不同水旱轮作体系稻田土壤剖面N2O的分布特征

通过原位采集淹水和排水状态下土壤剖面4个层次的气体,研究氧化亚氮(N2O)在水旱轮作体系稻田土壤剖面中的动态分布特征.试验设置小麦-单季稻和油菜-双季稻两种轮作体系,包括施N和不施N两种施肥方式.结果表明:施用N肥极显著促进了土壤剖面N2O的产生(P＜0.01),不同层次间N2O浓度相关性极显著(P＜0.01),小麦、油菜生长期施N和无N处理下层30 cm和50 cm处N2O浓度均高于表层7 cm和15 cm处;早稻无N处理则为表层7 cm和15 cm处高于下层30 cm和50 cm处(P＜0.05),其他水稻处理各层次间无显著差异.无N处理土壤N2O峰值出现在旱作向水稻的转变期,施N处理则出现在旱作第2次追肥后,季节转变期也有较高的N2O浓度.     

Diversity of soil fungal communities of Cerrado and its closely surrounding agriculture fields

Cerrado is a savanna-like region that covers a large area of Brazil. Despite its biological importance, the Cerrado has been the focus of few microbial diversity studies. A molecular approach was chosen to characterize the soil fungal communities in four areas of the Cerrado biome: a native Cerrado, a riverbank forest, an area converted to a soybean plantation, and an area converted to pasture. Global diversity of fungal communities in each area was assessed through Ribosomal intergenic spacer analysis which revealed remarkable differences among the areas studied. Sequencing of approximately 200 clones containing 18S rDNA sequences from each library was performed and, according to the genetic distance between sequences, these were assigned to operational taxonomic units (OTUs). A total of 75, 85, 85, and 70 OTUs were identified for the native Cerrado, riverbank forest, pasture, and soybean plantation, respectively. Analysis of sequences using a similarity cutoff value of 1% showed that the number of OTUs for the native Cerrado area was reduced by 35%; for the soybean plantation, a reduction by more than 50% was observed, indicating a reduction in fungal biodiversity associated with anthropogenic activity. This is the first study demonstrating the anthropogenic impact on Cerrado soil fungal diversity.     

Assessment of soil fungal communities using pyrosequencing

Pyrosequencing, a non-electrophoretic method of DNA sequencing, was used to investigate the extensive fungal community in soils of three islands in the Yellow Sea of Korea, between Korea and China. Pyrosequencing was carried out on amplicons derived from the 5′ region of 18S rDNA. A total of 10,166 reads were obtained, with an average length of 103 bp. The maximum number of fungal phylotypes in soil predicted at 99% similarity was 3,334. The maximum numbers of phylotypes predicted at 97% and 95% similarities were 736 and 286, respectively. Through phylogenetic assignment using BLASTN, a total of 372 tentative taxa were identified. The majority of true fungal sequences recovered in this study belonged to the Ascomycota (182 tentative taxa in 2,708 reads) and Basidiomycota (172 tentative taxa in 6,837 reads). The predominant species of Ascomycota detected have been described as lichen-forming fungi, litter/wood decomposers, plant parasites, endophytes, and saprotrophs: Peltigera neopolydactyla (Lecanoromycetes), Paecilomyces sp. (Sordariomycetes), Phacopsis huuskonenii (Lecanoromycetes), and Raffaelea hennebertii (mitosporicAscomycota). The majority of sequences in the Basidiomycota matched ectomycorrhizal and wood rotting fungi, including species of the Agaricales and Aphyllophorales, respectively. A high number of sequences in the Thelephorales, Boletales, Stereales, Hymenochaetales, and Ceratobasidiomycetes were also detected. By applying high-throughput pyrosequencing, we observed a high diversity of soil fungi and found evidence that pyrosequencing is a reliable technique for investigating fungal communities in soils.     

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.     

Vertical distribution of fungal communities in tallgrass prairie soil

We used 454 sequencing of the internal transcribed spacer region to characterize fungal communities in tallgrass prairie soils subdivided into strata 0-10, 10-20, 30-40 and 50-60 cm deep. The dataset included more than 14000 fungal sequences distributed across Basidiomycota, Ascomycota, basal fungal lineages and Glomeromycota in order of decreasing frequency. As expected the community richness and diversity estimators tended to decrease with increasing depth. Although species richness was significantly reduced for samples from the deeper profiles, even the deepest stratum sampled contained richness of more than a third of that in the topmost stratum. More importantly, nonparametric multidimensional scaling (NMS) ordination analyses indicated that the fungal communities differed across vertical profiles, although only the topmost and deepest strata were significantly different when the NMS axis scores were compared by ANOVA. These results emphasize the importance of considering the fungal communities across the vertical strata because the deeper soil horizons might maintain a distinct community composition and thus contribute greatly to overall richness. The majority of operational taxonomic units (OTUs) declined in frequency with increasing depth, although a linear regression analysis indicated that some increased with increasing depth. The OTUs and BLAST-assigned taxa that showed increasing frequencies were mainly unculturable fungi, but some showed likely affinities to families Nectriaceae and Venturiaceae or to genus Pachnocybe. Although the ecological roles of the fungi in the deeper strata remain uncertain, we hypothesize that the fungi with preferences for deeper soil have adequate access to substrates and possess environmental tolerances that enable their persistence in those environments.     

