Interactions of Azospirillum spp. in soils: a review

 This review summarizes and discusses the current knowledge and the, as yet, unanswered questions on the interactions of Azospirillum spp. in bulk soil (but not in the rhizosphere). It contains sections on the isolation of these bacteria from tropical to temperate soils, and on their short- and long-term persistence in bulk soil. The interactions of these bacteria with soil particles and minerals such as clay, sand and Ca, and the effect of soil pH, soil redox potential, and the cation exchange capacity of the soil on them is demonstrated. Data is presented on the distribution of Azospirillum spp. in soils, on their production of fibrillar material essential for anchoring the cells to soil particles, on the effects of soil irrigation, and of external soil treatments, and on the effect of soil C and C used in bacterial inoculants on the cells. It shows that root exudates possibly govern bacterial motility in the soil. Finally, the effect of pesticide applications, the relationships with other soil microorganisms such as Bdelovibrio spp., Bradyrhizobium spp., and phages, and the potential use of a community-control model of Azospirillum spp. in soil and in the rhizosphere is suggested. Received: 11 November 1998     

Azospirillum strains isolated from roots and rhizosphere soil of wheat (Triticum aestivum L.) grown under different soil moisture conditions

The present study deals with the isolation and characterization of Azospirillum strains isolated from roots and rhizosphere soil of wheat (at tillering and anthesis stages) plants grown under different moisture regimes in the field and in pots. The survival of Azospirillum isolates from plants of irrigated field and those from well-watered pots was higher than that of Azospirillum strains isolated from roots and rhizosphere soils of plants grown under arid and semiarid (14–8% soil moisture) field conditions and under water-stressed (8% soil moisture) conditions in pots. On the basis of carbon/nitrogen source utilization, the Azospirillum strains isolated from wheat under field and pot conditions were grouped in three groups. The unweighted pair group method with arithmetic means cluster analysis based on random amplification of polymorphic DNA showed that two groups of Azospirillum were similar. The strains isolated from plants (at tillering stage) grown under low moisture conditions either in pots or in field were genetically similar to strains isolated from plants grown under well-watered conditions in both pots and field. Inoculation of wheat with isolates from water-stressed plants induced tolerance to water stress in inoculated plants. Isolates from water-stressed conditions exhibited lower production of indole acetic acid, gibberellic acid, and trans zeatin riboside but a higher production of abscisic acid.     

健康与罹患青枯病的番茄土壤细菌群落特征比较

应用实时荧光定量PCR及MiSeq高通量测序技术,全面地研究了连作番茄田块中健康与感染青枯病植株周围土体及根际土壤细菌群落结构和组成.结果表明:健康番茄土体土壤的pH及全碳含量显著高于感病番茄土体土壤;土体及根际土壤的细菌群落结构和组成明显不同于感病番茄土体及根际土壤细菌群落.与感病番茄根际相比,健康番茄根际细菌的数量...     

Density,metabolic activity,and identity of cultivable rhizosphere bacteria on Salix viminalis in disturbed arable and landfill soils

The objective of this study was to provide fundamental data for a subsequent selection of willow growth and soil remediation promoting bacterial strains. The rhizosphere of willows (Salix viminalis) was screened for cultivable bacteria with high enzymatic activity (proteolytic, pectolytic, cellulolytic, amylolytic) and production of siderophores at four test sites with broad spectrum of anthropogenic soil disturbance: sewage‐sludge application, impoverishment by unfavorable arable use, ash dumping, and household‐waste depositing. The density of bacteria in the rhizosphere ranged from 7.92 to 8.56 log₁₀ of colony‐forming units per gram dry weight of soil and varied in a site‐ and willow‐clone‐specific manner. Within the 240 bacterial strains, a high diversity of metabolic activities was observed but was rarely combined in one strain (1.2% having six and 5.8% having five out of seven metabolic activities, respectively). The majority of strains (79.2%) revealed just one or two metabolic activities. Most common was a combination of lipolytic, proteolytic activities, and siderophore production as found in 13.8% of the bacterial strains. The 50 strains with the highest metabolic activity belonged predominantly to the Gammaproteobacteria (66%), the others to Flavobacteria (18%), Betaproteobacteria (8%), Actinobacteria (4%), and Bacilli (4%). The highest portion of cultivable strains of rhizosphere bacteria with high metabolic activities belonged to the genera Pseudomonas, Serratia, and Flavobacterium. We hypothesize that these genera include strains that support willow growth and soil remediation. Therefore, the described strain collection from the rhizosphere of S. viminalis provides a valuable basis for a subsequent selection of these candidates for applications in improvement of site adaptation of plants or remediation of soils.     

