Managing soil organic matter – implications for soil structure on organic farms

Abstract. This paper reviews current understanding of soil structure, the role of soil organic matter (SOM) in soil structure and evidence for or against better soil physical condition under organic farming. It also includes new data from farm case studies in the UK. Young SOM is especially important for soil structural development, improving ephemeral stability through fungal hyphae, extracellular polysaccharides, etc. Thus, to achieve aggregate stability and the advantages that this conveys, frequent input of fresh organic matter is required. Practices that add organic material are routinely a feature of organically farmed soils and the literature generally shows that, comparing like with like, organic farms had at least as good and sometimes better soil structure than conventionally managed farms. Our case studies confirmed this. In the reviewed papers, SOM was generally larger on the biodynamic/organic farms because of the organic additions and/or leys in the rotation. We can therefore hypothesize that, because it is especially the light fraction of SOM that is involved in soil structural development, soil structure will improve in a soil to which fresh organic residues are added regularly. Thus, we argue it is not the farming system per se that is important in promoting better physical condition, but the amount and quality of organic matter returned to a soil.     

Analysis of bacterial communities in soil by PCR-DGGE targeting protease genes

We studied the effects of the application of organic (OM) and inorganic fertilizer (CF) on soil protease activity and proteolytic bacterial communities in rhizosphere and bulk soil on an experimental lettuce field in Hokkaido, Japan. The protease activity always was higher in soils of the OM than with the CF treatment, and also higher in the rhizosphere than in the bulk soil. We analyzed proteolytic bacterial communities by denaturing gradient gel electrophoresis (DGGE) of the alkaline metalloprotease (apr) and neutral metalloprotease (npr) genes. Most apr forms detected were closely related to apr of Pseudomonas fluorescens, and all npr variants closely resembled the gene of Bacillus megaterium. These results were consistent with findings from tests using cultured bacterial communities, indicating a high specificity of our PCR-DGGE for amplifying apr and npr genes. The community compositions of proteolytic bacteria were assessed by principal component analysis of the DGGE profiles. There were significant differences in the effects of CF and OM on the community compositions of apr- and npr-expressing bacteria, and the communities of the two types of bacteria played different roles in rhizosphere and bulk soil. We found significant correlations between the protease activity and the communities of the two types of bacteria. The results indicate that different proteolytic bacteria release different amounts or activities of protease, and that the composition of proteolytic bacterial communities may play a major role in determining overall soil protease activity.     

Phosphorus dynamics in the rhizosphere of two wheat cultivars in a soil with high organic matter content

Soil organic matter (SOM) is a key of most nutrient cycling and its content influences labile phosphorus (P) pool. In order to promote P availability from SOM, some plant strategies could be important to increase organic P mineralization, which may change among cultivars of the same crop. This study evaluated phosphorus dynamics in the rhizosphere of two wheat cultivars in soil with high organic matter content. Experiment was established in a greenhouse using a Humic Cambisol in a randomized block design using Quartzo and Abalone as wheat cultivars and harvested 20 days after seedling. Pots with a horizontal mesh (25 µm) were used to isolate the soil from roots. At harvest, the soil under the mesh was sliced in five distances from the rhizoplane (0–3; 3–6; 6–10; 10–20; 20–30 mm). Organic P was the buffer to maintain P dynamics in the rhizosphere and there was phosphorus depletion in the first slice near the rhizoplane due to the root effect, regardless the cultivar. Quartzo showed high labile inorganic P, presumably due to the high amount of root hairs, which increased the acid phosphatase activity and consequently root P uptake. Quartzo was more efficient in changing rhizosphere regarding the P acquisition.     

Effect of organic mulches on soil bacterial communities one year after application

