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1.
There is a paucity of knowledge on microbial community diversity and naturally occurring seasonal variations in agricultural soil. For this purpose the soil microbial community of a wheat field on an experimental farm in The Netherlands was studied by using both cultivation-based and molecule-based methods. Samples were taken in the different seasons over a 1-year period. Fatty acid-based typing of bacterial isolates obtained via plating revealed a diverse community of mainly gram-positive bacteria, and only a few isolates appeared to belong to the Proteobacteria and green sulfur bacteria. Some genera, such as Micrococcus, Arthrobacter, and Corynebacterium were detected throughout the year, while Bacillus was found only in July. Isolate diversity was lowest in July, and the most abundant species, Arthrobacter oxydans, and members of the genus Pseudomonas were found in reduced numbers in July. Analysis by molecular techniques showed that diversity of cloned 16S ribosomal DNA (rDNA) sequences was greater than the diversity among cultured isolates. Moreover, based on analysis of 16S rDNA sequences, there was a more even distribution among five main divisions, Acidobacterium, Proteobacteria, Nitrospira, cyanobacteria, and green sulfur bacteria. No clones were found belonging to the gram-positive bacteria, which dominated the cultured isolates. Seasonal fluctuations were assessed by denaturing gradient gel electrophoresis. Statistical analysis of the banding patterns revealed significant differences between samples taken in different seasons. Cluster analysis of the patterns revealed that the bacterial community in July clearly differed from those in the other months. Although the molecule- and cultivation-based methods allowed the detection of different parts of the bacterial community, results from both methods indicated that the community present in July showed the largest difference from the communities of the other months. Efforts were made to use the sequence data for providing insight into more general ecological relationships. Based on the distribution of 16S rDNA sequences among the bacterial divisions found in this work and in literature, it is suggested that the ratio between the number of Proteobacteria and Acidobacterium organisms might be indicative of the trophic level of the soil.  相似文献   

2.
Genetic diversity of five wild populations and a cultured population of topmouth culter (Culter alburnus) was investigated using amplified fragment length polymorphism (AFLP). A total of 373 reproducible bands amplified with seven AFLP primer combinations were obtained from 163 fish. The percentage of polymorphic loci ranged widely from 37.0% to 69.2% within distinct populations. The cultured population appeared to have a lower level of polymorphism (37.0%), gene diversity (0.121 ± 0.188) and Shannon's Information index (0.183 ± 0.263) than the wild populations. Analysis of molecular variance (AMOVA) revealed that average FST value overall loci was 0.2671, and the percentage of variation within population (73.29%) was larger than among populations (26.71%) (P < 0.01). The six populations were clustered into two major clades with UPGMA. The results from analysis of population pairwise gene flow indicated moderate gene flow among populations. Our study indicated that the genetic diversity of the cultured population was reduced compared with the wild populations. Geographic isolation, habitat, and artificial selection all may have played important roles in population differentiation. The information may be beneficial to future broodstock selection and defining conservation management for the different populations of topmouth culter.  相似文献   

3.
Archaeal diversity in the 2012 terrestrial hot spring (Valley of Geysers, Kronotsky Nature Reserve, Kamchatka, Russia) was investigated using molecular and cultivation-based approaches. Analysis of the 16S rRNA gene sequences revealed predominance among archaea of uncultured microorganisms of the pSL12 and THSCG clusters. Analysis of the mcrA genes revealed that members of the order Methanomassiliicoccales were predominant (68%) among methanogens; the latter constituted 0.15% of the total number of archaea. Five stable thermophilic methanogenic associations utilizing hydrogen, formate, acetate, or methanol as substrates were obtained from the sediments of spring 2012. The diversity of cultured methanogens was limited to members of the genera Methanothermobacter, Methanothrix, and Methanomethylovorans. The association growing at 65°C and producing methane from methanol contained two components, which probably formed a syntrophic relationship: a Methanothermobacter methanogenic archaeon and a bacterium representing an separate cluster within the Firmicutes phylum, which was phylogenetically related to the genera Thermacetogenium and Syntrophaceticus. These data indicate high diversity of methanogens, notwithstanding their low abundance among archaea. The group of thermophilic Methanomassiliicoccales, which predominated among methanogens, is of special interest.  相似文献   

