Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition

Microbial composition and diversity of the tobacco leaf phyllosphere during plant development

Phyllosphere-associated microorganisms affect host plant's nutrients availability, its growth and ecological functions. Tobacco leaves provide a wide-area habitat for microbial life. Previous studies have mainly focused on phyllosphere microbiota at one time point of tobacco growth process, but more is unknown about dynamic changes in phyllospheric microbial composition from earlier to the late stage of plant development. In the current study, we had determined the bacterial and fungal communities succession of tobacco growth stages (i.e., seedling, squaring, and maturing) by using both 16S rRNA sequencing for bacterial and ITS sequencing for fungi. Our results demonstrated that among tobacco growth stages, the phyllospheric bacterial communities went through more distinct succession than the fungal communities did. Proteobacteria and Actinobacteria exerted the most influence in tobacco development from seedling to squaring stages. At maturing stage, Proteobacteria and Actinobacteria dominance was gradually replaced by Firmicutes and Bacteroidetes. Network analysis revealed that Proteobacteria, as the core phyllospheric microbia, played essential role in stabilizing the whole bacterial network during tobacco development, and consequently rendered it to more profound ecological functions. During tobacco development, the contents of leaf sugar, nicotine, nitrogen and potassium were significantly correlated with either bacterial or fungal communities, and these abiotic factors accounted for 39.3 and 51.5% of the total variation, respectively. We overall evinced that the development of tobacco phyllosphere is accompanied by variant dynamics of phyllospheric microbial community.

Mycorrhizae Enhance Soybean Plant Growth and Aluminum Stress Tolerance by Shaping the Microbiome Assembly in an Acidic Soil

Strongly acidic soils are characterized by high aluminum (Al) toxicity and low phosphorus (P) availability, which suppress legume plant growth and nodule development. Arbuscular mycorrhizal fungi (AMF) stimulate rhizobia and enhance plant P uptake. However, it is unclear how this symbiotic soybean-AMF-rhizobial trio promotes soybean growth in acidic soils. We examined the effects of AMF and rhizobium addition on the growth of two soybean genotypes, namely, Al-tolerant and Al-sensitive soybeans as well as their associated bacterial and fungal communities in an acidic soil. With and without rhizobial addition, AMF significantly increased the fresh shoot and root biomass of Al-tolerant soybean by 47%/87% and 37%/24%, respectively. This increase in plant biomass corresponded to the enrichment of four plant growth-promoting rhizobacteria (PGPR) in the rhizospheric soil, namely, Chitinophagaceae bacterium 4GSH07, Paraburkholderia soli, Sinomonas atrocyanea, and Aquincola tertiaricarbonis. For Al-sensitive soybean, AMF addition increased the fresh shoot and root biomass by 112%/64% and 30%/217%, respectively, with/without rhizobial addition. Interestingly, this significant increase coincided with a decrease in the pathogenic fungus Nigrospora oryzae as well as an increase in S. atrocyanea, A. tertiaricarbonis, and Talaromyces verruculosus (a P-solubilizing fungus) in the rhizospheric soil. Lastly, the compartment niche along the soil-plant continuum shaped microbiome assembly, with pathogenic/saprotrophic microbes accumulating in the rhizospheric soil and PGPR related to nitrogen fixation or stress resistance (e.g., Rhizobium leguminosarum and Sphingomonas azotifigens) accumulating in the endospheric layer. IMPORTANCE Taken together, this study examined the effects of arbuscular mycorrhizal fungi (AMF) and rhizobial combinations on the growth of Al-tolerant and Al-sensitive soybeans as well as their associated microbial communities in acidic soils and concluded that AMF enhances soybean growth and Al stress tolerance by recruiting PGPR and altering the root-associated microbiome assembly in a host-dependent manner. In the future, these findings will help us better understand the impacts of AMF on rhizosphere microbiome assembly and will contribute to the development of soybean breeding techniques for the comprehensive use of PGPR in sustainable agriculture.

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland

Distinct plant associated microbiomes live in rhizosphere soil, roots, and leaves. However, the differences in community assembly of fungi and bacteria along soil-plant continuum are less documented in ecosystems. We examined fungal and bacterial communities associated with leaves, roots, and rhizosphere soil of the dominant arbuscular mycorrhizal (AM) plants Taraxacum mongolicum and Elymus nutans and non-AM plant Carex enervis in the Zoige Wetland by using high throughput sequencing techniques. The operational taxonomic unit (OTU) richness of fungi and bacteria was significantly higher in rhizosphere soil than in roots and leaves, and their community compositions were significantly different in the rhizosphere soil, roots, and leaves in each plant species. The co-occurrence network analysis revealed that the sensitive fungal and bacterial OTUs with various taxonomic positions were mainly clustered into different modules according to rhizosphere soil, roots, and leaves in each plant species. Along the soil-plant continuum, the rhizosphere soil pool contributed more source on bacterial than on fungal communities in roots and leaves of the three plant species, and more source on bacterial and fungal communities in leaves of T. mongolicum and E. nutans compared with C. enervis. Furthermore, the root pool contributed more source on bacterial than on fungal communities in leaves of T. mongolicum and E. nutans but not that of C. enervis. This study highlights that the host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities along the soil-plant continuum in AM plants T. mongolicum and E. nutans and non-AM plant C. enervis in the Zoige Wetland. IMPORTANCE Elucidating the community microbiome assemblage alone the soil-plant continuum will help to better understand the biodiversity maintenance and ecosystem functioning. Here, we examined the fungal and bacterial communities in rhizosphere soil, roots, and leaves of two dominant AM plants and a non-AM plant in Zoige Wetland. We found that along the soil - plant continuum, host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities in the AM- and non-AM plants. This is the first report provides evidence of different assembly patterns of fungal and bacterial communities along the soil-plant continuum in the AM- and non-AM plants in the Zoige Wetland.