The application of organic mulches as a soil cover is effective in improving the quality of soil. However, very little information is available on the effect of mulches on the soil microbial community. In this study, we investigated the effect of various organic mulches on soil dehydrogenase activity (DHA) and microbial community structures in the top 1 cm and 5 cm below the soil surface 1 year after application of the mulches. DHA was stimulated at both depths in plots mulched with grass clippings (GC), but was not significantly different from the control for the other mulch treatments. Fatty acid methyl ester (FAME) analysis and denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction-amplified 16S rDNA fragments were used to assess changes in the soil microbial community structure. Cluster analysis and principle component analysis of FAME profiles showed that only soil mulched with pine chips distinctively clustered from the other treatments. At the soil surface, bacterial DGGE profiles revealed that distinct shifts in several bacterial populations occurred in soils mulched with GC and eucalyptus yardwaste (EY), while DGGE profiles from soil at the 5 cm depth revealed no distinct changes. Changes in bacterial diversity at the soil surface under different mulches were calculated based on the number of bands in the DGGE profile using the Shannon-Weaver index of diversity ( H). Compared to the control ( H =0.9), the GC- and EY-treated soils showed slightly increased bacterial diversity, with an H of 1.1 and 1.0, respectively. These results indicate that the long-term effect of organic mulches on the soil microbial activity and community structure is highly dependent upon the type of mulch and is mostly exerted in the top few centimeters of the soil profile.     

Application of DGGE analysis to the study of bacterial community structure in plant roots and in nonrhizosphere soil

To analyze the structure of bacterial communities in spinach roots and in the nonrhizosphere soil, we used PeR-amplified 16S rRNA gene fragments separated by denaturing gradient gel electrophoresis (DGGE). DGGE revealed a large number of band patterns, which were ascribed to various bacterial species composing each of the bacterial communities. The pattern from the roots was less complex than that from the soil. It is considered that DGGE analysis is suitable for studies of bacterial community structure in soil-plant ecosystems.     

Effect of long-term fertilization on bacterial communities in wheat endosphere

Fertilization has been shown to exert a significant influence on soil microorganisms and directly and indirectly influences plant growth and survival in agroecosystems. However, it is unknown whether fertilization affects endophytic microbial communities, which are ubiquitous and intimately associated with plant growth and health. Herein, we investigated endophytic bacterial communities in wheat leaves and roots under different long-term fertilization regimes, including NPK chemical fertilizer and NPK chemical fertilizer combined with wheat straw, pig manure, or cow manure. Endophytic bacterial community composition considerably differed in leaves and roots. Although different fertilization treatments did not affect the endophytic bacterial species richness or phylogenetic diversity in either leaves or roots, the community composition was significantly altered, particularly in roots. The endophytic bacterial co-occurrence network in leaves was more complex and stable than that in roots. Furthermore, many of the keystone species that were identified by their topological positions in the co-occurrence networks of leaves and roots were involved in plant growth and fitness. The total relative abundance of keystone species was the highest in the NPK plus cow manure treatment in both leaves and roots. Overall, our results suggest that different fertilization regimes can strongly affect endophytic bacterial communities, and the combination of NPK fertilizer and cow manure promoted the relative abundance of the key endophytic bacterial microbiota in both leaves and roots, which might be beneficial for plants in agroecosystems.     

连续施用解磷菌肥对复垦土壤磷酸酶和Hedley磷形态的影响

为了研究增施解磷菌肥对土壤供磷状况的改善和土壤中磷有效性的提高状况,通过田间小区试验研究了连续施用解磷菌肥对复垦5年土壤碱性磷酸酶活性及Hedley磷形态的影响。结果表明:施用无机肥+有机肥+解磷菌肥处理的土壤碱性磷酸酶活性最高,为30.65μg/(g·h),比对照提高了83.86%。本试验年与第3年复垦土壤相比,土壤中Hedley磷形态的含量都有不同程度的增加,H_2O-Po含量以无机肥+有机肥+解磷菌肥处理为最高,比对照提高了93.90%;NaOH-Pi、HCl-Pi、HCl-Po含量以无机肥+解磷菌肥处理最大,分别比对照提高了194.2%、61.87%、105.8%;残渣态磷含量以无机肥处理影响最大,比对照提高了22.87%;H_2O-Pi、NaHCO_3-Po含量以有机肥处理最大,比对照提高了129.2%、85.89%;NaHCO_3-Pi、NaOH-Po含量以有机肥+解磷菌肥处理提高最大,分别提高了176.9%、114.4%。可以得出:施用解磷菌肥的处理增加复垦土壤中H_2O-Po、NaHCO_3-Pi、NaOH-Pi、NaOH-Po、HCl-Pi、HCl-Po含量的效果较好。H_2O-Pi、H_2O-Po、NaHCO_3-Pi、NaHCO_3-Po、NaOH-Pi、NaOH-Po、HCl-Pi与碱性磷酸酶均呈极显著相关。解磷菌肥在一定程度上增强了复垦土壤碱性磷酸酶活性,影响土壤中Hedley磷分级的各形态磷素含量,从而提高磷的有效性。     

