Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

     

Functional and structural microbial diversity in organic and conventional viticulture: organic farming benefits natural biocontrol agents

Statistically significant differences in the structure and function of above-ground grapevine-associated microorganisms from organically and conventionally managed vineyards were found. Aureobasidium pullulans, a copper-detoxifying fungus and biocontrol agent, plays a key role in explaining these differences. The black fungus was strongly enriched in the communities of organically managed plants and yielded a higher indigenous antiphytopathogenic potential.     

Impact of long-term conventional and organic farming on the diversity of arbuscular mycorrhizal fungi

Previous work has shown considerably enhanced soil fertility in agroecosystems managed by organic farming as compared to conventional farming. Arbuscular mycorrhizal fungi (AMF) play a crucial role in nutrient acquisition and soil fertility. The objective of this study was to investigate the diversity of AMF in the context of a long-term study in which replicated field plots, at a single site in Central Europe, had been cultivated for 22 years according to two organic and two conventional farming systems. In the 23rd year, the field plots, carrying an 18-month-old grass-clover stand, were examined in two ways with respect to AMF diversity. Firstly, AMF spores were isolated and morphologically identified from soil samples. The study revealed that the AMF spore abundance and species diversity was significantly higher in the organic than in the conventional systems. Furthermore, the AMF community differed in the conventional and organic systems: Glomus species were similarly abundant in all systems but spores of Acaulospora and Scutellospora species were more abundant in the organic systems. Secondly, the soils were used to establish AMF-trap cultures using a consortium of Plantago lanceolata, Trifolium pratense and Lolium perenne as host plants. The AMF spore community developing in the trap cultures differed: after 12 months, two species of the Acaulosporaceae (A. paulinae and A. longula) were consistently found to account for a large part of the spore community in the trap cultures from the organic systems but were found rarely in the ones from the conventional systems. The findings show that some AMF species present in natural ecosystems are maintained under organic farming but severely depressed under conventional farming, indicating a potentially severe loss of ecosystem function under conventional farming.     

Effects of an integrated rice-crayfish farming system on soil organic carbon,enzyme activity,and microbial diversity in waterlogged paddy soil

A 10-year (2005–2015) field experiment was conducted to study the effects of an integrated rice-crayfish (CR) model on soil organic carbon, enzyme activity, and microbial diversity at soil depths of 0–10?cm, 10–20?cm, 20–30?cm, and 30–40?cm. Compared with a mid-season rice monoculture (MR) model, total organic carbon (TOC), particle organic carbon (POC), and water-soluble organic carbon (WSOC) were significantly higher in the 0–40?cm soil layers, and the content of microbial biomass carbon (MBC) was significantly higher in the 30–40?cm soil layer in the CR model. The ratios of WSOC to TOC and POC to TOC in the 0–40?cm soil layers in CR model exhibited an increasing trend, whereas the ratio of MBC to TOC in the 0–30?cm layers exhibited a decreasing trend with respect to that of the MR model, however, these differences were not statistically significant. The activity of soil invertase, acid phosphatase, and urease in the 0–40?cm soil layers in the CR model exhibited a decreasing trend with respect to that of the MR model, and the activity of urease in the 10–20?cm soil layer in the CR model was significantly lower than that in the MR model. Compared with the MR model, the CR model significantly enhanced the carbon utilization capacity of soil microbes, and the richness index, dominance index, and diversity index of the soil microbial community in the 20–30?cm layer, whereas it significantly decreased the number of dominant soil microorganism species and the carbon utilization capacity of soil microbes in the 0–10?cm layer. Soil organic carbon and its active components had a significant direct correlation with the microbial diversity index, and significantly positive correlations with invertase, urease, and acid phosphatase. With respect to the soil microbial diversity index, soil organic carbon and its active components had a closer relationship with soil enzyme activity.     

