Autoregulation of nodulation interferes with impacts of nitrogen fertilization levels on the leaf-associated bacterial community in soybeans

Interaction between C1-microorganisms and plants: contribution to the global carbon cycle and microbial survival strategies in the phyllosphere

C1-microorganisms that can utilize C1-compounds, such as methane and methanol, are ubiquitous in nature, and contribute to drive the global carbon cycle between two major greenhouse gases, CO2 and methane. Plants emit C1-compounds from their leaves and provide habitats for C1-microorganisms. Among C1-microorganisms, Methylobacterium spp., representative of methanol-utilizing methylotrophic bacteria, predominantly colonize the phyllosphere and are known to promote plant growth. This review summarizes the interactions between C1-mircroorganisms and plants that affect not only the fixation of C1-compounds produced by plants but also CO2 fixation by plants. We also describe our recent understanding of the survival strategy of C1-microorganisms in the phyllosphere and the application of Methylobacterium spp. to improve rice crop yield.

Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground?

Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.

Effects of Different Types of Additional Fertilizers on Root-associated Microbes of Napa Cabbage Grown in an Andosol Field in Japan

The effects of different types of additional fertilizations (a compound fertilizer and Chiyoda-kasei) on the root-associated microbes of napa cabbage grown in an Andosol field were investigated by molecular community ana-lyses. Most of the closest known species of the bacterial sequences whose relative abundance significantly differed among fertilizers were sensitive to nitrogen fertilization and/or related to the geochemical cycles of nitrogen. The fungal community on the roots of napa cabbage was dominated by two genera, Bipolaris and Olpidium. The relative abundance of these two genera was affected by the types of fertilizers to some extent and showed a strong negative correlation.

Phyllosphere bacterial assemblage is affected by plant genotypes and growth stages

The interaction between plants and microorganisms directly affects plant health and sustainable agricultural development. Leaves represent a wide-area habitat populated by a variety of microorganisms, whose impact on host environmental adaptability could influence plant growth and function. The driving factors for phyllosphere microbiota assemblage are the focus of current research. Here, we investigated the effect of growth stage (i.e., bolting, flowering, and maturation) and genotype of Arabidopsis thaliana (wild-type and the two photosynthetic mutants ndf4 and pgr5) on the composition of phyllosphere microbiota. Our results show that species abundance varied significantly between the three genotypes at different growth stages, whereas species richness and evenness varied only for ndf4. The leaf surface shared a core microbiota dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes in all tested growth stages and genotypes. Phyllosphere specificity varied more with respect to growth stage than to genotype. In summary, both the growth stage and genotype of A. thaliana are crucial in shaping phyllosphere bacterial composition, with the former being a stronger driver. Our findings provide a novel for investigating whether the host properties influence the phyllosphere community and favor healthy development of plants.

Nitrogen Deficiency-induced Bacterial Community Shifts in Soybean Roots

Nitrogen deficiency affects soybean growth and physiology, such as symbiosis with rhizobia; however, its effects on the bacterial composition of the soybean root microbiota remain unclear. A bacterial community analysis by 16S rRNA gene amplicon sequencing showed nitrogen deficiency-induced bacterial community shifts in soybean roots with the marked enrichment of Methylobacteriaceae. The abundance of Methylobacteriaceae was low in the roots of field-grown soybean without symptoms of nitrogen deficiency. Although Methylobacteriaceae isolated from soybean roots under nitrogen deficiency did not promote growth or nodulation when inoculated into soybean roots, these results indicate that the enrichment of Methylobacteriaceae in soybean roots is triggered by nitrogen-deficiency stress.

