Land-use intensification and agroforestry in the Kenyan highland: Impacts on soil microbial community composition and functional capacity

This study investigates microbial communities in soil from sites under different land use in Kenya. We sampled natural forest, forest plantations, agricultural fields of agroforestry farms, agricultural fields with traditional farming and eroded soil on the slopes of Mount Elgon, Kenya. We hypothesised that microbial decomposition capacity, biomass and diversity (1) decreases with intensified cultivation; and (2) can be restored by soil and land management in agroforestry. Functional capacity of soil microbial communities was estimated by degradation of 31 substrates on Biolog EcoPlates™. Microbial community composition and biomass were characterised by phospholipid fatty acid (PLFA) and microbial C and N analyses. All 31 substrates were metabolised in all studied soil types, i.e. functional diversity did not differ. However, both the substrate utilisation rates and the microbial biomass decreased with intensification of land use, and the biomass was positively correlated with organic matter content. Multivariate analysis of PLFA and Biolog EcoPlate™ data showed clear differences between land uses, also indicated by different relative abundance of PLFA markers for certain microorganism groups. In conclusion, our results show that vegetation and land use control the substrate utilisation capacity and microbial community composition and that functional capacity of depleted soils can be restored by active soil management, e.g. forest plantation. However, although 20–30 years of agroforestry farming practises did result in improved soil microbiological and chemical conditions of agricultural soil as compared to traditional agricultural fields, the change was not statistically significant.     

Long-term exclusion of plant-inputs to soil reduces the functional capacity of microbial communities to mineralise recalcitrant root-derived carbon sources

Microbial communities in soil are highly species-rich, recognition of which has led to the view that functional redundancy within communities may buffer many impacts of altered community structure on soil functions. In this study we investigated the impact of long-term (>50 years) exclusion of plant-inputs (bare-fallow treatment) on soil microbial community structure and on the ability of the microbial biomass to mineralise tracer additions of ¹³C-labelled plant-derived C-substrates. Exclusion of plant-inputs resulted in depletion of soil organic matter (SOM) and a reduction in microbial biomass size. The microbial community structure was also strongly affected, as indicated by the distinct phospholipid fatty acid (PLFA) profiles in bare-fallow and grassland soils. Mineralisation of labile plant-derived substrates was not perturbed by the bare-fallow treatment. The incorporation of labile plant-derived C into PLFA biomarkers was found to differ between soils, reflecting the distinct community structures of the soils and indicating that these substrates were utilised by a broad range of microbial groups. In contrast, the mineralisation of recalcitrant plant-derived substrates was reduced in bare-fallow soil and the fate of substrate-derived C within PLFA biomarkers was, initially, similar between the soils. These results indicate that utilisation of these recalcitrant substrates was a function restricted to specific groups, and that exclusion of plant-derived inputs to soil had reduced the capacity of bare-fallow microbial communities to utilise this substrate type. Therefore, the study suggests that long-term selective pressure on microbial communities, resulting in altered community structure, may also result in altered functional attributes. This structure-function relationship was apparent for utilisation of recalcitrant plant-derived substrates, but not for the more widely distributed attribute of labile C-substrate utilisation.     

Habitat selective factors influencing the structural composition and functional capacity of microbial communities in agricultural soils

Key physicochemical factors associated with microbial community composition and functions in Australian agricultural soils were identified. Soils from seven field sites, with varying long-term agricultural management regimes, were characterised physicochemically, on the basis of their bacterial and fungal community structures (using PCR-DGGE), and by assessing potential catabolic functions (MicroResp?). Soil type, rather than agricultural management practice, was the key determinant of microbial community structure and catabolic function (P<0.05). Following multivariate analysis, soil pH was identified as the key habitat-selective physicochemical soil property associated with variation in biological diversity and profiles of organic substrate utilisation. In particular, the capacity of soils to catabolise different C-substrates was closely correlated (ρ=0.604, P=0.001) to pH. With decreasing pH, the catabolism of common low molecular weight organic compounds (especially cysteine and aspartic acid) declined, however catabolism of two others (lysine and arginine) increased. Shifts in the capacity of soil microbiota to cycle common organic compounds have implications for overall geochemical cycling of C and N in acidifying soils. The genetic structure of the bacterial communities in soil strongly correlated with pH (ρ=0.722; P=0.001) and that of soil fungi with pH and % sand (ρ=0.323; P=0.006). Catabolic function was more closely associated with the structure of the bacterial than fungal communities. This work has shown that soil pH is a primary driver of microbial diversity and function in soil. Agricultural management practices thereby act to selectively shift populations and functions against this background.     

