous mounds. In spite of their abundance and activity in African savannas, few studies deal with the properties of underground nest structures (fungus-comb chambers) built by subterranean Macrotermitinae termites. We tested whether these termites significantly modify the soil physico-chemical properties within their nests in a humid tropical savanna and whether these effects are different for two termite species with differing building behaviour. Termite-worked soil material was collected from fungus-comb chamber walls of two widespread species: Ancistrotermes cavithorax, which builds diffuse and ephemeral nests and Odontotermes nr pauperans, which most often builds concentrated and permanent nests for a comparatively much longer period of time. Neither species influenced soil pH but both significantly modified soil texture and C-N content in their nest structures. A strong impact on clay-particle size was also detected but no significant differences in clay mineralogy. Thus Odontotermes has a greater effect on soil properties, that could be explained by its building behaviour and the concentration in space of its nest units. Therefore, spatial pattern and life-span of fungus-comb chambers should be an important parameter to be considered in the functional role of subterranean Macrotermitinae termites in the savanna.     

Use of RAPD markers for the study of microbial community similarity from termite mounds and tropical soils

In this study, we test the use of the RAPD (Random Amplified Polymorphic DNA) molecular markers as a way to estimate the similarity of the microbial communities in various termite mounds and soils. In tropical ecosystems, termite activities induce changes in the chemical and physical properties of soil. The question then arises as to whether or not termites affect the presence of natural microbial communities. Successful 16S rDNA amplifications provided evidence of the occurrence of bacterial DNA in termite constructions including both soil feeder and fungus grower materials. A phenetic dendrogram using the similarity distance calculated from pairwise data including 88 polymorphic RAPD markers was reconstructed and bootstrap scores mapped. The microbial communities of the mounds of the four soil-feeding termites were clustered in the same clade, while those of the mounds of the fungus-growing species were distinct like those of control soils. Microbial changes in nests result from termite building behavior, depending on whether they include feces in their constructions for soil-feeders or use saliva as particle cement for fungus-growers. It is argued that RAPDs are useful markers to detect differences in microbial community structure not only between termitaries and control soils but also between mounds of soil-feeders.     

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.     

Short-term effect of tillage and crop rotation on microbial community structure and enzyme activities of a clay loam soil

A field study was carried out to analyze the short-term (2 years) effect of tillage and crop rotation on microbial community structure and enzyme activities of a clay loam soil. The experimental design was a split-plot arrangement of treatments, consisting of two tillage treatments—ridge tillage (RT) and no-tillage (NT)—in combination with two crop rotation treatments—corn (Zea mays L.) monoculture and a 2-year corn-soybean (Glycine max L.) rotation. Phospholipid fatty acid (PLFA) profiles were used to assess soil microbial community structure. No-tillage resulted in significantly higher total PLFAs compared to the RT treatment, which was accompanied by higher activities of protease, β-glucosaminidase, and β-glucosidase. This suggests a close link between soil microbial communities and enzyme activities in response to tillage. The increase of total microbial lipid biomass in the NT soils was due to the increase in both fungal and bacterial PLFAs. Crop rotation had little effect on soil bacterial communities and enzyme activities, but it significantly influenced soil fungal communities, particularly arbuscular mycorrhizal fungi. Soils under monoculture corn had higher fungal biomass than soils under corn-soybean rotation regardless of tillage treatment.     

Unique soil microbial assemblages associated with grassland ant species with different nesting and foraging strategies

Ants are important ecosystem engineers and can be abundant in extensively managed grassland ecosystems. Different ant species create nests varying in structure and size, and tend to have a variety of feeding strategies. Differences in food imported to the nest and contrasting nesting behaviour may control soil microbial community structure in nest soil, with cascading effects on nutrient cycling, but this has not been tested in grassland ants. Soil and ants were sampled from nests of three ant species: two formicines; Lasius flavus (aphid farmer/scavenger, mound builder) and Formica lemani (scavenger/hunter, non-mound builder), and a myrmicine; Myrmica sabuleti (hunter/scavenger, non-mound builder), in an extensively grazed temperate grassland and compared to similar soils without ants. Microbial assemblages were determined using molecular approaches (terminal restriction length polymorphism and automated ribosomal intergenic spacer analysis). Both aboveground (vegetation diversity) and belowground (soil physico-chemical properties) components were measured to assess the potential of the different ant species to modify the environment. Stable isotope ratios (δ¹³C and δ¹⁵N) of ant tissues and nest soil organic matter confirmed differences in trophic distances. Significant changes in soil pH, moisture content, total C and total N, and in vegetation composition, demonstrated ant ecosystem engineering effects. In turn, nests of L. flavus, M. sabuleti and F. lemani had different microbial activities and harboured significantly different microbial assemblages (total bacteria, total fungi, ammonia-oxidising bacteria and nitrogen-fixing bacteria), but the diversity was similar. These findings suggest that grassland ants can control microbial assemblages via changes in physical and biological soil characteristics in their nests, and as such, different ant species harbour unique microbial assemblages in nests.     