Impact of Soybean Nodulation Phenotypes and Nitrogen Fertilizer Levels on the Rhizosphere Bacterial Community

The effects of nodulation properties of legumes on the rhizosphere bacterial community are still not clear. To determine the effects of nodulation phenotypes on bacterial communities in the rhizosphere of soybean plants, we performed high-throughput sequencing of the 16S rRNA gene to estimate the rhizosphere bacterial community of three soybean lines with different nodulation phenotypes grown in soil supplied with different levels of N fertilizer. The results revealed that both the soybean nodulation phenotypes and the N levels affected the rhizosphere bacteria community, but the nodulation phenotypes contributed more than the N-supply. The diversity of bacteria was decreased in the rhizosphere of super-nodulating phenotype. The response of rhizosphere bacterial communities to the soil available nitrogen (AN) concentrations was different than the response with the three nodulation phenotypes of soybean which was more stable in the wild-type (Nod⁺) soybean samples than that in the mutant samples (Nod^– and Nod⁺⁺). Bradyrhizobium in the rhizosphere was positively correlated with nodule number and negatively correlated to AN in the soil, while Burkholderia and Dyella were positively correlated with nodule biomass and nitrogenase activity. These results demonstrated that the nodulation phenotype of soybean affects the rhizosphere microbiome.

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.

Does reduced usage of antibiotics in livestock production mitigate the spread of antibiotic resistance in soil, earthworm guts, and the phyllosphere?

The overuse of antibiotics in animal husbandry is widespread and believed to significantly contribute to the selection of antibiotic resistance genes (ARGs) in animals. Thus, there is a global drive to reduce antibiotic use in the agricultural sector. However, it has not been established whether a reduction in the use of antibiotics in livestock production would be effective in reducing the spread of ARGs. A microcosm approach was used to determine how the addition of manure with either reduced antibiotic levels or with typical antibiotic levels could affect the spread of antibiotic resistance genes between soil, earthworms and the phyllosphere. When compared to the control soil, earthworm and phyllosphere samples had the greater increase in ARG abundance in conventional manure treatments (P < 0.05). Reduced antibiotic manure also enriched the abundance of ARGs in the phyllosphere and soil but not earthworm guts when compared to the control (P < 0.05). In both soil and earthworm guts, the enrichment of ARGs was lower in reduced antibiotic manure than in conventional manure. This study has identified bacterial transfer through the soil-earthworm-phyllosphere system as a potential means to spread ARGs between habitats after fertilization with livestock derived manures.

Growth Stage-dependent Bacterial Communities in Soybean Plant Tissues: Methylorubrum Transiently Dominated in the Flowering Stage of the Soybean Shoot

Plant-associated bacteria are critical for plant growth and health. However, the effects of plant growth stages on the bacterial community remain unclear. Analyses of the microbiome associated with field-grown soybean revealed a marked shift in the bacterial community during the growth stages. The relative abundance of Methylorubrum in the leaf and stem increased from 0.2% to more than 45%, but decreased to approximately 15%, with a peak at the flowering stage at which nitrogen metabolism changed in the soybean plant. These results suggest the significance of a time-series analysis for understanding the relationship between the microbial community and host plant physiology.

Phyllosphere of staple crops under pig manure fertilization, a reservoir of antibiotic resistance genes

In China, the common use of antibiotics in agriculture is recognized as a potential public health risk through the increasing use of livestock derived manure as a means of fertilization. By doing so this may increase the transfer of antibiotic resistance genes (ARGs) from animals, to soils and plants. In this study two staple crops (rice and wheat) were investigated for ARG enrichment under differing fertilization regimes. Here, we applied 4 treatments, no fertilizer, mineral fertilizer, clean (reduced antibiotic practice) and dirty (current antibiotic practice) pig manure, to soil microcosms planted with either rice or wheat, to investigate fertilization effects on the abundance of ARGs in the respective phyllospheres. For both rice and wheat, samples were collected after two separate fertilization periods. In total, 162 unique ARGs and 5 mobile genetic elements (MGEs) were detected from all rice and wheat samples. The addition of both clean and dirty manure, enhanced ARG abundance significantly when compared to no fertilizer treatments (P < 0.001), though clean manure enriched ARGs to a lesser extent than dirty manure, in all rice and wheat samples (P < 0.001). The classes of ARGs recorded were different between crops, with wheat samples having a higher ARG diversity than rice. These results revealed that staple crops in China such as rice and wheat may be a reservoir for ARGs when clean and dirty pig manure is used for fertilization.

Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era

Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant-microbe (PM) interactions are either beneficial or harmful. The role of microbiota in plant growth promotion (PGP) and protection against various stresses is well known. Recently, our knowledge of community composition of plant microbiome and significant driving factors have significantly improved. So, the use of plant microbiome is a reliable approach for a next green revolution and to meet the global food demand in sustainable and eco-friendly agriculture. An application of the multifaceted PM interactions needs the use of novel tools to know critical genetic and molecular aspects. Recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) tools are of great interest to explore PM interactions. A systematic understanding of the PM interactions will enable the application of GE tools to enhance the capacity of microbes or plants for agronomic trait improvement. This review focuses on applying GE techniques in plants or associated microbiota for discovering the fundamentals of the PM interactions, disease resistance, PGP activity, and future implications in agriculture.

Biological Control Agents Against Fusarium Wilt of Banana

In the last century, the banana crop and industry experienced dramatic losses due to an epidemic of Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f.sp. cubense (Foc) race 1. An even more dramatic menace is now feared due to the spread of Foc tropical race 4. Plant genetic resistance is generally considered as the most plausible strategy for controlling effectively such a devastating disease, as occurred for the first round of FWB epidemic. Nevertheless, with at least 182 articles published since 1970, biological control represents a large body of knowledge on FWB. Remarkably, many studies deal with biological control agents (BCAs) that reached the field-testing stage and even refer to high effectiveness. Some selected BCAs have been repeatedly assayed in independent trials, suggesting their promising value. Overall under field conditions, FWB has been controlled up to 79% by using Pseudomonas spp. strains, and up to 70% by several endophytes and Trichoderma spp. strains. Lower biocontrol efficacy (42-55%) has been obtained with arbuscular mycorrhizal fungi, Bacillus spp., and non-pathogenic Fusarium strains. Studies on Streptomyces spp. have been mostly limited to in vitro conditions so far, with very few pot-experiments, and none conducted in the field. The BCAs have been applied with diverse procedures (e.g., spore suspension, organic amendments, bioformulations, etc.) and at different stages of plant development (i.e., in vitro, nursery, at transplanting, post-transplanting), but there has been no evidence for a protocol better than another. Nonetheless, new bioformulation technologies (e.g., nanotechnology, formulation of microbial consortia and/or their metabolites, etc.) and tailor-made consortia of microbial strains should be encouraged. In conclusion, the literature offers many examples of promising BCAs, suggesting that biocontrol can greatly contribute to limit the damage caused by FWB. More efforts should be done to further validate the currently available outcomes, to deepen the knowledge on the most valuable BCAs, and to improve their efficacy by setting up effective formulations, application protocols, and integrated strategies.

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles

Many plants have natural partnerships with microbes that can boost their nitrogen (N) and/or phosphorus (P) acquisition. To assess whether wheat may have undiscovered associations of these types, we tested if N/P-starved Triticum aestivum show microbiome profiles that are simultaneously different from those of N/P-amended plants and those of their own bulk soils. The bacterial and fungal communities of root, rhizosphere, and bulk soil samples from the Historical Dryland Plots (Lethbridge, Canada), which hold T. aestivum that is grown both under N/P fertilization and in conditions of extreme N/P-starvation, were taxonomically described and compared (bacterial 16S rRNA genes and fungal Internal Transcribed Spacers-ITS). As the list may include novel N- and/or P-providing wheat partners, we then identified all the operational taxonomic units (OTUs) that were proportionally enriched in one or more of the nutrient starvation- and plant-specific communities. These analyses revealed: a) distinct N-starvation root and rhizosphere bacterial communities that were proportionally enriched, among others, in OTUs belonging to families Enterobacteriaceae, Chitinophagaceae, Comamonadaceae, Caulobacteraceae, Cytophagaceae, Streptomycetaceae, b) distinct N-starvation root fungal communities that were proportionally enriched in OTUs belonging to taxa Lulworthia, Sordariomycetes, Apodus, Conocybe, Ascomycota, Crocicreas, c) a distinct P-starvation rhizosphere bacterial community that was proportionally enriched in an OTU belonging to genus Agrobacterium, and d) a distinct P-starvation root fungal community that was proportionally enriched in OTUs belonging to genera Parastagonospora and Phaeosphaeriopsis. Our study might have exposed wheat-microbe connections that can form the basis of novel complementary yield-boosting tools.

