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1.
Here, we examine soil-borne microbial biogeography as a function of the features that define an American Viticultural Area (AVA), a geographically delimited American wine grape-growing region, defined for its distinguishing features of climate, geology, soils, physical features (topography and water), and elevation. In doing so, we lay a foundation upon which to link the terroir of wine back to the soil-borne microbial communities. The objective of this study is to elucidate the hierarchy of drivers of soil bacterial community structure in wine grape vineyards in Napa Valley, California. We measured differences in the soil bacterial and archaeal community composition and diversity by sequencing the fourth variable region of the small subunit ribosomal RNA gene (16S V4 rDNA). Soil bacterial communities were structured with respect to soil properties and AVA, demonstrating the complexity of soil microbial biogeography at the landscape scale and within the single land-use type. Location and edaphic variables that distinguish AVAs were the strongest explanatory factors for soil microbial community structure. Notably, the relationship with TC and TN of the <53 μm and 53–250 μm soil fractions offers support for the role of bacterial community structure rather than individual taxa on fine soil organic matter content. We reason that AVA, climate, and topography each affect soil microbial communities through their suite of impacts on soil properties. The identification of distinctive soil microbial communities associated with a given AVA lends support to the idea that soil microbial communities form a key in linking wine terroir back to the biotic components of the soil environment, suggesting that the relationship between soil microbial communities and wine terroir should be examined further.  相似文献   

2.
Nycodenz density centrifugation (NDC) is an isolation method that allows extraction of both culturable and unculturable bacterial cells from soil, to be used in further downstream analysis; however, to date there has been a lack of information concerning the efficiency of this method. The aim of this study was therefore to investigate the overall efficiency of NDC extractions from soil and to identify sampling bias, if any.Bacterial cells were extracted from three soil plots from the Danish CRUCIAL field trial using an already established NDC protocol. To evaluate all aspects of the NDC procedure, DNA was extracted directly from soil, from NDC-extracted cells, and from the soil pellets left after NDC. Bacterial diversity was assessed by PCR amplification of the V4-V6 regions of the 16S rRNA from the extracted DNA followed by sample-tagged amplicon-pyrosequencing using the 454 Genome Sequencer FLX system. Sequences were processed and analyzed using the Ribosomal Database Project’s (RDP) Pyrosequencing Pipeline tools.In this study, we show that extraction of bacteria from soil using NDC can result in significant biases in the form of either over- or underrepresentation of specific bacterial phyla commonly found in soil. Furthermore, rarefaction analysis, analysis of similarity, multidimensional scaling plots and analysis of variance showed that the diversity in the NDC-extracted sample was reduced significantly compared to both the original soil sample and the remaining NDC-pellet. To further study the soil diversity a mathematical model was employed to estimate how many sequences would be required in order to find 95% of all operational taxonomic units (OTUs) in the soil. The model estimated that the soil contains approximately 29,400 OTUs and that just 351,500 sequences are needed to cover 95% of the bacterial biodiversity, the equivalent of one full standard GS FLX run.  相似文献   

3.
Background, Aims, and Scope  Knowledge about shifts of microbial community structure and diversity following different agricultural management practices could improve our understanding of soil processes and thus help us to develop sound management strategies. A long-term fertilization experiment was established in 1989 at Fengqiu (35°00′N, 114°24′E) in northern China. The soil (sandy loam) is classified as aquic inceptisols and has received continuous fertilization treatments since then. The fertilization treatments included control (CK, no fertilizer), chemical fertilizers nitrogen (N) and potassium (K) (NK), phosphorous (P) and K (PK), NP, NPK, organic manure (OM), and half chemical fertilizers NPK plus half organic manure (1/2NPKOM). The objective of this study was to examine if the microbial community structure and diversity were affected by the long-term fertilization regimes. Materials and Methods  Soil samples were collected from the long-term experimental plots with seven treatments and four replications in April 2006. Microbial DNAs were extracted from the soil samples and the 16S rRNA genes were PCR amplified. The PCR products were analyzed by DGGE, cloning and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and the clone libraries constructed from the excised DGGE bands. Results  The bacterial community structure of the OM and PK treatments were significantly different from those of all other treatments. The bacterial community structures of the four Ncontaining treatments (NK, NP, NPK and 1/2NPKOM), as well as CK, were more similar to each other. The changes in bacterial community structures of the OM and PK treatments showed higher richness and diversity. Phylogenetic analyses indicated that Proteobacteria (30.5%) was the dominant taxonomic group of the soil, followed by Acidobacteria (15.3%), Gemmatimonadetes (12.7%), etc. Discussion  Irrespective of the two fertilization treatments of OM and PK, the cluster analysis showed that bacterial communities of the remaining five treatments of CK, NK, NP, NPK and 1/2NPKOM seemed to be more similar to each other, which indicated the relatively weak effects of the four N-containing treatments on soil bacterial communities. N fertilizer may be considered as a key factor to counteract the effects of other fertilizers on microbial communities. Conclusions  Our results show that long-term fertilization regimes can affect bacterial community structure and diversity of the agricultural soil. The OM and PK treatments showed a trend towards distinct community structures, higher richness and diversity when compared to the other treatments. Contrasting to the positive effects of OM and PK treatments on the bacterial communities, N fertilizer could be considered as a key factor in the soil to counteract the effects of other fertilizers on soil microbial communities. Recommendations and Perspectives  Because of the extremely high abundance and diversity of microorganisms in soil and the high heterogeneity of the soil, it is necessary to further examine the effects of fertilization regimes on microbial community and diversity in different type soils for comprehensively understanding their effects through the appropriate combination of molecular approaches. ESS-Submission Editor: Chengrong Chen, PhD (c.chen@griffith.edu.au)  相似文献   