The quality of exogenous organic matter: short-term effects on soil physical properties and soil organic matter fractions

We examined the short-term effect of five organic amendments and compared them to plots fertilized with inorganic fertilizer and unfertilized plots on aggregate stability and hydraulic conductivity, and on the OC and ON distribution in physically separated SOM fractions. After less than 1 year, the addition of organic amendments significantly increased ( P  <   0.01) the aggregate stability and hydraulic conductivity. The stability index ranged between 0.97 and 1.76 and the hydraulic conductivity between 1.23 and 2.80 × 10⁻³ m/s for the plots receiving organic amendments, compared with 0.34–0.43, and 0.42–0.64 × 10⁻³ m/s, respectively, for the unamended plots. There were significant differences between the organic amendments (P <  0.01), although these results were not unequivocal for both soil physical parameters. The total OC and ON content were significantly increased ( P  <   0.05) by only two applications of organic fertilizers: between 1.10 and 1.51% OC for the amended plots versus 0.98–1.08% for the unamended and between 0.092 and 0.131% ON versus 0.092–0.098% respectively. The amount of OC and ON in the free particulate organic matter fraction was also significantly increased ( P  <   0.05), but there were no significant differences ( P  <   0.05) in the OC and ON content in the POM occluded in micro-aggregates and in the silt + clay-sized organic matter fraction. The results showed that even in less than 1 year pronounced effects on soil physical properties and on the distribution of OC and ON in the SOM fractions occurred.     

Rhizosphere priming of soil organic matter by bacterial groups in a grassland soil

Plants often impact the rate of native soil organic matter turnover through root interactions with soil organisms; however the role of root-microbial interactions in mediation of the “priming effect” is not well understood. We examined the effects of living plant roots and N fertilization on belowground C dynamics in a California annual grassland soil (Haploxeralf) during a two-year greenhouse study. The fate of ¹³C-labeled belowground C (roots and organic matter) was followed under planted (Avena barbata) and unplanted conditions, and with and without supplemental N (20 kg N ha⁻¹ season⁻¹) over two periods of plant growth, each followed by a dry, fallow period of 120 d. Turnover of belowground ¹³C SOM was followed using ¹³C-phospholipid fatty acid (PLFA) biomarkers. Living roots increased the turnover and loss of belowground ¹³C compared with unplanted soils. Planted soils had 20% less belowground ¹³C present than in unplanted soils after 2 cycles of planting and fallow. After 2 treatment cycles, unlabeled soil C was 4.8% higher in planted soils than unplanted. The addition of N to soils decreased the turnover of enriched belowground ¹³C during the first treatment season in both planted and unplanted soils, however no effect of N was observed thereafter. Our findings suggest that A. barbata may increase soil C levels over time because root and exudate C inputs are significant, but that increase will be moderated by an overall faster C mineralization rate of belowground C. N addition may slow soil C losses; however, the effect was minor and transient in this system. The labeled root-derived ¹³C was initially recovered in gram negative (highest enrichment), gram positive, and fungal biomarkers. With successive growing seasons, the labeled C in the gram negative and fungal markers declined, while gram positive markers continued to accumulate labeled belowground C. The rhizosphere of A. barbata shifted the microbial community composition, resulting in greater abundances of gram negative markers and lower abundances of gram positive, actinobacteria and cyclopropyl PLFA markers compared to unplanted soil. However, the longer-term utilization of labeled belowground C by gram positive bacteria was enhanced in the rhizosphere microbial community compared with unplanted soils. We suggest that the activities of gram positive bacteria may be major controllers of multi-year rhizosphere-related priming of SOM decomposition.     

DGGE fingerprinting of culturable soil bacterial communities complements culture-independent analyses

Culture-dependent DGGE (CD DGGE) fingerprinting of the 16S rRNA gene was used to characterize mixed bacterial communities recovered on agar plates. Using R2A Agar as a growth medium, CD DGGE analysis resulted in clear banding patterns of sufficient complexity (16-32 major bands) and reproducibility to investigate differences in bacterial communities in a silt loam soil. Replicate CD DGGE profiles from plates inoculated with less-dilute samples (10⁻³) had a higher band count and were more similar (72-77%) than profiles from more-dilute samples (51-61%). Different culture media and incubation conditions resulted in distinct community fingerprints and increased the cumulative number of unique bands detected. When CD DGGE fingerprints were compared to profiles constructed from 16S rRNA genes obtained from culture-independent clone libraries (CB DGGE profiles) 34% of the bands were unique to the culture-dependent profiles, 32% were unique to the culture-independent profiles and 34% were found in both communities. These data demonstrate that culture-independent DGGE profiles are supplemented by the distinct bands detected in culture-dependent profiles. CD DGGE can be a useful technique to follow the dynamics of distinct culturable fractions of the soil bacterial community.     

