The effect of the native bacterial community structure on the predictability of E. coli O157:H7 survival in manure‐amended soil

Aims: The survival capability of pathogens like Escherichia coli O157:H7 in manure‐amended soil is considered to be an important factor for the likelihood of crop contamination. The aim of this study was to reveal the effects of the diversity and composition of soil bacterial community structure on the survival time (ttd) and stability (irregularity, defined as the intensity of irregular dynamic changes in a population over time) of an introduced E. coli O157:H7 gfp‐strain were investigated for 36 different soils by means of bacterial PCR‐DGGE fingerprints. Methods and Results: Bacterial PCR‐DGGE fingerprints made with DNA extracts from the different soils using bacterial 16S‐rRNA‐gene‐based primers were grouped by cluster analysis into two clusters consisting of six and 29 soils and one single soil at a cross‐correlation level of 16% among samples per cluster. Average irregularity values for E. coli O157:H7 survival in the same soils differed significantly between clusters (P = 0·05), whereas no significant difference was found for the corresponding average ttd values (P = 0·20). The irregularity was higher for cluster 1, which consisted primarily of soils that had received liquid manure and artificial fertilizer and had a significant higher bacterial diversity and evenness values (P < 0·001). Conclusions: Bacterial PCR‐DGGE fingerprints of 36 manure‐amended soils revealed two clusters which differed significantly in the stability (irregularity) of E. coli O157 decline. The cluster with the higher irregularity was characterized by higher bacterial diversity and evenness. Significance and Impact of the Study: The consequence of a high temporal irregularity is a lower accuracy of predictions of population behaviour, which results in higher levels of uncertainty associated with the estimates of model parameters when modelling the behaviour of E. coli O157:H7 in the framework of risk assessments. Soil community structure parameters like species diversity and evenness can be indicative for the reliability of predictive models describing the fate of pathogens in (agricultural) soil ecosystems.     

Patterns of diversity and adaptation in Glomeromycota from three prairie grasslands

Arbuscular mycorrhizal (AM) fungi are widespread root symbionts that often improve the fitness of their plant hosts. We tested whether local adaptation in mycorrhizal symbioses would shape the community structure of these root symbionts in a way that maximizes their symbiotic functioning. We grew a native prairie grass (Andropogon gerardii) with all possible combinations of soils and AM fungal inocula from three different prairies that varied in soil characteristics and disturbance history (two native prairie remnants and one recently restored). We identified the AM fungi colonizing A. gerardii roots using PCR amplification and cloning of the small subunit rRNA gene. We observed 13 operational taxonomic units (OTUs) belonging to six genera in three families. Taxonomic richness was higher in the restored than the native prairies with one member of the Gigaspora dominating the roots of plants grown with inocula from native prairies. Inoculum source and the soil environment influenced the composition of AM fungi that colonized plant roots. Correspondingly, host plants and AM fungi responded significantly to the soil–inoculum combinations such that home fungi often had the highest fitness and provided the greatest benefit to A. gerardii. Similar patterns were observed within the soil–inoculum combinations originating from two native prairies, where five sequence types of a single Gigaspora OTU were virtually the only root colonizers. Our results indicate that indigenous assemblages of AM fungi were adapted to the local soil environment and that this process occurred both at a community scale and at the scale of fungal sequence types within a dominant OTU.     

Wolbachia infection alters the relative abundance of resident bacteria in adult Aedes aegypti mosquitoes,but not larvae

Insect–symbiont interactions are known to play key roles in host functions and fitness. The common insect endosymbiont Wolbachia can reduce the ability of several human pathogens, including arboviruses and the malaria parasite, to replicate in insect hosts. Wolbachia does not naturally infect Aedes aegypti, the primary vector of dengue virus, but transinfected Ae. aegypti have antidengue virus properties and are currently being trialled as a dengue biocontrol strategy. Here, we assess the impact of Wolbachia infection of Ae. aegypti on the microbiome of wild mosquito populations (adults and larvae) collected from release sites in Cairns, Australia, by profiling the 16S rRNA gene using next‐generation sequencing. Our data indicate that Wolbachia reduces the relative abundance of a large proportion of bacterial taxa in Ae. aegypti adults, that is in accordance with the known pathogen‐blocking effects of Wolbachia on a variety of bacteria and viruses. In adults, several of the most abundant bacterial genera were found to undergo significant shifts in relative abundance. However, the genera showing the greatest changes in relative abundance in Wolbachia‐infected adults represented a low proportion of the total microbiome. In addition, there was little effect of Wolbachia infection on the relative abundance of bacterial taxa in larvae, or on species diversity (accounting for species richness and evenness together) detected in adults or larvae. These results offer insight into the effects of Wolbachia on the Ae. aegypti microbiome in a native setting, an important consideration for field releases of Wolbachia into the population.     

