Abiotic conditions and plant cover differentially affect microbial biomass and community composition on dune gradients

Dune systems are characterized by strong gradients of physical stress, with blowing sand and salt spray decreasing with distance from the ocean, and soil nutrients increasing. In this study we ask how soil microbial community composition and biomass change along transects away from the ocean, and whether these changes are regulated by abiotic stress or by resource availability. We collected bulk soil from under three plant species representative of the dune front, back, and flat: Ammophila breviligulata, Rosa rugosa, and Myrica pensylvanica. The biomass and composition of microbial communities were examined using phospholipid fatty acid (PLFA) analysis under patches of dominant vegetation, and in paired bare plots. We found that microbial biomass was strongly correlated with soil C, and thus the presence of vegetation. Community composition, on the other hand, varied with abiotic stresses, especially soil salinity. These variables in turn depended on distance from the shore, and were ameliorated in some cases by vegetation. These findings demonstrate that biomass and community composition are influenced by different environmental variables. Thus, relationships between biomass and composition are unlikely to be readily predicted on the basis of a single resource.     

Changes in soil microbial community composition in response to fertilization of paddy soils in subtropical China

Repeated fertilizer applications to cultivated soils may alter the composition and activities of microbial communities in terrestrial agro-ecosystems. In this study, we investigated the effects of different long term fertilization practices (control (CK), three levels of mineral fertilizer (N₁P₁K₁, N₂P₂K₂, and N₃P₃K₃), and organic manure (OM)) on soil environmental variables and microbial communities by using phospholipid fatty acid (PLFA) biomarkers analysis in subtropical China. Study showed that OM treatment led to increases in soil organic carbon (SOC), total nitrogen (TN) and total phosphorus (TP) contents, while the mineral fertilizer treatment led to increases in dissolved organic carbon (DOC) content. Changes in soil microbial communities (eg. bacteria, actinomycetes) were more noticeable in soils subjected to organic manure applications than in the control soils or those treated with mineral fertilizer applications. Fungal PLFA biomarkers responded differently from the other PLFA groups, the numerical values of fungal PLFA biomarkers were similar for all the OM and mineral fertilizer treatments. PCA analysis showed that the relative abundance of most PLFA biomarkers increased in response to OM treatment, and that increased application rates of the mineral fertilizer changed the composition of one small fungal PLFA biomarker group (namely 18:3ω6c and 16:1ω5c). Further, from the range of soil environmental factors that we examined, SOC, TN and TP were the key determinants affecting soil microbial community. Our results suggest that organic manure should be recommended to improve soil microbial activity in subtropical agricultural ecosystems, while increasing mineral fertilizer applications alone will not increase microbial growth in paddy soils.     

Temperature and substrate controls on microbial phospholipid fatty acid composition during incubation of grassland soils contrasting in organic matter quality

Soil incubations are often used to investigate soil organic matter (SOM) decomposition and its response to increased temperature, but changes in the activity and community composition of the decomposers have rarely been included. As part of an integrated investigation into the responses of SOM components in laboratory incubations at elevated temperatures, fungal and bacterial phospholipid fatty acids (PLFAs) were measured in two grassland soils contrasting in SOM quality (i.e. SOM composition), and changes in the microbial biomass and community composition were monitored. Whilst easily-degradable SOM and necromass released from soil preparation may have fuelled microbial activity at the start of the incubation, the overall activity and biomass of soil microorganisms were relatively constant during the subsequent one-year soil incubation, as indicated by the abundance of soil PLFAs, microbial respiration rate (r), and metabolic quotient (qCO₂). PLFAs relating to fungi and Gram-negative bacteria declined relative to Gram-positive bacteria in soils incubated at higher temperatures, presumably due to their vulnerability to disturbance and substrate constraints induced by faster exhaustion of available nutrient sources at higher temperatures. A linear correlation was found between incubation temperatures and the microbial stress ratios of cyclopropane PLFA-to-monoenoic precursor (cy17:0/16:1ω7c and cy19:0/18:1ω7c) and monoenoic-to-saturated PLFAs (mono/sat), as a combined effect of temperature and temperature-induced substrate constraints. The microbial PLFA decay patterns and ratios suggest that SOM quality intimately controls microbial responses to global warming.     

