Impact of cattle grazing and inorganic fertiliser additions to managed grasslands on the microbial community composition of soils

A study was undertaken to determine if cattle grazing on managed grasslands had an impact on the microbial community composition of soils. Microbial community molecular profiles of bacteria, actinomycetes, pseudomonads and fungi were generated by polymerase chain reaction (PCR) amplification of rDNA sequences from community DNA isolated from soils. PCR products were profiled using denaturing gradient gel electrophoresis (DGGE) and analysed by principal co-ordinate analysis. PCR–DGGE profiles indicated that cattle grazing had an impact on the pseudomonad community structure only, and that the addition of inorganic nitrogen (N) fertiliser impacted on bacterial, actinomycete and pseudomonad community structure. There was no difference in the community profiles of fungi from grazed and N fertilised grassland plots. Analysis of phospholipid fatty acid (PLFA) profiles revealed that both cattle grazing and N fertiliser impacted on microbial community structure. The abundance of individual PLFAs differed between treatments, with bacterial (15:0), actinomycete (10Me18:0) and fungal (18:2ω6) PLFAs not affected directly by grazing cattle and N fertiliser, however, there were significant grazing–fertiliser interactions. Bacterial plate counts were highest in the N fertilised plots and fungal plate counts were highest in the cattle grazed plots. Analysis of molecular microbial community profiles with PLFA and background soil data revealed several significant correlations. Notably, soil pH was positively correlated with PCO1 of the pseudomonad community profiles and negatively correlated with the fungal PLFA 18:2ω6. Fungal DGGE profiles were negatively correlated with the fungal PLFA 18:2ω6, and bacterial and fungal plate counts positively correlated with each other. Correlation analysis using PC1 from PLFA profile data showed no significant relationship with soil organic matter, pH, total C and total N. The results indicate that cattle grazing and N fertiliser addition to grasslands impact on the community composition of specific groups of micro-organisms. The consequences of such changes in population structure may have implications regarding the dynamics of nutrient turnover in soils.     

稻秸对土壤细菌群落分子多态性的影响

模拟稻秸原位还田条件,分别在水稻土和红壤中添加水稻秸秆培养70d ,第0、5、2 5、4 5、70天采集土样。采用非机械破壁法直接提取水稻土和红壤细菌总DNA ,水稻土细菌总DNA经过二次纯化;红壤细菌总DNA经过一次纯化后,PCR扩增其16SrDNAV3可变区,均可获得清晰的目的条带,对扩增产物进行DGGE分析,结果显示:水稻土和红壤样品的DGGE条带增加,说明稻秸能够增加土壤细菌群落分子多态性的丰富度,随着培养期的延长,施有稻秸的处理中土壤细菌群落多态性的变化远远复杂于空白对照土壤中的细菌群落变化;同时发现在稻秸刺激下不同土壤细菌群落多态性高峰期出现时间不同     

Long‐term effects of fertilizer and manure applications on soil quality and yields in a sub‐humid tropical rice‐rice system

Widespread yield stagnation and productivity declines in the rice–rice cropping system have been reported and many of the associated issues are related to soil quality. A long‐term experimental study was initiated in 1969 to assess the impact of continuous cultivation of rice as a single crop grown in wet as well as dry seasons using varying levels of chemical fertilizer and manure applications on soil quality indicators (physical, chemical and biological), a sustainable yield index (SYI) and a soil quality index (SQI). The treatments comprised chemical fertilizers and farmyard manure (FYM) either alone or in combination viz. control, N, NP, NK, NPK, FYM, N+FYM, NP+FYM, NK+FYM and NPK+FYM, laid out in a randomized complete block design with three replications. Soil samples were collected after the wet season rice harvest in 2010 and were analysed for physical, chemical and biological indicators of soil quality. A SYI based on long‐term yield data and SQI using principal component analysis (PCA) and nonlinear scoring functions were calculated. Application of NPK fertilizers in combination with FYM significantly increased the average grain yield of rice in both wet and dry seasons and enhanced the sustainability of the system compared to the control and plots in receipt of fertilizers. The SYI for the control was higher in the wet season than in the dry one, whereas the reverse was true for NPK+FYM treatment. The value of the dimensionless SQI varied from 1.46 in the control plot to 3.78 in the NPK+FYM one. A greater SYI and SQI in the NPK+FYM treatment demonstrated the importance of using a chemical fertilizer in combination with FYM. For the six soil quality indicators selected as a minimum data set (MDS), the contribution of DTPA‐Zn, available‐N and soil organic carbon to the SQI was substantial ranging from 59.4 to 85.7 per cent in NPK+FYM and control plots, respectively. Thus, these soil parameters could be used to monitor soil quality in a subhumid tropical rice–rice system.     

