Exploitation of endophytes for sustainable agricultural intensification

Intensive agriculture, which depends on unsustainable levels of agrochemical inputs, is environmentally harmful, and the expansion of these practices to meet future needs is not economically feasible. Other options should be considered to meet the global food security challenge. The plant microbiome has been linked to improved plant productivity and, in this microreview, we consider the endosphere – a subdivision of the plant microbiome. We suggest a new definition of microbial endophyte status, the need for synergy between fungal and bacterial endophyte research efforts, as well as potential strategies for endophyte application to agricultural systems.     

Bioactive chemical constituents produced by endophytes and effects on rice plant growth

We investigated the bioactive potential of fungal endophytes isolated from the roots of Glycine max (L.) Merr. and Cucumis sativus. Initial screening results showed that endophytes, (Chrysosporium pseudomerdarium, Aspergillus fumigates and Paecilomyces sp., Penicillium sp., Phoma glomerata, and Paecilomyces formosus) were promoting the growth attributes (shoot length, chlorophyll contents, and biomass) of mutant and wild-type rice. To know whether, these endophytes were producing bioactive chemical constituents; the endophytes were grown in potato dextrose, czapek broth, and ICI mediums that resulted in varying mycelia biomass. The advance chromatographic analysis of endophytic fungal culture filtrate showed gibberellins (GA) production namely GA₁ (0.05–10.55 ngml^?1), GA₃ (0.48–9.0 ngml^?1), GA₄ (0.2–8.0 ngml^?1), GA₇ (1.4–6.5 ngml^?1), and GA₉ (0.03–1.05 ngml^?1) while among endophytes, P. glomerata and P. formosus were highly potent in GAs production. Additionally, the endophyte's culture also contained indole-3-acetic acid (0.23–71.51 µgml^?1). Furthermore, oxalic (0.009–0.3 mgl^?1), quinic (0.019–0.22 mgl^?1), malic (1.94–17.2 mgl^?1), and citric (0.012–0.95 mgl^?1) acids were also present in the endophytic cultures. The biochemical potential of endophytes greatly varied depending on nutrient source and pH, however, czapek broth rich in carbon revealed higher potential for bioactive chemical constituent's production. In conclusion, the current findings suggest that endophyte can play a vital role in essential crop plant growth by synthesizing a wide array of bioactive metabolites. Furthermore, an increased production of chemical constituents can be achieved by changing the in vitro growth conditions of endophytes     

Fungal endophytes from Dioscorea zingiberensis rhizomes and their antibacterial activity

AIMS: The aim of the study was to isolate and characterize the endophytic fungi from the rhizomes of the Chinese traditional medicinal plant Dioscorea zingiberensis and to detect their antibacterial activities. METHODS AND RESULTS: After strict sterile sample preparation, nine fungal endophytes were isolated from rhizomes of the Chinese traditional medicinal plant D. zingiberensis. The endophytes were classified by morphological traits and internal transcribed spacer (ITS) rRNA gene sequence analysis. Their ITS rDNA sequences were 99-100% identical to Nectria, Fusarium, Rhizopycnis, Acremonium and Penicillium spp. respectively. Of these, the most frequent genera were Fusarium and Nectria. One isolate, Dzf7, was unclassified on the basis of its low sequence similarity. The next closest species was Alternaria longissima (c. 92.4% sequence similarity). Endophyte isolate Dzf5 showed the closest sequence similarity (c. 99.5%) to an uncultured soil fungus (DQ420800) obtained from Cedar Creek, USA. Bioassays using a modified broth dilution test were used to detect the antibacterial activity of n-butanol extracts of both mycelia and culture filtrates of D. zingiberensis showed biological activity against Bacillus subtilis, Staphylococcus haemolyticus, Escherichia coli and Xanthomonas vesicatoria. Minimal inhibitory concentration (MIC) values of the extracts were between 31 x 25 microg ml(-1) and 125 microg ml(-1). CONCLUSIONS: Endophytic fungus Dzf2 (c. 99 x 8% sequence similarity to Fusarium redolens) isolated from D. zingiberensis rhizome showed the most potent antibacterial activities. SIGNIFICANCE AND IMPACT OF THE STUDY: Endophytic fungi isolated from D. zingiberensis may be used as potential producers of antibacterial natural products.     

