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1.
J. T. Trevors 《Water, air, and soil pollution》1998,101(1-4):45-67
Microorganisms isolated from soil are sources of known and new microorganisms and genetic material. This review examines general principles of soil bacterial biodiversity, limitations in sampling soils, and examples of bacterial diversity in chemically-contaminated soils. Both conventional and molecular methods used to assess microbial biodiversity in soils will be addressed as well as selected examples of the effects of organic and inorganic pollutants on soil microbial diversity. 相似文献
2.
Assessing bacterial diversity in soil 总被引：1，自引：1，他引：0
3.
污染土壤的微生物多样性研究 总被引：10，自引：0，他引：10
土壤微生物多样性是土壤微生物生态学的重要研究内容，目前已成为国际上生态学发展的崭新方向之一。土壤微生物多样性包括微生物群落功能多样性、结构多样性及分子遗传多样性，是指示土壤生态系统稳定性及其功能的重要传感器。本文基于分离培养以及生物标志分子方法。从不同生态层次上认识微生物多样性，较全面、系统地综合评述国内外污染土壤环境的微生物群落功能、结构及分子遗传多样性的研究进展，并针对新形势下土壤污染所面临的新问题，探讨了近期土壤微生物生态学过程研究的重要手段与科学问题。 相似文献
4.
The narG gene is frequently used as a molecular marker for bacterial nitrate-reducing community analysis. In this study, a new set of primers targeting the narG gene was designed and applied to semi-nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay. The potential of the new primers was verified on DNA directly extracted from soils from five different experimental sites distributed in Central and Southern Italy. Specificity of the primers was determined by excision, amplification, and sequencing of bands resolved by DGGE. A phylogenetic analysis showed the correlation between the sequences retrieved from the soils studied and the narG sequences from β and γ-Proteobacteria. These primers expanded the existing molecular tools for ecological study on the size and diversity of nitrate-reducing bacterial community in soil. 相似文献
5.
Takeshi Terahara Seishi Ikeda Chiaki Noritake Katsuhiko Ando Shigeaki Harayama 《Soil biology & biochemistry》2009,41(3):473-480
The molecular diversity of bacterial chitinases in the bulk soils of arable land was investigated using culture-independent methods. The results demonstrate that bacterial chitinases in arable soils are highly diverse and comprise unique groups when their sequences were compared to those in public databases. The diversity of bacterial chitinases in arable soil was further evaluated using conventional phylogenetic analysis, the UniFrac analysis of the phylogenetic data, and the multidimensional scaling (MDS) analysis of T-RFLP profiles to elucidate the relationship between the diversity of bacterial chitinases and soil characteristics. These analyses indicate that environmental factors such as soil type and pH are responsible for shaping the composition of bacterial chitinases. 相似文献
6.
Kaare Johnsen Carsten S. Jacobsen Vigdis Torsvik Jan Sørensen 《Biology and Fertility of Soils》2001,33(6):443-453
According to guidelines for the approval of pesticides, side-effects on soil microorganisms should be determined by studying functional parameters such as carbon or nitrogen mineralisation. However, the microbial diversity may have been markedly changed following pesticide use despite unaltered metabolism, and such changes may affect soil fertility. This review evaluates new methods for measuring pesticide effects on bacterial diversity, and discusses how sampling should take temporal and spatial heterogeneity into account. Future research on pesticide approval protocols should establish the relationships between mineralisation assays and new and rapid bacterial diversity profiling methods, and should include the possible ecological implications of altered bacterial diversity for soil fertility. 相似文献
7.
等碳投入的有机肥和生物炭对红壤微生物多样性和土壤呼吸的影响 总被引：7，自引：2，他引：7
施用有机肥是快速培育瘠薄土壤的一个重要措施。针对中亚热带第四纪红黏土发育的红壤旱地,建立了玉米和花生单作系统等碳量投入有机肥和生物炭的田间试验,利用聚合酶链式反应—变性梯度凝胶电泳(polymerase chain reaction-denaturing gradient gel electrophoresis,PCR-DGGE)方法研究了土壤细菌和真菌群落组成和多样性的变化,分析了土壤呼吸速率(CO2通量)的变化及其与微生物多样性的关系。两年的试验表明,不同施肥方式导致微生物群落结构显著分异,施用有机肥和生物炭显著增加了细菌多样性,但施肥第二年真菌多样性有下降趋势。秸秆和猪粪配施显著增加了土壤呼吸速率,土壤呼吸速率与细菌和真菌多样性呈显著正相关,细菌多样性对土壤呼吸的影响(相对贡献率为71%)显著高于真菌(29%)。土壤磷素(全磷和速效磷)含量的变化是驱动红壤微生物多样性变化的主导因素,其对细菌和真菌多样性的相对贡献率分别为44.8%和47.4%。因此,合理配施秸秆和猪粪可以快速提高瘠薄红壤的生物功能。 相似文献
8.