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical–chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha‐ and Gamma‐Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta‐Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near‐surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw.     

Change in Bacterial Community Structure in Response to Disturbance of Natural Hardwood and Secondary Coniferous Forest Soils in Central Taiwan

Forest management often results in changes in the soil and its microbial communities. In the present study, differences in the soil bacterial community caused by forest management practices were characterized using small subunit (SSU) ribosomal RNA (rRNA) gene clone libraries. The communities were from a native hardwood forest (HWD) and two adjacent conifer plantations in a low-elevation montane, subtropical experimental forest at the Lienhuachi Experimental Forest (LHCEF) in central Taiwan. At this locality, the elevation ranges from 600 to 950 m, the mean annual precipitation is 2,200 mm, the mean annual temperature is 20.8°C, and the soil pH is 4. The conifer forests included a Cunninghamia konishii Hay (CNH) plantation of 40 years and an old growth Calocedrus formosana (Florin) Florin (CLC) forest of 80 years. A total of 476 clones were sequenced and assigned into 12 phylogenetic groups. Proteobacteria-affiliated clones (53%) predominated in the library from HWD soils. In contrast, Acidobacteria was the most abundant phylum and comprised 39% and 57% in the CLC and CNH libraries, respectively. Similarly, the most abundant OTUs in HWD soils were greatly reduced or absent in the CLC and CNH soils. Based on several diversity indices, the numbers of abundant OTUs and singletons, and rarefaction curves, the diversity of the HWD community (0.95 in evenness and Shannon diversity indices) was somewhat less than that in the CNH soils (0.97 in evenness and Shannon diversity indices). The diversity of the community in CLC soils was intermediate. The differences in diversity among the three communities may also reflect changes in abundances of a few OTUs. The CNH forest soil community may be still in a successional phase that is only partially stabilized after 40 years. Analysis of molecular variance also revealed that the bacterial community composition of HWD soils was significantly different from CLC and CNH soils (p = 0.001). These results suggest that the disturbance of forest conversion and tree species composition are important factors influencing the soil bacterial community among three forest ecosystems in the same climate.     

Soil conditioning effects of Phragmites australis on native wetland plant seedling survival

Interactions between introduced plants and soils they colonize are central to invasive species success in many systems. Belowground biotic and abiotic changes can influence the success of introduced species as well as their native competitors. All plants alter soil properties after colonization but, in the case of many invasive plant species, it is unclear whether the strength and direction of these soil conditioning effects are due to plant traits, plant origin, or local population characteristics and site conditions in the invaded range. Phragmites australis in North America exists as a mix of populations of different evolutionary origin. Populations of endemic native Phragmites australis americanus are declining, while introduced European populations are important wetland invaders. We assessed soil conditioning effects of native and non‐native P. australis populations on early and late seedling survival of native and introduced wetland plants. We further used a soil biocide treatment to assess the role of soil fungi on seedling survival. Survival of seedlings in soils colonized by P. australis was either unaffected or negatively affected; no species showed improved survival in P. australis‐conditioned soils. Population of P. australis was a significant factor explaining the response of seedlings, but origin (native or non‐native) was not a significant factor. Synthesis: Our results highlight the importance of phylogenetic control when assessing impacts of invasive species to avoid conflating general plant traits with mechanisms of invasive success. Both native (noninvasive) and non‐native (invasive) P. australis populations reduced seedling survival of competing plant species. Because soil legacy effects of native and non‐native P. australis are similar, this study suggests that the close phylogenetic relationship between the two populations, and not the invasive status of introduced P. australis, is more relevant to their soil‐mediated impact on other plant species.     

Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding

Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m⁻¹ and pH 7.80 (LOW soil), with EC 56 dS m⁻¹ and pH 10.11 (MEDIUM soil) and with EC 159 dS m⁻¹ and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the α- and γ-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.     

Fungi recovered from root-knot nematodes infecting vegetables under protected cultivation

A survey was conducted in root-knot nematode-infested plastic houses to determine the diversity and frequency of occurrence of fungi associated with the nematode. The relationships between percentage fungal parasitism and physicochemical properties of soil were also investigated. Fifty-nine plastic houses were sampled in southeastern Spain, 42 treated with nematicides and 17 left untreated. Eleven fungal genera and unidentified fungi were isolated from nematode eggs or juveniles. Fungal parasitism occurred more frequently in untreated (82.4%) than treated (50%) soils. The species richness in untreated soils ranged from 0 to 5, the Shannon–Wiener diversity index (a measurement of how many different fungi there are in site taking into account how evenly they are distributed among the site) from 0 to 2.01, and the evenness index from 0.46 to 0.99. In treated soils, species richness ranged from 0 to 4, the Shannon–Wiener diversity index from 0 to 1.61, and the evenness index from 0.81 to 1. Of the sites with nematophagous fungi, Arthrobotrys dactyloides (34%), Cylindrocarpon sp., Neosartoria hiratsukae (17%), and Fusarium solani (14%) were the fungi most frequently found. Physicochemical properties of soil were similar in nematicide treated and untreated soils. Percent fungal parasitism in untreated soils correlated positively with lime, silt and carbonate content of soil.     

Impacts of invasive annuals on soil carbon and nitrogen storage in southern California depend on the identity of the invader

Non‐native plant invasions can alter nutrient cycling processes and contribute to global climate change. In southern California, California sage scrub (hereafter sage scrub), a native shrub‐dominated habitat type in lowland areas, has decreased to <10% of its original distribution. Postdisturbance type‐conversion to non‐native annual grassland, and increasingly to mustard‐dominated invasive forbland, is a key contributor to sage scrub loss. To better understand how type‐conversion by common invasive annuals impacts carbon (C) and nitrogen (N) storage in surface soils, we examined how the identity of the invader (non‐native grasses, Bromus spp.; and non‐native forbs, Brassica nigra), microbial concentrations, and soil properties interact to influence soil nutrient storage in adjacent native and invasive habitat types at nine sites along a coast to inland gradient. We found that the impact of type‐conversion on nutrient storage was contingent upon the invasive plant type. Sage scrub soils stored more C and N than non‐native grasslands, whereas non‐native forblands had nutrient storage similar to or higher than sage scrub. We calculate that >940 t C km^?2 and >60 t N km^?2 are lost when sage scrub converts to grass‐dominated habitat, demonstrating that grass invasions are significant regional contributors to greenhouse gas emissions. We found that sites with greater total C and N storage were associated with high cation exchange capacities and bacterial concentrations. Non‐native grassland habitat type was a predictor of lower total C, and soil pH, which was greatest in invasive habitats, was a predictor of lower total N. We demonstrate that modeling regional nutrient storage requires accurate classification of habitat type and fine‐scale quantification of cation exchange capacity, pH, and bacterial abundance. Our results provide evidence that efforts to restore and conserve sage scrub enhance nutrient storage, a key ecosystem service reducing atmospheric CO₂ concentrations.     

Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem

Biofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third‐order stream at Konza Prairie over a 2‐ to 64‐day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations) increased and never plateaued during the experiment. Net primary productivity (net balance of oxygen consumption and production) of the developing biofilms did not differ statistically from zero until 64 days suggesting a balance of the use of autochthonous and allochthonous energy sources until late succession. Bacterial communities (MiSeq analyses of the V4 region of 16S rRNA) established quickly. Bacterial richness, diversity and evenness were high after 2 days and increased over time. Several dominant bacterial phyla (Beta‐, Alphaproteobacteria, Bacteroidetes, Gemmatimonadetes, Acidobacteria, Chloroflexi) and genera (Luteolibacter, Flavobacterium, Gemmatimonas, Hydrogenophaga) differed in relative abundance over space and time. Bacterial community composition differed across both space and successional time. Pairwise comparisons of phylogenetic turnover in bacterial community composition indicated that early‐stage succession (≤16 days) was driven by stochastic processes, whereas later stages were driven by deterministic selection regardless of site. Our data suggest that microbial biofilms predictably develop both functionally and structurally indicating distinct successional trajectories of bacterial communities in this ecosystem.     

BIODIVERSITY RESEARCH: Experimental introduction of the alien plant Hieracium lepidulum reveals no significant impact on montane plant communities in New Zealand

Aim There is debate over whether alien plants necessarily alter the communities they invade or can coexist with native species without discernable impacts. We followed the fate of montane plant communities in response to the experimental sowing of the alien weed Hieracium lepidulum, looking for changes in plant community composition and structure over 6 years. Location Craigieburn Range, New Zealand. Methods We used a replicated randomised block design, with 30 × 30 cm plots (n = 756) subdivided into 5 × 5 cm cells to examine and compare the effects of H. lepidulum at 0.09 m² (plot) and 0.0025 m² (cell) scales. Plots were sown with between 0 and 15,625 H. lepidulum seeds in 2003, forming gradients of invader density and cover. Measurements comprised community richness, evenness and diversity along with H. lepidulum density and cover at both scales. The relationships between the invader and local community attributes were modelled using hierarchical mixed‐effect models. Results Plant communities differed in the extent to which they became invaded, with H. lepidulum cover in the plots ranging from 0% to 52%, with a mean of only 1.89%. Plot species richness increased from 2003 to 2009, with a component of this increase (+0.002 species per year) associated with increasing H. lepidulum density. Other relationships between the plant community and H. lepidulum were generally non‐significant. Main conclusions In these montane plant communities, it appears H. lepidulum coexists with the native community with no measurable negative effects after 6 years on species richness, evenness or diversity, even where density and cover of the invader are highest. We suggest H. lepidulum has persisted preferentially at those sites with abiotic conditions sufficient to support a species‐rich assemblage.     

Responses of the soil fungal communities to the co‐invasion of two invasive species with different cover classes

• Soil fungal communities play an important role in the successful invasion of non‐native species. It is common for two or more invasive plant species to co‐occur in invaded ecosystems.
• This study aimed to determine the effects of co‐invasion of two invasive species (Erigeron annuus and Solidago canadensis) with different cover classes on soil fungal communities using high‐throughput sequencing.
• Invasion of E. annuus and/or S. canadensis had positive effects on the sequence number, operational taxonomic unit (OTU) richness, Shannon diversity, abundance‐based cover estimator (ACE index) and Chao1 index of soil fungal communities, but negative effects on the Simpson index. Thus, invasion of E. annuus and/or S. canadensis could increase diversity and richness of soil fungal communities but decrease dominance of some members of these communities, in part to facilitate plant further invasion, because high soil microbial diversity could increase soil functions and plant nutrient acquisition. Some soil fungal species grow well, whereas others tend to extinction after non‐native plant invasion with increasing invasion degree and presumably time. The sequence number, OTU richness, Shannon diversity, ACE index and Chao1 index of soil fungal communities were higher under co‐invasion of E. annuus and S. canadensis than under independent invasion of either individual species.
• The co‐invasion of the two invasive species had a positive synergistic effect on diversity and abundance of soil fungal communities, partly to build a soil microenvironment to enhance competitiveness of the invaders. The changed diversity and community under co‐invasion could modify resource availability and niche differentiation within the soil fungal communities, mediated by differences in leaf litter quality and quantity, which can support different fungal/microbial species in the soil.

