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

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

Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain

The elevational patterns of diversity for plants and animals have been well established over the past century. However, it is unclear whether there is a general elevational distribution pattern for microbes. Changbai Mountain is one of few well conserved natural ecosystems, where the vertical distribution of vegetation is known to mirror the vegetation horizontal zonation from temperate to frigid zones on the Eurasian continent. Here, we present a comprehensive analysis of soil bacterial community composition and diversity along six elevations representing six typical vegetation types from forest to alpine tundra using a bar-coded pyrosequencing technique. The bacterial communities differed dramatically along elevations (vegetation types), and the community composition was significantly correlated with soil pH, carbon/nitrogen ratio (C/N), moisture or total organic carbon (TOC), respectively. Phylogenetic diversity was positively correlated with soil pH (P = 0.024), while phylotype richness was positively correlated with soil pH (P = 0.004), total nitrogen (TN) (P = 0.030), and negatively correlated with C/N ratio (P = 0.021). Our results emphasize that pH is a better predictor of soil bacterial elevational distribution and also suggest that vegetation types may indirectly affect soil bacterial elevational distribution through altering soil C and N status.     

Search of environmental descriptors to explain the variability of the bacterial diversity from maize rhizospheres across a regional scale

The regional scale variability of the bacterial community inhabiting the rhizosphere was studied with soil collected from maize fields located in the Santo Domingo Valley (SDV; Baja California Sur, Mexico), a semi-arid agricultural ecosystem of approximately 200 km². The bacterial community structure was visualized by single-strand conformation polymorphism (SSCP) profiles of PCR-amplified partial 16S rRNA genes of directly extracted rhizosphere soil DNA. SSCP profiles of different SDV sites and an external field site in Germany were evaluated for their similarities and the contributing bacteria were characterized by DNA sequence analyses. SSCP profiles from each site were significantly different from the others, as revealed by permutation of pairwise similarities (P < 0.05). In comparison to the German site, SSCP profiles from SDV were more similar to each other despite contrasting soil salinity levels. Correspondence analysis revealed that among SDV sites, salinity levels, soil organic carbon and calcium (Ca²⁺) were most influential on the bacterial community structure. Depending on the phylogenetic group analyzed (Bacteria, Alphaproteobacteria, Pseudomonas), the importance of these soil variables varied. Interestingly, the East–West direction also revealed an effect, suggesting that future explorations of bacterial diversity patterns should also consider landscape topography in search of explaining patterns of bacterial diversity in soils.     

Characterization of cultivable heterotrophic bacterial communities in Cr-polluted and unpolluted soils using Biolog and ARDRA approaches

The bacterial communities of two soils with different chromium levels were characterized by Biolog carbon substrate utilization patterns and amplified 16S ribosomal DNA restriction analysis (ARDRA). For each bacterial community sample, cell suspensions containing 10,000 or 100 colony-forming units (CFU) were inoculated in each well of Biolog-GN microplates. The number of carbon compounds utilized by the bacterial community consisting of 100 CFU from unpolluted soil was significantly lower than that detected for the bacterial community consisting of 10,000 CFU. The size of inoculum did not substantially influence the percentage of carbon sources utilized by the Cr-polluted soil bacterial community. ARDRA approach was applied to about 100 bacterial isolates for each soil sample. A similar number of clusters for Gram-negative bacteria were found in both soils, but there were differences in percentages of isolates belonging to each group and specific genomic groups were found in each soil. Pseudomonas was the dominant taxon in both soils. Comparing the ARDRA clusters obtained from Gram-positive isolates it was evident that the culturable bacterial communities of Cr-polluted and unpolluted soils were dominated by the genus Arthrobacter and the genus Bacillus, respectively.     

Starved bacteria retain their size but lose culturability - Lessons from a 5000 years old undisturbed A-horizon

The vast majority of soil bacteria are unable to form visible colonies on agar media. One hypothesis is that unculturable soil bacteria are dwarf cells that may either be small starved forms derived from larger species or represent inherently small species. We test the hypotheses that cells of extremely starved soil bacterial communities are smaller and less culturable than cells of bacterial communities from a richer soil, and that culturability is related to cell size by comparing an extremely starved community from a 5200-year-old A-horizon buried under a burial mound with a community from a modern agricultural A-horizon.We serially filtered cell suspensions through filters with successively smaller pore sizes (0.8 μm, 0.6 μm and 0.4 μm) and assessed total cell number and culturability, i.e. the ability to form colonies on two types of agar media, in each size fraction. Cell size distributions were assessed in unfiltered suspensions. Average cell size was only moderately reduced in the starved community, where culturability was low for all size classes. In contrast, culturability was much higher in the modern community, where culturability decreased dramatically with decreasing cell sizes.     