Kinetics of acid phosphatase in calcium chloride extractable soil organic matter

The aim of this work was to compare the kinetic parameters of acid phosphatase (EC 3.1.3.2.) extracted from two forest soils under oak or pine. Soil was extracted with 4 mM CaCl₂ and the extract was divided into two fractions by filtration: one >0.2 μm containing microbial cells and soil particulates, and the other <0.2 μm containing fine particles and dissolved organic compounds of soil. The >0.2 μm fraction had higher K_m (0.26–0.82 vs. 0.12–0.39) and V_max (0.07–0.79 vs. 0.06–0.16) values than the <0.2 μm fraction, indicating a higher enzyme-substrate affinity and smaller amount of enzyme in fine particles and dissolved organic matter.     

Labile and stable pools of organic matter in soil amended with sewage sludge biochar

One of the main advantages of using biochar for agricultural purposes is its ability to store carbon (C) in soil for a long-term. Studies of labile and stable fractions of soil organic matter (SOM) may be a good indicator of the dynamics of biochar in soils. This study evaluated the effects of applying sewage sludge biochar (SSB) in combination with mineral fertilizer on fractions of SOM. To conduct this evaluation, 15 Mg ha^?1 of SSB combined or not with mineral fertilizer (NPK) was applied to the soil in two cropping seasons. Apart from total organic C (TOC), the labile and stable fractions of SOM were also determined. The combined use of SSB and NPK resulted in higher TOC, a 22% to 40% increase compared to the control and to the NPK treatments, respectively. The SSB produced at a lower temperature increased the labile fractions of SOM, especially the microbial biomass C, showing its capacity to supply nutrients in the short-term. The stable pools of SOM are increased after adding SSB produced at a higher temperature. It was concluded that pyrolysis temperature is a key-factor that determines the potential of SSB to accumulate C in labile and stable fractions of SOM.     

Single particle analysis reveals that bacterial community structures are semi-specific to the type of soil particle

Abstract

With the aim of understanding how diverse bacteria are distributed within a heterogeneous soil, we compared local bacterial communities on individual soil particles. We picked up 11 coarse sand-sized particles (quartz, whitish feldspar, yellow feldspar or unidentified brown particles) from a sandy soil, extracted DNA from each particle, and carried out partial 16S rDNA polymerase chain reaction denaturing gradient gel electrophoresis analysis. Bacterial communities located on soil particles of the same type were more similar in composition than communities located on particles of the other types. Thus, the local structure of a bacterial community is related to the type of soil particle, which suggests that a high diversity of soil bacteria emerges through a combination of local bacterial communities on different types of soil particles.     

耕作对土壤有机物和土壤团聚体稳定性的影响

Agricultural sustainability relates directly to maintaining or enhancing soil quality. Soil quality studies in Canada during the 1980‘s showed that loss of soil organic matter (SOM) and soil aggregate stability was standard features of non-sustainable land management in agroecosystems. In this study total soil organic carbon (SOC), particulate organic matter (POM), POM-C as a percentage of total SOC, and aggregate stability were determined for three cultivated fields and three adjacent grassland fields to assess the impact of conventional agricultural management on soil quality. POM was investigated using solid-state ^13C nuclear magnetic resonance (NMR) to determine any qualitative differences that may be attributed to cultivation. Results show a highly significant loss in total SOC, POM and aggregate stability in the cultivated fields as compared to the grassland fields and a significant loss of POM-C as a percentage of total SOC.Integrated results of the NMR spectra of the POM show a loss in carbohydrate-C and an increase in aromatic-C in the cultivated fields, which translates to a loss of biological lability in the organic matter. Conventional cultivation decreased the quantity and quality of SOM and caused a loss in aggregate stability resulting in an overall decline in soil quality.     

