连作土灭菌对葡萄根际土壤微生物群落功能的影响

In order to explore the correlation between soil microbial community function and plant growth, using 30 year continuous cropping soil of grapevines as research object, we studied the effects of sterilization of continuous cropping soil at different temperatures on the growth of grapevines and the microbial community function of rhizosphere soil. The results showed that plant height and stem diameter of grapevines grown in continuous cropping soil were lower than those in the other treatments. With the increasing sterilization temperature, the plant height and stem dia meter of grapevines increased. The ratio of bacteria to fungi in rhizosphere soil increased with the increasing sterilization temperature. The activity of rhizosphere microbes using carbon source was in order of continuous cropping soil sterilized at 100 ℃ > non continuous cropping soil > continuous cropping soil sterilized at 60 ℃ > continuous cropping soil. The regression analysis showed that amino acid (carbon source) in Biolog ECO plate had a significant correlation with microbial metabolic activity of rhizosphere soil. PCA analysis showed that lysine in root exudate had a highest contribution to the variance of principal components in each treatment, and it may play an important role in the obstacle of continuous cropping of grapevines.     

Soil microbial properties under different vegetation types on Mountain Han

This study investigated the influence of broadleaf and conifer vegetation on soil microbial communities in a distinct vertical distribution belt in Northeast China.Soil samples were taken at 0-5,5-10 and 10-20 cm depths from four vegetation types at different altitudes,which were characterized by poplar(Populus davidiana)(1250-1300 m),poplar(P.davidiana) mixed with birch(Betula platyphylla)(1370-1550 m),birch(B.platyphylla)(1550-1720 m),and larch(Larix principis-rupprechtii)(1840-1890 m).Microbial biomass and community structure were determined using the fumigation-extraction method and phospholipid fatty acid(PLFA) analysis,and soil fungal community level physiological profiles(CLPP) were characterized using Biolog FF Microplates.It was found that soil properties,especially soil organic carbon and water content,contributed significantly to the variations in soil microbes.With increasing soil depth,the soil microbial biomass,fungal biomass,and fungal catabolic ability diminished;however,the ratio of fungi to bacteria increased.The fungal ratio was higher under larch forests compared to that under poplar,birch,and their mixed forests,although the soil microbial biomass was lower.The direct contribution of vegetation types to the soil microbial community variation was 12%.If the indirect contribution through soil organic carbon was included,variations in the vegetation type had substantial influences on soil microbial composition and diversity.     

Modified micro suction cup/rhizobox approach for the in-situ detection of organic acids in rhizosphere soil solution

Root–soil interactions can strongly influence the soil solution chemistry in the rhizosphere. In the present study we propose a modification of the classical rhizobox/micro suction cup system to make it suitable for the collection and analysis of organic acids in the rhizosphere. In order to show the potential of the method, we tested the modified system with Lupinus albus L. as a model plant known to exude large amounts of citrate. The suction cups were installed through the transparent front plate of the rhizoboxes just after the emergence of cluster roots in order to allow optimal localized collection of soil solution. A small dead-volume allowed almost immediate stabilisation with formaldehyde of the sampled soil solutions in the collection container to prevent microbial degradation. The concentrations of organic acids were significantly larger in the rhizosphere soil solution of active cluster roots of Lupinus albus L. than in the bulk soil solution (about 400 μM of citrate versus <0.05 μM). We were able to follow the exudation process in-situ, which occurred during 2–3 days. Also the concentrations of other organic acids and inorganic anions differed between the bulk soil and the rhizosphere of cluster roots, normal roots, and nodules.     

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea

The deep-sea brines of the Red Sea include some of the most extreme and unique environments on Earth. They combine high salinities with increases in temperature, heavy metals,hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine–seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine–seawater interfaces were diverse and generally dominated by Caudovirales,yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface: the upper-interface was enriched with viruses associated with typical marine bacteria,while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, representing one of the first steps for ongoing and future sampling efforts and studies.     