Response of microbial activity and microbial community composition in soils to long-term arsenic and cadmium exposure

Arsenic (As) and cadmium (Cd) in soils can affect soil microbial function and community composition and, therefore, may have effects on soil ecosystem functioning. The aim of our study was to assess the effects of long-term As and Cd contamination on soil microbial community composition and soil enzyme activities. We analyzed soils that have been contaminated 25 years ago and at present still show enhanced levels of either As, 18 and 39 mg kg⁻¹, or Cd, 34 and 134 mg kg⁻¹. Soil without heavy metal addition served as control. Polymerase chain reaction (PCR) followed by denaturing gradient gel electrophoresis (DGGE) showed that bacterial community composition in As and Cd contaminated soils differed from that in the control soil. The same was true for the microbial community composition assessed by analysis of respiratory quinones. Soil fungi and Proteobacteria appeared to be tolerant towards As and Cd, while other groups of bacteria were reduced. The decline in alkaline phosphatase, arylsulphatase, protease and urease activities in the As- and Cd-contaminated soils was correlated with a decrease of respiratory quinones occuring in Actinobacteria and Firmicutes. Xylanase activity was unaffected or elevated in the contaminated soils which was correlated with a higher abundance of fungal quinones, and quinones found in Proteobacteria.     

Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest

Little is known about the organisms responsible for decomposition in terrestrial ecosystems, or how variations in their relative abundance may influence soil carbon (C) cycling. Here, we altered organic matter in situ by manipulating both litter and throughfall inputs to tropical rain forest soils, and then used qPCR and error-corrected bar-coded pyrosequencing to investigate how the resulting changes in soil chemical properties affected microbial community structure. The plot-scale manipulations drove significant changes in microbial community composition: Acidobacteria were present in greater relative abundance in litter removal plots than in double-litter plots, while Alphaproteobacteria were found in higher relative abundance in double-litter and throughfall reduction plots than in control or litter removal plots. In addition, the bacterial:archaeal ratio was higher in double-litter than no-litter plots. The relative abundances of Actinobacteria, Alphaproteobacteria and Gammaproteobacteria were positively correlated with microbial biomass C and nitrogen (N), and soil N and C pools, while acidobacterial relative abundance was negatively correlated with these same factors. Bacterial:archaeal ratios were positively correlated with soil moisture, total soil C and N, extractable ammonium pools, and soil C:N ratios. Additionally, bacterial:archaeal ratios were positively related to the relative abundance of Actinobacteria, Gammaproteobacteria, and Actinobacteria, and negatively correlated to the relative abundance of Nitrospira and Acidobacteria. Together, our results support the copiotrophic/oligotrophic model of soil heterotrophic microbes suggested by Fierer et al. (2007).     

Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest

To evaluate the importance of plant-soil feedbacks in forest ecosystems, it is fundamental to understand the spatial range within which plant species control soil physicochemical and microbial properties. We investigated the spatial pattern of soil properties associated with canopy trees in a tropical montane forest on Mt. Kianbalu, Borneo. We analyzed soil physicochemical properties and microbial communities (biomarker lipid abundance) as a function of soil depth and distance from the tree trunk of a conifer (Dacrydium gracilis) or a broadleaf tree (Lithocarpus clementianus). The concentration of condensed tannins and fungi-to-bacteria were higher beneath Dacrydium than beneath Lithocarpus. Furthermore, carbon-degrading enzyme activities were lower beneath Dacrydium. These effects of the tree species were more distinct on soil properties beneath the tree crown than on those outside the tree crown. These effects appeared to be largely due to differences in litter chemistry, and the distinct set of soil properties formed corresponding to the above canopy crown. In conclusion, the species-rich forest on the tropical mountain contains spatially distinct units of soil properties associated with canopy trees, and this spatial pattern can influence ecosystem dynamics in the forest through plant-soil feedback effects.     