     

Deep 16S rRNA gene sequencing of anterior foregut microbiota from the blue‐green sharpshooter (Graphocephala atropunctata)

Graphocephala atropunctata or the blue‐green sharpshooter (BGSS) has been long recognized as the principal native vector of Xylella fastidiosa in coastal, wine‐grape‐growing areas of California. X. fastidiosa is the causative agent of Pierce's disease of grapevine and of numerous other leaf‐scorching diseases of agronomically important plants. X. fastidiosa has been shown to colonize the cibarium and precibarium (anterior foregut) of sharpshooters, where it may encounter other naturally occurring bacterial species. Here, deep 16S rRNA sequencing was used to survey the microbiota associated with the BGSS anterior foregut. DNA was extracted from dissected cibaria and precibaria; a portion of the 16S rRNA gene was amplified and sequenced using Illumina MiSeq technology. An average of approximately 32 000 sequence reads per insect was obtained. Agrobacterium was the most common genus detected; additional sequencing of the full‐length 16S rRNA gene further identified this as Agrobacterium tumefaciens or A. fabrum. A number of additional plant‐associated bacterial genera were also detected (Pseudomonas and Ensifer), along with genera known to be associated with insects (Baumannia), and soil (Stenotrophomonas, Caulobacter, Delftia, Achromobacter, Acinetobacter and Novosphingobium). Approximately half of the genera reported here have been previously reported to be prevalent in the cibarium and precibarium of glassy‐winged sharpshooter (GWSS; Homalodisca vitripennis). Many of these cibarium‐ and precibarium‐associated genera likely interact with X. fastidiosa.     

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield

Spatial patterns of microbial communities have been extensively surveyed in well‐developed soils, but few studies investigated the vertical distribution of micro‐organisms in newly developed soils after glacier retreat. We used 454‐pyrosequencing to assess whether bacterial and fungal community structures differed between stages of soil development (SSD) characterized by an increasing vegetation cover from barren (vegetation cover: 0%/age: 10 years), sparsely vegetated (13%/60 years), transient (60%/80 years) to vegetated (95%/110 years) and depths (surface, 5 and 20 cm) along the Damma glacier forefield (Switzerland). The SSD significantly influenced the bacterial and fungal communities. Based on indicator species analyses, metabolically versatile bacteria (e.g. Geobacter) and psychrophilic yeasts (e.g. Mrakia) characterized the barren soils. Vegetated soils with higher C, N and root biomass consisted of bacteria able to degrade complex organic compounds (e.g. Candidatus Solibacter), lignocellulolytic Ascomycota (e.g. Geoglossum) and ectomycorrhizal Basidiomycota (e.g. Laccaria). Soil depth only influenced bacterial and fungal communities in barren and sparsely vegetated soils. These changes were partly due to more silt and higher soil moisture in the surface. In both soil ages, the surface was characterized by OTUs affiliated to Phormidium and Sphingobacteriales. In lower depths, however, bacterial and fungal communities differed between SSD. Lower depths of sparsely vegetated soils consisted of OTUs affiliated to Acidobacteria and Geoglossum, whereas depths of barren soils were characterized by OTUs related to Gemmatimonadetes. Overall, plant establishment drives the soil microbiota along the successional gradient but does not influence the vertical distribution of microbiota in recently deglaciated soils.     

土壤纤毛虫群落对不同退还模式生态恢复的响应

为了探究土壤纤毛虫群落对不同退还模式生态恢复的响应及利用其群落特征来评价退还效果,于2014年4月至2015年7月在甘肃省天祝藏族自治县朵什乡退耕还林区选取了3个不同退还林型样点(云杉、沙棘混交林A1,云杉林A2,沙棘林B1)和2个对照耕地样点(小麦地A0,豌豆地B0)为研究样地,采用"非淹没培养皿法"、活体观察法和培养直接计数法对土壤纤毛虫群落特征进行了研究,同时测定了各样点土壤的相关环境因子,并分析了不同恢复模式下土壤纤毛虫群落特征与植被群落参数、土壤环境因子间的相关性。研究共鉴定到125种土壤纤毛虫,隶属于9纲19目29科34属。结果显示:退还样点和对照样点的土壤纤毛虫群落结构特征存在明显差异(P0.05),退还样点间的物种相似性减小,群落组成复杂化;退还样点土壤纤毛虫物种数、密度、物种多样性指数、均匀度指数和丰富度指数均明显增高(P0.05),且各样点间表现为A1B1A2B0A0;各样点优势类群的演替趋势,由对照样点的肾形目演替为退还样点的散毛目。相关性分析和冗余分析结果表明,退耕还林后,对纤毛虫群落结构稳定影响最主要的是有机质、含水量和全氮的含量,不同林型间土壤纤毛虫群落组成差异较大,表明土壤纤毛虫群落结构可作为对退耕还林生态恢复的评价指标。     