4.
Little is known about abundances of the major bacterial taxa in agricultural soils and how they are affected by fertilization or other agricultural practices. Our aim was to determine the abundance and relative distribution of several bacterial phyla and one class, as well as the archaeal and crenarchaeal communities, and how they were affected by different fertilization regimes to examine whether specific responses of microorganisms could be identified at these high taxonomic ranks. We used real-time PCR with taxa specific primers to quantify the abundance of the Actinobacteria, Acidobacteria, Bacteriodetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Alphaproteobacteria and Crenarchaeota, as well as of the total bacteria and total archaea in soil sampled in 2002 and 2007 from a long term experimental field site subjected to six different fertilization regimes since 1956. The fertilization had affected soil pH, carbon and nitrogen, in addition to the C:N ratio. The total abundances of each taxon were affected in similar ways by the imposed treatments. By contrast, the relative abundance of certain taxa responded differently to the same fertilizer, with some taxa increasing while others decreased. Significant treatment effects were observed for the relative abundance of Alphaproteobacteria, Firmicutes, Verrucomicrobia and the Crenarchaeota and soil pH was the main driver for the observed differences. Differences between sampling years were also observed for the relative abundance of the Actinobacteria and the Bacteroidetes. Altogether, our results showed that agricultural practices can impact bacterial and archaeal phyla and classes in soil differently, which is consistent with recent work suggesting ecological coherence of members of bacterial clades at high taxonomic ranks.  相似文献   

5.
6.
The rhizosphere and the surrounding soil harbor an enormous microbial diversity and a specific community structure, generated by the interaction between plant roots and soil bacteria. The aim of this study was to address the influences of tree species, tree species diversity and leaf litter on soil bacterial diversity and community composition. Therefore, mesocosm experiments using beech, ash, lime, maple and hornbeam were established in 2006, and sampled in October 2008 and June 2009. Mesocosms were planted with one, three or five different tree species and treated with or without litter overlay.Cluster analysis of DGGE-derived patterns revealed a clustering of 2008 sampled litter treatments in two separated clusters. The corresponding treatments sampled in 2009 showed separation in one cluster. PCA analysis based on the relative abundance of active proteobacterial classes and other phyla in beech and ash single-tree species mesocosm indicated an effect of sampling time and leaf litter on active bacterial community composition. The abundance of next-generation sequencing-derived sequences assigned to the Betaproteobacteria was higher in the litter treatments, indicating a higher activity, under these conditions. The Deltaproteobacteria, Nitrospira and Gemmatimonadetes showed an opposite trend and were more active in the mesocosms without litter. The abundance of alphaproteobacterial sequences was higher in mesocosms sampled in 2009 (P = 0.014), whereas the Acidobacteria were more active in 2008 (P = 0.014). At the family level, we found significant differences of the litter vs. non-litter treated group. Additionally, an impact of beech and ash as tree species on soil bacterial diversity was confirmed by the Shannon and Simpson indices. Our results suggest that leaf litter decomposition in pH-stable soils affect the soil bacterial composition, while tree species influence the soil bacterial diversity.  相似文献   

