Development of microbial community during primary succession in areas degraded by mining activities

Together with plants, soil microbial communities play an essential role in the development of stable ecosystems on degraded lands, such as postmining spoil heaps. Our study addressed concurrent development of the vegetation and soil fungal and bacterial communities in the course of primary succession in a brown coal mine spoil deposit area in the Czech Republic across a chronosequence spanning 54 years. During succession, the plant communities changed from sparse plants over grassland and shrubland into a forest, becoming substantially more diverse with time. Microbial biomass increased until the 21st year of ecosystem development and later decreased. Although there was a close association between fungi and vegetation, with fungi mirroring the differences in plant community assemblages, the development of the bacterial community was different. The early succession community in the barren nonvegetated soil largely differed from that in the older sites, especially in its high abundance of autotrophic and free‐living N₂‐fixing bacteria. Later in succession, bacterial community changes were minor and reflected the chemical parameters of the soil, including pH, which also showed a minor change with time. Our results show that complex forest ecosystems developed over 54 years on the originally barren soil of the temperate zone and indicate an important role of bacteria in the initial stage of soil development. Although the arrival of vegetation affects substantially fungal as well as bacterial communities, it is mainly fungi that respond to the ongoing development of vegetation.     

Disentangling the contributions of arbuscular mycorrhizal fungi to soil multifunctionality

Soil multifunctionality represents a range of soil processes driven by the interactions between soil abiotic and biotic components. As a group of ubiquitous fungi that form mutualistic symbiotic associations with a vast array of terrestrial plants, arbuscular mycorrhizal (AM) fungi may play a critical role in maintaining soil multifunctionality, but the characteristics of their contributions remain to be unraveled. This mini review aims to disentangle the contributions of AM fungi to soil multifunctionality. We provide a framework of concepts about AM fungi making crucial contributions to maintaining multiple soil functions, including primary productivity, nutrient cycling, water regulation and purification, carbon and climate regulation, habitat for biodiversity, disease and pest control, and pollutant degradation and detoxification, via a variety of pathways, particularly contributing to soil and plant health. This review contends that AM fungi, as a keystone component of soil microbiome, can govern soil multifunctionality, ultimately promoting ecosystem services.     

土壤原生生物的类群及功能

土壤原生生物是生活在土表凋落物和土壤中最原始、最简单的真核生物。原生生物的演化进程快,种类多样,至今尚没有统一的系统发育分类体系。种类众多的土壤原生生物拥有多样的生态功能,在控制细菌的生长繁殖和群落组成、改变土壤营养物质的循环、调控植物生长发育及土壤污染物的净化等方面发挥着重要作用。本文从形态结构、进化过程及生态功能等几个方面,对土壤原生生物的系统分类及其功能、地理分布和研究方法,及其与土壤微生物、植物之间的生态关系,对土壤环境的潜在影响等领域的研究进展进行了总结,并对土壤原生生物研究中存在的问题进行了展望。旨在深入理解土壤原生生物类群和功能的多样性及其维持机制,为深化土壤原生生物与微生物、植物间的相互关系研究提供依据,为开发新的土壤和植物病害的生物防治技术提供参考。     

中国北方森林坡向对土壤细菌和从枝菌根真菌群落的影响

The effects of slope aspects on soil biogeochemical properties and plant communities in forested environments have been studied extensively; however, slope aspect influence on soil microbial communities remains largely unexamined, despite the central role of soil biota in ecosystem functioning. In this study, the communities of both soil bacteria and arbuscular mycorrhizal fungi (AMF) were investigated using tagged pyrosequencing for three types of slope aspects (south-facing aspect, north-facing aspect and flat area) in a boreal forest of the Greater Khingan Mountains, China. The bacterial and AMF community composition differed with slope aspects. Bacterial diversity was the lowest on the north-facing aspect, and AMF diversity was the lowest on the flat area. Aspects also had a significant impact on soil pH and available phosphorus (P) and shrubby biomass. Soil pH and understory shrub biomass were significantly correlated with bacterial communities, and soil available P and shrub biomass showed significant correlations with AMF communities. Our results suggested that slope aspects affected bacterial and AMF communities, mediated by aspect-induced changes in plant community and soil chemical properties (e.g., pH and available P), which improved the knowledge on the effects of forest slope aspects on aboveground and belowground communities.     