Grassland management influences spatial patterns of soil microbial communities

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

Spatial pattern and heterogeneity of soil properties in sand dunes under grazing and restoration in Horqin Sandy Land, Northern China

Applying a combination of classical and geostatistical methods, we identified soil properties and their spatial variation in a 5-year grazed sand dune (GSD5) and a 20-year recovered sand dune (RSD20) in Horqin Sandy Land, northern China. The paper assesses the effect of grazing, topography and vegetation restoration on spatial heterogeneity of soil properties. The results showed that soil organic carbon, total nitrogen, very fine sand (0.1–0.05 mm) content and their coefficients of variation were lower in GSD5 than in RSD20, while soil water contents (0–20 cm and 20–40 cm depths) were higher in GSD5 than in RSD20. Geostatistical analysis revealed that the spatial structured variance accounted for the largest proportion of total sample variance in soil properties at the measured scale under grazing and restoration. The spatial autocorrelation ranges were 66.30 m for soil organic carbon and 50.80 m for total nitrogen in GSD5 less than those in RSD20 (70.00 m and 76.10 m, respectively), while the spatial autocorrelation ranges of soil particle size fractions and soil water contents in RSD20 were less than those in GSD5. Kriging-interpolated maps also showed that the heterogeneity of soil organic carbon and total nitrogen and their degree of patch fragmentation were higher in GSD5 than in RSD20. These results suggested that continuous grazing resulted in an increase in spatial variability of soil nutrient and a decrease in spatial variability of soil particle size fractions and soil water content. Soil organic carbon and total nitrogen of sand dunes are associated closely with soil particle size fractions, relative height of sampling site and vegetation cover. Spatial patterns of soil properties are most strongly related to grazing, topography and plant-induced heterogeneity in sand dune ecosystems prone to wind erosion.     

Diversity of proteolytic community encoding for subtilisin in an arable field: spatial and temporal variability

The diversity of soil proteolytic community encoding for subtilisin (sub) was investigated at a cultivated field site with four different soil types and at three different depths in April, July, and October. A terminal restriction fragment length polymorphism (T-RFLP) analysis of subtilisin gene (sub) was applied to study dynamic of the sub gene pool. The aim of the present study was to relate differences in sub community structure to the vertical, site, and seasonal variations naturally occurring at the field site under investigation. A significant spatial variability in the community structure of sub-containing bacteria was observed. The richness of sub proteolytic bacterial population decreased with increasing soil depth, revealing the highest values in upper layers. A similar trend was observed among the different sites; the highest diversity was noticed at the site with the highest silt and nutrient content. The reasons behind the observed patterns in the community structure might be varying water amount and spatial isolation along the soil profile as well as variability of the quantity and quality of available substrates among different depths and different sites.     

Response of microbial communities to different doses of chromate in soil microcosms

The toxic effect of chromate on soil microbial communities is not well documented, although microorganisms control biogeochemical cycling, contribute to formation of soil structure, regulate the fate of organic matter applied to soil. In this study the effects of short- and middle-term chromate on the soil microbial community were investigated. The shifts in the size and in the diversity of culturable heterotrophic bacterial community, the resistance to Cr(VI) of heterotrophic bacteria, the presence of cyanobacteria, the activity of 19 enzymes, and the ATP content were monitored over time (120 days) in soil microcosms artificially contaminated with three concentrations of chromate (50, 250 and 1000 mg kg⁻¹ soil). The chromate contamination affected the structure and the diversity of the soil bacterial community. Bacterial strains isolated from the microcosm contaminated with the highest concentration of chromate were identified by 16S rDNA gene sequencing. All isolates belonged to the genus Pseudomonas, were able to reduce Cr(VI), and showed a high resistance to chromate. To our knowledge, this is the first report that shows Pseudomonas strains having the capability to resist up to 40 mM of Cr(VI) on minimal medium. The cyanobacterial group was more sensitive to chromate contamination than culturable heterotrophic bacteria. No cyanobacterial growth was detected in enrichment cultures from the soil polluted with the highest chromate concentration. Some enzymes were inhibited by high concentrations of chromate, whereas others were stimulated. The ATP content in microcosms was strongly affected by chromate. We conclude that the soil microbial community responds to chromate pollution through changes in community structure, in metabolic activity, and in selection for Cr(VI)-resistance.     

