Organic farming affects the potential of a granivorous carabid beetle to control arable weeds at local and landscape scales

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Fungicide Effects on Fungal Community Composition in the Wheat Phyllosphere

The fungicides used to control diseases in cereal production can have adverse effects on non-target fungi, with possible consequences for plant health and productivity. This study examined fungicide effects on fungal communities on winter wheat leaves in two areas of Sweden. High-throughput 454 sequencing of the fungal ITS2 region yielded 235 operational taxonomic units (OTUs) at the species level from the 18 fields studied. It was found that commonly used fungicides had moderate but significant effect on fungal community composition in the wheat phyllosphere. The relative abundance of several saprotrophs was altered by fungicide use, while the effect on common wheat pathogens was mixed. The fungal community on wheat leaves consisted mainly of basidiomycete yeasts, saprotrophic ascomycetes and plant pathogens. A core set of six fungal OTUs representing saprotrophic species was identified. These were present across all fields, although overall the difference in OTU richness was large between the two areas studied.     

Shared and unique features of bacterial communities in native forest and vineyard phyllosphere

Phyllosphere bacteria have received little attention despite their important roles in shaping plant performance traits. In this study, we characterize the bacterial communities on leaves of native trees inhabiting sclerophyllous forests in central Chile, one of the world's biodiversity hotspots. Additionally, we provide profiles of bacterial communities on grape leaves and berries of organic and conventional vineyards. Results of 16S rRNA gene amplicon sequence analysis showed that 45% of OTUs were shared across forest leaves, grape leaves, and grape berries. Conventional management had higher number of OTUs shared with forest leaves than organic management. In addition, grape leaves subjected to conventional management had higher alpha diversity than those with organic management, while no significant effect of agricultural management was observed in grape berries. Indicator analysis showed that Bdellovibrio, Beijerinckia, and Spirosoma were typical for forest leaves, whereas Enhydrobacter, Delftia, Proteiniclasticum, Arsenicicoccus, and Alkaliphilus were typical for the vineyard phyllosphere. Regarding agricultural managements, Beijerinckia, Sedimentibacter, Nesterenkonia, Gluconobacter, Conexibacter, and Anaeromyxobacter were typical for conventional grape leaves, whereas no genus‐level indicator was found for organic vineyard leaves. These results provide new insights of the diversity patterns of the phyllosphere microbiome in native and cultivated lands and suggest that both of these microbiomes are connected and integrated systems.     

Host Identity Impacts Rhizosphere Fungal Communities Associated with Three Alpine Plant Species

Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF) or non-arbuscular mycorrhizal (non-AMF) fungi and then tested whether habitat or host identity influenced these fungal communities. Approximately 14% of the sequences represented AMF taxa (44 OTUs) with the majority belonging to Glomus groups A and B. Non-AMF sequences represented 186 OTUs belonging to Ascomycota (58%), Basidiomycota (26%), Zygomycota (14%), and Chytridiomycota (2%) phyla. Total AMF and non-AMF richness were similar between habitats but varied among host species. AMF richness and diversity per root sample also varied among host species and were highest in T. ceratophorum compared with T. officinale and P. viscosum. In contrast, non-AMF richness and diversity per root sample were similar among host species except in the willow understory where diversity was reduced in T. officinale. Fungal community composition was influenced by host identity but not habitat. Specifically, T. officinale hosted a different AMF community than T. ceratophorum and P. viscosum while P. viscosum hosted a different non-AMF community than T. ceratophorum and T. officinale. Our results suggest that host identity has a stronger effect on rhizosphere fungi than habitat. Furthermore, although host identity influenced both AMF and non-AMF, this effect was stronger for the mutualistic AMF community.     