A plot experiment was conducted to understand the response of the soil bacterial community to manure application rates and the relationship between the composition of bacterial community and soil chemical properties. The experiment involved gradients of manure combined with chemical fertilizer in red soils from granite, red sandstone and red clay between 2013 and 2015. The soil bacterial community composition was significantly affected by different manure rates. The relative abundances of Burkholderiaceae, Micrococcaceae and Streptomycetaceae were higher at low manure rates (1.75 to 3.5 t·ha?1·yr.?1), whereas the relative abundance of Xanthomonadaceae was higher at high manure rates (7 to 28 t·ha?1·yr.?1). Manure application increased the bacterial abundance but decreased the diversity when its rates were higher than 7, 14 and 14 t·ha?1·yr.?1 in soils from granite, red sandstone and red clay, respectively. Redundancy analysis revealed that soils from different parent materials had different bacterial communities with soil pH and available phosphorus (AP) being determinant factors. The peanut yields exhibited significantly positive correlations with the bacterial diversity in soil, implying the importance of bacterial diversity for soil productivity. Soil AP was correlated with bacterial diversity by parabolic equations and probably AP may be an indicator of declining bacterial diversity at high manure rates. The critical value were 39.71, 65.75 and 90.16 mg·kg?1 in soils from granite, red sandstone and red clay, respectively. This study suggests the importance of maintaining soil bacterial diversity under moderate and balanced applications of manure. 相似文献
9.
Culture-dependent and culture-independent microbial investigation of pine litters and soil in subtropical Australia 总被引：1，自引：1，他引：0
Background, aim, and scope Forest plantations, widely grown for wood production, involve the selective promotion of single-tree species or replacement
of natural species by exotic tree species. Slash pine (Pinus elliottii) has been chosen for reforestation of infertile sandy soils in southeast Queensland, Australia. These exotic pine plantations
minimize soil and water losses and are important scientific study sites. The soil environment of these plantations, though
devoid of sufficient nutrients, organic carbon and other factors, harbors innumerable bacteria that may play a crucial role
in maintaining soil quality and ecosystem functions. These soil microorganisms also have the potential for use as sensitive
biological indicators to reflect environmental changes. It is therefore essential to understand the interrelationships among
bacterial communities and their environment by assessing their structural and functional diversity and their responses to
disturbances. The main aim of our investigation was to determine the diversity of bacterial communities in forest litters
and soil during the forest leaf litter decomposition using culture-dependent and culture-independent techniques.
Materials and methods A 25-cm (diameter) × 40-cm core sample was collected and fractionated into three subsamples designated E1 (L leaf litter layer),
E2 (F leaf litter layer), and E5 (0–10 cm soil layer). Both culture-dependent and culture-independent methods were applied
in this study. In the culture-independent study, a strategy of whole-community DNA extraction, polymerase chain reaction (PCR)
amplification followed by cloning and 16S rDNA sequence analysis was used; for culture-dependent study, the strategy included
sample plating and bacteria isolating, DNA extraction, PCR amplification, and 16S rDNA sequence analysis. The diversity similarities
between two bacterial communities and two methods are quantified using Jensen–Shannon divergence.
Results From culture-dependent study, 336 colonies in total were isolated and grouped from the three subsamples, and the 16S rRNA
sequence analysis from a representative isolate from each morphogroup (21 isolates) indicated that they belonged to the phyla
Actinobacteria, Firmicutes, and Proteobacteria. Culture-independent assessment based on 16S rRNA gene library comprising 194 clones revealed that members of the phylum Actinobacteria were absent in the culture-independent studies. Clones in libraries from E1 consisted exclusively of members of the Firmicutes. The majority of clones from E2 were related to Firmicutes (79%) and Proteobacteria (21%). Clones derived from E5 were mostly affiliated with Acidobacterium (42%), followed by unclassified bacteria (27%), Verrucomicrobiales (12%), Proteobacteria (11%), and Planctomycetes (8%).