Physiological, biochemical and molecular responses of the soil microbial community after afforestation of pastures with Pinus radiata

Afforestation and deforestation are key land-use changes across the world, and are considered to be dominant factors controlling ecosystem functioning and biodiversity. However, the responses of soil microbial communities to these land-use changes are not well understood. Because changes in soil microbial abundance and community structure have consequences for nutrient cycling, C-sequestration and long-term sustainability, we investigated impacts of land-use change, age of stand and soil physico-chemical properties on fungal and bacterial communities and their metabolic activities. This study was carried out at four sites in two geographical locations that were afforested on long-established pastures with Pinus radiata D. Don (pine). Two of the sites were on volcanic soils and two on non-volcanic soils and stand age ranged from 5 to 20 y. Microbial communities were analysed by biochemical (phospho-lipid fatty acids; PLFA) and molecular (multiplex-terminal restriction fragment length polymorphism; M-TRFLP) approaches. Both site and stand age influenced microbial properties, with changes being least detectable in the 5-y-old stand. Land use was a key factor influencing soil metabolic activities as measured by physiological profiling using MicroResp. Pasture soils had higher microbial biomass (P < 0.001), and metabolic activities (P < 0.001), and basal respiration rates were up to 2.8-times higher than in the pine soils. Microbial abundance analysis by PLFA showed that the fungal to bacterial ratio was higher in the pine soils (P < 0.01). Community analysis suggested that soil bacterial communities were more responsive to site (principal component 1; P < 0.001) than to land use (principal component 5; P < 0.001). In contrast, the fungal community was more affected by land-use change (principal component 1; P < 0.001) than by site, although site still had some influence on fungal community structure (principal component 2; P < 0.001). Redundancy analysis also suggested that bacterial and fungal communities responded differently to various soil abiotic properties, land-use change and location of sites. Overall, our results indicate that the change in land use from pasture to P. radiata stands had a direct impact on soil fungal communities but an indirect effect, through its effects on soil abiotic properties, on bacterial communities. Most of the changes in bacterial communities could be explained by altered soil physico-chemical properties associated with afforestation of pastures.     

Effects of Ant Mounds on the Plant and Soil Microbial Community in an Alpine Meadow of Qinghai–Tibet Plateau

Ants are important soil engineers, affecting the structure and function of ecosystems. To address the impacts of ants (Camponotus herculeanus ) on the properties of an alpine meadow ecosystem of Qinghai–Tibet Plateau, we investigated the effects of ant mounds on plant biomass, soil physicochemical properties, microbial diversity, and functions. We found that the total biomass of plant community was significantly greater in ant mound periphery. Plant species richness in ant mounds was reduced compared with that of control plots without ant mounds. Significant changes in physicochemical properties of soil were also observed. Soil organic matter, total nitrogen, available phosphorous, total potassium, and available potassium increased in ant mound soil due to the excavation activities by ants as well as the accumulation of organic matter and other nutrients during mound construction. For example, roots/soil contents (g/g) and soil moisture in ant mound soils were lower than those in controls. Microbial community composition and microbial biomass were clearly changed in ant mound soils. BIOLOG analysis further indicated that the functional diversity of the microbial community of ant mound soil increased and differed from that of controls. This study indicates that ant‐induced modification of soil properties indirectly influences plant biomass and species composition, and ant mounds have different microbial communities from those of control soil. Copyright © 2016 John Wiley & Sons, Ltd.     