Metagenomic Analysis Revealed Methylamine and Ureide Utilization of Soybean-Associated Methylobacterium

Methylobacterium inhabits the phyllosphere of a large number of plants. We herein report the results of comparative metagenome analyses on methylobacterial communities of soybean plants grown in an experimental field in Tohoku University (Kashimadai, Miyagi, Japan). Methylobacterium was identified as the most dominant genus (33%) among bacteria inhabiting soybean stems. We classified plant-derived Methylobacterium species into Groups I, II, and III based on 16S rRNA gene sequences, and found that Group I members (phylogenetically close to M. extorquens) were dominant in soybean-associated Methylobacterium. By comparing 29 genomes, we found that all Group I members possessed a complete set of genes for the N-methylglutamate pathway for methylamine utilization, and genes for urea degradation (urea carboxylase, urea amidolyase, and conventional urease). Only Group I members and soybean methylobacterial isolates grew in a culture supplemented with methylamine as the sole carbon source. They utilized urea or allantoin (a urea-related compound in legumes) as the sole nitrogen source; however, group III also utilized these compounds. The utilization of allantoin may be crucial in soybean-bacterial interactions because allantoin is a transported form of fixed nitrogen in legume plants. Soybean-derived Group I strain AMS5 colonized the model legume Lotus japonicus well. A comparison among the 29 genomes of plant-derived and other strains suggested that several candidate genes are involved in plant colonization such as csgG (curli fimbriae). Genes for the N-methylglutamate pathway and curli fimbriae were more abundant in soybean microbiomes than in rice microbiomes in the field. Based on these results, we discuss the lifestyle of Methylobacterium in the legume phyllosphere.

Rice Bran Amendment Suppresses Potato Common Scab by Increasing Antagonistic Bacterial Community Levels in the Rhizosphere

Potato common scab (PCS), caused by pathogenic Streptomyces spp., is a serious disease in potato production worldwide. Cultural practices, such as optimizing the soil pH and irrigation, are recommended but it is often difficult to establish stable disease reductions using these methods. Traditionally, local farmers in southwest Japan have amended soils with rice bran (RB) to suppress PCS. However, the scientific mechanism underlying disease suppression by RB has not been elucidated. The present study showed that RB amendment reduced PCS by repressing the pathogenic Streptomyces population in young tubers. Amplicon sequencing analyses of 16S ribosomal RNA genes from the rhizosphere microbiome revealed that RB amendment dramatically changed bacterial composition and led to an increase in the relative abundance of gram-positive bacteria such as Streptomyces spp., and this was negatively correlated with PCS disease severity. Most actinomycete isolates derived from the RB-amended soil showed antagonistic activity against pathogenic Streptomyces scabiei and S. turgidiscabies on R2A medium. Some of the Streptomyces isolates suppressed PCS when they were inoculated onto potato plants in a field experiment. These results suggest that RB amendment increases the levels of antagonistic bacteria against PCS pathogens in the potato rhizosphere.