Long‐term effects of fertilization on some soil properties under rainfed soybean‐wheat cropping in the Indian Himalayas

This study aims to examine the effects of long‐term fertilization and cropping on some chemical and microbiological properties of the soil in a 32 y old long‐term fertility experiment at Almora (Himalayan region, India) under rainfed soybean‐wheat rotation. Continuous annual application of recommended doses of chemical fertilizer and 10 Mg ha^–1 FYM on fresh‐weight basis (NPK + FYM) to soybean (Glycine max L.) sustained not only higher productivity of soybean and residual wheat (Triticum aestivum L.) crop, but also resulted in build‐up of total soil organic C (SOC), total soil N, P, and K. Concentration of SOC increased by 40% and 70% in the NPK + FYM–treated plots as compared to NPK (43.1 Mg C ha^–1) and unfertilized control plots (35.5 Mg C ha^–1), respectively. Average annual contribution of C input from soybean was 29% and that from wheat was 24% of the harvestable aboveground biomass yield. Annual gross C input and annual rate of total SOC enrichment from initial soil in the 0–15 cm layer were 4362 and 333 kg C ha^–1, respectively, for the plots under NPK + FYM. It was observed that the soils under the unfertilized control, NK and N + FYM treatments, suffered a net annual loss of 5.1, 5.2, and 15.8 kg P ha^–1, respectively, whereas the soils under NP, NPK, and NPK + FYM had net annual gains of 25.3, 18.8, and 16.4 kg P ha^–1, respectively. There was net negative K balance in all the treatments ranging from 6.9 kg ha^–1 y^–1 in NK to 82.4 kg ha^–1 y^–1 in N + FYM–treated plots. The application of NPK + FYM also recorded the highest levels of soil microbial‐biomass C, soil microbial‐biomass N, populations of viable and culturable soil microbes.     

Depth dynamics of soil N contents and natural abundances of 15N after 43 years of long-term fertilization and liming in sub-tropical Alfisol

The aim of this study was to understand impacts of long-term (43 years) fertilization on soil aggregation, N accumulation rates and δ¹⁵N in surface and deep layers in an Alfisol. Soil samples from seven treatments were analysed for N stocks, aggregate-associated N in 0–30 cm and the changes in δ¹⁵N in 0–90 cm depths. The treatments were: unfertilized control (control); recommended N dose (N); recommended N and phosphorus doses (NP); recommended N, P and potassium doses (NPK); 150% of recommended N, P and K doses (150% NPK); NPK + 10 Mg FYM ha^?1 (NPK + FYM) and NPK + 0.4 Mg lime ha^?1 (NPK + L). Results revealed that plots under NPK + FYM had ~39% higher total N concentrations than NPK + L in 0–30 cm soil layers. In NPK + L, macro-aggregates had 35 and 11% and microaggregates had 20 and 9% lower δ¹⁵N values than NPK + FYM in 0–15 and 15–30 cm soil layers, respectively. However, plots receiving NPK + FYM had ~39% greater deep soil (30–90 cm) N accumulation than NPK + L. These results would help understanding N supplying capacity by long-term fertilization and assist devising N management strategies in sub-tropical acidic Alfisols.     

