Metagenomic Characterization Reveals Pronounced Seasonality in the Diversity and Structure of the Phyllosphere Bacterial Community in a Mediterranean Ecosystem

Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere

Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.

Seasonal dynamics of phyllosphere epiphytic microbial communities of medicinal plants in farmland environment

Introduction

The phyllosphere of plants is inhabited by various microorganisms, which play a crucial role in plant physiological metabolism. Currently, there is limited research on the dynamic effects of species and seasons on plant phyllosphere microbial community diversity and microbial interactions.

Methods

In this study, high-throughput sequencing technology was used to sequence the leaf surface parasitic microorganisms of five medicinal plants (Bupleurum chinense, Atractylodes lancea, Salvia miltiorrhiza, Astragalus membranaceus, and Lonicera japonica).

Results

The results showed that bacteria and fungi clustered into 3,898 and 1,572 operational taxonomic units (OTUs), respectively. Compared to host species, seasons had a more significant impact on the a diversity of bacteria and fungi. The heterogeneity of phyllosphere microbial communities was greater in winter compared to summer. Key species analysis at the OTU level and Spearman correlation analysis demonstrated significant preferences in microbial interactions under plant and seasonal backgrounds. The network connections between bacterial and fungal communities significantly increased during seasonal transitions compared to connections with plants.

Discussion

This study enhances our understanding of the composition and ecological roles of plant-associated microbial communities in small-scale agricultural environments. Additionally, it provides valuable insights for assessing the biodiversity of medicinal plants.

Above- and below-ground microbiome in the annual developmental cycle of two olive tree varieties

The olive tree is a hallmark crop in the Mediterranean region. Its cultivation is characterized by an enormous variability in existing genotypes and geographical areas. As regards the associated microbial communities of the olive tree, despite progress, we still lack comprehensive knowledge in the description of these key determinants of plant health and productivity. Here, we determined the prokaryotic, fungal and arbuscular mycorrhizal fungal (AMF) microbiome in below- (rhizospheric soil, roots) and above-ground (phyllosphere and carposphere) plant compartments of two olive varieties 'Koroneiki' and 'Chondrolia Chalkidikis' grown in Southern and Northern Greece respectively, in five developmental stages along a full fruit-bearing season. Distinct microbial communities were supported in above- and below-ground plant parts; while the former tended to be similar between the two varieties/locations, the latter were location specific. In both varieties/locations, a seasonally stable root microbiome was observed over time; in contrast the plant microbiome in the other compartments were prone to changes over time, which may be related to seasonal environmental change and/or to plant developmental stage. We noted that olive roots exhibited an AMF-specific filtering effect (not observed for bacteria and general fungi) onto the rhizosphere AMF communities of the two olive varieties/locations/, leading to the assemblage of homogenous intraradical AMF communities. Finally, shared microbiome members between the two olive varieties/locations include bacterial and fungal taxa with putative functional attributes that may contribute to olive tree tolerance to abiotic and biotic stress.

Community structure and function of epiphytic bacteria attached to three submerged macrophytes

In aquatic ecosystems, large amounts of epiphytic bacteria living on the leaf surfaces of submerged macrophytes play important roles in affecting plant growth and biogeochemical cycling. The restoration of different submerged macrophytes has been considered an effective measure to improve eutrophic lakes. However, the community ecology of epiphytic bacteria is far from well understood for different submerged macrophytes. In this study, we used quantitative PCR, 16S rRNA gene high-throughput sequencing and functional prediction analysis to explore the structure and function of epiphytic bacteria in an aquatic ecosystem recovered by three submerged macrophytes (Hydrilla verticillata, Vallisneria natans and Potamogeton maackianus) during two growth periods. The results showed that the community compositions and functions of epiphytic bacterial communities on the submerged macrophyte hosts were different from those of the planktonic bacterial communities in the surrounding water. The alpha diversity of the epiphytic bacterial community was significantly higher in October than in July, and the community compositions and functions differed significantly in July and October. Among the three submerged macrophytes, the structures and functions of the epiphytic bacterial community exhibited obvious differences, and some specific taxa were enriched on the biofilms of the three plants. The alpha diversity and the abundance of functions related to nitrogen and phosphorus transformation were higher in the epiphytic bacteria of P. maackianus. In summary, these results provide clues for understanding the distribution and formation mechanisms of epiphytic bacteria on submerged macrophyte leaves and their roles in freshwater ecosystems.

Variations of Phyllosphere and Rhizosphere Microbial Communities of Pinus koraiensis Infected by Bursaphelenchus xylophilus

Pine wood nematode, Bursaphelenchus xylophilus, as one of the greatest threats to pine trees, is spreading all over the world. Plant microorganisms play an important role in the pathogenesis of nematodes. The phyllosphere and rhizosphere bacterial and fungal communities associated with healthy Pinus koraiensis (PKa) and P. koraiensis infected by B. xylophilus at the early (PKb) and last (PKc) stages were analyzed. Our results demonstrated that pine wood nematode (PWD) could increase the phyllosphere bacterial Pielou_e, Shannon, and Simpson index; phyllosphere fungal Chao 1 index, as well as rhizosphere bacterial Pielou_e, Shannon, and Simpson index; and rhizosphere fungal Pielou_e, Shannon, and Simpson index. What's more, slight shifts of the microbial diversity were observed at the early stage of infection, and the microbial diversity increased significantly as the symptoms of infection worsened. With the infection of B. xylophilus in P. koraiensis, Bradyrhizobium (rhizosphere bacteria), Massilia (phyllosphere bacteria), and Phaeosphaeriaceae (phyllosphere fungi) were the major contributors to the differences in community compositions among different treatments. With the infection of PWD, most of the bacterial groups tended to be co-excluding rather than co-occurring. These changes would correlate with microbial ability to suppress plant pathogen, enhancing the understanding of disease development and providing guidelines to pave the way for its possible management.