Endophytic fungal communities in woody perennials of three tropical forest types of the Western Ghats,southern India

Fungal endophytes of tropical trees are expected to be exceptionally species rich as a consequence of high tree diversity in the tropics and the purported host restriction among the endophytes. Based on this premise, endophytes have been regarded as a focal group for estimating fungal numbers because their possible hyperdiverse nature would reflect significantly global fungal diversity. We present our consolidated ten-year work on 75 dicotyledonous tree hosts belonging to 33 families and growing in three different types of tropical forests of the NBR in the Western Ghats, southern India. We conclude that endophyte diversity in these forests is limited due to loose host affiliations among endophytes. Some endophytes have a wide host range and colonize taxonomically disparate hosts suggesting adaptations in them to counter a variety of defense chemicals in their hosts. Furthermore, such polyphagous endophytes dominate the endophyte assemblages of different tree hosts. Individual leaves may be densely colonized but only by a few endophyte species. It appears that the environment (the type of forest in this case) has a larger role in determining the endophyte assemblage of a plant host than the taxonomy of the host plant. Thus, different tropical plant communities have to be studied for their endophyte diversity to test the generalization that endophytes are hyperdiverse in the tropics, estimate their true species richness, and use them as a predictor group for more accurate assessment of global fungal diversity.     

Diversity and ecology of soil fungal communities in rubber plantations

Monoculture rubber cultivation and its intensive associated human activities are known to have a negative impact on the biodiversity, ecology, and biological conservation of the ecosystems in which they occur. These negative impacts include changes to the biodiversity and function of soil fungal communities, which contribute towards nutrient cycling and interact with other organisms in belowground ecosystems, and may be pathogens. Despite the important role of soil fungi in rubber plantations, these communities have been poorly studied. In this paper, we review the existing literature on the diversity and ecology of belowground fungi in rubber plantations. Various groups of soil fungi, including saprobes, symbionts, and pathogens are discussed. Additionally, the role of plantation management is discussed in the context of both pathogenic soil fungi and the promotion of beneficial soil fungi. Management practices include clone selection, tree age and planting density, application of chemicals, and intercropping systems. Our review shows the strong need for further research into the effects of monoculture rubber plantations on soil fungal communities, and how we can best manage these systems in the future, in order to create a more sustainable approach to rubber production.     

Temporal variability in soil microbial communities across land-use types

Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.     

典型岩溶区域主要土壤类型分布特征与表层土壤保有量估算

在我国西南岩溶区域,土壤受地质和地形条件的影响程度较深,表现出强烈的非均一性;且在不同地质地形条件下,缺乏具体的量化参照系数,致使对土壤元素库容等方面的估算存在较大偏差。据此,本研究基于对贵阳市乌当区实地考察结果,归纳确立土壤在不同地质与地形下的分布特征,修正了现有的土壤图。利用地形图提取区域的坡度信息,再与土壤图和地质图进行叠加,乘以相应类型条件下土壤的经验系数,估算区域主要土壤类型表层(≤1m)土壤的保有量。结果表明,乌当区境内坡度>35°的碳酸盐岩地区无黄壤分布;石灰土的覆盖率和土壤剖面深度随坡度的增加,呈下降趋势,但连续性石灰岩分布区的石灰土变异程度较大;该区表层土壤(≤1m)保有量约为65656万t,主要集中分布在0°～15°碳酸盐岩分布区,且黄壤占50%以上。     

Diversity and distribution of soil fungal communities in a semiarid grassland

The fungal loop model of semiarid ecosystems integrates microtopographic structures and pulse dynamics with key microbial processes. However limited data exist about the composition and structure of fungal communities in these ecosystems. The goal of this study was to characterize diversity and structure of soil fungal communities in a semiarid grassland. The effect of long-term nitrogen fertilization on fungi also was evaluated. Samples of rhizosphere (soil surrounding plant roots) and biological soil crust (BSC) were collected in central New Mexico, USA. DNA was amplified from the samples with fungal specific primers. Twelve clone libraries were generated with a total of 307 (78 operational taxonomic units, OTUs) and 324 sequences (67 OTUs) for BSC and rhizosphere respectively. Approximately 40% of soil OTUs were considered novel (less than 97% identity when compared to other sequences in NCBI using BLAST). The dominant organisms were dark-septate (melanized fungi) ascomycetes belonging to Pleosporales. Effects of N enrichment on fungi were not evident at the community level; however the abundance of unique sequences, sampling intensity and temporal variations may be uncovering the effect of N in composition and diversity of fungal communities. The fungal communities of rhizosphere soil and BSC overlapped substantially in composition, with a Jaccard abundance similarity index of 0.75. Further analyses are required to explore possible functions of the dominant species colonizing zones of semiarid grassland soils.     