4.
《农业工程》2020,40(5):398-411
Understanding how topography-soil-disturbance drives spatial distribution of vegetation is the interest of ecologists. This study was, conducted to investigate the topography-soil-disturbance and vegetation relationships in Abune Yosef mountain range, Ethiopia. A total of 85 nested sample plots measuring 400 m2, 25 m2 and 1 m2 were established for trees, shrubs and herbs respectively. Topographic, soil and disturbance variables were also assessed from each plot. Plant community classification was described and identified by agglomerative hierarchical clustering using Ward's minimum variance clustering methods. Shannon diversity index was employed to determine community diversity. After detecting the length of the first Detrended Correspondence Analysis (DCA) axis, Canonical Correspondence Analysis (CCA) forward and backward stepwise selection of environmental variables was performed based on their p-value by running permutation tests. The first axis explained 43.63% of the overall inertia and is correlated with Elevation, pH, slope aspect, total Nitrogen, soil organic Carbon & Clay. On the other hand, the second axis explained 32.06% of the total inertia and is correlated with bulk density, slope, logging, & available Phosphorus. The present study revealed that topographic variables have a profound influence on vegetation spatial distribution than soil and disturbance factors.  相似文献   

5.
Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.  相似文献   

6.
利用ISSR分子标记对木荷种群在3个演替系列群落中的遗传多样性进行了研究。12个随机引物共检测到203个可重复的位点,其中多态位点183个,总多态位点百分率(P)为90.15%,平均多态位点百分率为82.27%。Shannon信息指数(I)估算的总遗传多样性为0.524 4,平均为0.477 8。Nei指数(h)计算的总基因多样性为0.358 7,平均为0.326 5。3个种群的P、I、h大小顺序均为针叶林>针阔混交林>常绿阔叶林。AMOVA分子变异显示91.56%变异来源于种群内,8.44%变异来源于种群间。种群间的遗传分化系数(GST)为0.089 7,基因流(Nm)为5.073 1。种群间的遗传相似度平均为0.928 4,遗传距离平均为0.074 4,针叶林种群与针阔混交林种群遗传相似度最高。  相似文献   

7.
江西井冈山自然保护区陆生贝类多样性   总被引:1,自引:0,他引:1  
2011年4~8月调查了江西井冈山自然保护区陆生贝类资源,共采得陆生贝类67种和亚种(含9个未定种),隶属4目19科31属,其中有1新种,即龙潭弯螺(Sinoennea sp.nov.)(另文报道);14种为江西省陆生贝类新纪录种;优势种为长柱倍唇螺(Diplommatina paxillus longipalatalis)、细锥倍唇螺(D.apicina)、灰尖巴蜗牛(Bradybaena ravida ravida)、双线巨蓬蛞蝓(Meghimatium bilineatum)。区系组成以东洋界成分为主,占种类总数的74.14%。阔叶林、灌木丛和农田生境陆生贝类种类较丰富,竹林和苔藓生境种类较少。根据调查数据,分别计算井冈山自然保护区5种不同生境类型中陆生贝类群落的多样性、丰富度和均匀度,结果表明,灌木丛生境陆生贝类的丰富度指数和多样性指数均最高,苔藓生境的均匀度指数最高。与邻近自然保护区比较,井冈山自然保护区陆生贝类物种较丰富,且与江西齐云山陆生贝类物种相似系数较高,与广东南岭物种相似系数较低。  相似文献   

8.
2009年5-9月,对荣成靖海湾大型养殖池塘海蜇(Rhopilema esculentum Kishinouye)养殖期间与养殖期前后底泥营养盐及大型底栖动物群落结构变化进行了研究。结果表明,7月份海蜇养殖期间,由于海蜇的避光性而产生的上下浮动的行为特征造成了对水体的扰动作用, 与海蜇的生物沉积作用共同导致养殖海区(实验点)与邻近非养殖海区(对照点)之间各项底泥营养盐指标均存在显著性差异,其中,实验点氨氮(NH4-N)、硝氮(NO3-N)和沉降速率(sedimentation rate, SR)显著高于对照点,实验点叶绿素a(Chla)、总有机物(TOM)和总有机碳(TOC)含量显著低于对照点。多变量聚类分析结果表明,海蜇养殖对养殖池塘的大型底栖动物群落结构产生显著影响,并且7月份实验点大型底栖动物生物多样性指数(H')和均匀度指数(J) 随海蜇放养显著增大,并显著高于对照点。大型底栖动物群落多样性指数与沉降速率(SR)和底泥TOM含量分别表现出显著正相关和负相关,而与其他营养盐指标无显著相关性。  相似文献   