Discussion This study showed that bacterial culturabilities in different fractions of leaf litters were similar, and both of them were
higher than the bacterial culturability in the soil. Unculturable bacterial diversity in the soil, however, was much higher
than the leaf litter bacterial diversity. The bacterial diversity on the top layer of leaf litters was slightly less than
that on the bottom layer of leaf litters. This might indicate that forest soils are a more complex environment than leaf litters
are and also that they might inhabit more unculturable microorganisms in the forest soils, which would need to be further
investigated. The leaf litter layer samples also demonstrate the significant difference between the bacterial community diversity
discovered by these two methods in this study. The information provided by assessing the different fractions of leaf litters
and forest soil has improved our understanding of the bacterial community distributions within the forest soil and the above-leaf
litters in an exotic pine plantation of subtropical Australia.
Conclusions This study represents the first attempt to examine the bacterial community in the different fractions of forest leaf litters
and soil in subtropical Australia. The data from this study show that the 16S rDNA clone libraries provided more comprehensive
phylogenetic diversity in the soil and leaf litter samples than the culture collections provided, and both the culture-dependent
and culture-independent studies revealed that the bacterial diversity present in the leaf litters was very different to that
present in the soil. The comparative analysis of bacterial communities in different fractions of leaf litters and soil samples
has also provided important baseline information about the bacterial diversity and composition in the exotic pine forest plantations.
Recommendations and perspectives The experimental data provided important information on the bacterial diversity in forest leaf litter and soil samples, though
additional surveys and comparisons at different locations would be needed to further characterize. In addition, combined methods
that can provide different parts of information on bacterial diversity are encouraged to be used in bacterial community study.
The established libraries of diverse 16S rRNA gene fragments from slash pine leaf litters and forest soil can be used to construct
specific DNA primers and probes to target bacterial groups of interest. It may then be possible to study the ecology of these
bacterial communities and the role of specific bacterial groups that contribute to the many interesting properties of these
environments. 相似文献
10.
国内首次运用FastPrep○R 核酸快速提取系统提取了重金属复合污染农田土壤的DNA ,并对其进行了聚合酶链反应—变性梯度凝胶电泳 (PCR DGGE)分析。结果表明 ,FastPrep○R核酸提取仪与相应的FastD NASPINKitforSoil试剂盒联用时 ,能有效地分离到纯度较高的重金属污染农田土壤的DNA。PCR DGGE电泳图谱表明 ,PCR产物经DGGE检测后得到的电泳条带清晰且分离效果好 ,可以明显反映出重金属复合污染导致了农田土壤微生物在基因上的损伤 ,影响到农田土壤生态系统的细菌丰富度 ,改变了土壤环境的优势菌群 ,从而使农田土壤微生物群落结构多样性发生变化。可见 ,FastPrep○R核酸提取系统同样适用于重金属污染农田土壤环境中微生物基因组DNA的快速分离和纯化 ,得到的DNA可直接用于PCR DGGE分析。 相似文献
11.
A central goal in soil microbial ecology research is to identify the biodiversity patterns and reveal the underlying mechanisms. Long-term soil acidification is known to reduce soil bacterial diversity, but the mechanisms responsible for this pattern have not been well explored. Soil acidification may reduce bacterial richness through ecological filtering (EF). In contrast, two types of processes may promote the maintenance of bacterial richness: species may adapt to the acidic pressure through evolution, and endemic species already adapted to the acidic pressure can colonize the acidified soils through dispersal. To identify the relative contribution of EF and evolution/dispersal (ED), we collected soils with a pH range of 4–7 from different ecosystems, conducted an acidification experiment with a similar pH range in a neutral soil, and proposed a conceptual framework that could distinguish the three potential types of mechanism (neither EF nor ED operate; EF operates alone; ED counteracts some effect of EF). We found that the entire bacterial domain was driven by the third type of mechanism, with ED counteracting about 42.4% (95% confidence interval: 32.7–50.4%) effect of EF. Meanwhile, different bacterial phyla/classes were governed by different types of mechanisms, and the dominant was the third type. Our results highlight the importance of both ecological and evolutionary mechanisms for regulating soil bacterial communities under environmental changes. 相似文献
12.