The status and fluxes of alkali and alkaline-earth metals in a savanna Alfisol under long-term cultivation

Information on the status and fluxes of alkali (Na, K and Rb) and alkaline-earth metals (Ba, Ca, Mg and Sr) in cultivated soils is required to predict their responses and sensitivity to acidification. The soils for this study were fertilized with NPK (NPK-plot), farmyard manure (FYM-plot) and combined application of FYM and NPK (FYM+NPK-plot) for 50 years. A control-plot, which neither received NPK nor FYM for 50 years, and a natural site were also sampled. Compared to the natural site, significant losses of alkali and alkaline-earth metals occurred in NPK-plot. The FYM+NPK-plot gained excess mass of Ca and Mg, but incurred losses of Na, Rb, K, Ba and Sr. In the FYM-plot, 4% excess mass of Mg and 65% excess mass of Ca were added to the soil, while in the FYM+NPK-plot, 18% excess mass of Mg and 61% excess mass of Ca were added to the soil. The excess masses of Ca and Mg added to these plots partly accounted for from incidental additions through FYM and NPK fertilization and from aeolian sources which, together, were accounted for between 40% and 56% of the Ca-enrichment and between 45% and 100% of Mg-enrichment. Evidence in the study supports the notion that sole application of NPK fertilizers leads to chemical degradation and increases the risk of acidification of savanna Alfisols under continuous cultivation.     

Changes in the microbial community of an arable soil caused by long-term metal contamination

The effects of past applications of farmyard manure (FYM, applied from 1942 to 1967), metal‐contaminated sewage sludge (applied from 1942 to 1961) and mineral fertilizer (NPK, applied from 1942 until now) on the microbial biomass and community structure in a sandy loam, arable soil from the Woburn Market Garden Experiment, UK, were investigated in 1998. Concentrations of Cu, Ni and Zn in soils which previously received sewage sludge were less than current European Union (EU) limits, but the soil Cd concentration was more than twice the permitted limit. Organic‐C concentration in the FYM‐treated soil and contaminated soils was about twice that of NPK‐treated soil. The initial microbial biomass‐C and estimates of total bacterial numbers by acridine orange direct count were significantly (P < 0.05) greater in the FYM‐treated soil compared with the NPK‐treated and the most contaminated soils. Total phospholipid fatty acid (PLFA) concentration (another measure of biomass) was significantly greater in the FYM‐treated soil compared with either the low or high metal‐contaminated soils, both of which contained similar PLFA concentrations. In the metal‐contaminated soils, in contrast, fluorescent Pseudomonas counts, as a percentage of total plate counts, were at least 1.5 times greater than in the uncontaminated soils. The concentrations of these microbial parameters were significantly (P < 0.05) less in the NPK soil than in all the other treatments. Biomass‐C as a percentage of organic‐C was also significantly (P < 0.05) greater in the uncontaminated soils compared with the metal‐contaminated soils. Biomass specific respiration rates in the metal‐contaminated soils were c. 1.5 times those in the FYM‐treated soil. In the metal‐contaminated soils, the concentration of mono‐unsaturated and hydroxy‐fatty acids (derived from phospholipids), and lipopolysaccharide hydroxy‐fatty acids (all indicative of Gram‐negative bacteria) were significantly (P < 0.05) greater than branched fatty acids (indicative of Gram‐positive bacteria). Furthermore, Gram‐negative counts were 62–68% greater than Gram‐positive counts in the metal‐contaminated soils. Branched fatty acid concentration was significantly (P < 0.05) greater in the FYM‐treated soil than in the metal‐contaminated soils. Gram‐positive counts were also 63% greater than Gram‐negative counts in the FYM‐treated soil. We found that effects of the relatively small heavy metal concentration caused measurable decreases in soil microbial biomass‐C concentrations, acridine orange direct counts and Gram‐positive counts. There were also increases in biomass specific respiration rates, and the microbial community had changed substantially, nearly 40 years after the metal inputs ceased. We conclude that, at the very least, the current EU permitted limits for heavy metals in agricultural soils should not be relaxed.     