Responses of arbuscular mycorrhizal fungi to nitrogen addition: A meta-analysis

Arbuscular mycorrhizal (AM) fungi play important roles in carbon (C), nitrogen (N) and phosphorus (P) cycling of terrestrial ecosystems. The impact of increasing N deposition on AM fungi will inevitably affect ecosystem processes. However, generalizable patterns of how N deposition affects AM fungi remains poorly understood. Here we conducted a global-scale meta-analysis from 94 publications and 101 sites to investigate the responses of AM fungi to N addition, including abundance in both intra-radical (host roots) and extra-radical portion (soil), richness and diversity. We also explored the mechanisms of N addition affecting AM fungi by the trait-based guilds method. Results showed that N addition significantly decreased AM fungal overall abundance (-8.0%). However, the response of abundance in intra-radical portion was not consistent with that in extra-radical portion: root colonization decreased (-11.6%) significantly, whereas extra-radical hyphae length density did not change significantly. Different AM fungal guilds showed different responses to N addition: both the abundance (spore density) and relative abundance of the rhizophilic guild decreased significantly under N addition (-29.8% and -12.0%, respectively), while the abundance and relative abundance of the edaphophilic guild had insignificant response to N addition. Such inconsistent responses of rhizophilic and edaphophilic guilds were mainly moderated by the change of soil pH and the response of root biomass, respectively. Moreover, N addition had an insignificant negative effect on AM fungal richness and diversity, which was strongly related with the relative availability of soil P (i.e. soil available N/P ratio). Collectively, this meta-analysis highlights that considering trait-based AM fungal guilds, soil P availability and host plant C allocation can greatly improve our understanding of the nuanced dynamics of AM fungal communities under increasing N deposition.

Plant Genetic Networks Shaping Phyllosphere Microbial Community

Phyllosphere microbial communities inhabit the aerial plant parts, such as leaves and flowers, where they form complex molecular interactions with the host plant. Contrary to the relatively well-studied rhizosphere microbiome, scientists are just starting to understand, and potentially utilize, the phyllosphere microbiome. In this article, we summarize the recent studies that have provided novel insights into the mechanism of the host genotype shaping the phyllosphere microbiome and the possibility to select a stable and well-adapted microbiome. We also discuss the most pressing gaps in our knowledge and identify the most promising research directions and tools for understanding the assembly and function of phyllosphere microbiomes - this understanding is necessary if we are to harness phyllosphere microbiomes for improving plant growth and health in managed systems.

Plant Growth and Soil Microbial Impacts of Enhancing Licorice With Inoculating Dark Septate Endophytes Under Drought Stress

This study mainly aimed to investigate the effects of dark septate endophytes (DSE) (Acrocalymma vagum, Paraboeremia putaminum, and Fusarium acuminatum) on the growth and microbial community composition in the rhizosphere soil of a medicinal plant, licorice (Glycyrrhiza uralensis), grown in the non-sterile soil under drought stress. The results showed that three DSE strains could effectively colonize the plant roots and form a strain-dependent symbiosis with licorice. Although drought stress declined the growth of licorice plants, these decreases were partly recovered by DSE inoculation. Specifically, the inoculation of A. vagum and P. putaminum significantly increased the biomass and glycyrrhizin content, whereas A. vagum and F. acuminatum increased glycyrrhizic acid content of host plants under drought stress. However, the inoculation of F. acuminatum showed significant negative effects on the shoot, root, and total biomass of licorice plants. In addition, the effects of DSE inoculation on the morphological, photosynthetic, and antioxidant parameters of licorice plants, and mineral nutrient and microbial community composition in the rhizosphere soil were dependent on the DSE species as well as water regime. Interestingly, DSE inoculation significantly increased AM fungi content under drought stress. In addition, DSE associated with water had a significant positive influence on soil organic matter, available phosphorus (P), AM fungi, leaf number, soluble protein, SOD activity, total root length, root branch, and glycyrrhizic acid content. Based on the results of variance partitioning analysis, 17.0, 34.0, 14.9, 40.1, 28.2, and 18.0% variations in shoot morphology, root morphology, plant biomass, active ingredient, photosynthetic parameters, and antioxidant parameters, respectively, were attributable to the presence of certain soil microorganisms. These findings suggest the possibility that DSE inoculation improved the root development and nutrient absorption of host plants, altered the soil microbiota, and might also contribute to plant growth and survival under drought conditions. As A. vagum exhibited positive effects on the plant biomass, morphological and physiological parameters, and active ingredient content in licorice plants under drought stress, it was considered to be the best fungus for licorice cultivation. These results contribute to the understanding of the ecological function of DSE fungi in dryland agriculture.

Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields

Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia, Cellulomonas, Microbacterium, Sphingomonas, and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae, Acetobacteraceae, Armatimonadaceae, and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.

Rhizobacterial communities of five co-occurring desert halophytes

BACKGROUND

Recently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.

METHODS

Five halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3-V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.

RESULTS

Significant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity of Halostachys caspica, Halocnemum strobilaceum and Kalidium foliatum associated bacterial communities was lower than that of Limonium gmelinii and Lycium ruthenicum communities. Furthermore, the composition of the bacterial communities of Halostachys caspica and Halocnemum strobilaceum was very different from those of Limonium gmelinii and Lycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.

DISCUSSION

Halophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.