Patterns of Plant Species Diversity in Remnant and Restored Tallgrass Prairies

To restore diversity of native vegetation, we must understand factors responsible for diversity in targeted communities. These factors operate at different spatial scales and may affect the number and relative abundances of species differently. We measured diversity of plant species and functional groups of species in replicated plots within paired restored and remnant (relic) tallgrass prairies at three locations in central Texas, U.S.A. To determine the contributions of species abundances and of spatial patterns of diversity to differences between prairie types, we separated diversity into richness and evenness (relative biomass) and into within‐plot (α), among‐plot (β), and prairie (γ) components. Species diversity was greater in remnant than in restored prairies at all spatial scales. At the γ scale, both species richness and species evenness were greater in remnants because of greater spatial variation in species composition. At the α scale, remnants were more diverse because of greater richness alone. Mean α richness correlated positively with the size of the species pool in restored prairies only, implying that in remnants, α richness was influenced more by colonization dynamics than by the number of species available for colonization. Plots in remnant prairies contained more functional groups and fewer species per group than did plots in restored prairies, suggesting that resource partitioning was greater in relic prairies. Our results are consistent with the interpretation that local ecological processes, like resource partitioning and limitations on seed dispersal, contribute to the greater diversity of remnant than restored prairies in central Texas. Restoration practices that limit abundances of competitive dominants, increase the number of species in seed mixtures, and increase the proximity of plants of different functional groups thus may be required to better simulate the plant diversity of tallgrass prairies.     

两种盐生植物根际土壤细菌多样性和群落结构

应用高通量测序技术对西北干旱区两种盐生植物黑果枸杞和里海盐爪爪根际土壤细菌的多样性和群落结构进行研究,旨在揭示两种耐盐植物根际土壤细菌之间以及根际与非根际细菌群落结构间的差异,为深入研究盐生植物根际土壤微生物与耐盐性之间的关系提供理论基础。结果表明:黑果枸杞、里海盐爪爪根际细菌多样性丰度高于非根际土,黑果枸杞根际土壤细菌多样性丰度高于里海盐爪爪。根际和非根际土壤细菌群落的组成和丰度存在差异,从黑果枸杞和里海盐爪爪根际土壤中分别检测出细菌21门289属和22门304属,而从非根际土壤中分别检测出28门285属和24门336属;在两种盐生植物根际土壤中,变形菌门和厚壁菌门均为优势门;拟杆菌门、放线菌门、蓝细菌门及浮霉菌门在根际土壤中的丰度显著高于非根际土壤,而厚壁菌门在根际土壤中的丰度低于非根际土壤。两种植物根际土壤中的细菌优势门和优势属的数量均高于非根际土壤,在黑果枸杞和里海盐爪爪的根际土壤中的细菌优势属分别有10个和9个,而二者非根际土壤中的细菌优势属各有4个,其中假单胞菌属是根际和非根际土壤中的共有优势属。黑果枸杞和里海盐爪爪根系细菌群落组成和丰度存在差异,只有假单胞菌属和盐单胞菌属是两种植物根际土壤中的共有优势属。Unifrac分析和聚类分析表明,两种盐生植物根际土壤细菌之间的相似性大于根际和非根际细菌群落间的相似性。细菌多样性与土壤有机碳、有机质、总氮正相关,与pH、电导率负相关,电导率和pH,有机碳和总氮分别是非根际土,根际土壤细菌群落物种组成的主要影响因素。     

Arbuscular mycorrhizal soil infectivity and spores distribution across plantations of tropical,subtropical and exotic tree species: a case study from the forest reserve of Bandia,Senegal