Soil microbial diversity affects soil organic matter decomposition in a silty grassland soil

Soil microorganisms play a pivotal role in soil organic matter (SOM) turn-over and their diversity is discussed as a key to the function of soil ecosystems. However, the extent to which SOM dynamics may be linked to changes in soil microbial diversity remains largely unknown. We characterized SOM degradation along a microbial diversity gradient in a two month incubation experiment under controlled laboratory conditions. A microbial diversity gradient was created by diluting soil suspension of a silty grassland soil. Microcosms containing the same sterilized soil were re-inoculated with one of the created microbial diversities, and were amended with ¹³C labeled wheat in order to assess whether SOM decomposition is linked to soil microbial diversity or not. Structural composition of wheat was assessed by solid-state ¹³C nuclear magnetic resonance, sugar and lignin content was quantified and labeled wheat contribution was determined by ¹³C compound specific analyses. Results showed decreased wheat O-alkyl-C with increasing microbial diversity. Total non-cellulosic sugar-C derived from wheat was not significantly influenced by microbial diversity. Carbon from wheat sugars (arabinose-C and xylose-C), however, was highest when microbial diversity was low, indicating reduced wheat sugar decomposition at low microbial diversity. Xylose-C was significantly correlated with the Shannon diversity index of the bacterial community. Soil lignin-C decreased irrespective of microbial diversity. At low microbial diversity the oxidation state of vanillyl–lignin units was significantly reduced. We conclude that microbial diversity alters bulk chemical structure, the decomposition of plant litter sugars and influences the microbial oxidation of total vanillyl–lignins, thus changing SOM composition.     

Chemical and biological indicators of soil quality in organic and conventional farming systems in Central Italy

In the past decade, there has been increased scientific interest in the so-called organic farming, especially in comparison with conventional agriculture. Many recent studies compare these two fundamentally different systems for soil properties, in different regions of the world. In this study, two adjacent fields in Central Italy, one managed according to organic, and the other according to conventional farming methods, were studied to determine the effects of these two agricultural systems on soil quality indicators at the farm level. Chemical and microbiological properties were chosen as indicators of soil quality and were measured at soil depth intervals of 5–20 and 20–35 cm, after 7 years of organic certified and conventional management methods. The field under organic management showed significantly better soil nutritional and microbiological conditions; with increased level of total nitrogen, nitrate and available phosphorus, and an increased microbial biomass content, and enzymatic activities (acid phosphatase, protease and dehydrogenase). No consistent increase in total organic carbon was observed. Results of the study suggest that, over the period of 7 year, organic management method strongly affects soil quality indicators. Large differences between the two soils were found in terms of microbiological properties, which are sensitive soil indicators of changes occurred under the different farming systems.     

Comparison of microbial diversity of edible flowers and basil grown with organic versus conventional methods

The consumption and use of edible flowers as food is growing; however, no study has been conducted to evaluate their role in the cause of food-borne illness or in food safety. Recent food-borne outbreaks traced to fresh herbs have raised concern about their processing and handling. Basil, one of the most commonly used fresh herbs, has been identified as a source of food-borne illness. Baseline assessments of microflora were performed, and the microbial diversity between growing methods (organic vs. conventional) was compared. DNA sequencing was used to identify the microbial flora present on fresh edible flower and basil samples. The most predominant species identified were Enterobacter hormaechei (10%), Acinetobacter calcoaceticus (10%), Enterobacter ludwigii (10%), Enterobacter asburiae (6%), and Enterobacter cowanii (6%). Pseudomonas aeruginosa (6%), Salmonella enterica (6%), and Bacillus amyloliquefaciens (2%) were also isolated. Phylogenetic analysis showed that most species of isolated bacteria belonged to the phyla Gammaproteobacteria (81.2%) and Firmicutes (18.8%). Statistical analysis, diversity index for species richness, and lineage-per-time plots showed that for basil, organically grown samples had a higher microbial diversity than conventionally grown samples. Edible flowers and basil are often grown using organic methods and are commonly consumed raw without any washing or cooking, to preserve aesthetic value, but these practices may pose a potential risk for food-borne illness. The baseline assessment, together with phylogenetic and statistical analyses, indicated possible microbial contamination in edible flowers and basil. The use of statistical estimation of molecular diversity based on the 16S rRNA sequences and lineage-per-time plots with phylogenetic analysis well served as a means for comparing microbial diversity in food samples between the growing methods (organic vs. conventional).     