Spatial variability of glyphosate mineralization and soil microbial characteristics in two Norwegian sandy loam soils as affected by surface topographical features

The aim of this study was to investigate the possible influence of surface topographical features on the spatial variability of glyphosate degradation and some microbial characteristics in sandy loam soil. Soil samples were taken from the ploughed layer across an agricultural field after seedbed preparation for grain (Grue site), and down to 1 m depth under a ridge tilled field (Målselv site), both sites having similar soil textural characteristics (sandy loam soil). Laboratory experiments were performed looking at glyphosate mineralization and soil microbial activity at the Grue site, as well as microbial biomass, activity and substrate utilization patterns at the Målselv site. Microbial biomass and activity decreased, and substrate utilization patterns changed with increasing soil depth, reflecting naturally occurring changes in quantity and quality of soil organic carbon. Further, our results show that considerable spatial heterogeneity in the degradation rate of glyphosate and general carbon utilization exists even across small areas within a single agricultural field. This horizontal variability was observed over several spatial scales, and could not be clearly explained. It evidently arose from differences in environmental factors affecting microbial activity and growth, and topographical features controlling redistribution of water and matter flow patterns were correlated to the investigated soil microbial variables.     

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

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

Environmental similarity is more important than distance in the community structuring processes of ammonia-oxidizing archaea in agricultural soils

Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has poorly been understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate the beta nearest taxon index to quantify the influence of stochastic and deterministic processes. We f...     

Response of microbial community composition and activity in agricultural and grassland soils after a simulated rainfall

Rainfall in Mediterranean climates may affect soil microbial processes and communities differently in agricultural vs. grassland soils. We explored the hypothesis that land use intensification decreases the resistance of microbial community composition and activity to perturbation. Soil carbon (C) and nitrogen (N) dynamics and microbial responses to a simulated Spring rainfall were measured in grassland and agricultural ecosystems. The California ecosystems consisted of two paired sets: annual vegetable crops and annual grassland in Salinas Valley, and perennial grass agriculture and native perennial grassland in Carmel Valley. Soil types of the respective ecosystem pairs were derived from granitic parent material and had sandy loam textures. Intact cores (30 cm deep) were collected in March 1999. After equilibration, dry soil cores (approx. −1 to −2 MPa) were exposed to a simulated Spring rainfall of 2.4 cm, and then were measured at 0, 6, 24, and 120 h after rewetting. Microbial biomass C (MBC) and inorganic N did not respond to rewetting. N₂O and CO₂ efflux and respiration increased after rewetting in all soils, with larger responses in the grassland than in the agricultural soils. Phospholipid fatty acid (PLFA) profiles indicated that changes in microbial community composition after rewetting were most pronounced in intensive vegetable production, followed by the relict perennial grassland. Changes in specific PLFA markers were not consistent across all sites. There were more similarities among microbial groups associated with PLFA markers in agricultural ecosystems than grassland ecosystems. Differences in responses of microbial communities may be related to the different plant species composition of the grasslands. Agricultural intensification appeared to decrease microbial diversity, as estimated from numbers of individual PLFA identified for each ecosystem, and reduce resistance to change in microbial community composition after rewetting. In the agricultural systems, reductions in both the measures of microbial diversity and the resistance of the microbial community composition to change after a perturbation were associated with lower ecosystem function, i.e. lower microbial responses to increased moisture availability.     

Soil sickness of peanuts is attributable to modifications in soil microbes induced by peanut root exudates rather than to direct allelopathy

The quantity and quality of peanut yields are seriously compromised by consecutive monoculture in the subtropical regions of China. Root exudates, which represent a growth regulator in peanut–soil feedback processes, play a principal role in soil sickness. The growth inhibition of a species in an in vitro bioassay enriched with root exudates and allelochemicals is commonly viewed as evidence of an allelopathic interaction. However, for some of these putative examples of allelopathy, the results have not been verified in more natural settings with plants continuously growing in soil. In this study, the phenolic acids in peanut root exudates, their retention characteristics in an Udic Ferrosol, and their effects on rhizosphere soil microbial communities and peanut seedling growth were studied. Phenolic acids from peanut root exudates were quickly metabolized by soil microorganisms and did not accumulate to high levels. The peanut root exudates selectively inhibited or stimulated certain communal bacterial and fungal species, with decreases in the relative abundance of the bacterial taxa Gelria glutamica, Mitsuaria chitosanitabida, and Burkholderia soli and the fungal taxa Mortierella sp. and Geminibasidium hirsutum and increases in the relative abundance of the bacterial taxon Desulfotomaculum ruminis and the fungal taxa Fusarium oxysporum, Bionectria ochroleuca and Phoma macrostoma. The experimental application of phenolic acids to non-sterile and sterile soil revealed that the poor performance of the peanut plants was attributed to changes in the soil microbial communities promoted by phenolic acids. These results suggest that pathogenic fungal accumulation at the expense of such beneficial microorganisms as plant growth promoting rhizobacteria, mycorrhizal fungi induced by root exudates, rather than direct autotoxicity induced by root exudates, might represent the principal cause underlying the soil sickness associated with peanut plants. We hope that our study will motivate researchers to integrate the role of soil microbial communities in allelopathic research, such that their observed significance in soil sickness during continuous monocropping of fields can be further explored.     