Effects of long-term fertilization with different substitution ratios of organic fertilizer on paddy soil

In recent years, the abuse of chemical fertilizers has caused numerous environmental problems, such as soil acidification and compaction. Replacing chemical fertilizers with organic fertilizers can effectively alleviate these problems. However, the effects of alternative organic fertilizers remain unclear. To explore the effects of organic fertilizer substitution on rice yield and paddy soil physicochemical properties and bacterial community structure, we conducted a 5-year experiment using different proportions of organic fertilizer substitution in a double-cropping rice field in Jiangxi, China. Our results showed that replacing chemical fertilizers with organic fertilizers can reduce soil acidification, increase soil organic matter content, nutrient contents, and enzyme activities, improve soil physicochemical properties and microbial community, and enhance soil metabolism. Appropriate organic substitution also had positive effects on rice production. These findings enhance our understanding of the effects of different alternative organic fertilization methods and have important theoretical significance for the promotion of the use of organic fertilizers in the future.     

Inputs of nitrogen and organic matter govern the composition of fungal communities in soil disturbed by overwintering cattle

Overwintering cattle outdoors causes soil surface disturbance, substantial increases of soil N_tot, C_org, and P and a shift in pH to alkaline levels. Since fungi predominate in unfertilized soils with acidic pH and have filamentous hyphae, we hypothesized that changes caused by overwintering cattle outdoors (trampling, excreta returns, and changes in soil chemistry) will lead to suppressed species richness, lower biomass, and alter the structure of fungal communities. The research was conducted on an upland pasture used more than 10 years for cattle overwintering. Both culture-dependent and -independent methods were used for the determination of either fungal species composition (cultivation; DGGE) or biomass (numbers of CFU; concentration of fungal PLFA marker 18:2ω6,9). Soils under three different levels of cattle disturbance (S - severe, M - moderate, C - no disturbance/control) were investigated during three subsequent years. In addition, the DGGE analysis of soils was completed by comparison with analysis of fresh cattle excrements (Ex). The composition of fungal communities showed significantly higher richness and a substantial shift in species composition in cattle-disturbed soils (S, M) in comparison to the non-disturbed soil (C). The number of separated DGGE bands was significantly higher in S (30.67 ± 1.63; mean ± SD) and M (25.50 ± 1.64) soils than in the C soil (19.33 ± 1.75). Sequencing of typical bands revealed common fungal genera - Alternaria, Penicillium, Fusarium, Rhizopus, Isaria, and Metarhizium. Profiles of the S soil were enriched by bands of rumen-born anaerobic fungi (Neocallimastix, Cyllamyces) occurring mainly in profiles of excrements, where relatively low band richness (14.33 ± 1.15) was observed. The increasing level of cattle disturbance induced an increase in the biomass of complex fungal community over the three-year experimental period from 3.39 ± 2.11 (mean ± SD) nmol of fungal PLFA per gram of the C soil to 5.87 ± 3.16 in the M soil and 9.21 ± 4.69 in the S soil. Concentrations of soil N_tot and C_org were evaluated as the parameters significantly correlating with biomass as well as composition of the fungal community.     

Changes in soil organic carbon fractions and bacterial community composition under different tillage and organic fertiliser application in a maize−wheat rotation system

ABSTRACT

The objective of this study was to assess the impact of different tillage and organic fertiliser regimes on soil carbon fractions and bacterial community composition within a maize–wheat cropping system. We conducted a six-year experiment on the Huang-Huai-Hai Plain of China. Six treatments were established: deep tillage (DT), shallow tillage (ST), no-tillage (NT), deep tillage with organic fertiliser (DTF), shallow tillage with organic fertiliser (STF), and no-tillage with organic fertiliser (NTF). Results indicated that during the winter wheat growing season, the highest contents of soil organic carbon (SOC) and easily-oxidised organic carbon (EOC) were in the STF treatment. During the summer maizegrowing season, the DTF treatment had the highest SOC and EOC contents. Compared with the other treatments, the NTF treatment had higher Chao1 and Shannon indices for bacteria; however, the relative abundance of Proteobacteria is highest in all treatments. A redundancy analysis (RDA) revealed that bacterial community composition was correlated with variation of the SOC, DOC, EOC, and microbial biomass carbon (MBC). Our results showed that combining the two components of the SOC fractions and bacterial community composition, STF practice in a maize–wheat rotation was a sustainable approach to optimising soil structure and improving soil quality.