The effects of mineral fertilizer and organic manure on soil microbial community and diversity

The effects of mineral fertilizer (NPK) and organic manure on phospholipid fatty acid profiles and microbial functional diversity were investigated in a long-term (21-year) fertilizer experiment. The experiment included nine treatments: organic manure (OM), organic manure plus fertilizer NPK (OM + NPK), fertilizer NPK (NPK), fertilizer NP (NP), fertilizer NK (NK), fertilizer N (N), fertilizer P (P), fertilizer K (K), and the control (CK, without fertilization). The original soil was extremely eroded, characterized by low pH and deficiencies of nutrients, particularly N and P. The application of OM and OM + NPK greatly increased crop yields, soil pH, organic C, total N, P and K, available N, P and K content. Crop yields, soil pH, organic C, total N and available N were also clearly increased by the application of mineral NPK fertilizer. The amounts of total PLFAs, bacterial, Gram-negative and actinobacterial PLFAs were highest in the OM + NPK treatment, followed by the OM treatment, whilst least in the N treatment. The amounts of Gram-positive and anaerobic PLFAs were highest in the OM treatment whilst least in the P treatment and the control, respectively. The amounts of aerobic and fungal PLFAs were highest in the NPK treatment whilst least in the N and P treatment, respectively. The average well color development (AWCD) was significantly increased by the application of OM and OM + NPK, and the functional diversity indices including Shannon index (H ^′ ), Simpson index (D) and McIntosh index (U) were also significantly increased by the application of OM and OM + NPK. Principal component analysis (PCA) of PLFA profiles and C source utilization patterns were used to describe changes in microbial biomass and metabolic fingerprints from nine fertilizer treatments. The PLFA profiles from OM, OM + NPK, NP and NPK were significantly different from that of CK, N, P, K and NK, and C source utilization patterns from OM and OM + NPK were clearly different from organic manure deficient treatments (CK, N, P, K, NP, NK 6 and NPK). Stepwise multiple regression analysis showed that total N, available P and soil pH significantly affected PLFA profiles and microbial functional diversity. Our results could provide a better understanding of the importance of organic manure plus balanced fertilization with N, P and K in promoting the soil microbial biomass, activity and diversity and thus enhancing crop growth and production.     

Molecular diversity of arbuscular mycorrhizal fungi in onion roots from organic and conventional farming systems in the Netherlands

Diversity and colonization levels of naturally occurring arbuscular mycorrhizal fungi (AMF) in onion roots were studied to compare organic and conventional farming systems in the Netherlands. In 2004, 20 onion fields were sampled in a balanced survey between farming systems and between two regions, namely, Zeeland and Flevoland. In 2005, nine conventional and ten organic fields were additionally surveyed in Flevoland. AMF phylotypes were identified by rDNA sequencing. All plants were colonized, with 60% for arbuscular colonization and 84% for hyphal colonization as grand means. In Zeeland, onion roots from organic fields had higher fractional colonization levels than those from conventional fields. Onion yields in conventional farming were positively correlated with colonization level. Overall, 14 AMF phylotypes were identified. The number of phylotypes per field ranged from one to six. Two phylotypes associated with the Glomus mosseae–coronatum and the G. caledonium–geosporum species complexes were the most abundant, whereas other phylotypes were infrequently found. Organic and conventional farming systems had similar number of phylotypes per field and Shannon diversity indices. A few organic and conventional fields had larger number of phylotypes, including phylotypes associated with the genera Glomus-B, Archaeospora, and Paraglomus. This suggests that farming systems as such did not influence AMF diversity, but rather specific environmental conditions or agricultural practices. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Authors Guillermo A. Galván and István Parádi contributed equally to this research and share first co-authorship.     

Methods of studying soil microbial diversity

Soil microorganisms, such as bacteria and fungi, play central roles in soil fertility and promoting plant health. This review examines and compares the various methods used to study microbial diversity in soil.     