Several fast‐growing and multipurpose trees such as exotic and valuable native species have been widely used in West Africa to reverse the tendency of massive degradation of plant cover and restore soil productivity. Although benefic effects have been reported on soil stabilization, a lack of information about their impact on soil symbiotic microorganisms still remains. This investigation has been carried out in field trees of 28 years old in a forest reserve at Bandia. To determine the mycorrhizal inoculum potential (MIP) of soils, a mycorrhizal bioassay was conducted using seedlings of Zea mays L. Spores concentration, arbuscular mycorrhizal (AM) fungi morphotypes and mycorrhizal colonization of field plants were examined. Results showed that fungal communities were dominated in all samples by the genus Glomus. Nevertheless, the others genera Gigaspora and Scutellospora occurred preferentially out of the plantations. The number and richness of spores as well as the MIP of soils were decreased in the tree plantations. Accordingly, the amount of annual herbaceous plants kept out of the tree plantations was much greater than those under the tree plantations. The colonization was higher in field root systems of herb plants in comparison with that of the tree plants. Comparisons allowed us to conclude that vegetation type modifies the AM fungal communities, and the results suggest further adoption of management practices that could improve or sustain the development of herbaceous layers and thus promote the AM fungal communities.     

Status of arbuscular mycorrhizal fungi (AMF) in the Sundarbans of India in relation to tidal inundation and chemical properties of soil

The arbuscular mycorrhizal status of fifteen mangroves and one mangrove associate was investigated from 27 sites of three inundation types namely, diurnal, usual springtide and summer springtide. Roots and rhizospheric soil samples were analysed for spore density, frequency of mycorrhizal colonization and some chemical characteristics of soil. Relative abundance, frequency and spore richness of AMF were assessed at each inundation type. All the plant species except Avicennia alba exhibited mycorrhizal colonization. The study demonstrated that mycorrhizal colonization and spore density were more influenced by host plant species than tidal inundation. Forty four AMF species belonging to six genera, namely Acaulospora, Entrophospora, Gigaspora, Glomus, Sclerocystis and Scutellospora, were recorded. Glomus mosseae exhibited highest frequency at all the inundation types; Glomus fistulosum, Sclerocystis coremioides and Glomus mosseae showed highest relative abundance at sites inundated by usual springtides, summer springtides and diurnal tides, respectively. Spore richness of AMF was of the order usual springtide > diurnal > summer springtide inundated sites. The mean spore richness was 3.27. Diurnally inundated sites had the lowest concentrations of salinity, available phosphorus, exchangeable potassium, sodium and magnesium. Statistical analyses indicated that mycorrhizal frequency and AMF spore richness were significantly negatively correlated to soil salinity. Spore richness was also significantly negatively correlated to available phosphorus. The soil parameters of the usual springtide inundated sites appeared to be favourable for the existence of maximum number of AMF. Glomus mosseae was the predominant species in terms of frequency in the soils of the Sundarbans.     

Assessment of the Bacterial Diversity in Fenvalerate-Treated Soil

The impact of the pesticide fenvalerate on the diversity of the bacterial community in soil was investigated in this study. After treatment with 0.1, 0.5 or 1.0 mg fenvalerate g^–1 soil in three soils and incubation for a 40-day period, the changes in diversity were monitored by two different methods. The cultivable heterotrophic diversity was investigated by colony morphology on solid LB medium. Genetic diversity was measured as bands on denaturing gradient gel electrophoresis (DGGE) gels by total genomic DNA extraction and purification, PCR-amplification of bacterial 16S rDNA fragments. The Shannon–Wiener index of diversity (H), richness (S) and evenness (E _H) were used to measure changes in the bacterial community in the soils. The results of the cultivable heterotrophic diversity and genetic diversity showed that there was an obvious decrease in diversity due to the application of fenvalerate to the soils, and the different amounts added had different impacts on the diversity. Bands appearing to be either enhanced or inhibited as a result of the fenvalerate treatments were excized and sequenced. Sequencing of excized DGGE bands indicated that application of fenvalerate had an obvious impact on several Pseudomonas spp., or Xanthomonas campestrisor Streptomyces avermitilis. This revealed that microbial community changes can occur due to the application of fenvalerate to soil.