9.
Aquilaria malaccensis is a fast-growing, tropical tree belonging to the family Thymelaeaceae and is locally known as Agar. Agarwood formation takes place in the stem or main branches of the tree where an injury has occurred. It is believed that the tree is first attacked by a pathogenic fungus, which causes it to weaken. Most fungal diversity studies have previously been based on morphological examination and cultivation methods. In this study, we used both culture-dependent and culture-independent approaches (metagenomic) to study the endophytic fungi on wood chips of A. malaccensis. The culture-based approach revealed Alternaria, Cladosporium, Curvularia, Fusarium, Phaeoacremonium and Trichoderma as members of the agarwood community. Also analysis of ITS sequencing of these culture isolates provided further verification of the identity of the cultured groups. Analysis of community DNA (metagenome) extracted from both infected and healthy wood samples revealed that the majority of fungi present had highest sequence similarity to members of Dothideomycetes, followed by Sordariomycetes and Saccharomycetes. Thus, morphological and genetic characteristics showed that most isolates from agarwood belong to phylum Ascomycota. A neighbour-joining tree showed the relationships between the isolates sequence data and the closest identified relatives from GenBank.  相似文献   

10.
Thirteen accessions of pearl millet (Pennisetum typhoides (L) Leeke) collected from different states of India and eight wild species of the genus Pennisetum across the world were analyzed for genetic diversity using AFLP markers. A combined analysis of eight primer combinations showed 35% polymorphism among P. typhoides accessions while analysis with five primer combinations showed 99% polymorphism among the wild species. The dendrogram constructed for the P. typhoides accessions based on the UPGMA method revealed two major clusters with samples from Gujarat forming a separate cluster from the rest of the samples. Principal component analysis of the same data set revealed similar results with the first principal component accounting for 65% of the total variation. The percentage of rare and common alleles contributing to the diversity in the sample was analyzed using the Shannon Weiner diversity index. The SW index revealed that the samples from Gujarat contributed significantly to the overall diversity among the accessions. Among accessions of each geographical region, considerable variation was revealed by SW index with samples from Tamil Nadu being most polymorphic. The genetic diversity in the accessions could be utilized for future breeding work. The dendrogram constructed for the wild species revealed the extent of genetic diversity among them. Analysis with one primer combination showed P. typhoides being closer to P. mollissimum than to the other analyzed species.  相似文献   

11.
Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20?years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40?% of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.  相似文献   

12.
《农业工程》2021,41(6):611-619
The integrity of the homestead pond supply depends on how various macrobenthic communities make their living more diversified and contribute to complex food webs. In addition, the macrobenthic community are significantly used as indicator organisms to detect the pollution impacts in aquatic ecosystems. In this study, we show the data about the diversity and community structure of macrobenthos and their relationship with environmental variables in homestead ponds of Noakhali coast from January 2019 to August 2019. The current study yielded 17 species belonging to seven taxonomic groups with a mean density of 3630 ind./m2. The Nematode community, comprising 48.86% of the total taxonomic groups with Prionchulus sp. as the dominant macrobenthic species represented more than 31% of the total macrobenthic taxa, and showed a significant negative correlation with the value of salinity, DO, pH. The environmental variables and diversity indices were detected significant variations (P < 0.05) among stations by the Kruskal-Wallis ANOVA, whereas Shannon-Wiener Diversity Index (H´) assessed moderate pollution, Evenness index (J) assessed uniform distributions of macrobenthic community, and environmental variables showed acceptable condition for the productivity of ponds. Cluster analysis (CA) and Non-metric multidimensional scaling (nMDS) demonstrate demarcations in the community structure of macrobenthos between samples. Within macrobenthic communities, Canonical Correspondence Analysis (CCA) provided insights and interpretations of the relationships between species and environmental gradients. Macrobenthic community reached the most abundance at a lower temperature, transparency and a higher DO, pH and salinity.  相似文献   