Effects of transportation direction of photosynthate on soil microbial processes in the rhizosphere of Phyllostachys bissetii北大核心CSCD

Aims Clonal integration contributes greatly to the adaption of clonal plants to heterogeneous habitats. However, effects of transportation direction of photosynthate on microbial processes need to be further investigated in the rhizosphere. The purpose of this study is to determine the effects of directional differences in photosynthate transport on microbial processes in the rhizosphere of clonal plant Phyllostachys bissetii. Methods By removing the aboveground parts of the ramets, acropetal treatment and basipetal treatment were applied in this study to control the transportation direction of photosynthate. In acropetal treatment, aboveground parts of distal ramets were cut off (with 20 cm above ground kept), and proximal ramets were left intact. While in basipetal treatment, aboveground parts of proximal ramets were cut off (with 20 cm above ground kept), and distal ramets were left intact. Rhizomes between the two ramets were either connected or severed. Carbon (C) and nitrogen (N) availabilities, and enzyme activities in the rhizosphere soils were measured. Important findings In acropetal treatment, total organic carbon (TOC), dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and soil inorganic nitrogen (NH4 +-N and NO3 --N) content in the rhizosphere soil of distal ramets with connected rhizomes were significantly higher than those with severed rhizome. The activities of urease, polyphenol oxidase (POXase), N-acetyl-β-D-Glucosaminidase (NAGase) were significantly enhanced. Further, clonal integration had a significant effect on C and N availability, and microbial processes in the rhizosphere soil of neighbouring ramets. In basipetal treatment, clonal integration did not show a significant effect on C availability in the rhizosphere soil of proximal ramets, but microbial processes along with soil enzyme activities were altered accordingly. Effects of transportation direction of photosynthate on microbial processes in the rhizosphere of P. bissetii provides insights into the adaptation mechanisms of clonal plant populations. © 2018 Editorial Office of Chinese Journal of Plant Ecology. All rights reserved.     

土壤微生物增强了外来植物紫茎泽兰对本地植物种的竞争力

【Background】The soil microbial community plays an important role in plant establishment, growth and nutrition. Invasion success may be linked to plant microbe interactions. 【Method】Under glasshouse conditions, we compared the effect of soil microbial communities to the growth and interactions between the exotic weed Ageratina adenophora and native plants. The microbial communities were from soil invaded by A.adenophora (IS) vs. that dominated by native weeds (NS). 【Result】A.adenophora which received inoculum from IS had higher arbuscular mycorrhizal colonization rate than that from NS, especially when Medicago falcata or Setaria viridis grew near A.adenophora. Microbial inoculum from IS accelerated the growth of A.adenophora, when planted in polyculture with the native plant S.viridis, but the native species growth was not affected. A.adenophora, receiving an inoculum from IS, inhibited the growth of its two neighboring native species, while no such effect was observed when using inoculum from NS. A.adenophora responded positively to the inoculum taken from IS in all planting combinations, but responded negatively to inoculum from NS both in monoculture and in polyculture with M.falcata. 【Conclusion and significance】Soil microbes, including arbuscular mycorrhizal fungi present in soil in the rhizosphere of A.adenophora enhanced the competiveness of this invasive weed against native species, which may be an important invasion mechanism of exotic plants.     

Spatial distribution of ant mounds and effects on soil physical properties in wetlands of the Sanjiang plain, China

Ants constitute a dominant element of soil mesofauna due to their biomass, abundance, richness of species and distribution within terrestrial ecosystems. They are important regulators of soil aggregate structure as they translocate large amounts of soil from the bottom to the soil surface. In doing so, they form biogenic structures (BS) made up of aggregates of different sizes and characteristics, i.e. ant mounds. These BS have varying characteristics according to the ant species and the soil where they carry their activities. Ants are considered soil engineers because of their effects on soil properties, availability of resource and flow of energy and nutrients in soil. Thus, it is important to gain information on their distribution and abundance. Relatively little is known about the spatial distribution of mounds and their role in the soil physical properties in wetlands of the Sanjiang plain, China. We conducted a survey of ant mounds and measured the density, height, and diameter and material composition of different ant mounds. The ecological characteristics of wetlands that ant mounds wide occurrence were also investigated, including soil type, hydrology characters and plant composition. Differences in soil particle composition, bulk density and soil moisture between ant mound and natural meadow were measured to assess the influences of ant mounds on soil physical properties. We also studied the effects of ant mounds on the microtopography of meadows. Ant mounds were found mainly in the transition zone between terrestrial and aquatic habitats, with wetland type, including Calamagrostis augustifolia wet meadow, C.augustifolia marsh meadow, shrubs marsh meadow and Carexmeyeriana–Carexappendiculata wetland, being a significant factor. Most of the mounds detected were inhabited by Lasius flavus Fabricius, Lasius niger Linnaeus and Formica sanguinea Latreille, which occupied 52.9%, 26.5% and 20.6% of the mounds surveyed, respectively. The density, height, diameter and mound composition were significantly different among the mounds of F. sanguinea Latreille, L. flavus Fabricius and L. niger Linnaeus. The average density and diameter of L. flavus mounds was significantly higher than those of other ant mounds. The average height of F. sanguinea mounds was highest among the mounds detected. Mound building activities changed soil particle size distribution, with the silt and clay content of mounds higher than for non-mound soil. Compared with adjacent, non-mound soil, the bulk density (0–30 cm) and water content (0–25 cm) of mound soil were significantly lower, but there were no significant differences between the mound soil of F. sanguinea Latreille and L. flavus Fabricius. The spatial distribution of ant mounds with different height and diameter also changed the micro-geomorphology of the soil surface, increasing the degree of fluctuation of the microtopography. The ant distribution characteristics and their ecological roles respond to a wide range of environmental alterations. The biogenic structures of ant and the specific environment associated with them have been defined as the “functional domain”, a sphere of influence that may significantly affect soil processes at certain spatial and temporal scales. Our results suggest that the distribution and structure of ant mounds can indicate wetland environmental changes, with mounds influencing ecosystem functions and enhancing wetland degradation.     