内生真菌对草坪植物病原真菌抑制作用的比较

分别从野生牧草羽茅(Achnatherum sibiricum (L.) Keng)、栽培种高羊茅(Festuca arundinacea Schreb.)(品种Millennium)、栽培种黑麦草(Lolium perenne L.) (品种Justus)中分离出内生真菌Neotyphodium sp.、N. coenophialum和N. lolli,通过体外培养法比较了这3种内生真菌对草坪植物病原真菌的抑制作用.结果表明,从羽茅中分离的内生真菌Neotyphodium sp.在两菌相交前对所有供试的病原真菌都有一定的抑制作用,其中对枝孢霉属(Cladosporium sp.)、弯孢霉属(Curvularia sp.)和拟茎点属(Phomopsis sp.)病原真菌的抑制效果尤为显著,对峙培养3d后的抑菌率分别达70.1%、52.3%和30.9%,营养竞争作用、重寄生作用是其主要的拮抗机制;从高羊茅中分离的内生真菌N. coenophialum对枝孢霉属病原真菌存在一定的抑制作用;而从黑麦草中分离的内生真菌N. lolli与病原真菌对峙培养时,病原真菌菌落慢慢侵占整个营养空间,内生真菌停止生长并逐渐褐变死亡.体外培养结果说明Neotyphodium sp.对供试病原真菌的拮抗效果优于N. coenophialum和N. lolli,由此推测Neotyphodium sp.与宿主植物羽茅的共生可能有利于宿主植物抵抗病原真菌的侵扰.     

Identification and characterization of PAH-degrading endophytes isolated from plants growing around a sludge dam

Abstract

This study involved the isolation of bacteria endophytes with PAH-degrading ability from plants growing around a sludge dam. A total of 19 distinct isolates that were morphologically identified were isolated from 4 species of plant with a follow-up confirmatory identification using the molecular technique. Polymerase chain reaction (PCR) of the 16S rRNA gene with specific primers (16S-27F PCR and 16S-1491R PCR) was carried out. The sequence of the PCR products was carried out, compared with similar nucleotides available in GenBank. Results of the phylogenetic analysis of the isolates indicated their belonging to 4 different clades including Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes. These were related to the genera Bacillus, Pseudomonas, Terribacillus, Virgibacillus, Stenotrophomonas, Paenibacillus, Brevibacterium, Geobacillus, Acinetobacter. From the result, Pseudomonas demonstrated a high incidence in the plants sampled. The in-vitro degradation study and the presence of dioxygenase genes indicated that these lists of endophytes are able to use the list of PAHs tested as their source of food and energy leading to their breakdown. This means that the bacterial endophytes contributed to the remediation of petroleum hydrocarbons in planta, a situation that may have been phytotoxic to plant alone. Therefore, these bacteria endophytes could be potential organisms for enhanced phytoremediation of PAHs.     

Survey of indigenous bacterial endophytes from cotton and sweet corn

The genotypic diversity of indigenous bacterial endophytes within stems and roots of sweet corn (Zea mays L.) and cotton (Gossypium hirsutum L.) was determined in field trials throughout one growing season. Strains were isolated from surface-disinfested tissues and identified by fatty acid analysis. Gram-negative bacteria comprised 70.5% of the endophytic bacteria and 27 of the 36 genera identified. The most frequently isolated groups from sweet corn roots, were Burkholderia pickettii and Enterobacter spp.; from sweet corn stems, Bacillus megaterium. Bacterial genera present in sweet corn roots were also generally present in sweet corn stems. However, Burkholderia gladioli, Burkholderia solanacearum and Enterobacter cloacae were isolated much more frequently from sweet corn roots than stems, whereas Methylobacterium spp. were found more frequently in sweet corn stems than roots. Agrobacterium radiobacter, Serratia spp. and Burkholderia solanacearum, were the most frequently isolated groups from cotton roots; and Bacillus megaterium and Bacillus pumilus from cotton stems. Acinetobacter baumannii and Arthrobacter spp. were present in cotton stems but not in cotton roots. There were 14 taxonomic groups present in cotton roots that were not in cotton stems; all but one were Gram-negative. These included, Agrobacterium radiobacter, Bacillus megaterium, Bacillus pumilus, Enterobacter asburiae, Pseudomonas chlororaphis, Serratia spp. and Staphylococcus spp. Rhizobium japonicum and Variovorax paradoxus were isolated, almost exclusively, from the roots of both crops. Bacterial taxa present in both sweet corn and cotton early in the season were generally present late in the season. The diversity of bacteria was greater in roots than stems for each crop.     