Fungal diversity and functionality are driven by soil texture in Taylor Valley,Antarctica

The McMurdo Dry Valleys surface is mainly constituted from unconsolidated permafrost. Despite the combination of cold and dry conditions, transiently wetted soils close to lake edges are hotspots of intense biological activity, that can support the surrounding soil ecosystems in such extreme environments. These soils host simple microbial communities that allow easy characterization of the parameters determining microbial establishment and diversification. Soil samples were collected close to three different glacial lakes (Lake Fryxell, Lake Hoare and Lake Joyce) located along a longitudinal gradient from the lower to the upper Taylor Valley. Fungal diversity and functionality of sampled soils were studied through ITS1 metabarcoding sequencing. The correlation between the parameters describing fungal diversity (i.e. total richness, relative richness of dominant taxonomic and functional groups, and community composition) and the edaphic physicochemical parameters (i.e. pH, moisture, C, N, P, Na⁺, K⁺, Mg²⁺ and Ca²⁺, cation exchange capacity, and soil granulometry) was assessed. The fungal communities showed low richness (48 ± 32 OTUs per sample). Their composition was highly diversified even within different sites close to the same lake. The main parameters affecting the diversity and composition of fungal communities were soil texture, in turn influencing the retention of water and nutrients, and physicochemical properties. This is of particular concern for the survival of these communities, given the expected environmental changes due to global warming.     

Farming practices change food web structures in cereal aphid–parasitoid–hyperparasitoid communities

Agricultural intensification has been shown to result in a decline in biodiversity across many taxa, but the changes in community structure and species interactions remain little understood. We have analysed and compared the structure of feeding interactions for cereal aphids and their primary and secondary parasitoids in organically and conventionally managed winter wheat fields using quantitative food web metrics (interaction evenness, generality, vulnerability, link density). Despite little variation in the richness of each trophic group, food web structures between the two farming systems differed remarkably. In contrast to common expectations, aphids and primary parasitoids were characterized by (1) a higher evenness of interaction frequencies (interaction evenness) in conventional fields, which cascaded to interactions at the next trophic level, with (2) a higher interaction evenness, (3) a higher ratio of primary parasitoid taxa per secondary parasitoid (generality) and (4) a higher link density. Aphid communities in the organically managed fields almost exclusively consisted of a single ear-colonizing species, Sitobion avenae, while highly fertilized conventional fields were mainly infested by leaf-colonizing aphids that benefit from the nutritional status of winter wheat. In conclusion, agricultural intensification appears to foster the complexity of aphid–parasitoid food webs, thereby not supporting the general expectation on the importance of organic farming practices for species richness and food web complexity.     

Decrease in diversity and changes in community composition of arbuscular mycorrhizal fungi in roots of apple trees with increasing orchard management intensity across a regional scale

Understanding which factors drive the diversity and community composition of arbuscular mycorrhizal fungi (AMF) is important due to the role of these soil micro‐organisms in ecosystem functioning and current environmental threats to AMF biodiversity. Additionally, in agro‐ecosystems, this knowledge may help to evaluate their use in making agriculture more sustainable. Here, we used 454‐pyrosequencing of small subunit rRNA gene amplicons to quantify AMF diversity and community composition in the roots of cultivated apple trees across 24 orchards in central Belgium. We aimed at identifying the factors (soil chemical variables, organic vs. conventional farming, and geographical location) that affect AMF diversity and community composition. In total, 110 AMF OTUs were detected, of which the majority belonged to the Glomeraceae (73%) and the Claroideoglomeraceae (19%). We show that soil characteristics and farming system, rather than the geographical location of the orchards, shape AMF communities on apple trees. Particularly, plant‐available P content of the soil was associated with lower AMF diversity. In orchards with a lower plant‐available P content of the soil (P < 100 mg/kg soil), we also found a significantly higher AMF diversity in organically managed orchards as compared to conventionally managed orchards. Finally, the degree of nestedness of the AMF communities was related to plant‐available P and N content of the soil, pointing at a progressive loss of AMF taxa with increasing fertilization. Overall, we conclude that a combination of organic orchard management and moderate fertilization may preserve diverse AMF communities on apple trees and that AMF in the roots of apple trees appear not to be dispersal limited at the scale of central Belgium.     