Spatial distribution of ant mounds and effects on soil physical properties in wetlands of the Sanjiang plain, China

Ants constitute a dominant element of soil mesofauna due to their biomass, abundance, richness of species and distribution within terrestrial ecosystems. They are important regulators of soil aggregate structure as they translocate large amounts of soil from the bottom to the soil surface. In doing so, they form biogenic structures (BS) made up of aggregates of different sizes and characteristics, i.e. ant mounds. These BS have varying characteristics according to the ant species and the soil where they carry their activities. Ants are considered soil engineers because of their effects on soil properties, availability of resource and flow of energy and nutrients in soil. Thus, it is important to gain information on their distribution and abundance. Relatively little is known about the spatial distribution of mounds and their role in the soil physical properties in wetlands of the Sanjiang plain, China. We conducted a survey of ant mounds and measured the density, height, and diameter and material composition of different ant mounds. The ecological characteristics of wetlands that ant mounds wide occurrence were also investigated, including soil type, hydrology characters and plant composition. Differences in soil particle composition, bulk density and soil moisture between ant mound and natural meadow were measured to assess the influences of ant mounds on soil physical properties. We also studied the effects of ant mounds on the microtopography of meadows. Ant mounds were found mainly in the transition zone between terrestrial and aquatic habitats, with wetland type, including Calamagrostis augustifolia wet meadow, C.augustifolia marsh meadow, shrubs marsh meadow and Carexmeyeriana–Carexappendiculata wetland, being a significant factor. Most of the mounds detected were inhabited by Lasius flavus Fabricius, Lasius niger Linnaeus and Formica sanguinea Latreille, which occupied 52.9%, 26.5% and 20.6% of the mounds surveyed, respectively. The density, height, diameter and mound composition were significantly different among the mounds of F. sanguinea Latreille, L. flavus Fabricius and L. niger Linnaeus. The average density and diameter of L. flavus mounds was significantly higher than those of other ant mounds. The average height of F. sanguinea mounds was highest among the mounds detected. Mound building activities changed soil particle size distribution, with the silt and clay content of mounds higher than for non-mound soil. Compared with adjacent, non-mound soil, the bulk density (0–30 cm) and water content (0–25 cm) of mound soil were significantly lower, but there were no significant differences between the mound soil of F. sanguinea Latreille and L. flavus Fabricius. The spatial distribution of ant mounds with different height and diameter also changed the micro-geomorphology of the soil surface, increasing the degree of fluctuation of the microtopography. The ant distribution characteristics and their ecological roles respond to a wide range of environmental alterations. The biogenic structures of ant and the specific environment associated with them have been defined as the “functional domain”, a sphere of influence that may significantly affect soil processes at certain spatial and temporal scales. Our results suggest that the distribution and structure of ant mounds can indicate wetland environmental changes, with mounds influencing ecosystem functions and enhancing wetland degradation.     

Effects of mercury on microbial biomass and enzyme activities in soil

Mercury (Hg) is a persistent soil pollutant that affects soil microbial activity. We monitored the changes in soil microbial biomass and activity of enzymes, including alkaline phosphatase, arylsulfatase, fluorescein diacetate (FDA) hydrolytic activity, and o-diphenol oxidase (o-DPO) in three soils contaminated with different concentrations of Hg. Increasing levels of Hg, from 0.5 to 10 μmol/g of dried soil, generally depressed microbial activity; however, the effects of Hg on soil microbial activity depended on soil type and composition, particularly organic matter content. o-DPO was less affected by Hg than the other three enzymes tested. Our results indicate that the analysis of microbial biomass content and soil-enzyme activities may be used to predict the soil quality contaminated with Hg.     