Soil microbial biomass and activity in organic tomato farming systems: Effects of organic inputs and straw mulching

Organic farming is rapidly expanding worldwide. Plant growth in organic systems greatly depends on the functions performed by soil microbes, particularly in nutrient supply. However, the linkages between soil microbes and nutrient availability in organically managed soils are not well understood. We conducted a long-term field experiment to examine microbial biomass and activity, and nutrient availability under four management regimes with different organic inputs. The experiment was initiated in 1997 by employing different practices of organic farming in a coastal sandy soil in Clinton, NC, USA. Organic practices were designed by applying organic substrates with different C and N availability, either in the presence or absence of wheat-straw mulch. The organic substrates used included composted cotton gin trash (CGT), animal manure (AM) and rye/vetch green manure (RV). A commercial synthetic fertilizer (SF) was used as a conventional control. Results obtained in both 2001 and 2002 showed that microbial biomass and microbial activity were generally higher in organically than conventionally managed soils with CGT being most effective. The CGT additions increased soil microbial biomass C and activity by 103-151% and 88-170% over a period of two years, respectively, leading to a 182-285% increase in potentially mineralizable N, compared to the SF control. Straw mulching further enhanced microbial biomass, activity, and potential N availability by 42, 64, and 30%, respectively, relative to non-mulched soils, likely via improving C and water availability for soil microbes. The findings that microbial properties and N availability for plants differed under different organic input regimes suggest the need for effective residue managements in organic tomato farming systems.     

Plant biomass, soil water content and soil N:P ratio regulating soil microbial functional diversity in a temperate steppe: A regional scale study

Soil microorganisms are influenced by various abiotic and biotic factors at the field plot scale. Little is known, however, about the factors that determine soil microbial community functional diversity at a larger spatial scale. Here we conducted a regional scale study to assess the driving forces governing soil microbial community functional diversity in a temperate steppe of Hulunbeir, Inner Mongolia, northern China. Redundancy analysis and regression analysis were used to examine the relationships between soil microbial community properties and environmental variables. The results showed that the functional diversity of soil microbial communities was correlated with aboveground plant biomass, root biomass, soil water content and soil N: P ratio, suggesting that plant biomass, soil water availability and soil N availability were major determinants of soil microbial community functional diversity. Since plant biomass can indicate resource availability, which is mainly constrained by soil water availability and N availability in temperate steppes, we consider that soil microbial community functional diversity was mainly controlled by resource availability in temperate steppes at a regional scale.     

Effect of tillage and N fertilization on microbial physiological profile of soils cultivated with wheat

Microbial diversity might be a good indicator of ecosystem disturbance and functioning. We determined the effect of soil disturbances, such as N fertilization and tillage management, on soil microbial communities in a Typic Argiudoll of the El Salado river basin (Argentina). Microbial activity and substrate utilization provided a metabolic fingerprint of the soil microbial community. Univariate and multivariate analyses were used to differentiate responses to N fertilization and tillage at each of three growth stages of wheat (Triticum aestivum L.). Tillage had an adverse effect on microbial diversity, in which reduced and conventional tillage treated soils had different populations. However, N fertilization also altered microbial diversity depending on the crop developmental stage considered. Metabolism of carboxylic acids and carbohydrates were the main indicators of functional microbial activity and diversity. Although the substrate consumption profile of 32 C substrates did not provide insights into the fundamental ecological interactions that may induce changes in microbial population, it allowed us to demonstrate the alterations of microbial diversity as a result of tillage. We conclude that tillage and N fertilization altered microbial diversity.     