DNA- versus RNA-based denaturing gradient gel electrophoresis profiles of a bacterial community during replenishment after soil fumigation

We compared the responsiveness and sensitivity to soil fumigation of DNA- and RNA-based analyses of a bacterial community. We first established an improved RNA extraction method using DNA as an adsorption competitor, because it is extremely difficult to extract nucleic acids from clay-rich volcanic ash soil (Andisol), which adsorbs nucleic acids. This novel method facilitated RNA extraction from 500 mg of Andisol for molecular analyses. Then we monitored 16S rDNA PCR and 16S rRNA RT-PCR denaturing gradient gel electrophoresis (DGGE) profiles of samples collected from a chloropicrin (CP)-treated field over 2 months. The difference between untreated control and CP-treated plots was detected clearly both in DNA- and RNA-based DGGE profiles after treatment. The temporal changes in DGGE profiles, however, differed between DNA- and RNA-based analyses in CP-treated plots. RNA-based DGGE showed quicker and greater changes in the bacterial community after CP treatment than did DNA-based DGGE, which showed similar trends to RNA-based DGGE but with a time lag. The extent of decrease in the diversity index (H′) and the change in principal response curves was larger in RNA-based analyses. These results indicate that the rDNA PCR-DGGE method also detects DNA of microbes no longer alive after fumigation, and that rRNA provides a more responsive biomarker than rDNA.     

基于实时荧光定量PCR技术的油气微生物勘探样品保存研究

针对一个油气藏和两个非油气藏上方的土壤剖面,围绕典型油气指示微生物甲烷氧化细菌,采用分子生态学技术比较了新鲜、自然风干和冷冻干燥3种处理下土壤中甲烷氧化细菌标靶基因pmoA的变化规律,研究了自然风干土壤能否用于油气资源微生物勘探.与新鲜土壤相比,自然风干和冷冻干燥显著降低了不同土壤剖面微生物总DNA含量,甲烷氧化细菌pmoA基因数量最多分别下降了90.7％和77.5％;然而,与非油气藏上方土壤剖面相比,自然风干和冷冻干燥处理后,油气藏上方不同土壤剖面依然检测到了大量的甲烷氧化细菌pmoA基因.本研究中,自然风干或冷冻干燥处理后的土壤适合于油气微生物勘探.     

Thermodynamics of K-Ca exchange in soils

The standard and differential thermodynamic properties of K-Ca exchange in soils from the Broadbalk (Batcombe series) and Saxmundham Rotation I (Beccles series) Experiments were evaluated for selected manurial treatments, using exchange isotherms and calorimetric measurements. The Beccles soil had a greater preference for K than the Batcombe soil in all the comparable treatments (Nil, PK and FYM). In all the soils, enthalpic forces favoured K preference but entropic forces Ca preference; in all but two cases the magnitude of the enthalpic forces were greater, resulting in K preference (positive -ΔG_o). The -ΔH_o values of the soils did not vary greatly, and the main cause of variation in -ΔG_o values was that in -TΔS_o values. Residual fertilizer K and FYM residues decreased preference for K at both locations, but more so at Broadbalk than at Saxmundham, presumably because of the greater duration and amount of K manuring at Broadbalk. FYM residues had a very complex effect on the exchange characteristics of Broadbalk soil. It is suggested that these differences are caused by the different pH values of the surface soils before they came into arable usage, which reflect their contrasting parent materials and pedogenic histories, and by the different durations and extents of manuring in the two experiments.     

不同年限毛竹林土壤固氮菌群落结构和丰度的演变

应用变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)和荧光定量PCR(real time fluorescent quantitative PCR,q PCR)方法研究了不同年限毛竹林土壤固氮菌群落结构和丰度的变化。结果表明:土壤p H、有机质、有效磷、速效钾和铵态氮含量在马尾松林改造成毛竹林5 a后明显提高,而后逐渐降低,并趋于稳定;土壤固氮菌多样性和nif H基因丰度也呈现相似的趋势。条带测序分析表明,毛竹林土壤固氮菌均为不可培养的固氮菌,与慢生根瘤菌(Bradyrhizobium sp.)具有较高的相似度。冗余分析结果表明,不同栽培年限毛竹林地土壤固氮菌群落组成发生了明显变化,长期栽培毛竹林引起的土壤养分变化对土壤固氮菌多样性具有重要影响。     

Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China

Background, Aims, and Scope  Knowledge about shifts of microbial community structure and diversity following different agricultural management practices could improve our understanding of soil processes and thus help us to develop sound management strategies. A long-term fertilization experiment was established in 1989 at Fengqiu (35°00′N, 114°24′E) in northern China. The soil (sandy loam) is classified as aquic inceptisols and has received continuous fertilization treatments since then. The fertilization treatments included control (CK, no fertilizer), chemical fertilizers nitrogen (N) and potassium (K) (NK), phosphorous (P) and K (PK), NP, NPK, organic manure (OM), and half chemical fertilizers NPK plus half organic manure (1/2NPKOM). The objective of this study was to examine if the microbial community structure and diversity were affected by the long-term fertilization regimes. Materials and Methods  Soil samples were collected from the long-term experimental plots with seven treatments and four replications in April 2006. Microbial DNAs were extracted from the soil samples and the 16S rRNA genes were PCR amplified. The PCR products were analyzed by DGGE, cloning and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and the clone libraries constructed from the excised DGGE bands. Results  The bacterial community structure of the OM and PK treatments were significantly different from those of all other treatments. The bacterial community structures of the four Ncontaining treatments (NK, NP, NPK and 1/2NPKOM), as well as CK, were more similar to each other. The changes in bacterial community structures of the OM and PK treatments showed higher richness and diversity. Phylogenetic analyses indicated that Proteobacteria (30.5%) was the dominant taxonomic group of the soil, followed by Acidobacteria (15.3%), Gemmatimonadetes (12.7%), etc. Discussion  Irrespective of the two fertilization treatments of OM and PK, the cluster analysis showed that bacterial communities of the remaining five treatments of CK, NK, NP, NPK and 1/2NPKOM seemed to be more similar to each other, which indicated the relatively weak effects of the four N-containing treatments on soil bacterial communities. N fertilizer may be considered as a key factor to counteract the effects of other fertilizers on microbial communities. Conclusions  Our results show that long-term fertilization regimes can affect bacterial community structure and diversity of the agricultural soil. The OM and PK treatments showed a trend towards distinct community structures, higher richness and diversity when compared to the other treatments. Contrasting to the positive effects of OM and PK treatments on the bacterial communities, N fertilizer could be considered as a key factor in the soil to counteract the effects of other fertilizers on soil microbial communities. Recommendations and Perspectives  Because of the extremely high abundance and diversity of microorganisms in soil and the high heterogeneity of the soil, it is necessary to further examine the effects of fertilization regimes on microbial community and diversity in different type soils for comprehensively understanding their effects through the appropriate combination of molecular approaches. ESS-Submission Editor: Chengrong Chen, PhD (c.chen@griffith.edu.au)     

Influence of continuous application of inorganic nutrients to a Maize–Wheat rotation on soil enzyme activity and grain quality in a rainfed Indian soil

To explore long-term impact of organic and inorganic fertilizers on soil health and grain quality, we monitored the enzyme activities and chemical properties of soil; and chemical composition of grain from eight treatments at an experimental field site established in 1996. There were eight treatments applied to both wheat and maize seasons: a control; four inorganic fertilizers, that is, nitrogen and phosphorus (NP), nitrogen and potassium (NK), phosphorous and potassium (PK) and nitrogen, phosphorus and potassium (NPK); farm yard manure alone (FYM) and addition of FYM at two different doses (100 and 50% of recommendation) to NPK that is, NPK + FYM and ½ NPK + FYM. After 11 years of the experiment the NPK + FYM and ½ NPK + FYM treatments had the highest yields, about 5 Mg maize ha⁻¹ and 2 Mg wheat ha⁻¹ with about 2 and 0.5 Mg ha⁻¹, respectively more than the NPK treatments. The dehydrogeanse activity of soils increased significantly in FYM and ½ NPK + FYM. Except urease all other enzymatic activities were increased in those treatments, which received manure. Urease activity was higher in mineral-N applied plots. Grain protein content of both maize and wheat was highest in mineral fertilized plots. Test weight also increased significantly on application of mineral fertilizer. Plots treated with half dose of recommended mineral fertilizer along with FYM were higher in urease, phosphomono and diesterase activities than that of NPK + FYM treated plots. Long-term application of inorganic nutrients along with FYM improved grain mineral composition and yield. Inhibition of few enzymatic activities were also observed upon application of inorganic nutrients either alone or in combination.     