13.
Revealing the relationship between plants and root-associated fungi is very important in understanding diversity maintenance and community assembly in ecosystems. However, the community assembly of root-associated fungi of focal plant species along a subtropical plant species diversity gradient is less documented. Here, we examined root-associated fungal communities associated with five ectomycorrhizal (EM) plant species (Betula luminifera, Castanea henryi, Castanopsis fargesii, C. sclerophylla, and Quercus serrate) in a Chinese subtropical woody plant species diversity (1, 2, 4, 8, 16 and 24 species) experiment, using paired-end Illumina MiSeq sequencing of the ITS2 region. In total, we detected 1933 root-associated fungal operational taxonomic units (OTUs) at a 97% sequence similarity level. Plant identity had a significant effect on total and saprotrophic fungal OTU richness, but plant species diversity level had a significant effect on saprotrophic and pathogenic fungal OTU richness. The community composition of total, saprotrophic and EM fungi was structured by plant identity and plant species diversity level. However, the community composition of pathogenic fungi was only shaped by plant identity. This study highlights that plant identity has a stronger effect on the root-associated fungal community than plant species diversity level in a diverse subtropical forest ecosystem.  相似文献   

14.
Maize (Zea mays L.) harbours significant genetic diversity not only in its centre of origin (Mexico) but also in several countries worldwide, including India, in the form of landraces. In this study, DNA fingerprinting of 48 landrace accessions from diverse regions of India was undertaken using 42 fluorescent dye-labeled Simple Sequence Repeat (SSR) markers, followed by allele resolution using DNA sequencer and analysis of molecular diversity within and among these landraces. The study revealed a large number of alleles (550), with high mean number of alleles per locus (13.1), and Polymorphism Information Content (PIC) of 0.60, reflecting the level of diversity in the landrace accessions. Besides identification of 174 unique alleles in 44 accessions, six highly frequent SSR alleles were detected at six loci (phi014, phi090, phi112, umc1367, phi062 and umc1266) with individual frequencies greater than 0.75, indicating that chromosomal regions harboring these SSR alleles are not selectively neutral. F statistics revealed very high genetic differentiation, population subdivision and varying levels of inbreeding in the landraces. Analysis of Molecular Variance showed that 63 % of the total variation in the accessions could be attributed to within-population diversity, and 37 % represented between population diversity. Cluster analysis of SSR data using Nei’s genetic distance and UPGMA revealed considerable genetic diversity in these populations, although no clear separation of accessions was observed based on their geographic origin.  相似文献   

15.
Phylogenetic analysis of the nucleotide sequences of 16S rRNA genes in the metagenomic community of Lubomirskia baicalensis has revealed taxonomic diversity of bacteria associated with the endemic freshwater sponge. Fifty-four operational taxonomic units (OTUs) belonging to six bacterial phyla (Actinobacteria, Proteobacteria (class ??-Proteobacteria and ??-Proteobacteria) Verrucomicrobia, Bacteroidetes, Cyanobacteria, and Nitrospira) have been identified. Actinobacteria, whose representatives are known as antibiotic producers, is the dominant phylum of the community (37%, 20 OTUs). All sequences detected shared the maximal homology with unculturable microorganisms from freshwater habitats. The wide diversity of bacteria closely coexisting with the Baikal sponge indicate the complex ecological relationships in the community formed under the unique conditions of Lake Baikal.  相似文献   