7.
Municipal solid waste (MSW) composts have been used to maintain the long-term productivity of agroecosystems and to protect the soil environment from overcropping, changes in climatic conditions and inadequate management; they also have the additional benefit of reducing waste disposal costs. Since MSW may contain heavy metals and other toxic compounds, amendments cannot only influence soil fertility, but may also affect the composition and activity of soil microorganisms. The effects of MSW compost and mineral N amendments in a 6-year field trial on some physical-chemical properties, enzyme activities and bacterial genetic diversity of cropped plots (Beta vulgaris-Triticum turgidum rotation) and uncropped plots were investigated. The compost was added at the recommended and twice the recommended dosage (12, 24 t ha−1). Amendments of cropped plots with MSW compost increased the contents of organic C from 13.3 to 15.0 g kg−1 soil and total N from 1.55 to 1.65 g kg−1 soil. There were significant increases in dehydrogenase (9.6%), β-glucosidase (13.5%), urease (15.4%), nitrate reductase (21.4%) and phosphatase (9.7%) activities. A significant reduction in protease activity (from 3.6 to 2.8 U g−1 soil) was measured when a double dose of compost was added to the cropped plots. No dosage effect was detected for the other enzymes. Changes in the microbial community, as a consequence of MSW amendment, were minimal as determined using denaturing gradient gel electrophoresis, rDNA internal spacer analysis and amplified ribosomal DNA restriction analysis of bacteria, archaea, actinomycetes, and ammonia oxidizers. This indicates that there was no significant variation in the overall bacterial communities nor in selected taxonomic groups deemed to be essential for soil fertility.  相似文献   

8.
9.
To analyze the structure of bacterial communities in spinach roots and in the nonrhizosphere soil, we used PeR-amplified 16S rRNA gene fragments separated by denaturing gradient gel electrophoresis (DGGE). DGGE revealed a large number of band patterns, which were ascribed to various bacterial species composing each of the bacterial communities. The pattern from the roots was less complex than that from the soil. It is considered that DGGE analysis is suitable for studies of bacterial community structure in soil-plant ecosystems.  相似文献   

10.
Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO2 (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.  相似文献   

11.
Knowledge of the cycling and compartmentalization of soil C that influence C storage may lead to the development of strategies to increase soil C storage potentials. The objective of this study was to use soil hydrolases and soil aggregate fractionation to explore the relationship between C cycling activity and soil aggregate structure. The prairie chronosequence soils were native prairie (NP) and agricultural (AG) and tallgrass prairies restored from agriculture in 1979 (RP-79) and 1993 (RP-93). Assays for -glucosidase (E.C. 3.2.1.21) and N-acetyl--glucosaminidase (NAGase, EC 3.2.1.30) activities were conducted on four aggregate size fractions (>2 mm, 1–2 mm, 250 m–1 mm, and 2–250 m) from each soil. There were significantly greater amounts of >2-mm aggregates in the RP-79 and RP-93 soils compared to the NP and AG soils due to rapid C accumulation from native plant establishment. Activities for both enzymes (g PNP g–1 soil h–1) were greatest in the microaggregate (2–250 m) compared to the macroaggregate (>2 mm) fraction; however, microaggregates are a small proportion of each soil (<12%) compared to the macroaggregates (75%). The RP soils have a hierarchical aggregate system with most of the enzyme activity in the largest aggregate fractions. The NP and AG soils show no hierarchical structure based on aggregate C accretion and significant C enzyme activity in smaller aggregates. The distribution of enzyme activity may play a role in the storage of C whereby the aggrading restored soils may be more susceptible to C loss during turnover of macroaggregates compared to the AG and NP soils with less macroaggregates.  相似文献   

12.
中亚热带四种森林土壤团聚体及其有机碳分布特征   总被引:7,自引:0,他引:7  
周纯亮  吴明 《土壤》2011,43(3):406-410
选择中亚热带地区4种典型森林类型:杉木林、湿地松林、毛竹林和次生林4种森林土壤为研究对象,研究了森林类型对土壤不同发生层水稳性团聚体及其有机碳分布特征的影响。结果表明:不同森林类型对>5 mm和2~5 mm土壤团聚体含量影响显著(p<0.05),表现为次生林>杉木林>毛竹林>湿地松林,而在其他粒径无显著差异。0~30 cm土层内团聚体R0.25和MWD次生林显著高于其他人工林,杉木林次之,湿地松林和毛竹林最低,其他土层无显著差异。各森林类型同土层不同粒径团聚体中有机碳含量随粒径大小变化,团聚体粒径越小,有机碳含量越高。0~10 cm土层同粒径土壤团聚体有机碳含量从大到小依次是次生林、杉木林、湿地松林和毛竹林,而在其他土层各森林类型之间差异不显著。  相似文献   