设施种植模式对土壤细菌多样性及群落结构的影响 总被引：4，自引：2，他引：4
为了研究有机和常规设施种植模式及轮作对土壤细菌多样性和群落结构的影响,本研究采用Illumina平台Hiseq 2500高通量测序技术,于2016年6月(作物处于收获期)对北京市顺义区不同设施种植模式(分别为有机设施种植模式和常规设施种植模式下的叶菜连作、茄果连作和叶茄轮作)下土壤细菌进行16S r RNA测序。测序质控后共获得17 278个操作分类单元(operational taxonomic units,OTUs),共计318 851条有效序列。比较不同种植模式和轮作下土壤细菌多样性、细菌群落结构组成、相对丰度及土壤理化性质与细菌群落多样性关系的差异性。结果表明:土壤微生物群落结构在有机和常规设施种植模式下差异明显,有机设施种植土壤细菌多样性高于常规设施种植;有机设施种植下轮作与连作土壤细菌群落结构表现出明显差异,而常规设施种植下,两者没有明显差异;有机种植模式下,轮作土壤细菌群落多样性高于连作土壤;设施种植土壤细菌群落主要属于鞘氨醇单胞菌属(Sphingomonas,5.05%)和芽孢杆菌属(Bacillus,4.84%),相对丰度大于0.5%的共有14个属。有机设施种植土壤含有较多促进植物生长、有机质分解的细菌,常规设施种植土壤中降解化学杀虫剂、防治土壤病害、促进硝化过程的细菌较多。RDA分析结果显示土壤细菌群落主要受全磷、速效磷、有机质的影响。Tumebacillus、Candidatus Solibacter和Acidothermus都是分解有机质、利用碳源的细菌属,与土壤有机质含量呈正相关关系。由此可见,设施条件下,有机和常规种植土壤微生物群落结构的差异性主要源于肥料使用、有害生物防治措施和管理方式的不同。有机设施种植模式下,轮作更有利于发挥其改良土壤营养循环和防治土壤病虫害的作用。上述结果为在微生物水平上研究设施条件下不同种植模式的土壤生态质量差异提供了参考。 相似文献
13.
Hermine Huot Jessica Joyner Alonso Córdoba Richard K. Shaw Michael A. Wilson Roxanne Walker Theodore R. Muth Zhongqi Cheng 《Journal of Soils and Sediments》2017,17(2):393-407
Purpose
The influence of human activities on the development and functioning of urban soils and their profile characteristics is still inadequately understood. Microbial communities can change due to anthropogenic disturbances and it is unclear how they exist along urban soil profiles. This study investigates the dynamic soil properties (DSPs) and the bacterial communities along the profiles of urban soils in New York City (NYC) with varying degree of human disturbances.Materials and methods
Eleven pedons were investigated across NYC as well as one control soil in a nearby non-urban area. Six soils are formed in naturally deposited materials (ND) and five in human-altered and human-transported materials (HAHT). For each soil, the profile was described and each horizon was sampled to assess DSPs and the bacterial community composition and diversity.Results and discussion
The development and the DSPs of NYC soils are influenced by the incorporation of HAHT materials and atmospheric deposits. The most abundant bacterial taxa observed in the NYC soils are also present in most natural and urban soils worldwide. The bacterial diversity was lower in some soils formed in ND materials, in which the contribution of low-abundance taxa was more restricted. Some differences in bacterial community composition separated the soils formed in ND materials and in dredged sediments from the soils formed in high artifact fill and serpentinite till. Changes in bacterial community composition between soil horizons were more noticeable in urban soils formed in ND materials than in those formed in HAHT materials which display less differentiated profiles and in the non-urban highly weathered soil.Conclusions
The bacterial diversity is not linked to the degree of disturbance of the urban soils but the variations in community composition between pedons and along soil profiles could be the result of changes in soil development and properties related to human activities and should be consistently characterized in urban soils.14.
15.