Rhizosphere microbiota assemblage associated with wild and cultivated soybeans grown in three types of soil suspensions

Soil microbial community composition is determined by the soil type and the plant species. By sequencing the V3-V4 region of the bacterial 16S rRNA gene amplicons, the current study assessed the bacterial community assemblage in rhizosphere and bulks soils of wild (Glycine soja) and cultivated (Glycine max) soybeans grown in the suspensions of three important soil types in China, including black, red and soda-saline-alkali soils. The alpha-diversity of the bacterial community in the rhizosphere was significantly higher than that of the bulk soils suggesting that bulk soil lacks plant nurturing effect under the current study conditions. Black and red soils were enriched with nitrifying and nitrogen-fixing bacteria but the soda-saline-alkali soil suspension had more denitrifying bacteria, which may reflect agronomic unsuitability of the latter. We also observed a high abundance of Bradyrhizobium and Pseudomonas, enriched cellulolytic bacteria, as well as a highly connected molecular ecological network in the G. soja rhizosphere soil. Taken all, the current study suggest that wild soybeans may have evolved to recruit beneficial microbes in its rhizosphere that can promote nutrients requisition, biostasis and disease-resistance, therefore ecologically more resilient than cultivated soybeans.     

盐沼湿地中植物根围土壤细菌群落结构和多样性的16S rDNA分析

The structure and diversity of the bacterial communities in rhizosphere soils of native Phragmites australis and Scirpus rnariqueter and alien Spartina alterniflora in the Yangtze River Estuary were investigated by constructing 16S ribosomal DNA （rDNA） clone libraries. The bacterial diversity was quantified by placing the clones into operational taxonomic unit （OTU） groups at the level of sequence similarity of 〉 97%. Phylogenetic analysis of the resulting 398 clone sequences indicated a high diversity of bacteria in the rhizosphere soils of these plants. The members of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria of the phylum Proteobacteria were the most abundant in rhizobacteria. Chao 1 nonpaxametric diversity estimator coupled with the reciprocal of Simpson＇s index （l/D） was applied to sequence data obtained from each library to evaluate total sequence diversity and quantitatively compare the level of dominance. The results showed that Phragmites, Scirpus, and Spartina rhizosphere soils contained 200, 668, and 382 OTUs, respectively. The bacterial communities in the Spartina and Phragraites rhizosphere soils displayed species dominance revealed by 1/D, whereas the bacterial community in Scirpus rhizosphere soil had uniform distributions of species abundance. Overall, analysis of 16S rDNA clone libraries from the rhizosphere soils indicates that the changes in bacterial composition may occur concomitantly with the shift of species composition in plant communities.     

生物有机肥对田间蔬菜根际土壤中病原菌和功能菌组成的影响

利用实时荧光定量PCR方法对田间条件下连作番茄和辣椒施用生物有机肥(BOF)和常规施肥(CK)的根际土壤微生物中青枯病原菌和功能菌群(固氮菌和荧光假单胞菌)的数量进行定量研究.结果表明:与CK相比,BOF处理的番茄和辣椒产量分别提高了26.0％和19.9％,青枯病发病率分别降低了41.5％和44.7％,番茄和辣椒植株根际土壤固氮菌数量分别增加了23.5％和25.8％、荧光假单胞菌数量分别增加了29.5％和20.2％、病原菌数量分别减少了73.2％和90.1％.生物有机肥能够调控根际微生物区系的组成,降低土传病害的发病率,促进作物健康生长;实时荧光定量PCR方法能够快速准确地检测根际土壤中功能微生物种群数量变化.     