Structural and functional diversity of bacterial community in soil treated with the herbicide napropamide estimated by the DGGE,CLPP and r/K-strategy approaches

Napropamide is one of the most commonly used herbicide in agricultural practice and can exhibit toxic effect to soil microorganisms. Therefore, the main objective of this study was to examine the genetic and functional diversity of microbial communities in soil treated with napropamide at field rate (FR, 2.25 mg kg⁻¹ of soil) and 10 times the FR (10 × FR, 22.5 mg kg⁻¹ of soil) by the denaturing gradient gel electrophoresis (DGGE) and the community level physiological profile (CLPP) methods. In addition, the r/K-strategy approach was used to evaluate the effect of this herbicide on the community structure of the culturable soil bacteria. DGGE patterns revealed that napropamide affected the structure of microbial community; however, the richness (S) and genetic diversity (H) values indicated that the FR dosage of napropamide experienced non-significant changes. In turn, the 10 × FR dosage of herbicide caused significant changes in the S and H values of dominant soil bacteria. DGGE profiles suggest an evolution of bacteria capable of degrading napropamide among indigenous microflora. Analysis of the CLPPs indicated that the catabolic activity of microbial community expressed as AWCD (average well-color development) was temporary positively affected after napropamide application and resulted in an increase of the substrate richness (S_R) as well as functional biodiversity (H) values. Analysis of the bacterial growth strategy revealed that napropamide affected the r- or K-type bacterial classes (ecotypes). In treated-soil samples K-strategists dominated the population, as indicated by the decreased ecophysiological (EP) index. Napropamide significantly affected the physiological state of culturable bacteria and caused a reduction in the rate of colony formation as well as a prolonged time of growth rate. Obtained results indicate that application of napropamide may poses a potential risk for soil functioning.     

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

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

Soil microbial community response to land-management and depth,related to the degradation of organic matter in English wetlands: Implications for the in situ preservation of archaeological remains

Wetlands are important habitats not only for their unique ecological value but also because they contain organic material that is fundamental to our understanding of precedent landscape and human past. This study compares the effects of two different land-management regimes on metabolic diversity and bacterial community structure with depth in order to relate them to the process of organic matter degradation and the potential for preservation in situ of organic archaeological artefacts in wetland soils. Soil cores were collected at five depths down to 100 cm from two wetlands sites in England. Environmental variables were monitored and the metabolic capabilities of the microbial community were studied using Biolog Ecoplates^®. DNA was extracted from soil, and the bacterial community structure was examined by polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE). To determine compositional changes in the bacterial community with depth, information about specific groups of bacteria at the site with higher water table (Hatfield Moor) was obtained by cloning and sequencing of 16S rRNA genes. Biolog and DGGE analyses showed depth variation and between-site variation. Carbon substrate utilization and bacterial diversity decreased with increasing depth. The wetland soil under an arable regime in which the water levels were kept elevated, showed higher metabolic capability and bacterial richness when compared with the soil under pasture and subjected to long-standing drainage. Cloning and sequencing showed that Proteobacteria and Acidobacteria were the predominant taxa within the soil profile, but there was a clear shift in bacterial community composition with increasing depth as several taxonomic groups (δ-Proteobacteria and Spirochaetes) were only detectable at 50 cm depth. Because the site with a high and stable water table presented higher metabolic activity and bacterial diversity, it may be that saturated conditions and a high water table are not sufficient to guarantee the preservation in situ of organic material such as archaeological artefacts.     