Decrease in diversity and shift in composition of the soil bacterial community were closely related to high available phosphorus in agricultural Fluvisols of North China

ABSTRACT

Our objectives were to investigate whether AP affects the soil bacterial community composition and diversity in high-level available phosphorus (AP) soils. The bacterial community was analysed through high-throughput sequencing using the Illumina MiSeq platform. Fifteen soils, including barren land, cropland and greenhouse soils which were sandy loam Fluvisols, were selected from different fields in Beijing, China, with AP contents ranging from 5.03 to 391.45 mg kg^?1. Statistical analyses revealed high AP (>100 mg kg^?1) decreased alpha diversity (Shannon’s index, H’) but not beta diversity of the soil bacterial community. The sequencing of 16S rRNA genes showed that Proteobacteria, Bacteroidetes and Acidobacteria were the dominant phyla in sandy loam Fluvisols. AP, soil organic carbon (SOC) and total nitrogen (TN) had synergistic influence on the shift of the bacterial community composition. Moreover, AP was the main driving factor affecting the soil bacterial community composition compared with other environmental factors. The members of the Proteobacteria, Bacteroidetes and Actinobacteria belonging to copiotrophic taxa typically increased in relative abundance in high-P soils, while oligotrophic taxa (mainly Acidobacteria) decreased in relative abundance. Our results demonstrated that the bacterial community composition would shift from oligotrophic to copiotrophic with increasing levels of AP.     

Microbiological characterization of the structures built by earthworms and ants in an agricultural field

The genesis and architecture of the structures built by ants and earthworms differ markedly, suggesting that—in addition to having different physical and chemical properties—the resident microbial community should also have unique properties. We characterized the inorganic N, biomass C, C mineralization rate, and functional diversity of the microbial communities of earthworm casts, earthworm burrow soil, ant mounds, and bulk soil from an agricultural field. Mound soil was most enriched in inorganic N and had the lowest pH, moisture content, and C mineralization rate. Functional diversity was evaluated by determining the ability of microorganisms to grow on 31 substrates using Biolog^®EcoPlates in combination with a most probable number (MPN) approach. Casts had MPNs that were one to two orders of magnitude higher than burrow, mound and bulk soil for most substrates. Casts also had the highest MPNs for particular substrate guilds relative to bulk soil, followed by mound and burrow soil. Indices of substrate diversity and evenness were highest for casts, followed by burrow, mound, and bulk soil. Differences in the type of habitat provided by the structures built by ants and earthworms result in the differential distribution of nutrients, microbial activity, and metabolic diversity of soils within an agricultural field that affect soil fertility and quality.     

Does altered rainfall regime change pesticide effects in soil? A terrestrial model ecosystem study from Mediterranean Portugal on the effects of pyrimethanil to soil microbial communities under extremes in rainfall

In this century, agroecosystems are subjected to multiple global change stressors acting in concert such as alterations in rainfall regimes and pesticide use. Alterations in rainfall regimes, characterised by more extreme intra-annual rainfall regimes, have been forecasted for the Mediterranean region. At the same time, the use of pesticides continues to rise. Here, we report the responses of soil microbial community to a model pesticide, i.e., fungicide pyrimethanil (PYR) under altered rainfall regimes (i.e., drought and heavy rainfall) two and eight weeks after PYR application. We measured the functional responses as enzyme activities, potential nitrification and BIOLOG carbon substrate utilisation. We also characterised the soil bacterial communities using polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) method. After two weeks, enzyme activities were mainly responsive to PYR and kinetic parameters, calculated from BIOLOG carbon substrate utilisation, indicated interaction effects from PYR and rain treatments. Bacterial band richness increased with PYR treatment under normal rain and drought regimes, but bacterial band richness was higher at 1X than 5X PYR under heavy rainfall. Bacterial community structure was also different with the PYR and rainfall treatments. By week eight, PYR treated soils remained functionally different from untreated soils. Bacterial band richness was consistent across PYR treatment regardless of rain regime. However, the bacterial community structure remained significantly different among the PYR treatments under different rain regimes. We conclude that rainfall extremes can alter the effect of PYR on the soil microbial community structure without altering PYR effects on soil functions (measured as enzyme activities, potential nitrification and BIOLOG carbon substrate utilisation).     