13.
The increasing frequency and severity of wildfires has led to growing attention to the effects of fire disturbance on soil microbial communities and biogeochemical cycling. While many studies have examined fire impacts on plant communities, and a growing body of research is detailing the effects of fire on soil microbial communities, little attention has been paid to the interaction between plant recolonization and shifts in soil properties and microbial community structure and function. In this study, we examined the effect of a common post-fire colonizer plant species, Corydalis aurea, on soil chemistry, microbial biomass, soil enzyme activity and bacterial community structure one year after a major forest wildfire in Colorado, USA, in severely burned and lightly burned soils. Consistent with past research, we find significant differences in soil edaphic and biotic properties between severe and light burn soils. Further, our work suggests an important interaction between fire severity and plant effects by demonstrating that the recolonization of soils by C. aurea plants only has a significant effect on soil bacterial communities and biogeochemistry in severely burned soils, resulting in increases in percent nitrogen, extractable organic carbon, microbial biomass, β-glucosidase enzyme activity and shifts in bacterial community diversity. This work propounds the important role of plant colonization in succession by demonstrating a clear connection between plant colonization and bacterial community structure as well as the cycling of carbon in a post-fire landscape. This study conveys how the strength of plant–microbe interactions in secondary succession may shift based on an abiotic context, where plant effects are accentuated in harsher abiotic conditions of severe burn soils, with implications for bacterial community structure and enzyme activity.  相似文献   

14.
Land-use change can have significant impacts on soil conditions and microbial communities are likely to respond to these changes. However, such responses are poorly characterized as few studies have examined how specific changes in edaphic characteristics do, or do not, influence the composition of soil bacterial and fungal communities across land-use types. Soil samples were collected from four replicated (n = 3) land-use types (hardwood and pine forests, cultivated and livestock pasture lands) in the southeastern US to assess the effects of land-use change on microbial community structure and distribution. We used quantitative PCR to estimate bacterial–fungal ratios and clone libraries targeting small-subunit rRNA genes to independently characterize the bacterial and fungal communities. Although some soil properties (soil texture and nutrient status) did significantly differ across land-use types, other edaphic factors (e.g., pH) did not vary consistently with land-use. Bacterial–fungal ratios were not significantly different across the land-uses and distinct land-use types did not necessarily harbor distinct soil fungal or bacterial communities. Rather, the composition of bacterial and fungal communities was most strongly correlated with specific soil properties. Soil pH was the best predictor of bacterial community composition across this landscape while fungal community composition was most closely associated with changes in soil nutrient status. Together these results suggest that specific changes in edaphic properties, not necessarily land-use type itself, may best predict shifts in microbial community composition across a given landscape. In addition, our results demonstrate the utility of using sequence-based approaches to concurrently analyze bacterial and fungal communities as such analyses provide detailed phylogenetic information on individual communities and permit the robust assessment of the biogeographical patterns exhibited by soil microbial communities.  相似文献   

15.
16.
通过在苏北滩涂地区开展田间试验,研究了不同施肥处理(不施肥、施农家肥、商品有机肥、无机肥)对滩涂地区围垦农田土壤有机碳及团聚体有机碳的影响。结果表明,与对照相比,不同施肥处理均能明显增加0~30 cm土层土壤有机碳含量和有机碳密度,施农家肥增加幅度最高,增加值分别为0.66 g kg-1和0.07 kg m-2。试验地区水稳性团聚体以5 mm和0.25~0.5 mm为主,含量分别为37%~57%和13%~20%;随着土层深度增加,5 mm团聚体含量降低,0.25~0.5 mm团聚体则增加;农家肥能显著增加5 mm团聚体含量,同时降低0.25~5 mm团聚体含量。团聚体中有机碳含量表现为,除0.25~0.5 mm团聚体外,5 mm至0.5~1 mm团聚体之间,粒径越小,有机碳含量越高,其中0.5~1 mm团聚体有机碳含量最高,为6.83 g kg-1;与其他处理相比,农家肥的施用能明显增加各粒级团聚体中有机碳含量。试验地区土壤有机碳含量与5 mm团聚体及其有机碳含量极显著正相关(p0.01),而与0.25~5 mm团聚体负相关(p0.01或p0.05)。  相似文献   