Selection for root colonising bacteria stimulating wheat growth in saline soils

High salinity of soils in arid and semi-arid regions results in desertification and decreased crop yield. One possibility to circumvent this problem is to use root colonising salt tolerant bacterial inoculants which can alleviate salt stress in plants. In the present work, the best five enhanced wheat root tip coloniser bacteria were selected from the rhizosphere of wheat grown in saline soil and were identified by the 16S rRNA gene sequence as Pseudomonas putida, Pseudomonas extremorientalis, Pseudomonas chlororaphis and Pseudomonas aurantiaca. The isolates tolerated salt of 5% NaCl and produced indole acetic acid under saline conditions. Four isolates proved to be very efficient in promoting a significant increase in the shoot, root and dry matter of wheat and were able to survive in saline soil. Four of the isolated strains appeared to be better competitive colonisers than reference strains and probably outcompeted with indigenous microorganisms of the rhizosphere. These results are promising for the application of selected environmentally save microbes in saline agricultural soils.     

Diversity of diazotroph populations in the rhizosphere of maize (Zea mays L.) growing on different French soils

Summary We studied the dominant diazotrophs associated with maize roots and rhizosphere soil originating from three different locations in France. An aseptically grown maize plantlet, the spermosphere model, was used to isolate N₂-fixing (acetylene-reducing) bacteria. Bacillus circulans was the dominant N₂-fixing bacterium in the rhizosphere of maize-growing soils from Ramonville and Trogny, but was not found in maize-growing sandy soil from Pissos. In the latter soil, Enterobacter cloacae, Klebsiella terrigena, and Pseudomonas sp. were the most abundant diazotrophs. Azospirillum sp., which has been frequently reported as an important diazotroph accociated with the maize rhizosphere, was not isolated from any of these soils. The strains were compared for their acetylene-reducing activity in the spermosphere model. The Bacillus circulans strains, which were more frequently isolated, also exhibited significantly greater acetylene-reducing activity (3100 nmol ethylene day^-1 plant^-1) than the Enterobacteriaceae strains (180 nmol ethylene day^-1 plant^-1). This work indicates for the first time that Bacillus circulans is an important maizerhizosphere-associated bacterium and a potential plant growth-promoting rhizobacterium.     

Evaluation of potassium application on tomato performance and rhizosphere bacterial communities under negative pressure irrigation of greenhouse-grown

Abstract

The study investigated the response to five levels of potassium (K) fertilizer addition on tomato (Solanum lycopersicum L.) performance and soil bacterial communities by negative pressure irrigation (NPI) over two consecutive years. The application of K fertilization positively affected tomato performance under NPI, as indicated by increased yield, quality, growth, and nutrients’ contents of tomato compared with no K addition treatment. High-throughput sequencing of the rhizosphere soil revealed that K additions significantly affected in the bacterial diversity indices according to Chao1, Ace, and Shannon. K addition significantly increased the relative abundance of Gemmatimonadetes and decreased the level of Planctomycetes. There were very prominent increases in the levels of the genus Opitutus, but reduced the content of Sphingomonas and Bdellovibrio compared with no K addition treatment. Furthermore, application of 150?kg K ha^?1 (K150) was considered to be beneficial for plant growth and rhizosphere bacterial diversity of tomato. The tomato yield under K150 was considerably increased by 58% and 47% compared with no K addition treatment in 2016 and 2017, respectively. The K150 showed the highest K fertilizer utilization efficiency compared with other K treatments, with K contribution rate and K agronomic efficiency reaching 36.7 and 62.9 as well as 32.0 and 53.6 in 2016 and 2017, respectively. Therefore, these findings also demonstrate that K application under NPI not only promotes yield and quality of tomato fruits but also positively affects the rhizosphere microbiome.     