Characterization of redox-related soil microbial communities along a river floodplain continuum by fatty acid methyl ester (FAME) and 16S rRNA genes

Redox states affect substrate availability and energy transformation, and, thus, play a crucial role in regulating soil microbial abundance, diversity, and community structure. We evaluated microbial communities in soils under oxic, intermittent, and anoxic conditions along a river floodplain continuum using fatty acid methyl ester (FAME) and 16S rRNA genes-based terminal-restriction fragment length polymorphism (T-RFLP) bacterial fingerprints. In all the soils tested, microbial communities clustered according to soil redox state by both evaluation techniques. Bacteria were dominant components of soil microbial communities, while mycorrhizal fungi composed about 12% of the microbial community in the oxic soils. Gram-positive bacteria consisted >10% of the community in all soils tested and their abundance increased with increasing soil depth when shifting from oxic to anoxic conditions. In the anoxic soils, Gram-positive bacteria composed about 16% of the total community, suggesting that their growth and maintenance were not as sensitive to oxygen supply as for other microbes. In general, microorganisms were more abundant and diverse, and distributed more evenly in the oxic layers than the anoxic layers. The decrease in abundance with increasing oxygen and substrate limitation, however, was considerably more drastic than the decrease in diversity, suggesting that growth of soil microorganisms is more energy demanding than maintenance. The lower diversity in the anoxic than the oxic soils was attributed primarily to the differences in oxygen availability in these soils.     

Effect of swine and dairy manure amendments on microbial communities in three soils as influenced by environmental conditions

Understanding the impacts of manure amendments on soil microorganisms can provide valuable insight into nutrient availability and potential crop and environmental effects. Soil microbial community characteristics, including microbial populations and activity, substrate utilization (SU) profiles, and fatty acid methyl ester (FAME) profiles, were compared in three soils amended or not amended with dairy or swine manure at two temperatures (18 and 25°C) and two soil water regimes (constant and fluctuating) in laboratory incubation assays. Soil type was the dominant factor determining microbial community characteristics, resulting in distinct differences among all three soil types and some differing effects of manure amendments. Both dairy and swine manures generally increased bacterial populations, substrate diversity, and FAME biomarkers for gram-negative organisms in all soils. Microbial activity was increased by both manures in an Illinois soil but only by dairy manure in two Maine soils. Dairy manure had greater effects than swine manure on SU and FAME parameters such as increased activity, utilization of carbohydrates and amino acids, substrate richness and diversity, and fungal FAME biomarkers. Temperature and water regime effects were relatively minor compared with soil type and amendment, but both significantly affected some microbial responses to manure amendments. Overall, microbial characteristics were more highly correlated with soil physical factors and soil and amendment C content than with N levels. These results indicate the importance of soil type, developmental history, and environmental factors on microbial community characteristics, which may effect nutrient availability from manure amendments and should be considered in amendment evaluations.Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture     

Structural and functional diversity of soil microbes is affected by elevated [CO<Subscript>2</Subscript>] and N addition in a poplar plantation