Modulation of R-gene expression across environments

Some environments are more conducive to pathogen growth than others, and, as a consequence, plants might be expected to invest more in resistance when pathogen growth is favored. Resistance (R-) genes in Arabidopsis thaliana have unusually extensive variation in basal expression when comparing the same R-gene among accessions collected from different environments. R-gene expression variation was characterized to explore whether R-gene expression is up-regulated in environments favoring pathogen proliferation and down-regulated when risks of infection are low; down-regulation would follow if costs of R-gene expression negatively impact plant fitness in the absence of disease. Quantitative reverse transcription-PCR was used to quantify the expression of 13 R-gene loci in plants grown in eight environmental conditions for each of 12 A. thaliana accessions, and large effects of the environment on R-gene expression were found. Surprisingly, almost every change in the environment--be it a change in biotic or abiotic conditions--led to an increase in R-gene expression, a response that was distinct from the average transcriptome response and from that of other stress response genes. These changes in expression are functional in that environmental change prior to infection affected levels of specific disease resistance to isolates of Pseudomonas syringae. In addition, there are strong latitudinal clines in basal R-gene expression and clines in R-gene expression plasticity correlated with drought and high temperatures. These results suggest that variation in R-gene expression across environments may be shaped by natural selection to reduce fitness costs of R-gene expression in permissive or predictable environments.

Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria

Methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and CO₂, the two most important greenhouse gases. This review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. Some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. Methanol-utilizing methylotrophs in the genus Methylobacterium are abundant in the phyllosphere and have the ability to promote the growth of some plants. Methanotrophs also inhabit the phyllosphere, and methanotrophs with high methane oxidation activities have been found on aquatic plants. Both plant and environmental factors are involved in shaping the methylotroph community on plants. Methanotrophic activity can be enhanced by heterotrophic bacteria that provide growth factors (e.g., cobalamin). Information regarding the biological interaction of methylotrophs with other organisms will facilitate a better understanding of the carbon cycle that is driven by methylotrophs.

Metagenomic analysis of the bacterial community associated with the taproot of sugar beet

We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 10(5) reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 10(5) reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the (15)N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.

Characterization of leaf blade- and leaf sheath-associated bacterial communities and assessment of their responses to environmental changes in CO₂, temperature, and nitrogen levels under field conditions

Rice shoot-associated bacterial communities at the panicle initiation stage were characterized and their responses to elevated surface water-soil temperature (ET), low nitrogen (LN), and free-air CO2 enrichment (FACE) were assessed by clone library analyses of the 16S rRNA gene. Principal coordinate analyses combining all sequence data for leaf blade- and leaf sheath-associated bacteria revealed that each bacterial community had a distinct structure, as supported by PC1 (61.5%), that was mainly attributed to the high abundance of Planctomycetes in leaf sheaths. Our results also indicated that the community structures of leaf blade-associated bacteria were more sensitive than those of leaf sheath-associated bacteria to the environmental factors examined. Among these environmental factors, LN strongly affected the community structures of leaf blade-associated bacteria by increasing the relative abundance of Bacilli. The most significant effect of FACE was also observed on leaf blade-associated bacteria under the LN condition, which was explained by decreases and increases in Agrobacterium and Pantoea, respectively. The community structures of leaf blade-associated bacteria under the combination of FACE and ET were more similar to those of the control than to those under ET or FACE. Thus, the combined effects of environmental factors need to be considered in order to realistically assess the effects of environmental changes on microbial community structures.

An assessment of urea-formaldehyde fertilizer on the diversity of bacterial communities in onion and sugar beet

The impact of a urea-formaldehyde (UF) fertilizer on bacterial diversity in onion bulbs and main roots of sugar beet were examined using a 16S rRNA gene clone library. The UF fertilizer markedly increased bacterial diversity in both plants. The results of principal coordinates analysis (PCoA) revealed that nearly 30% of the variance observed in bacterial diversity in both the onion and sugar beet was attributed to the fertilization conditions and also that the community structures in both plants shifted unidirectionally in response to the UF fertilizer.