The impact of long-term cultivation and management history on the status and dynamics of cobalt in a savanna Alfisol in Nigeria

The status of cobalt (Co) in savanna soils of Nigeria is largely unknown, and a long-term experiment including inorganic fertilizer (NPK) and farmyard manure (FYM) and uncultivated land provided information on the way management affected the dynamics of Co in the soil. Total Co increased with increasing depth, whereas readily extractable Co decreased. The mean concentration of Co (5.6–7.9 mg kg⁻¹) was close to the mean value of 8 mg kg⁻¹ reported for soils worldwide, whereas the concentration of extractable Co was less than that reported in most soils. Regression analysis indicated that total Fe predicted up to 78% of the soil Co. The potentially available Co correlated strongly with pedogenic or reducible Mn oxides extracted with dithionite–citrate–bicarbonate. Mass balance calculations showed that fertilization with either NPK or FYM caused losses of between 0.8 and 1.1 g Co m⁻² after 50 years of cultivation against the uncultivated site as a reference. However, Co increased by 1.8 g m⁻² in the soil receiving FYM + NPK, suggesting that the Co of the soil was best maintained under this management probably because of incidental additions of Co in the manures. Furthermore, the positive Co balance in the FYM + NPK plot was partly enhanced by its larger contents of clay, Fe and pedogenic Mn oxides than in either the FYM or NPK plots. Clay, Fe and pedogenic oxides served as Co sinks in this particular savanna soil.     

Long-term cattle manure application in soil. II. Effect on soil microbial populations and community structure

Studies were conducted to evaluate microbial populations and community structures in soils under different management systems in a long-term continuous winter wheat experiment. These soils had been treated with cattle manure for over a century, and P, NP, NPK, or NPK plus lime for over 70 years. Cattle manure application promoted the growth of bacteria, but not fungi, when compared with the control soil. Application of chemical fertilizers enriched the K-strategist bacterial community, while application of manure enriched both r- and K-strategists. DNA recovered was most abundant in the manure-treated soil. Effects on bacterial species richness and evenness following long-term soil treatments were also demonstrated by analyzing bacterial community DNA using amplified ribosomal DNA restriction analysis and repetitive extragenic palindromic-polymerase chain reaction fingerprinting. The richness and evenness of the bacterial community were enhanced by manure treatment and treatments that included N and P, which were positively correlated with soil productivity.     