Background, Aims, and Scope  The genetic structure and the functionality of soil microbes are both important when studying the role of soil in the C cycle in elevated CO₂ scenarios. The aim of this work was to investigate the genetic composition of the fungal community by means of PCR-DGGE and the functional diversity of soil micro-organisms in general with MicroResp-based community level physiological profiling (CLPP) in a poplar plantation (POPFACE) grown under elevated [CO₂] with and without nitrogen fertilization. Materials and Methods  The POPFACE experimental plantation and FACE facility are located in central Italy, Tuscania (VT). Clones of Populus alba, Populus nigra and Populus x euramericana were grown, from 1999 to 2004, in six 314 m² plots treated either with atmospheric (control) or enriched (550 μmol mol⁻¹) CO₂ with FACE (Free Air CO₂ Enrichment) technology in each growing season. Each plot is divided into six triangular sectors, with two sectors per poplar genotype: three species × two nitrogen levels. After removal of the litter layer one soil core per genotype (10 cm wide, 20 cm depth) was taken inside each of the three sectors in each plot, for a total of 36 soil cores (3 replicates × 2 [CO₂] × 2 fertilization × 3 species) in October 2004 and in July 2005. DNA was extracted with a bead beating procedure. 18S rDNA gene fragments were amplified with PCR using fungal primers (FR1 GC and FF390). Analysis of CLPP was performed using the MicroResp method. Carbon substrates were selected depending on their ecological relevance to soil and their solubility in water. In particular rhizospheric C sources (carboxylic acids and carbohydrates) were chosen considering the importance of root inputs for microbial metabolism. Results  The fertilization treatment differentiated the fungal community composition regardless of elevated [CO₂] or the poplar species; moreover the number of fungal species was lower in fertilized soil. The effect of elevated [CO₂] on the fungal community composition was evident only as interaction with the fertilization treatment as, in N-sufficient soils, the elevated [CO₂] selected a different microbial community. For CLPP, the differ ent poplar species were the main factors of variation. The FACE treatment, on average, resulted in lower C utilization rates in un-fertilized soils and higher in fertilized soils. Discussion  Fungal biomass and fungal composition depend on different factors: from previous studies we know that the greater quantity and the higher C/N ratio of organic inputs under elevated [CO₂] influenced positively the fungal biomass both in fertilized and in un-fertilized soil, whereas nitrogen availability resulted to be the main determinant of fungal community composition in this work. Whole active microbial community was directly influenced by the soil nutrient availability and the poplar species. Under elevated CO₂ the competition for N with plants strongly affected the microbial communities, which were not able to benefit from added rhizospheric substrates. Under Nsufficient conditions, the increase of microbial activity due to [CO₂] enrichment was related to a more active microbial community, favoured by the current availability of C and N. Conclusions  Different factors influenced the microbial community at different levels: poplar species and root exudates affected the functional properties of the microbial community, while the fungal specific composition (as seen with DGGE) remained unaffected. On the other hand, factors such as N and C availability had a strong impact on the community functionality and composition. Fungal community structure reflected the availability of N in soils and the effect of elevated [CO₂] on community structure and function was evident only in N-sufficient soils. The simultaneous availability of C and N was therefore the main driving force for microbial structure and function in this plantation. Recommendations and Perspectives  Using the soil instead of soil extracts for CLPP determination provides a direct measurement of substrate catabolism by microbial communities and reflects activity rather than growth because more immediate responses to substrates are measured. Further applications of this approach could include selective inhibition of different microbial functional groups to investigate specific CLPPs. To combine the structural analysis and the catabolic responses of specific microbial communities (i.e. fungi or bacteria) could provide new outlooks on the role of microbes on SOM decomposition. ESS-Submission Editor: Dr. Kirk Semple (k.semple@lancaster.ac.uk)     

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     

长期施用化肥对塿土微生物多样性的影响

【目的】土壤微生物在土壤有机质分解、营养循环、植物生长等方面都发挥着重要作用,研究长期施用化肥对其产生的影响可为农田合理施用化肥、培肥土壤和高产高效可持续性农业生产提供理论依据。【方法】以陕西杨凌"国家黄土肥力与肥料效益监测基地"的长期定位试验为基础,利用BIOLOG分析并结合常规分析研究了6种长期不同化肥施用方式不施肥(CK)、单施氮肥(N)、氮钾配施(NK)、磷钾配施(PK)、氮磷配施(NP)和氮磷钾配施(NPK)对土土壤微生物量和微生物功能多样性的影响。【结果】与不施肥CK相比,长期单施氮肥(N)的SMBC、SMBN没有显著变化,但明显降低了土壤微生物商和土壤微生物对氮素的利用;NP和NPK配施能够显著增加土SMBC和SMBN含量,明显提高了土壤微生物商,使土壤微生物种群结构发生了明显变化但土壤微生物对氮素的利用没有显著提高;长期偏施肥处理(NK、PK)的SMBC、SMBN和微生物商虽轻微增加,但土壤微生物种群结构没有显著改变。BIOLOG分析结果显示施磷处理(PK、NP和NPK)对微生物代谢活性的促进作用较大且在培养初期代谢活性较不施磷处理(CK、N和NK)增加显著。长期单施氮肥(N)对于提高土壤微生物多样性没有显著作用而其他化肥施用处理可以提高土土壤微生物群落的碳源利用能力、物种的丰富度和优势度,其中NP和NPK处理配施效果最好。化肥施用对土土壤微生物群落的均匀度没有显著影响。主成分分析的结果表明不同处理的土壤微生物对碳源利用表现出显著差异,氮磷养分的差异是产生分异的主要原因。【结论】土区小麦玉米轮作下,平衡施肥(NP或NPK配施)对于改善农田土壤微生物特性具有良好作用。     

Bacterial diversity in water-stable aggregates of soils under conventional and zero tillage management