Diversity and seasonal variations of mycorrhiza and rhizosphere bacteria in three common plant species at the Slovenian Ljubljana Marsh

Interactions between plants and microorganisms can significantly affect plant health and productivity as well as ecosystem functioning. Detailed knowledge of the tripartite relationships between plants, fungi, and bacteria, and their environment is still limited. In the present study, the soils adjacent to three plant species (Cruciata laevipes, Mentha piperita, Equisetum arvense) in the Ljubljana Marsh and the bulk, plant-free soil were analyzed for their bacterial community structure in June and October 2006. The terminal restriction fragment length polymorphism analysis indicated a different bacterial community structure in the rhizosphere and in bulk soil, however, with almost no seasonal changes between late spring and autumn samples and no apparent impact of the three plant species. In addition, root colonization of the three plant species by arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) was microscopically assessed monthly from May until October 2006. A presumably accidental correlation between monthly precipitation and the degree of arbuscule formation, with the latter lagging 1 month, was noted for M. piperita, the most heavily colonized of the three plant species. With all three plants, the phosphorus content in roots correlated positively with most AMF structures. Microsclerotia of DSE were mainly abundant in autumn samples. Fungal diversity in roots was estimated using temporal temperature gradient gel electrophoresis separation of the fungal polymerase chain reaction products obtained for both 18S-rDNA and the 5.8S-ITS2-28S rDNA segments. No specific effects of either plant species or seasonal changes on mycorrhizal community structure were discernible.     

Bacterial communities associated with natural and commercially grown rooibos (Aspalathus linearis)

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea. Symbiotic interactions between A. linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor, acidic fynbos soil. The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A. linearis, as well as the effect of seasonal changes on these communities. Bacterial communities were characterized using high throughput amplicon sequencing, and their correlations with soil chemical properties were investigated. The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction. Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant bacterial phyla detected in this study. Highly similar bacterial communities were associated with natural and commercially grown plants. Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season, while no significant differences were detected in the wet season. This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A. linearis.     

Effects of mineral and biofertilizers on barley growth on compacted soil

Abstract

Biofertilizers are an alternative to mineral fertilizers for increasing soil productivity and plant growth in sustainable agriculture. The objective of this study was to evaluate possible effects of three mineral fertilizers and four plant growth promoting rhizobacteria (PGPR) strains as biofertilizer on soil properties and seedling growth of barley (Hordeum vulgare) at three different soil bulk densities, and in three harvest periods. The application treatments included the control (without bacteria inoculation and mineral fertilizers), mineral fertilizers (N, NP and P) and plant growth promoting rhizobacteria species (Bacillus licheniformis RC04, Paenibacillus polymyxa RC05, Pseudomonas putida RC06, and Bacillus OSU-142) in sterilized soil. The PGPR, fungi, seedling growth, soil pH, organic matter content, available P and mineral nitrogen were determined in soil compacted artificially to three bulk density levels (1.1, 1.25 and 1.40 Mg m^?3) at 15, 30, and 45 days of plant harvest. The results showed that all the inoculated bacteria contributed to the amount of mineral nitrogen. Seed inoculation significantly increased the count of bacteria and fungi. Data suggest that seed inoculation of barley with PGPR strains tested increased root weight by 9–12.2%, and shoot weight by 29.7–43.3% compared with control. The N, NP and P application, however, increased root weight up to 18.2, 25.0 and 7.4% and shoot weight by 31.6, 43.4 and 26.4%, respectively. Our data show that PGPR stimulate barley growth and could be used as an alternative to chemical fertilizer. Soil compaction hampers the beneficial plant growth promoting properties of PGPR and should be avoided.     

Parasitism by Cuscuta australis affects the rhizhospheric soil bacterial communities of Trifolium repens L.

ABSTRACT

The effect of parasitism on belowground microbial communities is not well understood. 16S rRNA gene amplicon sequencing was used to test the effect of Cuscuta australis parasitism on the composition and diversity of bacterial community in the rhizospheric soil of the host plant Trifolium repens. 94569 sequences were obtained from the amplicons of non-parasitised, and 97172 sequences were obtained from the parasitised rhizospheric soil bacterial community. Parasitism of C. australis significantly decreased the relative abundance of the bacterial phylum Nitrospirae, while it significantly increased that of Verrucomicrobia. Parasitism of C. australis significantly decreased the relative abundance of 10 bacterial genera, while it significantly increased those of nine genera. The Chao 1 indexes of the rhizospheric soil bacterial community of parasitised T. repens were significantly lower than those of non-parasitised T. repens. Principal coordinate analysis (based on the genus) and principal component analysis (based on the predicted gene function of bacterial communities) showed that rhizospheric bacterial communities from parasitised and non-parasitised T. repens differed and can be divided into two groups. These results suggest that infection of the holoparasitic plant could indirectly change the composition, diversity, and function of rhizospheric soil bacteria of the host plant.     

