Bacterial communities associated with the rhizosphere of transgenic Bt 176 maize (Zea mays) and its non transgenic counterpart

The effect of transgenic Bt 176 maize on the rhizosphere bacterial community has been studied with a polyphasic approach by comparing the rhizosphere of Bt maize cultivated in greenhouse with that of its non transgenic counterpart grown in the same conditions. In the two plants the bacterial counts of the copiotrophic, oligotrophic and sporeforming bacteria, and the community level catabolic profiling, showed no significant differences; differences between the rhizosphere and bulk soil bacterial communities were evidenced. Automated ribosomal intergenic spacer analysis (ARISA) showed differences also in the rhizosphere communities at different plant ages, as well as between the two plant types. ARISA fingerprinting patterns of soil bacterial communities exposed to root growth solutions, collected from transgenic and non transgenic plants grown in hydroponic conditions, were grouped separately by principal component analysis suggesting that root exudates could determine the selection of different bacterial communities.     

Does disturbance and restoration of alpine grassland soils affect the genetic structure and diversity of bacterial and N2-fixing populations?

Responses of bacterial communities to disturbance and restoration processes were investigated on alpine grassland soil. Bulk soil, rhizosphere soil and two soil separates, i.e. sand-size (2000-200 microm) and silt-size (50-2 microm) were sampled from undisturbed grassland soil to soil under restoration for 1 month, 1 year, 4 years and 13 years after disturbance. Automated ribosomal intergenic spacer analysis (ARISA) and restriction fragment length polymorphism (RFLP) of nifH gene pools were used to assay genetic structure of the bacterial communities and N2-fixing guild. According to the distribution of ARISA band length in bacterial phyla, the dominance of ARISA bands below 400 bp showed that Gram-positive bacteria would be predominant in the studied grassland soil when not disturbed. Disturbance affected the genetic structure of bacterial community and of N2-fixing guild in relation to their location within the selected habitats. Shifts in IGS and nifH profiles of bulk soil metagenome were larger than those observed from sand-size- and silt-size-fractions, accounting for 40-50% of the variance in the profiles. Restoration of the genetic structure of telluric bacteria community and N2-fixing populations was found to be influenced by the spatial heterogeneity of the soil and niche diversification. Particular bacterial genetic structure within distinct habitats were evidenced and must be defined as subdivisions of the meta-community of bulk soil. Scale of soil microbial diversity/stability relationships is discussed with special attention to disconnected bacterial habitat compared with whole soil with multiple niches.     

Bacterial community diversity assessment in municipal solid waste compost amended soil using DGGE and ARISA fingerprinting methods

Bacterial community structure and diversity of Tunisian agricultural soil treated with different amounts of municipal solid waste compost (MSWC) and other fertilizers were studied using DGGE and ARISA fingerprinting methods. Sequence analysis of dominant DGGE bands revealed the presence of three major clusters, Cytophaga/Flexibacter/Bacteroides (CFB) group, Proteobacteria and Acidobacteria group. Using ARISA profiles, dominant populations were assigned to low and high GC Gram positive bacteria, Cyanobacteria, Spirochetes and Cytophagales. The two methods revealed the absence of significant bacterial community shifts related to the different MSWC applications. Moreover, indigenous bacterial population of the used loam-clayey soil was observed to limit proliferation and survival of Proteobacteria, initially dominant in MSWC and farmyard manure. Effectiveness of the two methods for soil bacterial community studying was shown. While DGGE was more accurate for bacterial identification, ARISA was more practical for handling and rapid estimation of dominant bacteria.     

Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.     

Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.     

NESTED AUTOMATED RIBOSOMAL INTERGENIC SPACER ANALYSIS: A RAPID AND ACCURATE METHOD FOR COMPARISON OF BACTERIAL COMMUNITY COMPOSITION

Nested automated ribosomal intergenic spacer analysis (ARISA) was used to examine the community structure of epilithic biofilms in freshwater streams experiencing different levels of human impact. This molecular fingerprinting technique generated reproducible profiles of bacterial community structure that varied significantly between stream sites. Nested ARISA was determined to be a cost-effective, high-throughput approach to assess bacterial community composition from very small sample volumes, requiring little sampling effort and without the need for taxonomic identification of individual organisms. In combination with multidimensional scaling, nested ARISA provides a rapid and sensitive method to carry out complex analyses of bacterial community structure.

PRACTICAL APPLICATIONS

Nested automated ribosomal intergenic spacer analysis (ARISA) provides a high-throughput molecular method with which to screen large numbers of environmental samples for differences in microbial community structure. This sensitive approach benefits assessments from small sample volumes or environments exhibiting reduced microbial biomass (both aquatic and terrestrial). Differences in bacterial community structure (obtained from ARISA profiles) could be used to characterize the impact of anthropogenic disturbance on freshwater systems, analogous to the current use of macroinvertebrate indicators of freshwater ecological health.     