Microbial communities in forest floors under four tree species in coastal British Columbia

We compare forest floor microbial communities in pure plots of four tree species (Thuja plicata, Tsuga heterophylla, Pseudotsuga menziesii, and Picea sitchensis) replicated at three sites on Vancouver Island. Microbial communities were characterised through community level physiological profiles (CLPP), and profiling of phospholipid fatty acids (PLFA).Microbial communities from cedar forest floors had higher potential C utilisation than the other species. The F layer of the forest floor under cedar contained significantly higher bacterial biomass (PLFA) than the F layer under the other three tree species. There were differences in microbial communities among the three sites: Upper Klanawa had the highest bacterial biomass and potential C utilisation; this site also had the highest N availability in the forest floors. Forest floor H layers under hemlock and Douglas-fir contained greater biomass of Gram positive, Gram negative bacteria and actinomycetes than F layers based on PLFA, and H layers under spruce contained greater biomass of Gram negative bacteria than F layers. There were no significant differences in bacterial biomass between forest floor layers under cedar. Fungal biomass displayed opposite trends to bacteria and actinomycetes, being lowest in cedar forest floors, and highest in the F layer and at the site with lowest N availability. There were also differences in community composition among species and sites, with cedar forest floors having a much lower fungal:bacterial ratio than spruce, hemlock and Douglas-fir. The least fertile Sarita Lake site had a much greater fungal:bacterial ratio than the more fertile San Juan and Upper Klanawa sites. Forest floor layer had the greatest effect on microbial community structure and potential function, followed by site, and tree species. The similarity in trends among measures of N availability and microbial communities is further evidence that these techniques provide information on microbial communities that is relevant to N cycling processes in the forest floor.     

Impact of coloniser plant species on the development of decomposer microbial communities following deglaciation

The effects of coloniser plant species on microbial community growth and composition were investigated on recently deglaciated terrain at Glacier Bay, south-east Alaska. Analysis of microbial communities using phospholipids fatty acid analysis (PLFA) revealed that Alnus and Rhacomitrium had the greatest impact on microbial growth, increasing total PLFA by some 6-7 fold relative to bare soil, whereas Equisetum led to a 5.5 fold increase in total PLFA relative to bare soil. These coloniser species also had significant effects on the composition of their associated microbial communities. Rhacomitrium, Alnus, and Equisetum increased bacterial PLFA, a measure of bacterial biomass, relative to bare soil. Rhacomitrium and Alnus also dramatically increased the concentration of the fungal fatty 18:2ω6 in soil relative to bare soil, by 12-fold and 8-fold, respectively. The net effect of the above changes was a significant increase in the ratio of fungal: bacterial fatty acids in soil associated with Alnus and Rhacomitrium, but not Equisetum. Possible reasons for these effects of particular plants on microbial communities are discussed, as is their significance in relation to the development of microbial communities in relatively sterile, recently deglaciated ground.     

Soil microbial communities of no-till dryland agroecosystems across an evapotranspiration gradient

In degraded agricultural soils, organic C levels can be increased and conserved by adopting alternative management strategies such as no-tillage and increased cropping intensity. However, soil microbial community responses to increased soil organic C (SOC) may be constrained due to water limitations in semi-arid dryland agroecosystems. The purpose of this study was to assess SOC, microbial biomass C (MBC) and community ester-linked fatty acid methyl ester (EL-FAME) composition under winter wheat (Triticum aestivum L.) in no-till systems of wheat–corn (Zea mays L.)–fallow (WCF), wheat–wheat–corn–millet (Panicum miliaceum L.) (WWCM), wheat–corn–millet (WCM), opportunity cropping (OPP), and perennial grass across a potential evapotranspiration gradient in eastern Colorado. Rotations of WWCM and OPP, in which crops are chosen based on available soil water at the time of planting rather than according to a predetermined rotation schedule, increased levels of SOC to those measured under perennial grass. However, MBC under OPP cropping accounted for the smallest fraction (2.0–3.6%) of SOC compared to other systems, in which MBC ranged from 2.4 to 6.3% of SOC. Microbial community structure was most divergent between OPP-cropped and perennial grass soils, whereas few differences were observed among microbial communities of the WCF, WCM, and WWCM rotations. Compared to perennial grass and other cropping systems, microbial biomass in OPP-cropped soil was low and contained less of the arbuscular mycorrhizal fungal biomarker 16:1ω5c. Microbial stress, as indicated by the ratio of 17:0 cy to 16:1ω7c, was greatest under OPP and WCF cropping. In contrast, soils under perennial grass contained lower ratios of bacterial:fungal EL-FAMEs and higher levels of MBC, ratios of MBC:SOC, and relative abundances of 16:1ω5c. Across locations, SOC and moisture content increased as soil texture became finer, whereas trends in MBC and community structure followed the potential evapotranspiration gradient. Soil from the high potential evapotranspiration site contained the lowest level of MBC but greater relative amounts of 16:1ω5c and lower ratios of stress indicator and bacterial:fungal EL-FAMEs compared to soil located at the moderate and low potential evapotranspiration sites. Indistinct microbial communities under WCF, WCM, and WWCM could be explained by EL-FAME limitations to detecting slight differences in microbial community structure or to the overwhelming response of microbial communities to environmental rather than management conditions. Further research is needed to assess potential legacy effects of long-term agricultural management that may mask microbial responses to recent management change, as well as to identify conditions that lead to high microbial community resiliency in response to management so that communities are similar under a given crop despite different preceding crops.     