根结线虫接种对黄瓜植株根际土壤pH和微生物的影响

通过人工接种不同数量的根结线虫卵,测定了黄瓜植株根际土壤的pH和微生物数量。结果表明,随接种数量的增加,根际土壤好气性细菌数量、厌气性细菌数量、细菌总数及细菌/真菌(B/F)逐渐降低;真菌数量却逐渐升高;放线菌数量在接种量为2000个·株-1时显著升高,之后随着接种量的增加逐渐降低;放线菌/真菌(A/F)在接种量为2000个·株-1时略有升高,之后随着接种量的增加逐渐降低。接种根结线虫后,黄瓜植株根际土壤中好气性细菌数量和B/F值与pH呈显著正相关,厌气性细菌数量、细菌总数、放线菌数量以及A/F值与pH呈极显著正相关,真菌数量与pH呈显著负相关。根结线虫侵染黄瓜植株导致根际土壤发生"真菌化",显示土壤质量下降。     

Deep incorporation of corn straw benefits soil organic carbon and microbial community composition in a black soil of Northeast China

‘Deep incorporation of corn straw’ (CSDI) is to concentrate the burial of corn straw into the subsurface soil layer (20–40 cm) and to break the plough pan, thereby creating a loosened plough layer (0–20 cm) and a fertile subsurface soil layer. However, its impacts on soil organic carbon (SOC) and the microbial community remain poorly understood. A field experiment was conducted to investigate the effects of 1-year CSDI (CD1), 3-year CSDI (CD3) and 5-year CSDI (CD5) on soil aggregates and aggregate-associated SOC, as well as bacterial and fungal community characteristics (examined by the high-throughput gene sequencing method). The results demonstrated that SOC and soil fungal diversity were decreased by CD1, but increased by CD3 and CD5. Compared with the control, CD5 promoted 2–0.25 mm soil macroaggregation, significantly increased SOC by 8.94% and aggregate-associated SOC by 5.96%–8.84%, consequently improving the physical protection of SOC by soil aggregates. CD3 and CD5 enhanced the richness and diversity of soil bacteria and fungi, and altered community composition. For soil bacteria, the relative abundance of Acidobacteria and Chloroflexi was increased, while that of Firmicutes, Gemmatimonadetes, Sphingomonas and Bacillus was decreased. For soil fungi, the relative abundance of Ascomycota, Zygomycota, Mortierella and Fusarium was greatly improved, but that of Basidiomycota was reduced. These obvious variations in microbial community structure were beneficial to straw degradation and SOC accumulation. Overall, the optimization of microbial community with CSDI plays a positive role in promoting soil organic matter, nutrient cycling and carbon sequestration, and thus improving soil fertility.     

Rhizosphere microbiota assemblage associated with wild and cultivated soybeans grown in three types of soil suspensions

Soil microbial community composition is determined by the soil type and the plant species. By sequencing the V3-V4 region of the bacterial 16S rRNA gene amplicons, the current study assessed the bacterial community assemblage in rhizosphere and bulks soils of wild (Glycine soja) and cultivated (Glycine max) soybeans grown in the suspensions of three important soil types in China, including black, red and soda-saline-alkali soils. The alpha-diversity of the bacterial community in the rhizosphere was significantly higher than that of the bulk soils suggesting that bulk soil lacks plant nurturing effect under the current study conditions. Black and red soils were enriched with nitrifying and nitrogen-fixing bacteria but the soda-saline-alkali soil suspension had more denitrifying bacteria, which may reflect agronomic unsuitability of the latter. We also observed a high abundance of Bradyrhizobium and Pseudomonas, enriched cellulolytic bacteria, as well as a highly connected molecular ecological network in the G. soja rhizosphere soil. Taken all, the current study suggest that wild soybeans may have evolved to recruit beneficial microbes in its rhizosphere that can promote nutrients requisition, biostasis and disease-resistance, therefore ecologically more resilient than cultivated soybeans.     

Mycorrhizal diversity: Cause and effect?