烤后不同霉变程度烟叶际真菌群落组成与多样性分析

【目的】为了解烤后不同霉变程度烟叶真菌群落组成与多样性。【方法】基于IlluminaMiSeq高通量测序平台对烤后烟叶叶柄和叶片叶际样品的真菌群落组成进行了分析。【结果】霉变重烟叶叶片(BQ)、霉变重烟叶叶柄(BZ)、霉变轻烟叶叶片(JQ)、霉变轻烟叶叶柄(JZ) 4类样品真菌分布于子囊菌门(Ascomycota)、担子菌门(Basidiomycota)、接合菌门(Zygomycota)等7个菌门、27个纲、58个目、104个科、171个属的360个真菌分类单元(OTUs)。不同霉变程度烟叶叶际真菌群落组成、分类单元的相对丰度及优势分类单元皆存在不同程度差异。在属的水平上,霉变重烟叶叶片(BQ)的优势菌属为Aspergillus (89.64%)、Myrothecium (2.54%)、Rhodotorula (2.48%)、Gibberella (1.49%);霉变重烟叶叶柄(BZ)的优势菌属为Aspergillus(96.93%)和Alternaria(1.92%);霉变轻烟叶叶片(JQ)的优势菌属为Aspergillus(40.13%)、Rhodotorula(31.81%)、Alternaria(16.75%);霉变轻烟叶叶柄(JZ)的优势菌属为Aspergillus (62.77%)、Alternaria (9.74%)、Rhodotorula (5.20%)。【结论】霉变轻烟叶叶片样品真菌群落的多样性最高,霉变轻烟叶叶柄的真菌群落丰富度最高。霉变重烟叶样品的叶片部位的真菌群落丰富度和多样性均高于叶柄。烟叶霉烂为烤房常见病害,其病原真菌种类多样,且广泛分布于烟叶和环境中。该研究结果为烤房烟叶霉烂病的防治可根据不同发病程度的不同部位的真菌群落构成特征,制定相应的防治方案提供了参考依据。     

Diversity of spiders after spring sowing – influence of farming system and habitat type

Spiders contribute considerably to diversity in agroecosystems and are important components of natural pest control. Farming system and adjacent habitats may influence spider diversity. In this study, diversity of the spider families Lycosidae and Linyphiidae was studied after spring sowing until the time when a common pest (Rhopalosiphum padi) colonizes cereal fields. The spiders were collected with pitfall traps at eight organically or conventionally managed farms around Uppsala, Sweden, in three different habitats at each site: field margin, crop field and the edge between the two. The effects of farming system and habitat type on diversity of lycosids and linyphiids were considered using three different measures (activity density, species richness and composition). The most dominant species of each spider family, Pardosa agrestis (Lycosidae) and Oedothorax apicatus (Linyphiidae), had higher activity density at organic sites, and farming systems also contained different species compositions of both lycosid and linyphiid spiders. Also, linyphiid species richness was higher on conventional sites and linyphiid species composition was influenced by habitat type, in contrast with lycosids. Activity density and species richness of lycosid spiders were, on the other hand, more associated with field margins than linyphiid spiders.     

青杨雌雄株叶际微生物群落多样性和结构的差异

【目的】本论文探究了青杨雌雄株的叶际微生物的群落结构差异及其主要环境影响因素。【方法】以河北小五台山的天然青杨林为研究对象,采用基于16S rRNA/ITS1基因的MiSeq高通量测序技术,分析了青杨雌雄株叶际细菌和真菌的群落结构,并耦合分析其与叶片理化性质的相关性。【结果】测序结果表明细菌和真菌的多样性指数ACE、Chao1、Shannon、Simpson在雌雄株间都无显著性差异(P>0.05)。Metastats组间群落显著性差异分析表明,在门水平,青杨雌雄株叶际细菌和真菌都无显著差异。而在属水平,青杨雌雄株的叶际细菌Amnibacterium和Spingomonas及真菌Aureobasidium、Elmerina、Exobasidium、Endoconidioma、Monilinia和Rhodotorula的相对丰度在雌雄株叶际有显著差异(P<0.05)。基于OTUs的菌群分析表明,青杨雌株和雄株的叶际环境上都有其各自的特有菌群,如雌株的特有真菌Pringsheimia(0.15%)和细菌Chitinophaga(0.04%)。RDA冗余分析表明,叶片含水量与青杨叶际真菌的群落结构有显著相关性(P<0.05),而未发现青杨细菌群落结构与测定的叶片理化性质有显著相关。【结论】青杨雌雄株叶际微生物在属水平有显著分异的菌属,且可能受叶片理化性质影响,该结果为揭示雌雄异株植物的叶际微生物差异有重要借鉴意义。     