阔叶林改种毛竹(Phyllostachys pubescens)后土壤固氮细菌 nifH 基因多样性的变化

【目的】毛竹是喜氮植物,土壤氮素水平对毛竹生长至关重要。生物固氮是土壤氮素的重要来源,因此,探索阔叶林改种毛竹后土壤固氮细菌和土壤氮素的变化具有重要意义。【方法】选择立地条件相近的毛竹林(100多年前由阔叶林改种而来)和阔叶林,每种林地在东北坡向位置随机选择4个10 m×10 m标准样地,每个标准样地选取5个采样点,分层采集0—20 cm(表层)和20—40 cm(次表层)土壤样品,分析了土壤pH、有机碳、碱解氮、有效磷、速效钾和含水量等常规理化性质; 采用引物对AQER和PolF,以土壤总DNA为模板扩增了固氮细菌功能基因(nifH )片段,应用变性梯度凝胶电泳(DGGE)和实时荧光定量PCR(Real-time PCR),分析了固氮细菌群落结构、多样性以及丰度(nifH 基因拷贝数)变化; 通过基因克隆测序对土壤固氮细菌进行初步鉴定。【结果】阔叶林改种毛竹后土壤pH显著(P0.05)提高; 毛竹林土壤的含水量、碱解氮以及表层土壤的速效钾显著高于(P0.05)同层的阔叶林土壤,而有效磷则显著(P0.05)低于同层的阔叶林土壤。总体来说,阔叶林改种毛竹后土壤养分含量明显提高; 阔叶林土壤固氮细菌DGGE条带数以及多样性指数(Shannon-Wiener index)都高于毛竹林; 基于DGGE条带信息的聚类分析和主成分分析(PCA)结果表明,阔叶林和毛竹林区分为2个类群,而同一林分的不同土层之间差异较小; 实时荧光定量PCR结果显示,毛竹林土壤的固氮细菌 nifH 基因丰度显著(P0.05)高于阔叶林土壤; 通过克隆测序,14个阳性克隆分别属于2个不同的菌属,其中13个均为Bradyrhizobium,1个为Azohydromonas lata,条带序列与已知序列的相似度为93%~98%。【结论】阔叶林改种毛竹后土壤固氮细菌的种类减少,而功能基因丰度却明显增加; 土壤氮素水平明显提高,这可能是土壤固氮能力增强的结果。     

Methanogenic archaeal communities developed in paddy fields in the Kojima Bay polder, estimated by denaturing gradient gel electrophoresis, real-time PCR and sequencing analyses

Methanogenic archaeal communities inhabiting the paddy field soils in the Kojima Bay polder were investigated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), real-time PCR and sequencing analyses. Soil samples of the plow and subsoil layers were collected in 2006 from four paddy fields that were reclaimed between 1692 and 1954. The DGGE band patterns of the targeted 16S rRNA genes amplified from the extracted DNA from the samples were different from the patterns from the paddy field soils in diluvial and alluvial areas. The numbers of targeted 16S rRNA genes, which were involved with methanogenic archaeal and other archaeal sequences, were approximately 10⁷–10⁸ and 10⁶ g⁻¹ dry soil in the plow and subsoil layers, respectively. Sequences of methanogenic archaeal 16S rRNA genes belonging to Methanocellales (Rice cluster I), Methanosarcinales and Methanobacteriales were obtained from the major DGGE bands. Whereas sequences in Methanomicrobiales, which were predominant methanogens in the diluvial and alluvial paddy fields, were not recovered. Known halophilic and methylotrophic methanogens, which are characteristic of saline and marine environments, were not detected. These results indicate that distinctive methanogenic archaeal communities have developed in the paddy field soils in the Kojima Bay polder.     

Effect of Integrated Nutrient Management on Soil Physical Properties and Crop Productivity under a Maize (Zea mays)–Mustard (Brassica campestris) Cropping Sequence in Acidic Soils of Northeast India

A five-year (2001/02–2006/07) field experiment was carried out on acidic clay loam soil classified as Typic Hapludalf with a maize–mustard crop sequence to study the effect of continuous application of nitrogen, phosphorus, and potassium (NPK) fertilizers alone and in combination with lime, farmyard manure (FYM), and biofertilizers on soil physical properties, soil organic carbon (SOC), soil microbial biomass carbon (SMBC), and crop yields on the hilly ecosystem of Meghalaya. Significant improvement in the soil physical conditions of the soil was observed under integrated application of organic manure and inorganic fertilizers. Addition of NPK fertilizers along with organic manure, lime, and biofertilizers increased soil organic carbon (SOC) content, aggregate stability, moisture-retention capacity, and infiltration rate of the soil while reducing bulk density. The SOC content under the treatment of 100% NPK + lime + biofertilizer + FYM was significantly greater (68.58%) than in control plots. Maize and mustard crop yields also significantly increased (4.73- and 21.09-folds, respectively) with continuous application of balanced inorganic (100% NPK) + lime + biofertilizer + FYM as compared to the control plots. However, crop yields drastically reduced under application of integrated nutrients without FYM as compared to the treatment with FYM application. Thus, the results suggest that integrated use of a balanced inorganic fertilizer in combination with lime and organic manure sustains a soil physical environment that is better for achieving higher crop productivity under intensive cropping systems in the hilly ecosystem of northeastern India.     