Mycorrhizal fungi play a critical role in nutrient cycling and ecosystem function. They improve plant growth and survival through a mutualistic relationship in which photosynthates are exchanged for increased access to water and nutrients. Because the benefits realized are not equal among different plant–fungal species combinations, mycorrhizal fungi may help govern plant community structure and successional trajectories. In fact, both plant productivity and plant diversity have been shown to increase with increasing diversity of mycorrhizal fungi. The diversity and species composition of plant communities also exert a reciprocal influence on associated mycorrhizal communities, although edaphic factors may also play a role. Given this inherent bi-directionality of mycorrhizal relationships, the potential exists for positive feedback mechanisms which may promote and maintain both plant and mycorrhizal fungal diversity. This review considers recent literature on both arbuscular and ectomycorrhizal fungal–plant community relationships within a variety of environments, including artificially constructed systems and naturally occurring grasslands and forests.     

土壤原生动物——研究方法及其在土传病害防控中的作用

原生动物是原生生物的一种,是土壤食物网中的消费者,能捕食细菌和真菌等其他微生物。除了对土壤微生物群落和物质循环产生重要影响外,根际原生动物与细菌、真菌等土壤微生物共同组成生物网络屏障,并在抵御土传病原菌入侵作物根系的过程中发挥着重要作用。然而,相对于根际有益细菌和有益真菌,国内外关于原生动物防控土传病害的效果及作用机制的研究非常有限。本文梳理了土壤原生动物在土传病害防控中的效果、作用机制及其相关研究方法,并对未来原生动物的研究和应用作出了展望。呼吁更多学者关注土壤原生动物及其在生态系统中的功能,挖掘其在土壤健康和农业可持续发展中的重要价值。     

Soil bacterial community response to sulfadiazine in the soil–root zone

Sulfonamide antibiotics reach soil via manure and adversely affect microbial diversity. Clear effects of these bacteriostatic, growth‐inhibiting antibiotics occur in the presence of a parallel input of microbial activity stimulating manure. Natural hot spots with already increased soil microbial activity are located in the rhizosphere, comprising microorganism such as Pseudomonas with plant growth promoting and pathogenic strains. The hypothesis was therefore that the antibiotic activity of sulfonamides is promoted in the rhizosphere even in the absence of manure, followed by shifts of the natural plant‐specific microbial community structure. This was evaluated by a laboratory experiment with Salix fragilis L. and Zea mays L. After 40 d of incubation, sub‐areas such as non‐rhizosphere soil, rhizosphere soil and plant roots were sampled. Effects on microbial community structure were analyzed using 16S rRNA gene fragment patterns of total bacteria community and Pseudomonas. Selected exoenzymes of N‐, P‐, and C‐cycling were used to test effects on microbial functions. Compared to the factors soil sub‐area and sulfadiazine (SDZ) content, plant species had the largest influence on the bacterial community structure and soil exoenzyme activity pattern. This was also reflected by an up to 1.5‐fold higher acid phosphatase activity in samples from maize‐ compared to willow‐planted soil. We conclude that antibiotic effects on the bacterial community structures are influenced by the antibiotic concentration and root influence.     

芒萁侵入红壤退化裸地对土壤理化性质和细菌组成的影响

芒萁是最早侵入红壤退化裸地的先锋植物,其侵入过程对土壤环境的改变在退化裸地生态恢复进程中具有重要意义。以福建省长汀县红壤侵蚀裸地为研究对象,分析测定退化裸地中芒萁侵入区和非侵入区土壤理化性质和细菌组成及多样性。结果表明：芒萁侵入裸地显著提高土壤最大持水量、土壤含水率、全碳、全氮、全钾、有机质和pH,并显著降低土壤容重;芒萁侵入区增加根瘤菌目和慢生根瘤菌属等14种土壤优势细菌,变形菌门和甲型(α)变形杆菌的相对丰度显著提高(p<0.05),而土壤绿弯菌门和AD3菌纲的相对丰度显著降低(p<0.05),这些土壤细菌主要功能为化能异养、好氧化能异养和纤维素分解;芒萁侵入裸地显著提高土壤细菌群落结构多样性(p<0.05);芒萁侵入区和非侵入区土壤细菌群落结构差异显著(p<0.05);土壤细菌群落结构的主要影响因子是土壤含水率、全碳、有机质、土壤容重和pH。这些影响因子与疣微菌门、变形菌门、疣微菌纲和甲型(α)变形杆菌纲正相关。综上所述,芒萁侵入后可显著改善红壤侵蚀退化裸地的土壤理化性质,改善土壤细菌群落组成,增加土壤细菌群落多样性和优势菌群,对土壤细菌群落有积极效应。     