黑老虎内生真菌及根际土壤真菌的群落结构与生态功能分析

为探讨黑老虎(Kadsura coccinea)根际土壤和组织内生真菌菌群的组成及其生态功能，该研究采用ITS高通量测序技术对成熟黑老虎(根、茎、叶)内生真菌及根际土壤真菌群落结构、多样性和生态功能进行了分析。结果表明：(1)从12个样品中共获得2 241个可操作分类单元(OTU),涉及10门、41纲、95目、212科、367属，内生真菌(根、茎、叶)和根际土壤真菌OTU数分别为386、536、258、1 435个，其中共有的OTU为18个。在门水平上，黑老虎内生真菌及根际土壤真菌优势群落均为子囊菌门和担子菌门，其中子囊菌门在叶和茎中占比分别高达96.99%和95.37%;在属水平上，黑老虎根际土壤真菌中腐生真菌被孢霉属占比较高(为13.5%),叶和茎等生长旺盛的组织中子囊菌门未分类属和痂囊腔菌属占比较高。(2)α多样性分析结果显示，黑老虎根际土壤真菌群落的丰度和多样性明显高于内生真菌，茎中内生真菌丰度显著高于根和叶，而根、茎和叶组织间内生真菌多样性差异不显著；PCoA分析结果显示，叶和茎的真菌群落结构相似性更高。(3)利用FUNGuild数据库进行的功能预测分析结果显示，黑老虎根际土...     

Culture-dependent and culture-independent assessment of bacteria in the apple phyllosphere

Aims: Bacterial communities in the apple phyllosphere were examined quantitatively and qualitatively by applying culture‐dependent and culture‐independent methods. Methods and Results: Populations estimated by viewing cells stained with 4′,6‐diamidino‐2‐phenylindole generally were at least 100–1000 times greater than populations estimated by culturing on tryptic soy agar (TSA). Of the 44 operational taxonomic units (OTUs; cut‐off threshold of 97%) detected in total, five bacterial orders containing 23 OTUs were identified by culturing on TSA, whereas nine orders containing 33 OTUs were identified by 16S rRNA gene cloning of DNA extracted from apple leaf surfaces. Twelve of the 44 OTUs were shared between cultured isolates and 16S rRNA gene clones and included the orders Burkholderiales, Pseudomonadales, Rhizobiales and Sphingomonadales. Three OTUs within the genus Sphingomonas accounted for 40% of isolates and 68% of clones. The Actinomycetales were found only among isolates, whereas the Bacteroidales, Enterobacteriales, Myxococales and Sphingobacteriales were represented in the 16S rRNA gene clone libraries but were absent among isolates. Conclusions: Culture‐independent methods revealed greater numbers and greater richness of bacteria on apple leaves than found by culturing. Significance and Impact of the Study: This is the first study to directly compare culture‐dependent and independent approaches for assessing bacterial communities in the phyllosphere. The biases introduced by different methods will have a significant impact on studies related to phyllosphere ecology, biological control of plant diseases, reservoirs of antibiotic resistance genes and food safety.     

Midgut fungal and bacterial microbiota of Aedes triseriatus and Aedes japonicus shift in response to La Crosse virus infection

Understanding how midgut microbial communities of field‐collected mosquitoes interact with pathogens is critical for controlling vector infection and disease. We used 16S rRNA and internal transcribed spacer sequencing to characterize the midgut bacterial and fungal communities of adult females of Aedes triseriatus and Aedes japonicus collected as pupae in tree holes, plastic bins and waste tires and their response to La Crosse virus (LACV) infection. For both mosquito species and across all habitat and virus treatments, a total of 62 bacterial operational taxonomic units (OTUs) from six phyla and 21 fungal OTUs from two phyla were identified. The majority of bacterial (92%) and fungal (71%) OTUs were shared between the mosquito species; however, several OTUs were unique to each species. Bacterial and fungal communities of individuals that took either infectious or noninfectious bloodmeals were less diverse and more homogeneous compared to those of newly emerged adults. Interestingly, LACV‐infected A. triseriatus and A. japonicus had higher bacterial richness and lower fungal richness compared to individuals that took a noninfectious bloodmeal, suggesting that viral infection was associated with an increase in bacterial OTUs and a decrease in fungal OTUs. For both mosquito species, several OTUs were identified that had both high fidelity and specificity to mosquito midguts that were infected with LACV. Overall, these findings demonstrate that bacterial and fungal communities that reside in mosquito midguts respond to host diet and viral infection and could play a role in modulating vector susceptibility to LACV.     