17.
受枸杞道地产区土地资源等因素限制,连作障碍已成为影响枸杞产业发展的重要原因之一,导致严重的经济损失.研究连作条件下枸杞农田土壤生态系统微生物群落的演替规律对枸杞产业的可持续发展具有重要的理论意义.以宁夏银川市南梁农场连作多年的枸杞地为研究对象,利用Illumina MiSeq测序技术分析了连作对再植枸杞根际/非根际细菌群落的影响.结果表明,连作地显著抑制再植枸杞苗地径的增加,且其土壤pH较对照样地显著降低(p<0.05).测序结果证实,与对照样地相比,连作地再植枸杞根际土壤细菌物种数显著降低(p<0.05),细菌群落α多样性下降(p>0.05).主坐标分析表明,连作和对照样地间枸杞非根际细菌群落结构无明显差异,但连作显著改变再植枸杞根际细菌的群落结构.对细菌群落丰度的统计分析发现,连作地枸杞根际浮霉菌门、非根际假单胞菌门的相对丰度较对照样地显著降低(p<0.05).此外,冗余分析结果表明:枸杞园土壤pH和有效磷含量是影响枸杞非根际土壤细菌群落结构变化的主要因素,分别解释了41.8%和35.4%的群落结构变化(p<0.05),其他土壤因子无统计学意义,但土壤理化因子对再植枸杞根际细菌群落结构变化的影响均未达显著水平.这些结果证实连作能够显著抑制再植枸杞生长、影响再植枸杞根际细菌群落结构和多样性,干扰枸杞与土壤细菌群落间的互作关系.这些研究结果将为解析枸杞连作障碍机制提供理论基础.  相似文献   

18.
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   

19.
为研究不同深度土壤控水对壤土稻田土壤水势、微生物区系和细菌群落多样性的影响,通过土培池栽试验,在水稻生育后期设置土壤深度0~5 cm(S05)、0~10 cm(S10)和0~15 cm(S15)控水处理,以保持水层为对照,分析了不同深度控水处理下5 cm、10 cm、15 cm深土壤水势与土壤微生物区系、细菌群落多样性的变化。结果表明:土壤5 cm、10 cm、15 cm深度的水势随着控水深度增加而降低,S05控水处理主要影响上层(5 cm)土壤水势,S10控水处理影响上、中层(10 cm)土壤水势,S15控水处理土壤水势随土层深度的增加而升高。花后8 d和32 d,S05控水处理上层土壤细菌数量显著高于S10、S15控水处理;花后16~24 d,S05控水处理中层、下层(15 cm)土壤细菌数量均显著高于S15控水处理;土壤水势与水稻生育后期中、下层土壤细菌数量呈极显著正相关关系。S05控水处理10 cm、15 cm土层的细菌丰富度Chao指数均显著高于S15控水处理及CK。3个控水处理中,5 cm土层细菌的多样性Shannon指数以S05控水处理最低。优势细菌菌群分析发现,优势群落主要为变形菌门、绿弯菌门、酸杆菌门、拟杆菌门,四者总相对丰度在80%以上;S15控水处理中层土壤变形菌门相对丰度低于S05和S10控水处理。3个控水处理土壤样品中优势纲(相对丰度大于2%)达15个,主要包括α-变形菌纲、β-变形菌纲、δ-变形菌纲、厌氧绳菌纲等,这4个纲的总相对丰度在47%以上,其中厌氧绳菌纲相对丰度最高;上层土壤中S05控水处理的β-变形菌纲相对丰度显著低于S10和S15控水处理。因此,不同深度土壤控水对壤土土壤水势、细菌数量存在影响,改变了细菌的多样性及丰富度,对土壤细菌优势菌种类无显著影响。  相似文献   

20.
Fourteen agricultural soils from various areas of Tuscany were characterized by a range of measurements indicative of soil biological activity. The objective of our research was to identify soil parameters suitable as indicators for evaluating their quality. In general, enzyme activities were found to vary widely, with the highest activity for each enzyme being distributed among only five of the 14 soils studied. The narrowest range (14-fold) in enzyme activities for the various soils was observed for catalase and the widest range (577-fold) for g -glucosidase. Biomass C and, among the measured enzyme activities, amylase, were well correlated with total organic carbon, total N, cation and anion exchange capacity. Positive correlations were found between the maximum water holding capacity and dehydrogenase, amylase, biomass C, FDA hydrolytic activity, the biological index of fertility and the enzyme activity number, so showing that soil moisture may play an important role in affecting soil biological characteristics. No significant correlations were observed among the soil enzymes themselves. The FDA hydrolytic activity appeared to be the index most related with the other biological characteristics tested in this study and, for this reason, can be considered the most effective index for putting in evidence relationships existing between the different biological characteristics in the soils investigated.  相似文献   

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