Root, rhizosphere and root-free respiration in soils under grassland and forest plants

Plants significantly affect rates of carbon (C) turnover in soils, both because they are sources of carbon through exudation in the rhizosphere and litter‐fall, and because rhizosphere microbes stimulated by roots also metabolize native soil carbon. Different plant species affect these components of soil carbon turnover in different ways, but the quantitative information on this is lacking for different ecosystems and soil‐plant combinations. To compare the effects of grassland and forest plant species on the components of rhizosphere respiration in different soils, we grew ryegrass (Lolium perenne) and radiata pine (Pinus radiata D. Don) in two silt loam soils in pots in a glasshouse, and in seven samplings over 45 weeks measured total (R_total), root (R_root) and root‐free soil respiration (R_rfs), the latter from respiration in unplanted controls. We calculated rhizosphere respiration (R_rhizo), defined here as the net of that fuelled by native soil C and root‐derived C, from R_total less R_root+R_rfs. We also measured plant growth and total, water‐soluble and microbial biomass C in the soils at each sampling. Results showed that R_rfs decreased over the experimental period in both soils. Under ryegrass, R_root, R_rhizo and R_total increased up to 14 weeks after planting and then stabilized, whereas under radiata pine, they continued to increase throughout the experiment. By the end of the experiment, the R_root, R_rhizo and R_rfs components accounted for 49–58, 31–50 and 1–11% of soil total respiration under ryegrass, respectively, and 43–66, 29–53 and 1–5% under radiata pine. The greater R_root, R_rhizo and R_total values under radiata pine were related to greater root biomass and root‐derived organic C, and enhanced microbial mineralization of native soil organic C.     

盐地碱蓬根际土壤细菌群落结构及其功能

盐地碱蓬作为生物改良盐碱地的理想材料,其根际土壤微生物对土壤改良发挥着重要作用。为了深入探索环渤海滨海盐碱地碱蓬根际土壤细菌群落结构组成及其功能,采用Illumina Misep高通量测序平台对环渤海地区滨海盐碱地盐地碱蓬根际土壤和裸地土壤进行测序。从16个样本中获得有效序列734 792条, 4 285个OTUs,归属于41门、100纲、282目、400科、892属、1 577种。盐地碱蓬根际土壤细菌群落由变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、绿弯曲门(Chloroflexi)、拟杆菌门(Bacteroidetes)、芽单胞菌门(Gemmatimonadetes)、酸杆菌门(Acidobacteria)、厚壁菌门(Firmicutes)、蓝藻细菌门(Cyanobacteria)、髌骨细菌门(Patescibacteria、浮霉菌门(Planctomycetes)组成。Alpha多样性计算结果表明,盐地碱蓬根际土壤细菌群落结构多样性高并与裸地土壤间差异显著;LEfSe(LDAEffectSize)分析发现,盐地碱蓬与裸地差异指示种明显不同。PCoA与相关性Heatmap表明,盐地碱蓬、速效氮、速效钾、速效磷、电导率是影响土壤细菌目类水平群落组成的主要因子。PICRUSt(Phylogenetic InvestigationofCommunitiesbyReconstructionofUnobserved States)分析表明微生物群落在新陈代谢等40个功能方面盐地碱蓬根际土壤比裸地土壤高。本研究表明盐地碱蓬覆盖能够降低土壤盐分,增加土壤养分,对土壤细菌群落多样性及其功能有积极作用。     

Bacterial communities associated with natural and commercially grown rooibos (Aspalathus linearis)

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea. Symbiotic interactions between A. linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor, acidic fynbos soil. The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A. linearis, as well as the effect of seasonal changes on these communities. Bacterial communities were characterized using high throughput amplicon sequencing, and their correlations with soil chemical properties were investigated. The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction. Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant bacterial phyla detected in this study. Highly similar bacterial communities were associated with natural and commercially grown plants. Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season, while no significant differences were detected in the wet season. This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A. linearis.     