Low nitrogen fertilization adapts rice root microbiome to low nutrient environment by changing biogeochemical functions

Reduced fertilizer usage is one of the objectives of field management in the pursuit of sustainable agriculture. Here, we report on shifts of bacterial communities in paddy rice ecosystems with low (LN), standard (SN), and high (HN) levels of N fertilizer application (0, 30, and 300 kg N ha⁻¹, respectively). The LN field had received no N fertilizer for 5 years prior to the experiment. The LN and HN plants showed a 50% decrease and a 60% increase in biomass compared with the SN plant biomass, respectively. Analyses of 16S rRNA genes suggested shifts of bacterial communities between the LN and SN root microbiomes, which were statistically confirmed by metagenome analyses. The relative abundances of Burkholderia, Bradyrhizobium and Methylosinus were significantly increased in root microbiome of the LN field relative to the SN field. Conversely, the abundance of methanogenic archaea was reduced in the LN field relative to the SN field. The functional genes for methane oxidation (pmo and mmo) and plant association (acdS and iaaMH) were significantly abundant in the LN root microbiome. Quantitative PCR of pmoA/mcrA genes and a ¹³C methane experiment provided evidence of more active methane oxidation in the rice roots of the LN field. In addition, functional genes for the metabolism of N, S, Fe, and aromatic compounds were more abundant in the LN root microbiome. These results suggest that low-N-fertilizer management is an important factor in shaping the microbial community structure containing key microbes for plant associations and biogeochemical processes in paddy rice ecosystems.

Impact of Azospirillum sp. B510 inoculation on rice-associated bacterial communities in a paddy field

Rice seedlings were inoculated with Azospirillum sp. B510 and transplanted into a paddy field. Growth in terms of tiller numbers and shoot length was significantly increased by inoculation. Principal-coordinates analysis of rice bacterial communities using the 16S rRNA gene showed no overall change from B510 inoculation. However, the abundance of Veillonellaceae and Aurantimonas significantly increased in the base and shoots, respectively, of B510-inoculated plants. The abundance of Azospirillum did not differ between B510-inoculated and uninoculated plants (0.02-0.50%). These results indicate that the application of Azospirillum sp. B510 not only enhanced rice growth, but also affected minor rice-associated bacteria.

Molecular characterization of the bacterial community in a potato phytosphere

The bacterial community of a potato phytosphere at the flowering stage was examined using both culture-dependent and -independent methods. Tissues (leaves, stems, roots and tubers) were sampled from field-grown potato plants (cultivar Matilda), and the clone libraries of 16S rRNA genes and the isolate collections using R2A medium were constructed. By analyzing the combined data set of 16S rRNA gene sequences from both clone libraries and isolate collections, 82 genera from 8 phyla were found and 237 OTUs (≥97% identity) at species level were identified across the potato phytosphere. The statistical analyses of clone libraries suggested that stems harbor the lowest diversity among the tissues examined. The phylogenetic analyses revealed that the most dominant phylum was shown to be Proteobacteria for all tissues (62.0%-89.7% and 57.7%-72.9%, respectively), followed by Actinobacteria (5.0%-10.7% and 14.6%-39.4%, respectively). The results of principal coordinates analyses of both clone libraries and isolate collections indicated that distinct differences were observed between above- and below-ground tissues for bacterial community structures. The results also revealed that leaves harbored highly similar community structures to stems, while the tuber community was shown to be distinctly different from the stem and root communities.