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.     

The influence of soil properties on the structure of bacterial and fungal communities across land-use types

Land-use change can have significant impacts on soil conditions and microbial communities are likely to respond to these changes. However, such responses are poorly characterized as few studies have examined how specific changes in edaphic characteristics do, or do not, influence the composition of soil bacterial and fungal communities across land-use types. Soil samples were collected from four replicated (n = 3) land-use types (hardwood and pine forests, cultivated and livestock pasture lands) in the southeastern US to assess the effects of land-use change on microbial community structure and distribution. We used quantitative PCR to estimate bacterial–fungal ratios and clone libraries targeting small-subunit rRNA genes to independently characterize the bacterial and fungal communities. Although some soil properties (soil texture and nutrient status) did significantly differ across land-use types, other edaphic factors (e.g., pH) did not vary consistently with land-use. Bacterial–fungal ratios were not significantly different across the land-uses and distinct land-use types did not necessarily harbor distinct soil fungal or bacterial communities. Rather, the composition of bacterial and fungal communities was most strongly correlated with specific soil properties. Soil pH was the best predictor of bacterial community composition across this landscape while fungal community composition was most closely associated with changes in soil nutrient status. Together these results suggest that specific changes in edaphic properties, not necessarily land-use type itself, may best predict shifts in microbial community composition across a given landscape. In addition, our results demonstrate the utility of using sequence-based approaches to concurrently analyze bacterial and fungal communities as such analyses provide detailed phylogenetic information on individual communities and permit the robust assessment of the biogeographical patterns exhibited by soil microbial communities.     

Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite’s impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C₃ perennial grasses, C₄ midgrasses, C₄ shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt to characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.     

Pineapple–banana rotation reduced the amount of Fusarium oxysporum more than maize–banana rotation mainly through modulating fungal communities

Continuous cropping with banana results in an enrichment of Fusarium oxysporum f. sp. cubense race 4 (FOC) in soil, causing the soil-borne disease Fusarium wilt. Crop rotation has been an effective method of controlling various soil-borne diseases. However, no information is currently available concerning variations in soil microbial community structure in banana crop rotations. Thus, the influence of two-year crop rotation systems of pineapple–banana and maize–banana on the population density of FOC and soil microbial community structure was investigated to identify which rotation system is more effective in FOC suppression and differences in microbial community composition among different rotations. Bacterial and fungal communities were interrogated by pyrosequencing of the 16 S RNA gene and the internal transcribed spacer (ITS) region. The pineapple–banana rotation was more effective than maize–banana in reducing FOC abundances and suppressing Fusarium wilt disease incidence. Allelopathic effects of pineapple root exudates on FOC were not observed. Greater fungal community variations than bacterial were identified between the two rotation systems, suggesting that fungal communities may play a more important role in regulating FOC abundances. Furthermore, in the pineapple–banana rotation, Acidobacteria, Planctomycetes, Chloroflexi phyla, Gp1, Gp2 and Burkholderia bacterial genera increased while the fungal phyla Basidiomycota, (esp. Gymnopilus) increased and Sordariomycetes decreased. Such changes may be important microbial factors in the decrease in FOC.     