Ability of different plant species to promote microbiological processes in semiarid soil

In semiarid climate soils, the establishment of a plant cover is fundamental to avoid degradation and desertification processes. A better understanding of the ability of plants to promote soil microbial processes in these conditions is necessary for successful soil reclamation. Six different plant species were planted in a semiarid soil, in order to know which species are the most effective for the reclamation of semiarid areas. Six years after planting, the rhizosphere soils were studied by measuring chemical (pH, electrical conductivity, total organic carbon and other carbon fractions), physical (% of saggregates), microbiological (microbial biomass carbon and soil respiration), and biochemical (dehydrogenase, phosphatase, β-glucosidase and urease activities) parameters. In general, in all the soil–plant systems plant nutrients, organic matter and microbial activity increased compared to the control soil. For some species, such as Rhamnus lycioides, the increase in the total organic carbon content (TOC) in the rhizosphere zone was almost 200%. A positive correlation was found between TOC and water-soluble carbon (p<0.001); both parameters were negatively correlated with electrical conductivity. Microbial biomass carbon and soil respiration were highest in the rhizosphere of Stipa tenacissima (98% and 60%, respectively, of increase on soil control values) and Rosmarinus officinalis (94% and 51%, respectively, of increase on soil control values). These microbiological parameters were correlated with the percentage of stable aggregates (p<0.01). Enzyme activities were affected by the rhizosphere, their values depending on the shrub species.     

Überleben inokulierter Rhizosphärenbakterien und deren Einfluß auf native Bakterienpopulationen im Wurzelraum von Luzerne

Survival of inoculated rhizosphere bacteria and their influence on native bacterial populations in the rhizosphere of alfalfa The survival of inoculated bacteria and their influence on native bacterial populations in the rhizosphere of alfalfa were investigated in a greenhouse experiment. The plant growth promoting strains Rhizobium meliloti me18 and Pseudomonas fluorescens PsIA12 were reisolated from the rhizosphere about 7 weeks after single and mixed strain inoculation. They did not induce lasting changes in the diversity of the native bacterial communities of the rhizosphere. Only within the first week after inoculation was an increase in total bacterial abundance observed. In general, the diversity of bacterial communities increased with plant age and with proximity to the root tip.     

Abundance of Frankia from Gymnostoma spp. in the rhizosphere of Alphitonia neocaledonica, a non-nodulated Rhamnaceae endemicto New Caledonia

The capacity of different soils of New Caledonia to induce nodulation in Gymnostoma poissonianum was studied. The soils were sampled under five Gymnostoma species, Alphitonia neocaledonica (a non-nodulated endemic Rhamnaceae) and Pinus caribea (an introduced species) growing in various ecological conditions. Using G. poissonianum as trap-host, we observed a higher abundance of Frankia from Gymnostoma spp. in the rhizosphere of A. neocaledonica as compared with bare soils and P. caribea rhizosphere. The nodulating capacity of A. neocaledonica rhizosphere was almost similar to that of the five Gymnostoma species (symbiotic host) studied in the same stations. In comparison, bare soils or rhizosphere of P. caribea had poor nodulating capacities. We isolated fourteen Frankia strains from nodules of G. poissonianum after baiting with the rhizospheric soils of five Gymnostoma and A. neocaledonica. Using the PCR/RFLP method, we confirmed the similarity with those already described. Frankia was abundant in the rhizosphere of A. neocaledonica in all the sites studied. One explanation could be a positive tropism of Frankia towards species belonging to families having nodulated species, which is the case of A. neocaledonica endemic in New Caledonia. We can suppose that the non-nodulated plants belonging to these families can excrete some chemical substances able to attract Frankia and to induce its proliferation.     

Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils

A number of studies have reported species specific selection of microbial communities in the rhizosphere by plants. It is hypothesised that plants influence microbial community structure in the rhizosphere through rhizodeposition. We examined to what extent the structure of bacterial and fungal communities in the rhizosphere of grasses is determined by the plant species and different soil types. Three grass species were planted in soil from one site, to identify plant-specific influences on rhizosphere microbial communities. To quantify the soil-specific effects on rhizosphere microbial community structure, we planted one grass species (Lolium perenne L.) into soils from three contrasting sites. Rhizosphere, non-rhizosphere (bulk) and control (non-planted) soil samples were collected at regular intervals, to examine the temporal changes in soil microbial communities. Rhizosphere soil samples were collected from both root bases and root tips, to investigate root associated spatial influences. Both fungal and bacterial communities were analysed by terminal restriction fragment length polymorphism (TRFLP). Both bacterial and fungal communities were influenced by the plant growth but there was no evidence for plant species selection of the soil microbial communities in the rhizosphere of the different grass species. For both fungal and bacterial communities, the major determinant of community structure in rhizospheres was soil type. This observation was confirmed by cloning and sequencing analysis of bacterial communities. In control soils, bacterial composition was dominated by Firmicutes and Actinobacteria but in the rhizosphere samples, the majority of bacteria belonged to Proteobacteria and Acidobacteria. Bacterial community compositions of rhizosphere soils from different plants were similar, indicating only a weak influence of plant species on rhizosphere microbial community structure.     