京郊荒滩地短期植被恢复对土壤理化性质及微生物群落结构的影响

为了揭示京郊荒滩地植被恢复初期土壤理化性质与微生物群落结构的变化特征,以补播苜蓿(Medicago sativa L.)、补播无芒雀麦(Bromus inermis Leyss)为研究对象,自然撂荒地为对照,采用高通量测序方法研究不同植被恢复模式土壤细菌与真菌的群落结构。结果表明:(1)2种植被恢复方式下土壤全氮含量显著高于对照,补播无芒雀麦土壤全磷含量最高;(2)2种植被恢复方式短期内显著改善了土壤物理性质,土壤容重显著低于对照,补播无芒雀麦土壤田间持水量、毛管持水量与最大持水量最高,补播苜蓿土壤饱和导水率最高;(3)2种植被恢复方式短期内对土壤微生物群落结构产生影响,真菌中的子囊菌门、细菌中的蓝细菌门相对丰度增加,真菌与细菌的生物多样性降低;(4)相关性分析表明,土壤有机质含量与真菌中的子囊菌门、细菌中的变形菌门、蓝细菌门数量存在显著正相关关系。2种植被恢复方式短期内均不同程度的改善了土壤理化性质,增加了固氮及降解有机质的微生物的数量及活性。     

Identification and performance of stress‐tolerant phosphate‐solubilizing bacterial isolates on Tagetes minuta grown in sodic soil

Tagetes minuta is moderately adapted to a wide range of climate and due to its tolerance to larger salt, pH and exchangeable sodium percentage (ESP) in soil it is considered to be a potential crop for salt‐affected soil. Its tolerance to adverse condition and association with halophilic microbes can combine to play a greater role in crop production and improvement in soil health. After screening, the potential phosphate‐solubilizing bacteria (PSB) RS‐1, RS‐2 and RS‐3 were isolated from sodic soils and tested in pot experiment using a naturally occurring sodic soil of pH 9.3 and an ESP of about 45. Under optimum conditions in the laboratory, these bacteria showed phosphorus solubilization potential in liquid medium containing tricalcium phosphate (TCP). Inoculation of PSB significantly increased plant growth in terms of height, number of branches, dry matter accumulation and nutrient uptake. Significant changes were also found in content and quality of essential oil. It was observed that PSB also improved the physical, chemical and biological properties of soil. The bacterial strains tested in this study have the potential for use as a biofertilizer in sustaining the growth of Tagetes minuta in salt stress soil and mitigating soil stress problems.     

Effects of silver nanoparticles on soil microorganisms and maize biomass are linked in the rhizosphere

Silver nanoparticles hold great promise as effective anti-microbial compounds in a myriad of applications but may also pose a threat to non-target bacteria and fungi in the environment. Because microorganisms are involved in extensive interactions with many other organisms, these partner species are also prone to indirect negative effects from silver nanoparticles.Here, we focus on the effects of nanosilver exposure in the rhizosphere. Specifically, we evaluate the effect of 100 mg kg⁻¹ silver nanoparticles on maize plants, as well as on the bacteria and fungi in the plant's rhizosphere and the surrounding bulk soil. Maize biomass measurements, microbial community fingerprints, an indicator of microbial enzymatic activity, and carbon use diversity profiles are used. Hereby, it is shown that 100 mg kg⁻¹ silver nanoparticles in soil increases maize biomass, and that this effect coincides with significant alterations of the bacterial communities in the rhizosphere. The bacterial community in nanosilver exposed rhizosphere shows less enzymatic activity and significantly altered carbon use and community composition profiles. Fungal communities are less affected by silver nanoparticles, as their composition is only slightly modified by nanosilver exposure. In addition, the microbial changes noted in the rhizosphere were significantly different from those noted in the bulk soil, indicated by different nanosilver-induced alterations of carbon use and community composition profiles in bulk and rhizosphere soil.Overall, microorganisms in the rhizosphere seem to play an important role when evaluating the fate and effects of silver nanoparticle exposure in soil, and not only is the nanosilver response different for bacteria and fungi, but also for bulk and rhizosphere soil. Consequently, assessment of microbial populations should be considered an essential parameter when investigating the impacts of nanoparticle exposure.     