Diversity and complexity of microbial communities from a chlor-alkali tailings dump

Revegetation of the tailings dumps produced by various industrial activities is necessary to prevent dust storms and erosion and represents a great challenge for ecological restoration. Little is known about the microbial colonisation and community structure of revegetated tailings following site exploitation. Here, we report the sequencing of 16S rRNA and internal transcribed spacer (ITS) fungal RNA gene amplicons from chlor-alkali residue and from an adjacent undisturbed soil to define the composition and assembly of the rhizosphere microbial communities. After quality filtering, a total of 72,373 and 89,929 bacterial sequences and 122,618 and 111,209 fungal sequences remained for community analysis from undisturbed soil and tailings dump samples, respectively. These reads were affiliated with 45 bacterial and 9 fungal phyla and 113 bacterial and 35 fungal classes. We observed a clear dominance of Gammaproteobacteria at our study site (24% of total sequences), especially of the Pseudomonas genera (72% of Gammaproteobacteria sequences), together with the dominance of a few fungal taxa, such as Hebeloma and Geopora. However, we also noticed that the core microbiome comprised 64.4% and 62.4% of the bacterial and fungal genera, respectively, despite marked differences in soil physico-chemical properties. A heatmap of correlations between soil parameters and taxa confirmed that approximately 50% of the 33 dominant taxa colonised both types of soil. We further demonstrated that the global bacterial-fungal network topology of the dump approximated that of the undisturbed soil. Our approach illuminates the importance of studying more than just a single component of the microbial community and represents a step forward in uncovering the microbial ecology of disturbed environments beyond what is generally found in conventional studies. Our study also provides novel global community proxies that have led us to conclude that environmental filtering is more likely to occur through the activity of tree roots rather than as a result of specific soil characteristics and could be an important force in the assembly of at least some microbial communities.     

Soil moisture is the major factor influencing microbial community structure and enzyme activities across seven biogeoclimatic zones in western Canada

Although soil microorganisms play a central role in the soil processes that determine nutrient availability and productivity of forest ecosystems, we are only beginning to understand how microbial communities are shaped by environmental factors and how the structure and function of soil microbial communities in turn influence rates of key soil processes. Here we compare the structure and function of soil microbial communities in seven mature, undisturbed forest types across a range of regional climates in British Columbia and Alberta, and examine the variation in community composition within forest types. We collected the forest floor fermentation (F) and humus (H) layers and upper 10 cm of mineral soil at 3 sites in each of seven forest types (corresponding to seven Biogeoclimatic zones) in both spring and summer. Phospholipid fatty acid analysis was used to investigate the structure of soil microbial communities and total soil microbial biomass; potential activities of extra-cellular enzymes indicated the functional potential of the soil microbial community in each layer at each site.Multivariate analysis indicated that both structure and enzyme activities of soil microbial communities differed among the forest types, and significantly separated along the regional climate gradient, despite high local variation. Soil moisture and organic matter contents were most closely related to microbial community characteristics. Forests in the Ponderosa Pine and Mountain Hemlock zones were distinct from other forests and from each other when comparing potential enzyme activities and had the most extreme moisture and temperature values. Forest floors from the hot and dry Ponderosa Pine forests were associated with enzymes characteristic of water-stress and high concentrations of phenols and other recalcitrant compounds. The wet and cold Mountain Hemlock forests were associated with low enzyme activity.An influence of tree species was apparent at the three sites within the Coastal Western Hemlock zone; high bacterial:fungal biomass ratios were found under western redcedar (Thuja plicata) which also had high pH and base-cation levels, and under Douglas-fir (Pseudotsuga menziesii), which had high N availability. Potential activities enzymes differed among soil layers: potential activities of phenol oxidase and peroxidase were highest in mineral soil, whereas phosphatase, betaglucosidase, NAGase, sulfatase, xylosidase and cellobiohydrolase were highest in the forest floors.     