不同稻作模式下稻田土壤活性有机碳变化动态

通过大田试验,研究了稻鸭复合种养(RD)、间歇灌溉(RW)、常规淹水灌溉(CK)3种不同稻作模式下稻田土壤可溶性有机碳(DOC)、易氧化态有机碳(ROC)和微生物生物量碳(MBC)3种活性有机碳组分的动态变化规律.结果表明:3种稻作模式下土壤DOC、MBC在水稻拔节-齐穗阶段含量最高;ROC在水稻整个生育期内变化平稳,没有表现出显著的阶段性差异.MBC受水稻生育期的影响最大;DOC受水稻生育期和稻作模式的影响均较大;而ROC主要受稻作模式的影响.与CK相比,RD能显著提高土壤DOC和ROC及其有效率;而RW极显著降低了DOC及其有效率,明显提高了ROC及其有效率.3处理间MBC及微生物熵均没有显著差异.     

淹水培养条件下土壤微生物生物量碳、氮和可溶性有机碳、氮的动态

以洞庭湖区2个典型水稻土(红黄泥和紫潮泥)为对象,研究了25 ℃、淹水培养条件下稻草-硫铵配施和单施硫铵处理土壤微生物生物量碳、氮(SMBC、SMBN)和可溶性有机碳、氮(SDOC、SDON)的动态变化.结果表明,SMBC、SMBN和SDOC、SDON在培养前期达到峰值,之后降低,并趋于稳定.添加底物后,2种土壤不同处理土壤微生物生物量碳与有机碳(SMBC/TC)和土壤微生物生物量氮与全氮(SMBN/TN)的平均值都在2%～3%之间变化;可溶性碳与全碳(SDOC/TC)的平均值为1%左右,可溶性氮与全氮(SDON/TN)平均值为5%～6%.2种土壤中SMBC峰值单施硫铵处理最大,但与稻草-硫铵配施处理差异均不显著;SMBN、SDOC和SDON峰值稻草-硫铵配施最大.稻草-硫铵配施与单施硫铵处理中,低肥力红黄泥的SMBN、SDOC和SDON峰值差异显著;而高肥力紫潮泥SMBN和SDOC峰值差异不显著.前7 d,SMBC/SMBN＜10;14 d后,同一时刻单施硫铵处理SMBC/SMBN＞稻草-硫铵配施.不同处理的SDOC/SDON 3 d时最大,28 d时最小.     

Arbuscular mycorrhizal fungal diversity and species dominance in a temperate soil with long-term conventional and low-input cropping systems

The aim of this work was to study the effect of long-term contrasting cropping systems on the indigenous arbuscular mycorrhizal fungal (AMF) spore populations in the soil of a field experiment located in western Finland. Conventional and low-input cropping systems were compared, each with two nutrient management regimes. The conventional cropping system with a non-leguminous 6-year crop rotation (barley–barley–rye–oat–potato–oat) was fertilized at either full (rotation A) or half (rotation B) the recommended rate. In the low-input cropping system, plant residues were returned to the plots either as such (rotation C) or composted (rotation D). In the rotation of this system, 1 year with barley was replaced by clover, and oat was cultivated mixed with pea. Thus, the 6-year rotation was barley–red clover–rye–oat + pea–potato–oat + pea. Each rotation was replicated three times, starting the 6-year rotation in three different years, these being designated point 1, point 2, and point 3, respectively. In the low-input system, biotite and rock phosphate were used to compensate for K and P in the harvested yield, while animal manure was applied at the start only. After 13 years, rotation points 1 and 3 were studied. Barley was the standing crop in all plots of rotation point 1, while oat and oat + pea were grown in rotations C and D, respectively. AMF spores were studied by direct extraction and by trapping, sampled on 15 June and 15 August. In addition, a special assay was designed for isolation of fast colonizing, dominating AMF. The cropping system did not significantly affect AMF spore densities, although the low-input cropping system with composted plant residues had the highest density with 44 spores on average and the conventional system with full fertilization 24 spores per 100 cm³ soil in the autumn samples. Species richness was low in the experimental area. Five Glomus spp., one Acaulospora, and one Scutellospora were identified at the species level. In addition to these, three unidentified Glomus spp. were found. Species richness was not affected by cropping system, rotation point, or their interactions. The Shannon–Wiener index of AMF spore distributions was significantly higher in the fully fertilized than in the half-fertilized conventional plots. Glomus claroideum was the most commonly identified single species in the experimental area. It occurred in all the cropping systems and their various rotation points, representing about 30% of the total number of identified spores. In August, G. claroideum accounted for as much as 45–55% of the total numbers of spores identified in the conventional system with halved fertilization. In contrast, Glomus mosseae occurred more commonly in June (26%) than in August (9%). A bioassay using roots as inoculum for isolation and culture of dominating AMF was successfully developed and yielded only G. claroideum. This indicates a high probability of being able to more generally identify, isolate, and culture fast colonizing generalist AMF for use as inoculants in agriculture and horticulture.     