Black soils (Mollisols) are one of the most important soil resources for maintaining food security in China, and they are mainly distributed in northeast China. A previous comprehensive study revealed the biogeographical distribution patterns of bacterial communities in the black soil zone. In this study, we used the same soil samples and analyzed the 454 pyrosequencing data for the nuclear ribosomal internal transcribed spacer (ITS) region to examine the fungal communities in these black soils. A total of 220,812 fungal ITS sequences were obtained from 26 soil samples that were collected across the black soil zone. These sequences were classified into at least 5 phyla, 20 classes, greater than 70 orders and over 350 genera, suggesting a high fungal diversity across the black soils. The diversity of fungal communities and distribution of several abundant fungal taxa were significantly related to the soil carbon content. Non-metric multidimensional scaling and canonical correspondence analysis plots indicated that the fungal community composition was most strongly affected by the soil carbon content followed by soil pH. This finding differs from the bacterial community results, which indicated that soil pH was the most important edaphic factor in determining the bacterial community composition of these black soils. A variance partitioning analysis indicated that the geographic distance contributed 20% of the fungal community variation and soil environmental factors that were characterized explained approximately 35%. A pairwise analysis revealed that the diversity of the fungal community was relatively higher at lower latitudes, which is similar to the findings for the bacterial communities in the same region and suggests that a latitudinal gradient of microbial community diversity might occur in the black soil zone. By incorporating our previous findings on the bacterial communities, we can conclude that contemporary factors of soil characteristics are more important than historical factor of geographic distance in shaping the microbial community in the black soil zone of northeast China. 相似文献
16.
Chenxu Liu Qimei Lin Guitong Li 《Acta Agriculturae Scandinavica, Section B - Plant Soil Science》2013,63(7):618-630
ABSTRACT Our objectives were to investigate whether AP affects the soil bacterial community composition and diversity in high-level available phosphorus (AP) soils. The bacterial community was analysed through high-throughput sequencing using the Illumina MiSeq platform. Fifteen soils, including barren land, cropland and greenhouse soils which were sandy loam Fluvisols, were selected from different fields in Beijing, China, with AP contents ranging from 5.03 to 391.45 mg kg?1. Statistical analyses revealed high AP (>100 mg kg?1) decreased alpha diversity (Shannon’s index, H’) but not beta diversity of the soil bacterial community. The sequencing of 16S rRNA genes showed that Proteobacteria, Bacteroidetes and Acidobacteria were the dominant phyla in sandy loam Fluvisols. AP, soil organic carbon (SOC) and total nitrogen (TN) had synergistic influence on the shift of the bacterial community composition. Moreover, AP was the main driving factor affecting the soil bacterial community composition compared with other environmental factors. The members of the Proteobacteria, Bacteroidetes and Actinobacteria belonging to copiotrophic taxa typically increased in relative abundance in high-P soils, while oligotrophic taxa (mainly Acidobacteria) decreased in relative abundance. Our results demonstrated that the bacterial community composition would shift from oligotrophic to copiotrophic with increasing levels of AP. 相似文献
17.
Rima Upchurch Chih-Yu Chiu Karin Everett Glen Dyszynski David C Coleman William B Whitman 《Soil biology & biochemistry》2008,40(6):1294-1305
Differences in the bacterial communities of soils caused by disturbances and land management were identified in rRNA gene libraries prepared from conventional tilled (CT) and no tilled (NT) cropland, a successional forest after 30 y of regrowth (NF) and an old forest of >65 y (OF) at Horseshoe Bend, in the southern Piedmont of Georgia (USA). Libraries were also prepared from forests after 80 y of regrowth at the Coweeta Long Term Ecological Research site (CWT) in the Southern Appalachians of western North Carolina (USA). The composition of the bacterial communities in cropland soils differed from those of the Horseshoe Bend OF and CWT forest soils, and many of the most abundant OTUs were different. Likewise, the diversity of bacterial communities from forest was less than that from cropland. The lower diversity in forest soils was attributed to the presence of a few, very abundant taxa in forest soils that were of reduced abundance or absent in cropland soils. After 30 y of regrowth, the composition of the bacterial soil community of the NF was similar to that of the OF, but the diversity was greater. These results suggested that the bacterial community of soil changes slowly within the time scale of these studies. In contrast, the composition and diversity of the bacterial communities in the Horseshoe Bend OF and Coweeta soils were very similar. Thus, this forest soil bacterial community was widely distributed in spite of the differences in soil properties, vegetation, and climate as well as resilient to disturbances of the above ground vegetation. 相似文献
18.