Soil microbial biomass,crop yields,and bacterial community structure as affected by long-term fertilizer treatments under wheat-rice cropping

Soil microbial biomass carbon (SMBC) and nitrogen (SMBN), soil microbial community structure, and crop yields were studied in a long-term (1982–2004) fertilization experiment carried out in Suining, Sichuan province of PR China. Eight treatments included three chemical fertilizer (CF) treatments (N, NP, NPK), three CF + farmyard manure (M) treatments (NM, NPM, NPKM), M alone and no fertilizer (CK) as control. The results showed that the soil microbial biomass was higher in soil treated with CFM than in soil treated with CF alone, and that NPKM gave the highest rice and wheat yields. The SMBC and SMBN were higher after rice than those after wheat cropping. SMBC correlated closely with soil organic matter. Average yields of wheat and rice for 22 years were higher and more stable in the fertilized plots than in control plots. Bacterial community structure was analyzed by PCR-DGGE targeting eubacterial 16S rRNA genes. A higher diversity of the soil bacterial community was found in soil amended with CFM than in other fertilizer treatments. Some specific band emerged in the soil amended with M. The highest diversity of bacterial communities was found in the NPKM treated soil. The bacterial community structures differed in rice and wheat plots. Sequencing of PCR products separated in DGGE showed that some of the common and dominant bands were closely related to Aquicella lusitana and to Acidobacteria. This study demonstrated that mixed application of N, P, and K with additional M amendment increased soil microbial biomass, diversified the bacterial communities and maintained the crop production in the Calcareous Purplish Paddy soil.     

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.     

Seven years of enhanced water availability influences the physiological,structural, and functional attributes of a soil microbial community

Water availability is known to influence many aspects of microbial growth and physiology, but less is known about how complex soil microbial communities respond to changing water status. To understand how long-term enhancement of soil water availability (without flooding) influences microbial communities, we measured the seasonal dynamics of several community-level traits following >7 years of irrigation in a drought-prone tallgrass prairie soil. From late May to mid-September, water was supplied to the irrigated treatments based on calculated plant water demand. Phospholipid fatty acids (PLFA) were used to assess changes in microbial community structure and physiology. To assess the community-level physiological profile, microbial utilization of BIOLOG substrates was determined. After incubation for 2 days, the distribution of added ¹³C-glucose in microbial and respired pools was used as an index of substrate utilization efficiency. We also measured the relative contribution of fungi and bacteria to soil microbial biomass via substrate-induced respiration (SIR). Multivariate analysis of mol% PLFA and BIOLOG substrate utilization indicated that both water availability and sampling time influenced both the physiological and structural characteristics of the soil microbial community. Specific change in biomarker PLFA revealed a decreased ratio of cyclopropyl to ω7-precursors due to water addition, suggesting community-level stresses were reduced. Over the growing season, continuously greater water availability resulted in a 53% greater ratio of fungal to bacterial biomass using SIR, and a 65% increase in fungal PLFA. The number of substrates utilized by the cultivable microbial community tended to be greater in continuously wetted soil, especially during periods of low rainfall. While water dynamics appeared to be associated with some of the shifts in microbial community activity, structural and functional changes in the community appeared to be more closely linked to the cumulative effects of water regime on ecosystem properties. Seasonality strongly influenced microbial communities. The environmental factors associated with seasonal change need to be more closely probed to better understand the drivers of community structure and function.     

Microbial activity and community structure of a soil after heavy metal contamination in a model forest ecosystem

We assessed the effects of chronic heavy metal (HM) contamination on soil microbial communities in a newly established forest ecosystem. We hypothesized that HM would affect community function and alter the microbial community structure over time and that the effects are more pronounced in combination with acid rain (AR). These hypotheses were tested in a model forest ecosystem consisting of several tree species (Norway spruce, birch, willow, and poplar) maintained in open top chambers. HMs were added to the topsoil as filter dust from a secondary metal smelter and two types of irrigation water acidity (ambient rain vs. acidified rain) were applied during four vegetation periods. HM contamination strongly impacted the microbial biomass (measured with both fumigation-extraction and quantitative lipid biomarker analyses) and community function (measured as basal respiration and soil hydrolase activities) of the soil microbial communities. The most drastic effect was found in the combined treatment of HM and AR, although soil pH and bioavailable HM contents were comparable to those of treatments with HM alone. Analyses of phospholipid fatty acids (PLFAs) and terminal restriction fragment length polymorphisms (T-RFLPs) of PCR-amplified 16S ribosomal DNA showed that HM treatment affected the structure of bacterial communities during the 4-year experimental period. Very likely, this is due to the still large bioavailable HM contents in the HM contaminated topsoils at the end of the experiment.