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose (¹³C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO₃ ^? as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.     

Mycorrhizal fungal spore community structure in a manipulated prairie

Most plant communities support a diverse assemblage of arbuscular mycorrhizal fungi (AMF). AMF communities have the potential to affect plant community structure and vice versa. We examined AMF sporulation in a 4.5‐ha reconstructed prairie in Eau Claire County, Wisconsin. In fall 2003, the site was planted with varied numbers and combinations of native prairie species from four functional guilds: C₃ grasses/sedges, C₄ grasses, legume, and nonleguminous forbs. We hypothesized that more diverse plant seeding mixtures would promote AMF diversity. To examine the interaction between plant and fungal communities, plots were divided and subplots treated with the fungicide chlorothalonil to suppress AMF, enriched with ammonium nitrate fertilizer, treated with both fungicide and nitrogen, or remained untreated (control). Soil samples were collected during the summers of 2004, 2006, and 2007 from each subplot. Spores of AMF were extracted, identified to species, and enumerated. Initial plant seeding diversity did not significantly influence spore abundance, fungal diversity, plant productivity, or plant richness 4 years after establishment. Fungal species richness was positively, but weakly, correlated with plant productivity (r² = 0.11) and plant richness (r² = 0.09). Fungal community composition changed significantly over time; nitrogen addition, fungicide application, and site characteristics also shaped community composition. After 4 years of treatment, nitrogen and fungicide reduced AMF richness, changed sporulation patterns among AMF taxa, and reduced diversity and productivity in plant communities. Divergence in AMF community is being mirrored by changes in the plant community independent of initial seeding treatments, though causation could not be determined.     

Generalist predators in organically and conventionally managed grass‐clover fields: implications for conservation biological control

Organically managed agroecosystems rely in part on biological control to prevent pest outbreaks. Generalist predators (Araneae, Carabidae and Staphylinidae) are a major component of the natural enemy community in agroecosystems. We assessed the seasonal dynamics of major generalist predator groups in conventionally and organically managed grass–clover fields that primarily differed by fertilisation strategy. We further established an experiment, manipulating the abundant wolf spider genus Pardosa, to identify the importance of these predators for herbivore suppression in the same system and growth period. Organic management significantly enhanced ground‐active spider numbers early and late in the growing season, with potentially positive effects of plant cover and non‐pest decomposer prey. However, enhancing spider numbers in the field experiment did not improve biological control in organically managed grass–clover fields. Similar to the survey results, reduced densities of Pardosa had no short‐term effect on any prey taxa; however, spider guild structure changed in response to Pardosa manipulation. In the presence of fewer Pardosa, other ground‐running spiders were more abundant; therefore, their impact on herbivore numbers may have been elevated, possibly cancelling increases in herbivore numbers because of reduced predation by Pardosa. Our results indicate positive effects of organic farming on spider activity density; however, our survey data and the predator manipulation experiment failed to find evidence that ground‐running spiders reduced herbivore numbers. We therefore suggest that a positive impact of organic fertilisers on wolf spiders in grass–clover agroecosystems may not necessarily improve biological control when compared with conventional farming.     

Metabarcoding of fungal communities associated with bark beetles

Many species of fungi are closely allied with bark beetles, including many tree pathogens, but their species richness and patterns of distribution remain largely unknown. We established a protocol for metabarcoding of fungal communities directly from total genomic DNA extracted from individual beetles, showing that the ITS3/4 primer pair selectively amplifies the fungal ITS. Using three specimens of bark beetle from different species, we assess the fungal diversity associated with these specimens and the repeatability of these estimates in PCRs conducted with different primer tags. The combined replicates produced 727 fungal Operational Taxonomic Units (OTUs) for the specimen of Hylastes ater, 435 OTUs for Tomicus piniperda, and 294 OTUs for Trypodendron lineatum, while individual PCR reactions produced on average only 229, 54, and 31 OTUs for the three specimens, respectively. Yet, communities from PCR replicates were very similar in pairwise comparisons, in particular when considering species abundance, but differed greatly among the three beetle specimens. Different primer tags or the inclusion of amplicons in separate libraries did not impact the species composition. The ITS2 sequences were identified with the Lowest Common Ancestor approach and correspond to diverse lineages of fungi, including Ophiostomaceae and Leotiomycetes widely found to be tree pathogens. We conclude that Illumina MiSeq metabarcoding reliably captures fungal diversity associated with bark beetles, although numerous PCR replicates are recommended for an exhaustive sample. Direct PCR from beetle DNA extractions provides a rapid method for future surveys of fungal species diversity and their associations with bark beetles and environmental variables.     