Response of Soil Bacterial Community Structure to Permafrost Degradation in the Upstream Regions of the Shule River Basin,Qinghai–Tibet Plateau

Permafrost degradation affects soil properties and vegetation, but little is known about its consequent effects on the soil bacterial community. In this study, we analyzed the bacterial community structure of 12 permafrost-affected soil samples from four principal permafrost types, sub-stable permafrost (SSP), transition permafrost (TP), unstable permafrost (UP) and extremely unstable permafrost (EUP), to investigate the effects of vegetation characteristics and soil properties on bacterial community structure during the process of permafrost degradation. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the predominant phyla in all four permafrost soil types. The relative abundance of Proteobacteria decreased in the order SSP > TP> UP > EUP, whereas the abundance of Actinobacteria increased in the order SSP < TP < UP < EUP. Moreover, the Actinobacteria/Proteobacteria ratio increased significantly in the order SSP < TP < UP < EUP along with permafrost degradation, which may be useful as a sign of permafrost degradation. Redundancy analysis (RDA) showed that bacterial communities could be clustered by permafrost types. Analysis of single factors revealed that soil moisture (SM) was the most important factor affecting the bacterial community structure and diversity, followed by soil total nitrogen (STN) and vegetation cover (VC). Partial RDA analysis showed that the soil properties and vegetation characteristics jointly shaped the bacterial community structure. Hence, we can conclude that permafrost degradation, caused by global warming, affects vegetation and soil properties and consequently drives changes in the soil bacterial community structure.     

Impact of catchment land use on bacterial communities within stream biofilms

The bacterial community structure in epilithic biofilms within 18 different streams was characterised using a community DNA fingerprinting technique (automated ribosomal intergenic spacer analysis—ARISA). Each stream has previously been described in terms of the dominant catchment land use, relative level of human disturbance and using a broad suite of water quality variables. Combination of ARISA with multivariate statistical analysis and ordination revealed that bacterial communities in streams located within rural catchments were significantly different to those within urban catchments. Broad-scale catchment land use described the largest component of the observed variation with no single water quality variable found to be a dominant determinant of the observed bacterial community variability, assessed using distance based redundancy analysis (dbRDA) of the ARISA data. This study highlights the potential of bacterial ARISA to provide a rapid and cost-effective approach to monitor the impact of catchment land use on aquatic ecosystems, such as the influence of encroaching urban development on the ecological health of rural streams.     

Moderate Warming in Microcosm Experiment Does Not Affect Microbial Communities in Temperate Vineyard Soils

Changes in the soil microbial community structure can lead to dramatic changes in the soil ecosystem. Temperature, which is projected to increase with climate change, is commonly assumed to affect microbial communities, but its effects on agricultural soils are not fully understood. We collected soil samples from six vineyards characterised by a difference of about 2 °C in daily soil temperature over the year and simulated in a microcosm experiment different temperature regimes over a period of 1 year: seasonal fluctuations in soil temperature based on the average daily soil temperature measured in the field; soil temperature warming (2 °C above the normal seasonal temperatures); and constant temperatures normally registered in these temperate soils in winter (3 °C) and in summer (20 °C). Changes in the soil bacterial and fungal community structures were analysed by automated ribosomal intergenic spacer analysis (ARISA). We did not find any effect of warming on soil bacterial and fungal communities, while stable temperatures affected the fungal more than the bacterial communities, although this effect was soil dependent. The soil bacterial community exhibited soil-dependent seasonal fluctuations, while the fungal community was mainly stable. Each soil harbours different microbial communities that respond differently to seasonal temperature fluctuations; therefore, any generalization regarding the effect of climate change on soil communities should be made carefully.     

Microbial biodiversity of thermophilic communities in hot mineral soils of Tramway Ridge, Mount Erebus, Antarctica

Tramway Ridge, located near the summit of Mount Erebus in Antarctica, is probably the most remote geothermal soil habitat on Earth. Steam fumaroles maintain moist, hot soil environments creating extreme local physicochemical differentials. In this study a culture-independent approach combining automated rRNA intergenic spacer analysis (ARISA) and a 16S rRNA gene library was used to characterize soil microbial (Bacterial and Archaeal) diversity along intense physicochemical gradients. Statistical analysis of ARISA data showed a clear delineation between bacterial community structure at sites close to fumaroles and all other sites. Temperature and pH were identified as the primary drivers of this demarcation. A clone library constructed from a high-temperature site led to the identification of 18 novel bacterial operational taxonomic units (OTUs). All 16S rRNA gene sequences were deep branching and distantly (85–93%) related to other environmental clones. Five of the signatures branched with an unknown group between candidate division OP10 and Chloroflexi . Within this clade, sequence similarity was low, suggesting it contains several yet-to-be described bacterial groups. Five archaeal OTUs were obtained and exhibited high levels of sequence similarity (95–97%) with Crenarchaeota sourced from deep-subsurface environments on two distant continents. The novel bacterial assemblage coupled with the unique archaeal affinities reinvigorates the hypotheses that Tramway Ridge organisms are relics of archaic microbial lineages specifically adapted to survive in this harsh environment and that this site may provide a portal to the deep-subsurface biosphere.     