Influence of soil temperature on methane emission from rice paddy fields

Methane emission rates from an Italian rice paddy field showed diel and seasonal variations. The seasonal variations were not closely related to soil temperatures. However, the dieL changes of CH₄ fluxes were significantly correlated with the diel changes of the temperature in a particular soil depth. The soil depths with the best correlations between CH4 flux and temperature were shallow (1–5cm) in May and June, deep (10–15cm) in June and July, and again shallow (1–5 cm) in August. Apparent activation energies (E_a) calculated from these correlations using the Arrhenius model were relatively low (50–150 kJ mol^–1) in May and June, but increased to higher values (80–450 kJ mol^–1) in August. In the laboratory, CH₄ emission from two rice cultures incubated at temperatures between 20 and 38°C showed E . values of 41 and 53 kJ mol^–1) Methane production in anoxic paddy soil suspensions incubated between 7 and 43°C showed E values between 53 and 132 kJ mol^–1 with an average value of 85 kJ mol^–1) and in pure cultures of hydrogenotrophic methanogenic bacteria E _a values between 77 and 173 (average 126) kJ mol^–1. It is suggested that diel changes of soil properties other than temperature affect CH₄ emission rates, e.g. diel changes in root exudation or in efficiency of CH⁴ oxidation in the rhizosphere.     

徐州权台煤矿井下700 m水平微生物群落分布特征

煤矿井下与表生环境具有明显差异,研究其微生物群落分布及多样性对深入探讨井下水-岩-气-生作用机制具有重要意义.本研究在徐州权台煤矿井下700 m水平采集了8个沉积物样本,对样品进行了理化指标测试和Miseq高通量测序.结果表明,煤矿井下具有丰富的微生物多样性,8个样本共检测到35个细菌门类,其中变形菌门(Proteob...     

Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields

Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.     

Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics

The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants.     

Diversity and structure of ectomycorrhizal and co-associated fungal communities in a serpentine soil

The community of ectomycorrhizal (ECM) and co-associated fungi from a serpentine site forested with Pinus sylvestris and Quercus petraea was explored, to improve the understanding of ECM diversity in naturally metalliferous soils. ECM fungi were identified by a combination of morphotyping and direct sequencing of the nuclear ribosomal internal transcribed spacer region 2 and of a part of the large-subunit region. Co-associated fungi from selected ECM were identified by restriction fragment length polymorphism and sequencing of representative clones from libraries. Polymerase chain reaction with species-specific primers was applied to assess patterns of association of ECM and co-associated fungi. Twenty ECM species were differentiated. Aphyllophoralean fungi representing several basidiomycete orders and Russulaceae were dominant. Phialocephala fortinii was the most frequently encountered taxon from the diverse assemblage of ECM co-associated fungi. A ribotype representing a deeply branching ascomycete lineage known from ribosomal deoxyribonucleic acid sequences only was detected in some ECM samples. A broad taxonomic range of fungi have the potential to successfully colonise tree roots under the extreme edaphic conditions of serpentine soils. Distribution patterns of ECM-co-associated fungi hint at the importance of specific inter-fungal interactions, which are hypothesised to be a relevant factor for the maintenance of ECM diversity.     

Ectomycorrhizal fungal community in alkaline-saline soil in northeastern China

Alkaline-saline soil is widespread in arid and semiarid regions of the world and causes severe environmental and agricultural problems. To advance our understanding of the adaptation of ectomycorrhizal fungi (EMF) to alkaline-saline soil, we investigated EMF communities on Mongolian willow (Salix linearistipularis) growing in alkaline-saline soil (up to pH 9.2) in northeastern China. In total, 75 root samples were collected from 25 willow individuals over 4.7 ha. To identify fungal species in ectomycorrhizal root tips, we used terminal restriction fragment length polymorphism and sequencing analyses of the internal transcribed spacer region of ribosomal DNA. We detected 11 EMF species, including species of Inocybe, Hebeloma, and Tomentella of the Basidiomycota and three Ascomycota species. The EMF richness of the study site was estimated to be 15–17 using major estimators. The most abundant species was Geopora sp. 1, while no Geopora-dominated EMF communities have been reported so far. Phylogenetic analysis showed that the phylogroup including Geopora sp. 1 has been found mostly in alkaline soil habitats, indicating its adaptation to high soil pH. Because EMF are indispensable for host plant growth, the EMF species detected in this study may be useful for restoration of alkaline-saline areas.     

Long-term continuously monocropped peanut significantly disturbed the balance of soil fungal communities

Journal of Microbiology - Balancing soil microbial diversity and abundance is critical to sustaining soil health, and understanding the dynamics of soil microbes in a monocropping system can help...