T. G. Dobrovol’skaya E. A. Leont’evskaya A. A. Sneg P. N. Balabko 《Eurasian Soil Science》2010,43(4):442-446
The analysis of the taxonomic structure of the bacterial complexes in the alluvial soils of the Oka River valley allowed revealing
the distinct differences in the spectrum of the bacterial dominants in the virgin and cultivated soils. Arthrobacter and pigment coryneform bacteria are shown to predominate in the virgin soil; bacilli and pseudomonades are common in the
soil under vegetables. On cabbage leaves and carrot roots (both healthy and rotten), the spectrum of dominants is composed
of two genera of enterobacteria: Pantoea and Erwinia. As a result of the plowing in of vegetables into the soil, enterobacteria accumulate; among them, phytopathogenic species
are present. Within a year after this plowing in and the new yield, the enterobacteria practically disappeared, but myxobacteria
and cytophages developed. Since these bacteria belong to the cellulose-destroying prokaryotes, the increase in their contents
in the soil testified to their participation in the decomposition of the buried vegetable residues. Weeds are known to concentrate
various bacterial forms in the phylloplane; they enter from different ecological niches: soil, water, meadow, and agricultural
plants. Representatives of phytopathogenic bacteria as minor components were found on weeds. 相似文献
19.
黄河三角洲刺槐根际与非根际细菌结构及多样性 总被引：4，自引：0，他引：4
为精确分析黄河三角洲刺槐根际与非根际土壤细菌群落定殖情况,本研究采用高通量测序方法对刺槐根际与非根际土壤细菌结构及多样性进行了研究。研究表明,根际土壤细菌共有36门214属,非根际土壤细菌共有33门153属。变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、酸杆菌门(Acidobacteria)细菌丰度超过15%,是根际与非根际土壤中的优势菌落。根际与非根际土壤中酸杆菌门、硝化螺旋菌门(Nitrospirae)丰度差异显著。根际土壤中红游动菌属(Rhodoplanes)、溶杆菌属(Lysobacter)、热单胞菌属(Thermomonas)、链霉菌属(Streptomyces)及非根际土壤中红游动菌属、溶杆菌属、链霉菌属、Kaistobacter细菌丰度超过4%。根际土壤中固氮菌丰度显著高于非根际土壤,解磷、解钾细菌丰度差异不显著。根际与非根际土壤细菌Chao丰富度分别为2 054、2 376,差异显著。根际与非根际土壤细菌之间的权重(Weighted Unifrac)距离在0.12~0.25之间。综上所述,黄河三角洲刺槐根际与非根际土壤细菌结构具有一定差异,多样性差异显著。 相似文献
20.
基于高通量测序的两种植被恢复类型根际土壤细菌多样性研究 总被引：21，自引：1，他引：20
为研究库布齐沙地生态恢复过程中不同植被恢复类型土壤微生物细菌群落结构、多样性的变化特征,以流动沙地为对照,运用高通量测序技术,对自然恢复的油蒿群落、人工种植的中间锦鸡儿群落根际和非根际土壤细菌多样性进行了研究,并分析了土壤理化性质对其分布的影响。结果表明:(1)与流沙对照相比,两种植被恢复类型对细菌多样性产生了正效应,细菌群落丰度、多样性和均匀度明显增加。其中,自然恢复的油蒿群落土壤细菌丰度高于人工种植的中间锦鸡儿群落;(2)变形菌门、酸杆菌门和放线菌门为研究区土壤中的优势细菌类群,其中变形菌门在各样地丰度比例最高,变形菌的4个亚群变化趋势一致,α-变形菌相对含量在油蒿和中间锦鸡儿群落根际土壤中明显增加,尤其是自然恢复的油蒿群落根际土壤中α-变形菌得到了很好的恢复;(3)土壤有机质、全氮、速效氮、速效钾含量和土壤含水量是影响土壤细菌群落丰度和多样性的主要土壤因子,典型相关分析表明土壤有机质、全氮、全钾、速效钾、速效氮含量对于研究区土壤细菌群落遗传多样性的变化起着重要作用。 相似文献