Diversity and functional analysis of Chinese bumblebee gut microbiota reveal the metabolic niche and antibiotic resistance variation of Gilliamella

Bumblebees play an important role in maintaining the balance of natural and agricultural ecosystems,and the characteristic gut microbiota of bumblebees exhibit significant mutualistic functions.China has the highest diversity of bumblebees;however,gut microbiota of Chinese bumblebees have mostly been investigated through cultureindependent studies.Here,we analyzed the gut communities of bumblebees from Sichuan,Yunnan,and Shaanxi provinces in China through 16S ribosomal RNA amplicon sequencing and bacterial isolation.It revealed that the bumblebees examined in this study harbored two gut enterotypes as previously reported:one is dominated by Gilliamella and Snodgrassella,and the other is distinguished by prevalent environmental species.The gut compositions obviously varied among different individual bees.We then isolated 325 bacterial strains and the comparative genomic analysis of Gillianiella strains revealed that galactose and pectin digestion pathways were conserved in strains from bumblebees,while genes for the utilization of arabinose,mannose,xylose,and rhamnose were mostly lost.Only two strains from the Chinese bumblebees possess the multidrug-resistant gene emrB,which is phylogenetically closely related to that from the symbionts of soil entomopathogenic nematode.In contrast,tetracycline-resistant genes were uniquely present in three strains from the USA.Our results illustrate the prevalence of strain-level variations in the metabolic potentials and the distributions of antibiotic-resistant genes in Chinese bumblebee gut bacteria.     

内蒙草原不同植物功能群及物种对土壤微生物组成的影响

为了分析不同植物群落组成对内蒙古典型草原土壤微生物群落组成的影响,本研究利用植物功能群剔除处理实验平台,采用荧光定量PCR(real-timePCR)和自动核糖体间隔区基因分析(automated ribosomal intergenic spacer analysis,ARISA)技术,对不同植物功能群组成的非根际土壤和常见物种的根际土壤中细菌和真菌的数量及群落结构进行了分析。结果表明,在非根际土壤中,不同植物功能群组成对细菌数量有显著影响,而对真菌数量及细菌和真菌的群落结构影响不明显;在根际土壤中,不同植物物种对细菌、真菌的数量都有显著影响。此外,聚类分析表明,不同物种的根际土中细菌和真菌的群落结构也有所不同,尤其以细菌的群落结构变化较为明显。研究结果表明不同植物物种可以通过根系影响土壤微生物群落组成。     

Light Structures Phototroph,Bacterial and Fungal Communities at the Soil Surface

The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0–3 mm) and bulk soil (3–12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.     

Fungal diversity increases soil fungistasis and resistance to microbial invasion by a non resident species

Biodiversity decline is a major concern for ecosystem functioning. Recent research efforts have been mostly focused on terrestrial plants, while, despite their importance in both natural and artificial ecosystems, little is known about soil microbial communities. This work aims at investigating the effects of fungal species richness on soil invasion by non resident microbes. Synthetic fungal communities with a species diversity ranging from 1 to 8 were assembled in laboratory microcosms and used in three factorial experiments to assess the effect of diversity on soil fungistasis, microbial invasion of soil amended with plant litter and of plant rhizosphere. The capability of different microbes to colonize environments characterized by different resident microbial communities was measured. The number of microbial species in the microcosms positively affected soil fungistasis that was also induced more rapidly in presence of synthetic communities with more species. Moreover, the increase of resident fungal diversity dramatically reduced the invasibility of both soil and plant rhizosphere. We found lower variability of soil fungistasis and invasibility in microcosms with higher species richness of microbial communities. Our study pointed out the existence of negative relationships between fungal diversity and soil invasibility by non resident microbes. Therefore, the loss of microbial species may adversely affect ecosystem functionality under specific environmental conditions.     

p-Coumaric Acid Influenced Cucumber Rhizosphere Soil Microbial Communities and the Growth of Fusarium oxysporum f.sp. cucumerinum Owen

Background

Autotoxicity of cucumber root exudates or decaying residues may be the cause of the soil sickness of cucumber. However, how autotoxins affect soil microbial communities is not yet fully understood.