Methane oxidation activity and bacterial community composition in a simulated landfill cover soil is influenced by the growth of Chenopodium album L.

Oxygen availability in landfill cover soil is a major limitation to the growth and activity of methanotrophs as methane oxidation is an aerobic microbial process. Plants tolerant to high concentrations of landfill gas (LFG) may play an important role in improving methane oxidation within landfill cover soil and reducing emission of methane, a greenhouse gas, from it. In this study, the effect of an LFG tolerant plant Chenopodium album L. on methane oxidation activity (MOA) and bacterial community composition in landfill cover soil was investigated. Soil samples from four simulated lysimeters with and without LFG and plant vegetation were taken at 4 stages during the plant's development cycle. Results showed that the total number of culturable bacteria in soil could be significantly increased (P < 0.05) by the growth of C. album. The total number of methanotrophs and MOA in soils with LFG was significantly higher (P < 0.05) than in soils without LFG on sampling days 90, 150 and 210. The total number of methanotrophs and MOA in lysimeters with LFG added increased in the presence of C. album when the plant entered the seed setting stage. Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) gel patterns of 16S rDNA gene fragment and band sequencing analyses showed apparent differences in soil bacterial communities in the presence of LFG and plant vegetation. Members of the genus Methylosarcina were found to be the active and dominant methanotrophs in rhizosphere soil of C. album with LFG, while Methylococcus, Methylocystis, and Methylosinus were the primary methanotroph genera in LFG soil without C. album. Thus, C. album appears to select for specific methanotrophic bacteria in the presence of LFG. Soil MOA and microbial diversity can also be significantly affected by the presence of this plant.     

Growth,phosphorus uptake,and rhizosphere microbial‐community composition of a phosphorus‐efficient wheat cultivar in soils differing in pH

In a pot experiment, the P‐efficient wheat (Triticum aestivum L.) cultivar Goldmark was grown in ten soils from South Australia covering a wide range of pH (four acidic, two neutral, and four alkaline soils) with low to moderate P availability. Phosphorus (100 mg P kg^–1) was supplied as FePO₄ to acidic soils, CaHPO₄ to alkaline, and 1:1 mixture of FePO₄ and CaHPO₄ to neutral soils. Phosphorus uptake was correlated with P availability measured by anion‐exchange resin and microbial biomass P in the rhizosphere. Growth and P uptake were best in the neutral soils, lower in the acidic, and poorest in the alkaline soils. The good growth in the neutral soils could be explained by a combination of extensive soil exploitation by the roots and high phosphatase activity in the rhizosphere, indicating microbial facilitation of organic‐P mineralization. The plant effect (soil exploitation by roots) appeared to dominate in the acidic soils. Alkaline phosphatase and diesterase activities in acidic soils were lower than in neutral soils, but strongly increased in the rhizosphere compared with the bulk soil, suggesting that microorganisms contribute to P uptake in these acidic soils. Shoot and root growth and P uptake per unit root length were lowest in the alkaline soils. Despite high alkaline phosphatase and diesterase activities in the alkaline soils, microbial biomass P was low, suggesting that the enzymes could not mineralize sufficient organic P to meet the demands of plants and microorganisms. Microbial‐community composition, assessed by fatty acid methylester (FAME) analysis, was strongly dependent on soil pH, whereas other soil properties (organic‐C or CaCO₃ content) were less important or not important at all (soil texture).