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

Background, aim, and scope  Fertilization is an important agricultural practice for increasing crop yields. In order to maintain the soil sustainability, it is important to monitor the effects of fertilizer applications on the shifts of soil microorganisms, which control the cycling of many nutrients in the soil. Here, culture-dependent and culture-independent approaches were used to analyze the soil bacterial and fungal quantities and community structure under seven fertilization treatments, including Control, Manure, Return (harvested peanut straw was returned to the plot), and chemical fertilizers of NPK, NP, NK, and PK. The objective of this study was to examine the effects on soil microbial composition and diversity of long-term organic and chemical fertilizer regimes in a Chinese upland red soil. Materials and methods  Soil samples were collected from a long-term experiment station at Yingtan (28°15′N, 116°55′E), Jiangxi Province of China. The soil samples (0–20 cm) from four individual plots per treatment were collected. The total numbers of culturable bacteria and fungi were determined as colony forming units (CFUs) and selected colonies were identified on agar plates by dilution plate methods. Moreover, soil DNAs were extracted and bacterial 16S rRNA genes and fungal 18S rRNA genes were polymerase chain reaction amplified, and then analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. Results  The organic fertilizers, especially manure, induced the least culturable bacterial CFUs, but the highest bacterial diversity ascertained by DGGE banding patterns. Chemical fertilizers, on the other hand, had less effect on the bacterial composition and diversity, with the NK treatment having the lowest CFUs. For the fungal community, the manure treatment had the largest CFUs but much fewer DGGE bands, also with the NK treatment having the lowest CFUs. The conventional identification of representative bacterial and fungal genera showed that long-term fertilization treatments resulted in differences in soil microbial composition and diversity. In particular, 42.4% of the identified bacterial isolates were classified into members of Arthrobacter. For fungi, Aspergillus, Penicillium, and Mucor were the most prevalent three genera, which accounted for 46.6% of the total identified fungi. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Discussion  It was evident that more representative fungal genera appeared in organic treatments than other treatments, indicating that culturable fungi were more sensitive to organic than to chemical fertilizers. A very notable finding was that fungal CFUs appeared maximal in organic manure treatments. This was quite different from the bacterial CFUs in the manure, indicating that bacteria and fungi responded differently to the fertilization. Similar to bacteria, the minimum fungal CFUs were also observed in the NK treatment. This result provided evidence that phosphorus could be a key factor for microorganisms in the soil. Thus, despite the fact that culture-dependent techniques are not ideal for studies of the composition of natural microbial communities when used alone, they provide one of the more useful means of understanding the growth habit, development, and potential function of microorganisms from soil habitats. A combination of culture-dependent and culture-independent approaches is likely to reveal more complete information regarding the composition of soil microbial communities. Conclusions  Long-term fertilization had great effects on the soil bacterial and fungal communities. Organic fertilizer applications induced the least culturable bacterial CFUs but the highest bacterial diversity, while chemical fertilizer applications had less impact on soil bacterial community. The largest fungal CFUs were obtained, but much lower diversity was detected in the manure treatment. The lowest bacterial and also fungal CFUs were observed in the NK treatment. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Phosphorus fertilizer could be considered as a key factor to control the microbial CFUs and diversity in this Chinese upland red soil. Recommendations and perspectives  Soil fungi seem to be a more sensitive indicator of soil fertility than soil bacteria. Since the major limitation of molecular methods in soil microbial studies is the lack of discrimination between the living and dead, or active and dormant microorganisms, both culture-dependent and culture-independent methods should be used to appropriately characterize soil microbial diversity.     

基于高通量测序研究草莓根际微生物群落结构和多样性

研究草莓根际土壤微生物群落组成和结构,对健康草莓土壤生态系统的构建和保持具有重要意义。以不同地区草莓根际土壤为研究样本,利用MiSeq平台Illumina第二代高通量测序技术并结合相关生物信息学分析土壤细菌16S rRNA基因V4+V5区域和真菌ITS1+ITS2区域的丰富度和多样性指数以及群落结构。结果表明:从15个草莓根际土壤样本中获得4554个细菌分类操作单元OTU和1298个真菌OTU,草莓根际土壤的优势细菌门为变形菌门、厚壁菌门、放线菌门、酸杆菌门和绿弯菌门,主要的优势细菌属有16种;优势真菌门为子囊菌门、接合菌门和担子菌门,主要的优势真菌属有8种。冗余分析(RDA)显示,全氮和pH对土壤微生物群落结构的影响最大,共解释了61%的群落变化,各因子的贡献率大小依次为土壤全氮pH有效磷全钾全磷有机质速效钾碱解氮;相关性分析也表明,土壤理化指标均与不同优势菌门存在密切的相关关系。本研究结果加深了对草莓根际微生物群落结构和多样性的认识,为深入研究草莓根际微生物多样性及功能与环境因子之间的关系提供了借鉴。