Capacity of fatty acid profiles and substrate utilization patterns to describe differences in soil microbial communities associated with increased salinity or alkalinity at three locations in South Australia

 Fatty acid methyl ester (FAME) profiles, together with Biolog substrate utilization patterns, were used in conjunction with measurements of other soil chemical and microbiological properties to describe differences in soil microbial communities induced by increased salinity and alkalinity in grass/legume pastures at three sites in SE South Australia. Total ester-linked FAMEs (EL-FAMEs) and phospholipid-linked FAMEs (PL-FAMEs), were also compared for their ability to detect differences between the soil microbial communities. The level of salinity and alkalinity in affected areas of the pastures showed seasonal variation, being greater in summer than in winter. At the time of sampling for the chemical and microbiological measurements (winter) only the affected soil at site 1 was significantly saline. The affected soils at all three sites had lower organic C and total N concentrations than the corresponding non-affected soils. At site 1 microbial biomass, CO₂-C respiration and the rate of cellulose decomposition was also lower in the affected soil compared to the non-affected soil. Biomarker fatty acids present in both the EL- and PL-FAME profiles indicated a lower ratio of fungal to bacterial fatty acids in the saline affected soil at site 1. Analysis of Biolog substrate utilization patterns indicated that the bacterial community in the affected soil at site 1 utilized fewer carbon substrates and had lower functional diversity than the corresponding community in the non-affected soil. In contrast, increased alkalinity, of major importance at sites 2 and 3, had no effect on microbial biomass, the rate of cellulose decomposition or functional diversity but was associated with significant differences in the relative amounts of several fatty acids in the PL-FAME profiles indicative of a shift towards a bacterial dominated community. Despite differences in the number and relative amounts of fatty acids detected, principal component analysis of the EL- and PL-FAME profiles were equally capable of separating the affected and non-affected soils at all three sites. Redundancy analysis of the FAME data showed that organic C, microbial biomass, electrical conductivity and bicarbonate-extractable P were significantly correlated with variation in the EL-FAME profiles, whereas pH, electrical conductivity, NH₄-N, CO₂-C respiration and the microbial quotient were significantly correlated with variation in the PL-FAME profiles. Redundancy analysis of the Biolog data indicated that cation exchange capacity and bicarbonate-extractable K were significantly correlated with the variation in Biolog substrate utilization patterns. Received: 8 March 2000     

Effects of cattle-lagoon slurry on a soil microbial community can be observed until depths of 50 m

The large amount of effluent generated by concentrated animal feeding operations (CAFOs) has raised concerns about contamination of groundwater and pollution of streams by compounds that penetrate the vadose zone. However, the possibility that a microbial community in the vadose zone under cattle-slurry lagoons (CSLs) may also be affected has not been considered. In the present study, we investigated the influence of long-term (30 years) accumulation of cattle slurry on the vertical distribution of a soil microbial community (microbial biomass [MB], CO₂ evolution, substrate utilization ability), until a 50-m depth, compared to a control site. Total soluble nitrogen (TSN) was found to be elevated fourfold, and MB was found to be threefold higher under the CSL compared to a control site. In general, the increase in MB is associated with higher soil moisture and higher nitrogen content. Substrate utilization ability was found to be significantly higher in a CSL in comparison to the control site. At the CSL site, a higher utilization of aromatic carboxylic acids typical of cattle slurry was obtained in the deeper soil layers (7–30 m), indicating a degree of microbial adaptation even at these depths. The soil layers under the CSL were more dynamic as the microbial functional diversity was significantly different between the layers, while no such difference was seen at the reference site. Our results, therefore, suggest that the infiltration of cattle slurry can affect the microbial community throughout the vadose zone. We also suggest that activity of the microbial community, as characterized by its substrate utilization ability, can be a bioindicator for anthropogenic activities and environmental changes even at depths below the rhizosphere (30 cm).     

Changes in microbial community structure following herbicide (glyphosate) additions to forest soils

Glyphosate applied at the recommended field rate to a clay loam and a sandy loam forest soil resulted in few changes in microbial community structure. Total and culturable bacteria, fungal hyphal length, bacterial:fungal biomass, carbon utilization profiles (BIOLOG), and bacterial and fungal phospholipid fatty acids (PLFA) were unaffected 1, 3, 7, or 30 days after application of a commercial formulation (Roundup^®). In contrast, a high concentration of glyphosate (100× field rate) simulating an undiluted chemical spill substantially altered the bacterial community in both soils. Increases in total bacteria, culturable bacteria, and bacterial:fungal biomass were rapid following application. Culturable bacteria increased from about 1% of the total population in untreated soil to as much as 25% at the high concentration by day 7, indicating enrichment of generalist bacteria. Community composition in both soils shifted from fungal dominance to an equal ratio of bacteria to fungi. Functional diversity of culturable bacteria, estimated by C substrate utilization, also increased at the high glyphosate concentration, particularly in the clay loam soil. Unlike the other bacterial indices, only minor changes in bacterial PLFA resulted after the third day following the 100× field rate application. Apparently the herbicide resulted in an across-the-board stimulation of bacteria that was not reflected by the finer-scale PLFA community structure. Changes in fungal properties (hyphae, propagules, PLFA biomarkers) were few and transient. We conclude that the commercial formulation of glyphosate has a benign affect on community structure when applied at the recommended field rate, and produces a non-specific, short-term stimulation of bacteria at a high concentration.     