Fungal endophyte communities differ between chestnut galls and surrounding foliar tissues

Foliar endophytic fungi are present in almost all vascular plants. The composition of endophyte communities varies among plant individuals. Likely, but understudied, sources of this variation are the species composition of the plant community and initial attacks by insect herbivores. We addressed these issues by characterizing fungal endophyte communities on leaves of chestnut (Castanea sativa) grown in pure vs. mixed stands. We used ITS metabarcoding methods to identify endophytic fungi associated with galls caused by the invasive gall wasp, Dryocosmus kuriphilus, and with surrounding chestnut leaf tissues. We found 1378 different OTUs. The richness, diversity and composition of endophyte communities differed between galls and surrounding leaf tissues but were independent of forest stand composition. Fungal endophyte richness was lower in galls than in surrounding leaf tissues. Most differences in the composition of fungal endophyte communities between galls and foliar tissues were due to OTU turnover. These results suggest that insect-induced galls provide a particular habitat condition for endophytic microorganisms, regardless of forest species composition. A better understanding of endophyte biology is important to improve their use as biocontrol agents of galling insects.     

Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars

Fungal endophytes are micro-organisms that colonize healthy plant tissues without causing disease symptoms. They are described as plant growth and disease resistance promoters and have shown antimicrobial activity. The spatial-temporal distribution of endophytic communities in olive cultivars has been poorly explored. This study aims to investigate the richness and diversity of endophytic fungi in different seasons and sites, within the Alentejo region, Portugal. Additionally, and because the impact of some pathogenic fungi (e.g. Colletotrichum spp.) varies according to olive cultivars; three cultivars, Galega vulgar, Cobrançosa and Azeiteira, were sampled. 1868 fungal isolates were identified as belonging to 26 OTUs; 13 OTUs were identified to the genera level and 13 to species level. Cultivar Galega vulgar and season autumn showed significant higher values in terms of endophytic richness and diversity. At site level, Elvas showed the lowest fungal richness and diversity of fungal endophytes. This study reinforces the importance of exploring the combined spatio-temporal distribution of the endophytic biodiversity in different olive cultivars. Knowledge about endophytic communities may help to better understand their functions in plants hosts, such as their ecological dynamics with pathogenic fungi, which can be explored for their use as biocontrol agents.     

Diversity and functional traits of culturable microbiome members,including cyanobacteria in the rice phyllosphere

The diversity and abundance of culturable microbiome members of the rice phyllosphere was investigated using cv. Pusa Punjab Basmati 1509. Both diversity and species richness of bacteria were significantly higher in plants in pots in a semi‐controlled environment than those in fields. Application of fertilisers reduced both diversity and species richness in field‐grown plants under a conventional flooded system of rice intensification (SRI) and in dry‐seeded rice (DSR) modes. Sequence analyses of 16S rDNA of culturable bacteria, those selected after amplified ribosomal DNA restriction analysis (ARDRA), showed the dominance of α‐proteobacteria (35%) and actinobacteria (38%); Pantoea, Exiguobacterium and Bacillus were common among the culturable phyllospheric bacteria. About 34% of 83 culturable bacterial isolates had higher potential (>2 μg·ml^?1) for indole acetic acid production in the absence of tryptophan. Interestingly, the phyllosphere bacterial isolates from the pot experiment had significantly higher potential for nitrogen fixation than isolates from the field experiment. Enrichment for cyanobacteria showed both unicellular forms and non‐heterocystous filaments under aerobic as well as anaerobic conditions. PCR‐DGGE analysis of these showed that aerobic and anaerobic conditions as well as the three modes of cultivation of rice in the field strongly influenced the number and abundance of phylotypes. The adaptability and functional traits of these culturable microbiome members suggest enormous diversity in the phyllosphere, including potential for plant growth promotion, which was also significantly influenced by the different methods of growing rice.