16.
The small-subunit ribosomal DNA (rDNA) diversity was found to be very high in a Hawaiian soil community that might be expected to have lower diversity than the communities in continental soils because the Hawaiian soil is geographically isolated and only 200 years old, is subjected to a constant climate, and harbors low plant diversity. Since an underlying community structure could not be revealed by analyzing the total eubacterial rDNA, we first fractionated the DNA on the basis of guanine-plus-cytosine (G+C) content by using bis-benzimidazole and equilibrium centrifugation and then analyzed the bacterial rDNA amplified from a fraction with a high biomass (63% G+C fraction) and a fraction with a low biomass (35% G+C fraction). The rDNA clone libraries were screened by amplified rDNA restriction analysis to determine phylotype distribution. The dominant biomass reflected by the 63% G+C fraction contained several dominant phylotypes, while the community members that were less successful (35% G+C fraction) did not show dominance but there was a very high diversity of phylotypes. Nucleotide sequence analysis revealed taxa belonging to the groups expected for the G+C contents used. The dominant phylotypes in the 63% G+C fraction were members of the Pseudomonas, Rhizobium-Agrobacterium, and Rhodospirillum assemblages, while all of the clones sequenced from the 35% G+C fraction were affiliated with several Clostridium assemblages. The two-step rDNA analysis used here uncovered more diversity than can be detected by direct rDNA analysis of total community DNA. The G+C separation step is also a way to detect some of the less dominant organisms in a community.  相似文献   

17.
The structure and specific characteristics of the hydrolytic microbial complexes from chestnut paleosols buried under the barrows of different ages (~4500 and ~3500 years) was compared with their modern analogue in microcosm experiments. Potential activity of the hydrolytic complex of the microbial community of the barrow paleosols was found to be higher than in the modern soil complex. The share of metabolically active cells revealed by FISH after the introduction of a growth-stimulating polysaccharide into the paleosol microcosm was 50% of the whole prokaryotic cell number. The paleosol community exhibited a more pronounced response to addition of the substrate than the modern soil community. The differences in the phylogenetic taxonomic structure of the prokaryotic metabolically active hydrolytic complex in the buried and modern soils were revealed. The hydrolytic complex of modern soil was more diverse, while the dominant hydrolytic organisms revealed in paleosols were unicellular and mycelial Actinobacteria, as well as Proteobacteria.  相似文献   

18.
Bacteria in the phycosphere have a unique ecological relationship with host algae due to their utilization of algal extracellular products as nutrients. Some bacteria control the growth of algal cells and even lyse them. The diversity of bacteria and their community dynamics in the phycosphere of microalgae are still relatively little understood, especially of those associated with red tide-causing algae. In this study, scanning electron microscope (SEM) images of algal cell morphology revealed that the phycosphere bacteria of the red tide-causing algae, Skeletonema costatum and Scrippsiella trochoidea, could lyse them within 72 h. The community level physiology of the algicidal bacteria was studied using Biolog ECO microplates, a common method for the ecological study of microbial communities. The average well color development (AWCD) values of bacteria in the phycospheres of both species were low, indicating that the bacteria had low metabolic activity overall. The diversity indices were both lower than the bacterial diversity from natural environments. However, the bacteria associated with S. trochoidea demonstrated a higher AWCD value and diversity than those in the phycosphere of S. costatum. The utilization of carbon sources significantly changed at different lytic times, reflecting that the bacterial community structure changed during the algae-lysing process. These results revealed that the bacterial communities in phycospheres had a simple structure and low diversity. When the balance between algae and bacteria broke down, the total bacterial density increased while the algicidal bacteria accumulated and became the dominant species, changing the bacterial community structure in this micro-ecosystem.  相似文献   

19.
Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers.  相似文献   

20.
道路边坡坡度对植被恢复中物种多样性的影响研究   总被引:2,自引:0,他引:2  
以成都平原周边的5条道路的边坡植被群落作为研究对象,采用样线法,研究坡度对道路边坡的植物群落多样性的影响。选取101个海拔在300~400 m间并且土壤质地相同的边坡样方进行坡度分析。结果显示:(1)选取的样方中,共出现142种植物,属于61个科,121属。(2)边坡坡度对阳坡和阴坡的灌木层与草本层的植物群落物种多样性具有显著的影响(P<0.05)。(3)边坡坡度对阴坡群落的均匀度指数影响显著(P<0.05);而对阳坡群落的丰富度影响相对较大,呈现先增加后降低的趋势。分析表明,边坡坡度对成都平原周边地区道路边坡的植物群落多样性具有显著影响;在坡度<35°的条件下,植被群落恢复效果较好,群落的多样性高;而对>35°的边坡来说,多样性指数呈下降趋势,不利于后期边坡恢复。  相似文献   

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