Influence of irrigated agriculture on soil microbial diversity

Organic carbon (C), bacterial biomass and structural community diversity were measured in Southern Idaho soils with long term cropping histories. The soils tested were native sagebrush vegetation (NSB), irrigated moldboard plowed crops (IMP), irrigated conservation – chisel – tilled crops (ICT) and irrigated pasture systems (IP). Organic C concentration in soils decreased in the order NSB 0–5 cm > IP 0–30 cm = ICT 0–15 cm > IMP 0–30 cm > NSB 5–15 cm = NSB 15–30 cm. Active bacterial, fungal and microbial biomass correlated with soil C as measured by the Walkely Black method in positive curvilinear relationships (r² = 0.93, 0.80 and 0.76, respectively). Amplicon length heterogeneity (LH-PCR) DNA profiling was used to access the eubacterial diversity in all soils and at all depths. The Shannon–Weaver diversity index was used to measure the differences using the combined data from three hypervariable domains of the eubacterial 16S rRNA genes. Diversity was greatest in NSB 15–30 cm soil and lowest in the IMP soil. With the exception of IMP with the lowest diversity index, the samples highest in C (NSB 0–5 cm, IP 0–30 cm, ICT 0–15 cm) reflected lower diversity indices. However, these indices were not significantly different from each other. ICT and IP increase soil C and to some extent increase diversity relative to IMP. Since soil bacteria respond quickly to environmental changes, monitoring microbial communities may be one way to assess the impact of agricultural practices such as irrigation and tillage regimes.     

Differences in the composition and diversity of bacterial communities from agricultural and forest soils

Differences in the bacterial communities of soils caused by disturbances and land management were identified in rRNA gene libraries prepared from conventional tilled (CT) and no tilled (NT) cropland, a successional forest after 30 y of regrowth (NF) and an old forest of >65 y (OF) at Horseshoe Bend, in the southern Piedmont of Georgia (USA). Libraries were also prepared from forests after 80 y of regrowth at the Coweeta Long Term Ecological Research site (CWT) in the Southern Appalachians of western North Carolina (USA). The composition of the bacterial communities in cropland soils differed from those of the Horseshoe Bend OF and CWT forest soils, and many of the most abundant OTUs were different. Likewise, the diversity of bacterial communities from forest was less than that from cropland. The lower diversity in forest soils was attributed to the presence of a few, very abundant taxa in forest soils that were of reduced abundance or absent in cropland soils. After 30 y of regrowth, the composition of the bacterial soil community of the NF was similar to that of the OF, but the diversity was greater. These results suggested that the bacterial community of soil changes slowly within the time scale of these studies. In contrast, the composition and diversity of the bacterial communities in the Horseshoe Bend OF and Coweeta soils were very similar. Thus, this forest soil bacterial community was widely distributed in spite of the differences in soil properties, vegetation, and climate as well as resilient to disturbances of the above ground vegetation.     

Labile,recalcitrant, microbial carbon and nitrogen and the microbial community composition at two Abies faxoniana forest elevations under elevated temperatures