Methodology/Principal Findings

The aims of this study were to study the effects of an artificially applied autotoxin of cucumber, p-coumaric acid, on cucumber seedling growth, rhizosphere soil microbial communities, and Fusarium oxysporum f.sp. cucumerinum Owen (a soil-borne pathogen of cucumber) growth. Abundance, structure and composition of rhizosphere bacterial and fungal communities were analyzed with real-time PCR, PCR-denaturing gradient gel electrophoresis (DGGE) and clone library methods. Soil dehydrogenase activity and microbial biomass C (MBC) were determined to indicate the activity and size of the soil microflora. Results showed that p-coumaric acid (0.1–1.0 µmol/g soil) decreased cucumber leaf area, and increased soil dehydrogenase activity, MBC and rhizosphere bacterial and fungal community abundances. p-Coumaric acid also changed the structure and composition of rhizosphere bacterial and fungal communities, with increases in the relative abundances of bacterial taxa Firmicutes, Betaproteobacteria, Gammaproteobacteria and fungal taxa Sordariomycete, Zygomycota, and decreases in the relative abundances of bacterial taxa Bacteroidetes, Deltaproteobacteria, Planctomycetes, Verrucomicrobia and fungal taxon Pezizomycete. In addition, p-coumaric acid increased Fusarium oxysporum population densities in soil.

Conclusions/Significance

These results indicate that p-coumaric acid may play a role in the autotoxicity of cucumber via influencing soil microbial communities.     

不同生境黑果枸杞根际与非根际土壤微生物群落多样性

研究典型生境黑果枸杞根际与非根际土壤微生物群落多样性及其与土壤理化性质间的关系,为进一步研究黑果枸杞抗逆性提供理论数据。采集新疆精河县艾比湖地区(EB)盐碱地、乌苏市(WS)路旁荒地、五家渠市(WQ)人工林带的黑果枸杞根际与非根际土壤,利用Illumina-MiSeq高通量测序技术分析细菌和真菌群落组成和多样性。结果表明:根际土壤细菌多样性高于非根际土壤(WQ除外),而根际真菌多样性低于非根际土壤。WQ非根际土壤细菌和真菌多样性均高于EB和WS;根际细菌多样性排序为EBWSWQ,根际真菌多样性排序为WSEBWQ。根际土壤优势细菌门依次是变形菌门、拟杆菌门、放线菌门、酸杆菌门,真菌优势门为子囊菌门、担子菌门。根际土壤细菌变形菌门、拟杆菌门、酸杆菌门的相对丰度高于非根际土壤,而厚壁菌在根际土壤中的丰度显著降低,真菌优势门丰度在根际土和非根际土中的变化趋势因地区而异; Haliea、Gp10、Pelagibius、Microbulbifer、假单胞菌属、Thioprofundum、Deferrisoma是根际土壤细菌优势属;多孢子菌属、支顶孢属、Corollospora、Cochlonema是根际真菌优势属。细菌、真菌优势类群(门、属)的组成以及丰富度存在地区间差异,厚壁菌门在EB地区的丰富度显著高于含盐量较低的WS、WQ;盐碱生境EB中根际土壤嗜盐细菌的丰度高于非盐碱生境(WQ、WS),如盐单胞菌属、动性球菌属、Geminicoccu、Pelagibius、Gracilimonas、Salinimicrobium等。小囊菌属是EB根际真菌的最优势属,Melanoleuca是WQ和WS的最优势属,地孔菌属、Xenobotrytis、Brachyconidiellopsis、多孢子菌属等在EB根际土壤中的丰度显著高于WQ和WS。非盐碱生境(WS和WQ)的微生物群落之间的相似性较高,并且高于与盐碱环境(EB)之间的相似性,表明土壤含盐量对微生物群落组成丰度具有重要的影响。     