Introduced Plant Viruses and the Invasion of a Native Grass Flora

Weed and native grasses from the South Island of New Zealand were surveyed for virus infection. Cocksfoot mottle virus (CfMV) and Ryegrass mosaic virus (RgMV) were restricted to a few introduced species; however, Barley yellow dwarf viruses (BYDVs) have invaded native grasses in New Zealand. Virus incidence was significantly lower in the native species (2%) than in the introduced species (12%). Four different serotypes (RMV, RPV, PAV, MAV) were detected in the introduced grass flora but only two (RMV, PAV) were detected in native species. In experimental transmission tests the aphid vector Rhopalosiphum padi's survival was variable on the 20 native species tested but this was not due to the presence or absence of endophytic fungi as none were detected in the New Zealand species. Aphid numbers increased and plants were killed when R. padi fed on Agrostis muelleriana and Festuca multinodis. R. padi transmitted a PAV isolate to these and six other native species. BYDVs infected 4/5 of the subfamilies tested. Virus incidence in native Arundinoideae and Pooideae was significantly lower than in introduced Pooideae and Panicoideae. One species of Bambusoideae collected from the field was not infected but was found susceptible in glasshouse tests. Agrostis capillaris, Dactylis glomerata and Lolium perenne were identified as the most likely reservoirs of infection for the native flora. Anthoxanthum odoratum was not infected but if the SGV serotype and its vector Schizaphis graminum were ever introduced, A. odoratum could form an effective reservoir from near sea level into alpine areas. This revised version was published online in July 2006 with corrections to the Cover Date.     

Plant growth‐promoting endophytic bacteria augment growth and salinity tolerance in rice plants

• Salt stress negatively affects growth and development of plants. However, it is hypothesized that plant growth‐promoting endophytic bacteria can greatly alleviate the adverse effects of salinity and can promote growth and development of plants. In the present research, we aimed to isolate endophytic bacteria from halotolerant plants and evaluate their capacity for promoting crop plant growth.
• The bacterial endophytes were isolated from selected plants inhabiting sand dunes at Pohang beach, screened for plant growth‐promoting traits and applied to rice seedlings under salt stress (NaCl; 150 mm ).
• Out of 59 endophytic bacterial isolates, only six isolates, i.e. Curtobacterium oceanosedimentum SAK1, Curtobacterium luteum SAK2, Enterobacter ludwigii SAK5, Bacillus cereus SA1, Micrococcus yunnanensis SA2, Enterobacter tabaci SA3, resulted in a significant increase in the growth of Waito‐C rice. The cultural filtrates of bacterial endophytes were tested for phytohormones, including indole‐3‐acetic acid, gibberellins and organic acids. Inoculation of the selected strains considerably reduced the amount of endogenous ABA in rice plants under NaCl stress, however, they increased GSH and sugar content. Similarly, these strains augmented the expression of flavin monooxygenase (OsYUCCA1) and auxin efflux carrier (OsPIN1) genes under salt stress.
• In conclusion, the pragmatic application of the above selected bacterial strains alleviated the adverse effects of NaCl stress and enhanced rice growth attributes by producing various phytohormones.

     

Fungal endophytes of proteaceae, with particular emphasis onBotryosphaeria proteae

Fungal endophytes occurring in leaves and stems of three species of Proteaceae,Protea cynaroides, Leucospermum cordifolium andLeucadendron salignum×laureolum were investigated on farms in three locations in the Western Cape province of South Africa. The aims of this study were to determine ifBotryosphaeria proteae, a fungus that has been recorded from leaf spots ofProtea spp., was mostly restricted to leaf tissue, and whether it could occur as an endophyte in different members of Proteaceae. In this studyB. proteae was routinely isolated inProtea andLeucospermum, although it was not a dominant taxon and did not occur inLeucadendron. Botryosphaeria proteae occurred mostly in leaves, rather than stems, suggesting that it is not important as a stem canker pathogen.     

Geographical and seasonal influences on the distribution of fungal endophytes in Quercus ilex

A systematic survey of the endophytic assemblages of Quercus ilex in central Spain has been performed, with the goal of evaluating the importance of geographical and seasonal factors on these fungal communities. Four sampling sites were selected; one of them was sampled twice, in the spring and the autumn. The collected plant material consisted of bark, twigs and leaves from eight trees per site. Fungal strains were isolated with the use of a surface-sterilization method with sodium hypochlorite. A total of 2921 fungal strains grouped into 149 'species' or morphological types were recovered. The 10 dominant species, with isolation frequencies >1.5%, were Pyrenochaeta sp., Periconiella anamorph of Biscogniauxia mediterranea (De Not.) Kuntze, Pseudonectria sp., Cryptosporiopsis quercina Petrak, Alternaria alternata (Fr:) Keissl., two undetermined coelomycetes, Penicillium funiculosum Thom, Diplodia mutila Fr. apud Mont. and Ascochyta sp. Medians of fungal species per tree were significantly different among the sampled sites. The isolation frequencies of the dominant species, as well as other less frequent species, were significantly dependent on the sampling site. The degree of endophytic infection and the diversity of fungal species were significantly higher in the spring. The frequencies of all dominant species at one of the sites depended significantly on the season, except for C. quercina , Acremonium sclerotigenum (F & V Moreau ex Valenta) Gams. and D. mutila . Cluster analysis of the whole endophytic mycoflora of the sampled trees suggested that the geographical factor affects the endophytic distribution patterns more significantly than the seasonal factor.     