Factors Structuring the Epiphytic Archaeal and Fungal Communities in a Semi-arid Mediterranean Ecosystem

The phyllosphere microbiome exerts a strong effect on plants' productivity, and its composition is determined by various factors. To date, most phyllosphere studies have focused on bacteria, while fungi and especially archaea have been overlooked. We studied the effects of plant host and season on the abundance and diversity of the epiphytic archaeal and fungal communities in a typical semi-arid Mediterranean ecosystem. We collected leaves in two largely contrasting seasons (summer and winter) from eight perennial species of varying attributes which could be grouped into the following: (i) high-canopy, evergreen sclerophyllοus shrubs with leathery leaves, and low-canopy, either semi-deciduous shrubs or non-woody perennials with non-leathery leaves, and (ii) aromatic and non-aromatic plants. We determined the abundance of epiphytic Crenarchaea, total fungi, Alternaria and Cladosporium (main airborne fungi) via q-PCR and the structure of the epiphytic archaeal and fungal communities via amplicon sequencing. We observed a strong seasonal effect with all microbial groups examined showing higher abundance in summer. Plant host and season were equally important determinants of the composition of the fungal community consisted mostly of Ascomycota, with Hypocreales dominating in winter and Capnodiales and Pleosporales in summer. In contrast, the archaeal community showed plant host driven patterns dominated by the Soil Crenarchaeotic Group (SCG) and Aenigmarchaeota. Plant habit and aromatic nature exhibited filtering effects only on the epiphytic fungal communities. Our study provides a first in-depth analysis of the key determinants shaping the phyllosphere archaeal and fungal communities of a semi-arid Mediterranean ecosystem.

The Microbiome of the Medicinal Plants Achillea millefolium L. and Hamamelis virginiana L

In the recent past many studies investigated the microbiome of plants including several medicinal plants (MP). Microbial communities of the associated soil, rhizosphere and the above-ground organs were included, but there is still limited information on their seasonal development, and in particular simultaneous investigations of different plant organs are lacking. Many studies predominantly addressed either the prokaryotic or fungal microbiome. A distinction of epi- and endophytic communities of above-ground plant organs has rarely been made. Therefore, we conducted a comprehensive investigation of the bacterial and fungal microbiome of the MP Achillea millefolium and studied the epi- and endophytic microbial communities of leaves, flower buds and flowers between spring and summer together with the microbiome of the associated soil at one location. Further, we assessed the core microbiome of Achillea from four different locations at distances up to 250 km in southern Germany and Switzerland. In addition, the bacterial and fungal epi- and endophytic leaf microbiome of the arborescent shrub Hamamelis virginiana and the associated soil was investigated at one location. The results show a generally decreasing diversity of both microbial communities from soil to flower of Achillea. The diversity of the bacterial and fungal endophytic leaf communities of Achillea increased from April to July, whereas that of the epiphytic leaf communities decreased. In contrast, the diversity of the fungal communities of both leaf compartments and that of epiphytic bacteria of Hamamelis increased over time indicating plant-specific differences in the temporal development of microbial communities. Both MPs exhibited distinct microbial communities with plant-specific but also common taxa. The core taxa of Achillea constituted a lower fraction of the total number of taxa than of the total abundance of taxa. The results of our study provide a basis to link interactions of the microbiome with their host plant in relation to the production of bioactive compounds.

Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems

The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant's compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.

A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand

The phyllosphere microbiome is increasingly recognised as an influential component of plant physiology, yet it remains unclear whether stable host-microbe associations generally exist in the phyllosphere. Leptospermum scoparium (mānuka) is a tea tree indigenous to New Zealand, and honey derived from mānuka is widely known to possess unique antimicrobial properties. However, the host physiological traits associated with these antimicrobial properties vary widely, and the specific cause of such variation has eluded scientists despite decades of research. Notably, the mānuka phyllosphere microbiome remains uncharacterised, and its potential role in mediating host physiology has not been considered. Working within the prevailing core microbiome conceptual framework, we hypothesise that the phyllosphere microbiome of mānuka exhibits specific host association patterns congruent with those of a microbial community under host selective pressure (null hypothesis: the mānuka phyllosphere microbiome is recruited stochastically from the surrounding environment). To examine our hypothesis, we characterised the phyllosphere and associated soil microbiomes of five distinct and geographically distant mānuka populations across the North Island of New Zealand. We identified a habitat-specific and relatively abundant core microbiome in the mānuka phyllosphere, which was persistent across all samples. In contrast, non-core phyllosphere microorganisms exhibited significant variation across individual host trees and populations that was strongly driven by environmental and spatial factors. Our results demonstrate the existence of a dominant and ubiquitous core microbiome in the phyllosphere of mānuka, supporting our hypothesis that phyllosphere microorganisms of mānuka exhibit specific host association and potentially mediate physiological traits of this nationally and culturally treasured indigenous plant. In addition, our results illustrate biogeographical patterns in mānuka phyllosphere microbiomes and offer insight into factors contributing to phyllosphere microbiome assembly.