Seasonal and management influences on bacterial community structure in an upland grassland soil

Floristically diverse Nardo-Galion upland grasslands are common in Ireland and the UK and are valuable in agricultural, environmental and ecological terms. Under improvement (inputs of lime, fertiliser and re-seeding), they convert to mesotrophic grassland containing very few plant species. The effects of upland grassland improvement and seasonality on soil microbial communities were investigated at an upland site. Samples were taken at five times in one year in order to observe seasonal trends, and bacterial community structure was monitored using automated ribosomal intergenic spacer analysis (ARISA), a DNA-fingerprinting approach. Differences in soil chemistry and bacterial community structure between unimproved and improved grassland soils were noted. Season was also found to cause mild fluctuations in bacterial community structure, with soil samples from colder months (October and December) more correlated with change in ribotype profiles than samples from warmer months. However, for the majority of seasons clear differences in bacterial community structures from unimproved and improved soils could be seen, indicating seasonal influences did not obscure effects associated with improvement.     

Drivers of bacterial diversity dynamics in permeable carbonate and silicate coral reef sands from the Red Sea

Permeable sediments and associated microbial communities play a fundamental role in nutrient recycling within coral reef ecosystems by ensuring high levels of primary production in oligotrophic environments. A previous study on organic matter degradation within biogenic carbonate and terrigenous silicate reef sands in the Red Sea suggested that observed sand-specific differences in microbial activity could be caused by variations in microbial biomass and diversity. Here, we tested this hypothesis by comparing bacterial abundance and community structure in both sand types, and by further exploring the structuring effects of time (season) and space (sediment depth, in/out-reef). Changes in bacterial community structure, as determined via automated ribosomal intergenic spacer analysis (ARISA), were primarily driven by sand mineralogy at specific seasons, sediment depths and reef locations. By coupling ARISA with 16S-ITS rRNA sequencing, we detected significant community shifts already at the bacterial class level, with Proteobacteria (Gamma-, Delta-, Alpha-) and Actinobacteria being prominent members of the highly diverse communities. Overall, our findings suggest that reef sand-associated bacterial communities vary substantially with sand type. Especially in synergy with environmental variation over time and space, mineralogical differences seem to play a central role in maintaining high levels of bacterial community heterogeneity. The local co-occurrence of carbonate and silicate sands may thus significantly increase the availability of microbial niches within a single coral reef ecosystem.     

Structural diversity of bacterial communities in a heavy metal mineralized granite outcrop

This laboratory study of a variably mineralized and hydrothermally altered granite outcrop investigated the influences of rock-surface chemistry and heavy metal content on resident bacterial populations. Results indicated that elevated heavy metal concentrations had a profound impact on bacterial community structure, with strong relationships found between certain ribotypes and particular chemical/heavy metal elements. Automated ribosomal intergenic sequence analysis (ARISA) was used to assess the nature and extent of bacterial diversity, and this was combined with chemical analysis and multivariate statistics to identify the main geochemical factors influencing bacterial community structure. A randomization test revealed significant changes in bacterial structure between samples, while canonical correspondence analysis (CCA) related each individual ARISA profile to linear combinations of the chemical variables (mineralogy, major element and heavy metal concentrations) revealing the geochemical factors that correlated with changes in the ARISA data. anova was performed to further explore interactions between individual ribotypes and chemical/heavy metal composition, and revealed that a high proportion of ribotypes correlated significantly with heavy metals.     

植物群落和土壤理化性质对碧塔海湿地土壤细菌群落的影响

土壤微生物是湿地生态系统中土壤-植物系统生源要素迁移转化的引擎.探究湿地生态系统地上植物群落、土壤理化性质和空间结构与土壤细菌间的相互关系是维护湿地生态系统健康和稳定的关键.本研究运用双向指示种分析法(TWINSPAN)对碧塔海湿地采集的35个样方中的植物群落进行分类,并采用高通量测序技术对样方的表层土壤细菌进行测序,...     