黄河三角洲不同类型盐生植物土壤真菌群落结构特征

盐生植物种类及其所具有的不同耐盐调节方式影响着根际微生物群落的结构与组成。为明确不同类型盐生植物根际与非根际土壤中真菌群落结构与组成的差异及其与土壤环境间的相互关系,该研究采集了黄河三角洲地区芦苇、盐地碱蓬、獐毛3种不同类型盐生植物0~20 cm土层的根际和非根际土壤,通过高通量测序对其真菌群落多样性和结构进行了分析,以探究真菌群落特征与土壤理化因子间的关系。结果表明：(1)3种不同类型盐生植物根际土壤真菌群落丰富度显著大于各自非根际土,且獐毛根际土壤真菌群落丰富度显著大于芦苇和盐地碱蓬的根际土。(2)距离热图分析表明,芦苇和盐地碱蓬非根际土壤真菌群落间的相似性最大。(3)土壤真菌多样性和丰富度与土壤总碳、总氮、有效磷、pH呈正相关关系,与土壤盐分含量呈负相关关系。(4)3种不同类型盐生植物的根际与非根际土壤中,球囊菌门(Glomeromycota)均为绝对优势门,盾巨孢囊霉属(Scutellospora)为优势属。(5)RDA分析表明,土壤盐分含量是影响土壤真菌群落结构的重要因子,球囊菌门丰度与土壤总氮、总碳、有效磷、有机碳、pH呈正相关关系,与盐分呈负相关关系。(6)植物土壤真菌群落特征随盐生植物类型的变化以及样本土壤距宿主植物根系远近存在差异。     

Despite Long-Term Compost Amendment Seasonal Changes are Main Drivers of Soil Fungal and Bacterial Population Dynamics in a Tuscan Vineyard

The effect of long-term (8 years) compost treatments (compost or compost plus mineral fertilizer) on genetic structure of bacterial and fungal populations in both bulk soil and rhizosphere of grapevine (Vitis vinifera) was analyzed in respect to a control constituted by the soil treated with mineral fertilization. Soils were sampled in early summer (July), mid-summer (August), and before harvest (October). Bacterial and fungal populations were characterized by genetic fingerprints generated by the application of 16S rDNA and ITS rDNA Multiplex Terminal Fragment Length Polymorphism (M-TRFLP) technique. Compost induced no significant differences at any time on microbial communities from bulk soil samples, whereas seasonal variations significantly affected both bacterial and fungal populations as indicated by the Multi Dimensional Scaling (MDS) ordination method of the M-TRFLPs results. MDS analysis of grapevine rhizosphere M-TRFLPs showed that temporal separation was significant for the bacterial population only. Results suggested that soil microbial populations in vineyard productive ecosystems may be sensitive to environmental changes induced by seasonal variations and show a certain degree of resilience to different agricultural practices.     

Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis,a Living Fossil

Welwitschia mirabilis is an ancient and rare plant distributed along the western coast of Namibia and Angola. Several aspects of Welwitschia biology and ecology have been investigated, but very little is known about the microbial communities associated with this plant. This study reports on the bacterial and fungal communities inhabiting the rhizosphere of W. mirabilis and the surrounding bulk soil. Rhizosphere communities were dominated by sequences of Alphaproteobacteria and Euromycetes, while Actinobacteria, Alphaproteobacteria, and fungi of the class Dothideomycetes jointly dominated bulk soil communities. Although microbial communities within the rhizosphere and soil samples were highly variable, very few “species” (OTUs defined at a 97% identity cut-off) were shared between these two environments. There was a small ‘core’ rhizosphere bacterial community (formed by Nitratireductor, Steroidobacter, Pseudonocardia and three Phylobacteriaceae) that together with Rhizophagus, an arbuscular mycorrhizal fungus, and other putative plant growth-promoting microbes may interact synergistically to promote Welwitschia growth.     

Weeds influence soil bacterial and fungal communities

Background and aims

Vineyards harbour a variety of weeds, which are usually controlled since they compete with grapevines for water and nutrients. However, weed plants may host groups of fungi and bacteria exerting important functions.

Methods

We grew three different common vineyard weeds (Taraxacum officinalis, Trifolium repens and Poa trivialis) in four different soils to investigate the effects of weeds and soil type on bacterial and fungal communities colonising bulk soil, rhizosphere and root compartments. Measurements were made using the cultivation-independent technique Automated Ribosomal Intergenic Spacer Analysis (ARISA).

Results

Weeds have a substantial effect on roots but less impact on the rhizosphere and bulk soil, while soil type affects all three compartments, in particular the bulk soil community. The fungal, but not the bacterial, bulk soil community structure was affected by the plants at the late experimental stage. Root communities contained a smaller number of Operational Taxonomic Units (OTUs) and different bacterial and fungal structures compared with rhizosphere and bulk soil communities.

Conclusions

Weed effect is localised to the rhizosphere and does not extend to bulk soil in the case of bacteria, although the structure of fungal communities in the bulk soil may be influenced by some weed plants.