Reduced tillage of agricultural soils has been shown to result in greater macroaggregation, microbial biomass and microbial diversity. While it has been shown that macroaggregates contain more microbial biomass per unit soil mass than microaggregates, it is unclear how microbial diversity varies with soil aggregation. We investigated the functional diversity (catabolic potential) of bacteria, evaluated by calculating Shannon’s diversity index (H′), substrate richness (S) and substrate evenness (E) from potential substrate utilization patterns, in whole soil (i.e. not separated into different aggregate sizes) and aggregates of different sizes (2–4, 1–2, 0.5–1, 0.25–0.5, and 0.1–0.25 mm diameter) in loam and silt loam soils grown to barley and managed for 6 years under conventional tillage (CT) or zero tillage (ZT) systems in northern British Columbia. There were no significant tillage effects on bacterial diversity in whole soils. In soil aggregates, H′ and E were significantly higher under CT than under ZT on the loam at barley planting time, with no significant aggregate size effects. However, at barley-heading stage, all diversity indices in both soils were significantly higher under ZT than under CT, and they tended to increase with increasing aggregate size. Cluster analysis and principal component analysis of substrate utilization patterns also revealed differences in bacterial community structures between CT and ZT, but the substrates that were utilized differently between the two tillage systems were not the same between soil types or sampling times. The results during the cropping cycle imply that deterioration of soil structure is probably one factor that explains the adverse effects of soil tillage on soil microbial biomass and diversity.     

Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil

Low molecular weight carbon (C) substrates are major drivers of bacterial activity and diversity in the soil environment. However, it is not well understood how specific low molecular weight C compounds, which are frequently found in root exudates and litter leachates, influence bacterial community structure or if there are specific groups of soil bacteria that preferentially respond to these C inputs. To address these knowledge gaps, we added three simple C substrates representative of common root exudate compounds (glucose, glycine, and citric acid) to microcosms containing three distinct soils from a grassland, hardwood forest, and coniferous forest. CO₂ production was assessed over a 24 h incubation period and, at the end of the incubation, DNA was extracted from the samples for assessment of bacterial community structure via bar-coded pyrosequencing of the 16S rRNA gene. All three C substrates significantly increased CO₂ production in all soils; however, there was no relationship between the magnitude of the increase in CO₂ production and the shift in bacterial community composition. All three substrates had significant effects on overall community structure with the changes primarily driven by relative increases in β-Proteobacteria, γ-Proteobacteria, and Actinobacteria. Citric acid additions had a particularly strong influence on bacterial communities, producing a 2-5-fold increase in the relative abundance of the β-Proteobacteria subphylum. These results suggest that although community-level responses to substrate additions vary depending on the substrate and soil in question, there are specific bacterial taxa that preferentially respond to the substrate additions across soil types.     

Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe

Serious nitrogen (N) deposition in terrestrial ecosystems causes soil acidification and changes the structure and function of the microbial community. However, it is unclear how these changes are dependent on N deposition rates, other factors induced by N (e.g., pH), and their interactions. In this study, we investigated the responses of soil prokaryotic community structure and stability after a 13-year N addition in the semi-arid Leymus chinensis steppe in Inner Mongolia, China. Our results demonstrated that the prokaryotic community structure changed at the low N addition rate of 1.75 g N m⁻² yr⁻¹; however, dramatic changes in microbial abundance, respiratory quotient, and prokaryotic diversity occurred at N addition rates of more than 5.25 g N m⁻² yr⁻¹ when the soil pH dropped below 6.0. The two patterns indicated the difference in driving forces for different microbial properties. The N-driven and pH-driven processes are likely the most important mechanisms determining the responses of bacterial community to N. Some copiotrophic/oligotrophic bacteria, e.g., Proteobacteria and Acidobacteria, changed their relative abundances with the N addition continuously even at a low rate, indicating that they were more sensitive to N directly. Some bacterial groups significantly changed their relative abundance at a high N addition rate when pH dropped below 6.0, e.g., Verrucomicrobia and Armatimonadetes, indicating that they were more sensitive to pH below 6.0. N addition altered the prokaryotic community structure through enrichment of copiotrophic bacteria (species adjustment) at low N addition rates and through enrichment of nitrophilous taxa and significant loss of diversity at high N rates. The results also demonstrated that a high N addition diminished the stability of the prokaryotic community structure and activity through reduction in species diversity and bacterial interaction. Overall, this study supported the hypothesis that the responses of prokaryota to N were dependent on deposition rates, and N-driven and pH-driven processes were the important mechanisms to control the shift of the prokaryotic community.     