Microbial biomass dynamics in recently air-dried and rewetted soils compared to others stored air-dry for up to 103 years

Our aim was to compare the soil microbial biomass concentration and its activity (measured as CO₂-C evolved) following the rewetting and aerobic incubation of soils which have previously been stored air-dry for different periods. Some of the soils have been stored in the Rothamsted sample archive for 103 years, others were comparable freshly sampled soils following air-drying and rewetting and other soils were stored air-dry for 2 years then rewetted for the work described here. Following air-drying, soil ATP concentrations were variable in recently air-dried soil, comprising about 10-35% of the initial ATP concentrations in fresh soil. Following rewetting, the percentage recovery of ATP increased in all soils by 7 days, then declined to between 73% and 87% of the original ATP concentration in the air-dried soils by day 12. Storage of air-dried soils decreased the ability of the microbial biomass to restore its ATP concentrations. For example, the ATP concentration in a soil sampled from stubbed (i.e. tree seedling, saplings and bushes cut frequently to ground level) grassland of the Broadbalk continuous wheat experiment at Rothamsted then air-dried for 2 years was only about 14% of that in the fresh soil at 2 days after rewetting. In other soils from the Hoosfield Barley Experiment, also at Rothamsted, previously given NPK or FYM since 1852, and sampled then stored air-dry for between 13 and 83 years, from 52% to 57% of the ATP in the comparable fresh soils was measured at two days after rewetting. The soil ATP concentration then changed little more up to 12 days. One of the most interesting findings was that while the microbial biomass ATP concentration in the above NPK soils only ranged from about 2 to 4 μmol ATP g⁻¹ biomass C, in the FYM soil the microbial biomass ATP concentrations (range 11.5-13.6 μmol ATP g⁻¹ biomass C) were the same as we repeatedly measure in fresh moist aerobic soil. We do not yet know the reasons for this. More than twice as much CO₂-C was evolved from the long-term stored soils than from freshly sampled ones. However, the specific respiration of the microbial biomass did not change much after the first 12 years of storage, indicating that loss of viability mainly occurred in the earlier years.     

Soil boron status: impact of lime and fertilizers in an Indian long-term field experiment on a Typic Paleustalf

In Indian agriculture, nitrogen (N) and phosphorus (P) fertilizers are predominantly used by the farmers, often ignoring secondary and micronutrients. Significance of boron (B) in nutrient management studies has been increasingly underlined under intensive cropping systems particularly in acid soils. In order to understand the distribution of soil native B in different fractions and their contribution to plant B uptake as influenced by nutrient management, soil samples collected after wheat (2009–2010) from a long-term experiment (LTE) continuing since 1972–1973 on Typic Paleustalf of Ranchi were subjected to sequential fractionation of soil B. Treatments included N alone, NP, NPK, 150% of recommended NPK, NPK + farmyard manure (FYM), NPK + lime, and an unfertilized-control. Five soil B fractions were determined along with hot CaCl₂-extractable (available) B. Averaged across the treatments, the soil had low organic carbon (C), pH and cation exchange capacity (CEC), and high free sesquioxides. Total B content was 21.7 mg kg^?1. Among different B fractions, residual B was the major contributor to total B and other fractions collectively shared 7% of total B only. Application of N alone depleted readily soluble, specifically adsorbed and organically bound B bringing the contents even below unfertilized-control. Conjoint use of lime or FYM with NPK increased significantly these fractions, whereas a decrease in oxide bound B was noticed under these treatments. Available B was positively correlated with these fractions indicating their significance in controlling B availability in the soil. The study revealed that use of lime or FYM helped modifying the distribution of soil B in different fractions by way of changing soil pH and organic C content, resulting in enrichment of plant available pool. A drastically low available B content in different treatments receiving fertilizers alone, however, suggested the necessity of B fertilization at prescribed rates for maintaining soil B fertility as also high crop yields.