淹水培养条件下土壤微生物生物量碳、氮和可溶性有机碳、氦的动态

以洞庭湖区2个典型水稻土（红黄泥和紫潮泥）为对象,研究了25℃、淹水培养条件下稻草-硫铵配施和单施硫铵处理土壤微生物生物量碳、氮（SMBC、SMBN）和可溶性有机碳、氦（SDOC、SDON）的动态变化．结果表明,SMBC、SMBN和SDOC、SDON在培养前期达到峰值,之后降低,并趋于稳定．添加底物后,2种土壤不同处理土壤微生物生物量碳与有机碳（SMBC／TC）和土壤微生物生物量氮与全氮（SMBN／TN）的平均值都在2％-3％之间变化;可溶性碳与全碳（SDOC／TC）的平均值为1％左右,可溶性氮与全氮（SDON／TN）平均值为5％-6％．2种土壤中SMBC峰值单施硫铵处理最大,但与稻草-硫铵配施处理差异均不显著;SMBN、SDOC和SDON峰值稻草-硫铵配施最大．稻草．硫铵配施与单施硫铵处理中,低肥力红黄泥的SMBN、SDOC和SDON峰值差异显著;而高肥力紫潮泥SMBN和SDOC峰值差异不显著．前7d,SMBC／SMBN〈10;14d后,同一时刻单施硫铵处理SMBC／SMBN〉稻草．硫铵配施．不同处理的SDOC!SDON3d时最大．28d时最小．     

Reclamation of abandoned saline-alkali soil increased soil microbial diversity and degradation potential

Plant and Soil - Reclamation of saline-alkali soils to grow cotton (Gossypium spp.) is very common in the arid Manas River Basin in Northwest China. However, little is known about the degradation...     

Impact of soil leachate on microbial biomass and diversity affected by plant diversity

Plant and Soil - High plant diversity is usually linked with high soil microbial diversity, which is hypothesized to be attributed to a high diversity of components in the soil leachate, but...     

Transient peak in moth diversity as a response to organic farming

Few initiatives to preserve and enhance biodiversity on farmland have been as thoroughly evaluated and debated as the agri-environment schemes (AES). Yet, little is known how confounding factors co-varying with the specific AES measures may affect species responses. Here, we quantify the influence of one such factor, the time since transition to organic farming, on moth diversity patterns. We found that species richness and abundance of moths were higher on new organic farms (years since transition ≤6) compared to old organic (≥15 years) and conventional farms, indicating a transient diversity peak. This correlates with the abundance patterns of the weed Cirsium arvense, which also reached its highest densities on new organic farms. Weeds such as C. arvense constitute a notorious problem in organic farming. However, they also provide various resources for farmland biodiversity, and our results strongly suggest that the transient weed peak may be important in influencing the parallel peak among the moths. This stresses the problem in balancing out production and conservation values. More generally, our results show that rather than having static effects on the environment, AES can have an important temporal component and result in a dynamic interplay between different trophic levels.