Aureimonas jatrophae sp. nov. and Aureimonas phyllosphaerae sp. nov., leaf-associated bacteria isolated from Jatropha curcas L

Four orange-pigmented isolates, L7-456, L7-484T, L9-479 and L9-753T, originating from surface-sterilized leaf tissues of Jatropha curcas L. cultivars were characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that all four isolates belong to the genus Aureimonas . In these analyses, strain L7-484T appeared to be most closely related to Aureimonas ureilytica 5715S-12T (95.7 % sequence identity). The 16S rRNA gene sequences of strains L7-456, L9-479 and L9-753T were found to be identical and also shared the highest similarity with A. ureilytica 5715S-12T (97.5 %). Both L7-484T and L9-753T contained Q-10 and Q-9 as predominant ubiquinones and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, sulfoquinovosyldiacylglycerol and an aminophospholipid as the major polar lipids. C18 : 1ω7c and C16 : 0 were the major fatty acids. Similar to other species in the genus Aureimonas , hydroxylated fatty acids (e.g. C18 : 1 2-OH) and cyclic fatty acids (C19 : 0 cyclo ω8c) were also present. The DNA G+C contents of L7-484T and L9-753T were 66.1 and 69.4 mol%, respectively. Strains L7-484T and L9-753T exhibited less than 40 % DNA–DNA hybridization both between themselves and to A. ureilytica KACC 11607T. Our results support the proposal that strain L7-484T represents a novel species within the genus Aureimonas , for which the name Aureimonas jatrophae sp. nov. is proposed, and that strains L9-753T, L7-456 ( = KACC 16229  = DSM 25023) and L9-479 ( = KACC 16228  = DSM 25024) represent a second novel species within the genus, for which the name Aureimonas phyllosphaerae sp. nov. is proposed. The type strains of Aureimonas jatrophae sp. nov. and Aureimonas phyllosphaerae sp. nov. are respectively L7-484T ( = KACC 16230T  = DSM 25025T) and L9-753T ( = KACC 16231T  = DSM 25026T).

Microbial life in the phyllosphere

Our knowledge of the microbiology of the phyllosphere, or the aerial parts of plants, has historically lagged behind our knowledge of the microbiology of the rhizosphere, or the below-ground habitat of plants, particularly with respect to fundamental questions such as which microorganisms are present and what they do there. In recent years, however, this has begun to change. Cultivation-independent studies have revealed that a few bacterial phyla predominate in the phyllosphere of different plants and that plant factors are involved in shaping these phyllosphere communities, which feature specific adaptations and exhibit multipartite relationships both with host plants and among community members. Insights into the underlying structural principles of indigenous microbial phyllosphere populations will help us to develop a deeper understanding of the phyllosphere microbiota and will have applications in the promotion of plant growth and plant protection.

Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica)

Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes, and leaves) by Denaturing Gradient Gel Electrophoresis (DGGE). A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units) were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ, and δ subclasses) and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.

The genotype of the calcium/calmodulin-dependent protein kinase gene (CCaMK) determines bacterial community diversity in rice roots under paddy and upland field conditions

The effects of the Oryza sativa calcium/calmodulin-dependent protein kinase OsCCaMK genotype (dominant homozygous [D], heterozygous [H], recessive homozygous [R]) on rice root-associated bacteria, including endophytes and epiphytes, were examined by using a Tos17 rice mutant line under paddy and upland field conditions. Roots were sampled at the flowering stage and were subjected to clone library analyses. The relative abundance of Alphaproteobacteria was noticeably decreased in R plants under both paddy and upland conditions (0.8% and 3.0%, respectively) relative to those in D plants (10.3% and 17.4%, respectively). Population shifts of the Sphingomonadales and Rhizobiales were mainly responsible for this low abundance in R plants. The abundance of Anaerolineae (Chloroflexi) and Clostridia (Firmicutes) was increased in R plants under paddy conditions. The abundance of a subpopulation of Actinobacteria (Saccharothrix spp. and unclassified Actinosynnemataceae) was increased in R plants under upland conditions. Principal coordinate analysis revealed unidirectional community shifts in relation to OsCCaMK gene dosage under both conditions. In addition, shoot length, tiller number, and plant weight decreased as the OsCCaMK gene dosage decreased under upland conditions. These results suggest significant impacts of OsCCaMK on both the diversity of root-associated bacteria and rice plant growth under both paddy and upland field conditions.