不同水稻组织内生细菌的群落多样性

[目的]为详细了解水稻不同组织内生细菌群落多样性。[方法]对宁粳43号内生细菌的总DNA提取后,采用高通量测序技术对水稻内生细菌的16S rRNA基因进行了序列测定,分析了水稻不同组织部位内生细菌群落结构特征。[结果]叶部共获得内生细菌OTUs 610个,茎部411个,根部174个。物种分类显示,叶部内生细菌种类隶属于22门40纲103目198科399属,其中优势类群是红球菌属（Rhodococcus）和乳酸杆菌属（Lactobacillus）,它们的相对丰度分别为21.00%和9.19%;茎部内生细菌种类隶属于19门31纲85目169科306属,其中优势类群是红球菌属和罗尔斯通菌属（Ralstonia）,它们的相对丰度分别为19.25%和13.52%;根部内生细菌种类隶属于9门19纲44目82科140属,其中优势类群是肠杆菌属（Enterobacter）和埃希氏杆菌属（Escherichia）,它们的相对丰度分别为81.13%和10.89%。根茎叶中相同的OTU有78个,放线菌门（Actinobacteria）与大多数细菌具有相关性。根系内生细菌中具有调控各种代谢网络功能的物种丰度高于茎部和叶部。[结论]不同水稻组织内生细菌具有丰富的群落多样性,其中叶部的内生细菌物种最丰富,根系参与各种代谢调控的细菌丰度最高,各个组织部位的优势菌属各不相同,变形菌门是最重要的水稻内生细菌。     

In vitro salt and thermal tolerance of fungal endophytes of Nicotiana spp. growing in arid regions of north-western Australia

Abstract

Endophytic fungal strains isolated from indigenous Nicotiana plants naturally growing in dry and hot regions of north-western Australia were characterised based on their tolerance to salinity and temperature. Sixty-eight fungal isolates were tested on eight levels (0.5 M, 1.0 M, 1.5 M, 2.0 M, 2.5 M, 3.0 M, 3.5 M and 4.0 M) of five different of salts solutions NaCl, KCl, MgCl₂, CaCl₂ and MgSO₄ and at various temperatures (25–50?°C). The salt adaptation test indicated that the fungal strains namely Aspergillus niger (E-202), A. ochraceous-A (E-134), Aurantiporus sp. (E-135), Cladosporium halotolerance (E-128), Pleurostomophora richardsiae (E-13) and Trichoderma sp. (E-185.1) were tolerant to higher concentrations of various salts. The most growth-limiting salt turned out to be MgCl₂ followed by the chaotrope CaCl₂. Responses to temperature tolerance revealed that most fungi tested could grow at 30?°C. About 50% all the fungi did not show any growth when the temperature was raised above 30?°C. When the temperature was raised up to 50?°C all the fungi failed to grow but the fungus Rasamsonia piperina (E-172). Endophyte strains identified could be promising candidates for future research in investigating the fungus–plant interactions and their roles in plant adaptation to inhospitable environments.     

水稻OsCIPK10基因的克隆和功能分析

利用反向遗传学的方法对水稻OsCIPK10基因的功能进行了分析。结果表明,过量表达OsCIPK10基因的转基因水稻与野生型水稻在株型、抗高盐和耐低钾能力方面没有明显差异,但是小RNA干扰表达OsCIPK10基因的转基因水稻表现出显著的抗盐性。在缺钾胁迫条件下OsCIPK10基因的表达升高,推测该基因在应答高盐和低钾的非生物胁迫过程中起作用。OsCIPK10基因启动子与报告基因GUS融合表达的转基因水稻的染色结果显示:OsCIPK10基因呈组成型表达,但是在维管组织表达水平更高。     

Occurrence of fungal endophytes in cultivars ofTriticum aestivum in South Africa

Fungal endophytes were isolated from leaves, roots and stems of four wheat cultivars and a breeding line at three different sampling dates during the 1993 growing season. Of the 55 different fungal taxa encountered, 19 were present at relative importance values of more than 5%. No cultivar-related differences in the assembleges of endophytes were observed.Phoma glomerata was not restricted to only one tissue type, whereasAlternaria alternata, basidiomycete sp. 1,Pleospora herbarum andEpicoccum nigrum occurred primarily in the leaves, andFusarium avenaceum was extremely frequent in roots. In general, colonization by endophytes increased with the age of the plants. Most endophytes were isolated from wheat leaves. Successional colonization of a given tissue type was quantitative rather than qualitative, with a given fungal taxon increasing or decreasing over the period sampled, rather than replacing the fungi initially encountered.Present address: Téra d'Sott 5, CH-6949, Comano, Switzerland.