Short-term effects of biochar amendment on soil microbial community in humid tropics

Biochar is known to ameliorate soil fertility and improve crop production but information regarding soil microbiota responses on biochar amendment remains limited. The experiment was conducted to study the effect of biochars from palm kernel (pyrolysed at 400°C) and rice husk (gasified at 800°C) in a sandy loam Acrisol from Peninsular Malaysia. The soil was amended with palm kernel shell biochar (PK), rice husk biochar (RH), palm kernel biochar with fertilizer (FPK), rice husk biochar with fertilizer (FRH), fertilizer and control soil. Soil samples were taken during maize harvesting and were analysed for physico-chemical properties, microbial biomass, microbial abundance and microbial diversity. Increase in pH, moisture content, CEC, organic C, and labile C were recorded in all biochar amended soils. Microbial biomass C was 65% and 36% higher in RH and FRH, respectively, than control. Microbial biomass N was greatest in FPK and FRH with respective increment of 359% and 341% than control. β-glucosidase and xylanase activities were significantly increased in all biochar treated soils than control. A shift in microbial diversity was not detected. The biochar affects the microbial community by altering the soil environment and increasing labile active carbon sources in the short-term amendment.     

Carbon and net nitrogen mineralisation in two forest soils amended with different concentrations of biuret

Biuret is a known contaminant of urea fertilisers that might be useful as a slow release N fertiliser for forestry. We studied carbon (C), net nitrogen (N) mineralisation and soil microbial biomass C and N dynamics in two forest soils (a sandy loam and a silt loam) during a 16-week long incubation following application of biuret (C 23.3%, N 40.8%, O 30.0% and H 4.9%) at concentrations of 0, 2, 10, 100 and 1000 mg kg⁻¹ (oven-dried) soil to assess the potential of biuret as a slow-release N fertiliser. Lower concentrations of biuret specifically increased C mineralisation and soil microbial biomass C in the sandy loam soil, but not in the silt loam soil. A significant decrease of microbial biomass C was found in both soils at week 16 after biuret was applied at higher concentrations. C mineralisation declined with duration of incubation in both soils due to decreased C availability. Biuret at concentrations from 10 to 100 mg kg⁻¹ soil had a significantly positive priming effect on soil organic N mineralisation in both soils. The causes for the priming effects were related to the stimulation of microbial growth and activity at an early stage of the incubation and/or the death of microbes at a later stage, which was biuret-concentration-dependent. The patterns in NH₄⁺-N accumulation differed markedly between the two soils. Net N mineralisation and nitrification were much greater in the sandy loam soil than in the silt loam soil. However, the onset of net nitrification was earlier in the silt loam soil. Biuret might be a potential slow-release N source in the silt loam soil.     

Clay Addition to Sandy Soil——Influence of Clay Type and Size on Nutrient Availability in Sandy Soils Amended with Residues Differing in C/N ratio

Addition of clay-rich subsoil to sandy soil results in heterogeneous soil with clay peds(2-mm) or finely ground( 2 mm) clay soil(FG), which may affect the nutrient availability. The aim of this study was to assess the effect of clay soil particle size(FG or peds)and properties on nutrient availability and organic C binding in sandy soil after addition of residues with low(young kikuyu grass,KG) or high(faba bean, FB) C/N ratio. Two clay soils with high and low smectite percentage, clay and exchangeable Fe and Al were added to a sandy soil at a rate of 20%(weight/weight) either as FG or peds. Over 45 d, available N and P as well as microbial biomass N and P concentrations and cumulative respiration were greater in soils with residues of KG than FB. For soils with KG residues,clay addition increased available N and initial microbial biomass C and N concentrations, but decreased cumulative respiration and P availability compared to sandy soil without clay. Differences in measured parameters between clay type and size were inconsistent and varied with time except the increase in total organic C in the 53 μm fraction during the experiment, which was greater for soils with FG than with peds. We concluded that the high exchangeable Fe and Al concentrations in the low-smectite clay soil can compensate a lower clay concentration and proportion of smectite with respect to binding of organic matter and nutrients.