We investigated the interactions of altitude and artificial warming on the soil microbial community structure in a subalpine Abies faxoniana forest in southwestern China after four years of warming. Open top chambers (OTCs) at two elevations (3000 m and 3500 m) were established, and their soil microbial characteristics, organic carbon (C) and nitrogen (N) were measured. The microbial community structure was quantified by phospholipid fatty acid (PLFA) analysis. A two-step sulfuric acid hydrolysis was used to quantify the labile and recalcitrant C fractions in the soil organic matter. The results showed that bacterial PLFAs and gram-negative bacterial PLFAs increased and the fungal PLFAs and the fungi/bacteria ratio decreased with warming at the high altitude. By contrast, the warming effects on those parameters at low altitude were small. The higher proportion of labile easily decomposable soil C may explain the different responses of the microbial community composition at the two altitudes. An RDA analysis confirmed that the variations in the soil community structure were significantly associated with soil organic matter properties such as the sizes of the soil labile N pool (LP-N), the recalcitrant N pool (RP-N), and the labile C pool as well as dissolved organic C (DOC) and dissolved organic N concentrations (DON). Our results also showed that labile C and N pools increased with the altitude, but the microbial biomass C as measured with chloroform fumigation techniques decreased. Warming increased only the recalcitrant C pools at the high altitude. Given the longer mean residence time for recalcitrant C and the much greater size of this soil organic carbon pool, the results indicated that a rise in temperature in our case increased soil C pools at higher altitudes, at least during the early stages of experimental soil warming. Warming could also cause changes in the composition of the microbial community and enzyme activities, consequently leading to functional changes in soil ecosystem processes at the high altitude.     

Interactive effects of elevation and land use on soil bacterial communities in the Tibetan Plateau

The Tibetan Plateau of China is uniquely vulnerable to the global climate change and anthropogenic disturbances. As soil bacteria exert a considerable influence on the ecosystem function, understanding their response to different climates and land-use types is important. Here, we characterized the bacterial community composition and diversity across three major ecosystems (cropland, forest, and grassland) in the Sygera Mountains of Tibet, along a typical elevational gradient (3 300-4 600 m). The abundance of taxa that preferentially inhabit neutral or weak alkaline soil environments (such as Actinobacteria, Thermoleophilia, and some non-acidophilus Acidobacteria) was significantly greater in the cropland than in the forest and grassland. Furthermore, the diversity of soil bacterial communities was also significantly greater in the cropland than in the forest and grassland. We observed a unimodal distribution of bacterial species diversity along the elevation gradient. The dominant phyla Acidobacteria and Proteobacteria exhibited consistent elevational distribution patterns that mirrored the abundance of their most abundant classes, while different patterns were observed for Acidobacteria and Proteobacteria at the class level. Soil pH was the primary edaphic property that regulated bacterial community composition across the different land-use types. Additionally, soil pH was the main factor distinguishing bacterial communities in managed soils (i.e., cropland) from the communities in the natural environments (i.e., forest and grassland). In conclusion, land use (particularly anthropogenic disturbances such as cropping) largely controlled soil environment, played a major role in driving bacterial community composition and distribution, and also surpassed climate in affecting bacterial community distribution.     

Bacterial communities in soil mimic patterns of vegetative succession and ecosystem climax but are resilient to change between seasons

Organism succession during ecosystem development has been researched for aboveground plant communities, however, the associated patterns of change in below-ground microbial communities are less described. In 2008, a study was initiated along a developmental sand-dune soil chronosequence bordering northern Lake Michigan near Wilderness Park (WP). It was hypothesized that soil bacterial communities would follow a pattern of change that is associated with soil, plant, and ecosystem development. This study included 5 replicate sites along 9 soils (n = 45) ranging in age from ∼105 to 4010 years since deposition. Soil bacterial community composition and diversity were studied using bacterial tag-encoded FLX amplicon pyrosequencing of the 16S rRNA gene. Bray–Curtis ordination indicated that bacterial community assembly changed along the developmental soil and plant gradient. The changes were not affected by seasonal differences, despite likely differences in plant root C (e.g. exudates), temperature, and water availability in soil. Soil base cations (Ca, Mg) and pH declined, showing log-linear correlations with soil age (r ∼ 0.83, 0.84 and 0.81; P < 0.01). Bacterial diversity (Simpson's 1/D) declined rapidly during the initial stages of soil development (∼105–450 y) and thereafter (>450 y) did not change. Turnover of plant taxa was also more rapid early during ecosystem development and correlated with bacterial community structural change (P < 0.000001; r = 0.56). It is hypothesized that plants help to drive pedogenic change during early (<450 y) soil development (e.g. pH decline, cation leaching) which drive selection of soil bacterial communities. In mature soils (∼450–4000 y), resilient and stable soil bacterial community structures developed, mimicking steady-state climax communities that were observed during latter stages of primary plant succession. These relationships point to possible feedbacks between plant and bacterial communities during ecosystem development.