Occurrence of vesicular-arbuscular mycorrhizae with Amaranthaceae in soils of the Indian semi-arid region

Summary Some members of the family Amaranthaceae, which has mostly been reported as non-mycorrhizal, were examined for a symbiotic association with mycorrhizae in the semiarid and arid zones. Ten species belonging to five genera, Achyranthes, Aerva, Alternanthera, Amaranthus, and Celosia were examined, using 1.0-cm long root standards. Intercellular hyphae, vesicles and arbuscules were observed in the root cortex. The number of different types of spores in the rhizosphere soil of different plants ranged from one to three. The spores isolated represented nine species belonging to four genera, Glomus, Gigaspora, Sclerocystis, and Scutellospora. No correlation could be established between spore counts and either soil pH or soil moisture.     

Arbuscular mycorrhizal fungi of a Mediterranean island (Pianosa), within a UNESCO Biosphere Reserve

In this work we have determined the community composition of spore-forming arbuscular mycorrhizal fungi (AMF) in a maquis site on Pianosa island, a protected area within the Tuscan Islands UNESCO Biosphere Reserve, Italy. We have analysed rhizosphere soil of the dominant plant species Pistacia lentiscus, Smilax aspera, Rosmarinus officinalis and of the endemic plant Helichrysum litoreum. The AMF species recovered were: Scutellospora dipurpurescens, Glomus coronatum, Glomus mosseae, Glomus etunicatum, Glomus geosporum, Glomus viscosum, Entrophospora sp., Pacispora sp. and Glomus rubiforme. The identification of native S. dipurpurescens and G. coronatum was carried out on spores isolated from rhizosphere soil of H. litoreum, by combining morphological traits and 18S (SSU) and ITS rDNA sequences. Therefore, AMF species of Pianosa rhizosphere soils represent an important repository for the conservation and maintenance in their natural habitat of such beneficial symbionts, key microorganisms of soil fertility.     

黄土丘陵沟壑区典型林地土壤微生物、酶活性和养分特征

通过对陕西吴起县黄土沟壑区退耕还林地不同林分(沙棘、刺槐、油松、小叶杨)根际与非根际土壤养分、酶活性和微生物特征进行研究,比较4种典型林分及退耕草地“根际效应”及根际对养分的截留效应,评价根际效应对土壤特性产生不同改良效果,为黄土沟壑区退耕地人工林科学选择造林树种提供理论支持。研究表明:1根际与非根际土壤中有机质含量、有效磷含量、碱解氮含量和速效钾含量表现出显著差异,有机质、有效磷、速效钾含量均呈现明显的根际聚集现象。2根际土壤微生物数量和土壤酶活性总体高于非根际,仅油松样地中过氧化氢酶活性和小叶杨样地中脲酶活性根际低于非根际。3根际土壤中脲酶活性与细菌和真菌数量相关性达到显著水平,过氧化氢酶活性与真菌相关性达到显著水平;有机质含量与细菌、放线菌数量和脲酶活性相关性达到显著水平;碱解氮、有效磷含量均与细菌、真菌数量和脲酶活性相关性达到显著水平。在非根际土壤中,土壤养分含量与土壤微生物、土壤酶活性的相关性明显降低。4从土壤肥力综合水平看,根际土壤肥力水平综合得分总体上大于非根际土壤,其中根际土壤中沙棘小叶杨油松刺槐草地。沙棘能大幅度提高土壤肥力,具有较好的土壤改良效果。