Litter quality versus soil microbial community controls over decomposition: a quantitative analysis

The possible effects of soil microbial community structure on organic matter decomposition rates have been widely acknowledged, but are poorly understood. Understanding these relationships is complicated by the fact that microbial community structure and function are likely to both affect and be affected by organic matter quality and chemistry, thus it is difficult to draw mechanistic conclusions from field studies. We conducted a reciprocal soil inoculum × litter transplant laboratory incubation experiment using samples collected from a set of sites that have similar climate and plant species composition but vary significantly in bacterial community structure and litter quality. The results showed that litter quality explained the majority of variation in decomposition rates under controlled laboratory conditions: over the course of the 162-day incubation, litter quality explained nearly two-thirds (64 %) of variation in decomposition rates, and a smaller proportion (25 %) was explained by variation in the inoculum type. In addition, the relative importance of inoculum type on soil respiration increased over the course of the experiment, and was significantly higher in microcosms with lower litter quality relative to those with higher quality litter. We also used molecular phylogenetics to examine the relationships between bacterial community composition and soil respiration in samples through time. Pyrosequencing revealed that bacterial community composition explained 32 % of the variation in respiration rates. However, equal portions (i.e., 16 %) of the variation in bacterial community composition were explained by inoculum type and litter quality, reflecting the importance of both the meta-community and the environment in bacterial assembly. Taken together, these results indicate that the effects of changing microbial community composition on decomposition are likely to be smaller than the potential effects of climate change and/or litter quality changes in response to increasing atmospheric CO₂ concentrations or atmospheric nutrient deposition.     

Soil Bacterial and Fungal Community Structure Across a Range of Unimproved and Semi-Improved Upland Grasslands

Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects.     

Role of exogenous nitric oxide in alleviating iron deficiency-induced peanut chlorosis on calcareous soil

This study examined the effects of exogenous nitric oxide (NO) on physiological characteristics of peanut (Arachis hypogaea L.) growing on calcareous soil. Sodium nitroprusside (SNP), a NO donor, was root application (directly; slow-release bag; slow-release capsule; slow-release particle) and foliar application. The results showed that SNP application alleviated iron (Fe) deficiency-induced chlorosis, increased the yield of peanut and increased the Fe concentration in peanut grain. SNP, especially supplied by slow-release particle improved the available Fe in soil by reducing pH of soil and increasing available Fe of soil. Furthermore, SNP application significantly increased the H⁺-ATPase and Fe³⁺ reductase activities and increased the total Fe concentration in the leaves. Meanwhile, SNP application, especially foliar application enhanced the availability of Fe in the plant by significantly increasing the active Fe content and chlorophyll content in the leaves. In addition, SNP also increased the antioxidant activities, but decreased the superoxide anion (O₂^??) generation rate and malondialdehyde content, which protected peanut against the Fe deficiency-induced oxidative stress. Therefore, these results support a physiological action of SNP on the availability, uptake and transport of Fe in the plant and foliar application SNP had the best effects in leaves and SNP supplied by slow-release particle had the best effects in roots. In addition, on the whole, the effects of SNP supplied by slow-release ways were better than directly supplied into the soil.     

文峪河上游河岸带不同植被类型土壤nirS反硝化菌群结构及功能

以文峪河上游河岸带不同演替阶段的8种植被类型五花草甸(WH)、沙棘林(HR)、柳树林(SS)、山杨林(PC)、山杨白桦林(PQ)、山杨白桦落叶松林(PQL)、落叶松云杉林(LP)和云杉林(PM)土壤为研究对象,采用高通量测序技术测定nirS反硝化细菌群落组成及相对丰度,乙炔抑制法测定反硝化酶活性(DEA)。对其土壤理化性质及反硝化细菌群落组成及相对丰度进行方差分析,采用冗余分析(RDA)和Spearman相关性分析不同植被类型及土层反硝化细菌群落结构及功能及土壤理化因子的关联性。结果表明:1)不同植被类型及土层土壤理化因子存在显著差异,柳树林(SS)0—15 cm土层硝态氮(NO~+_3-N)含量显著高于其他植被类型各土层;2)土壤反硝化菌群多样性指数在五花草甸(WH)、山杨白桦林(PQ)和云杉林(PM)中较其他植被类型高;3)沙棘林(HR)及柳树林(SS)反硝化酶活性(DEA)显著高于其他植被类型;4)不同植被类型反硝化优势菌群分布存在显著差异及特异性,如浮霉菌门(Planctomycetes)仅在落叶松云杉混交林(LP)和云杉林(PM)植被类型15—30 cm土层中分布;5)土壤pH、土壤有机碳(SOC)、土壤铵态氮(NH~+_4-N)和硝态氮(NO~+_3-N)等是影响土壤反硝化细菌群落结构及组成的重要因子,其中土壤铵态氮和硝态氮含量变化是导致土壤反硝化菌群多样性和反硝化酶活性差异的关键因子。本研究揭示了文峪河上游河岸带不同植被类型土壤反硝化细菌群落结构及功能的变化和分布特征,为进一步研究该区域河岸带氮素循环及水体污染防治提供重要参考依据。     

Soil microbial community successional patterns during forest ecosystem restoration

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.