Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils

The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.

Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere

Stable isotope probing of microbial nucleic acids applied in the rhizosphere enables (a) the identification of the active microbial community involved in root exudate assimilation and those involved in soil organic matter degradation, and (b) the study of the impact of plants via root exudates on the in situ expression of microbial functions. By incubating plants under ¹³CO₂, fresh carbon exuded by the plant will be labeled and hence the microbial community assimilating ¹³C-root exudates will incorporate ¹³C into their cellular macromolecules. Labeled DNA, RNA, and proteins can be used to identify microorganisms that assimilated the root exudates. We provide a step-by-step protocol on how to apply stable isotope probing of DNA and RNA in the plant rhizosphere to identify the active microbial communities and analyze their gene expression.

Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize

Phyllosphere contains various microorganisms that may harbor diverse antibiotic resistance genes (ARGs). However, we know little about the composition of antibiotic resistome and the factors influencing the diversity and abundance of ARGs in the phyllosphere. In this study, 16S rRNA gene amplicon sequencing and high-throughput quantitative PCR approaches were employed to investigate the effects of long-term (over 10 years) organic fertilization on the phyllosphere bacterial communities and antibiotic resistome. Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes dominated in the phyllosphere bacterial communities. Long-term application of sewage sludge and chicken manure altered the phyllosphere bacterial community composition, with a remarkable decrease in bacterial alpha-diversity. A total of 124 unique ARGs were detected in the phyllosphere. The application of sewage sludge and chicken manure significantly increased the abundance of ARGs, with a maximum 2638-fold enrichment. Variation partitioning analysis (VPA) together with network analysis indicated that the profile of ARGs is strongly correlated with bacterial community compositions. These results improve the knowledge about the diversity of plant-associated antibiotic resistome and factors influencing the profile of ARGs in the phyllosphere.

Comparative Genomics of Aspergillus flavus S and L Morphotypes Yield Insights into Niche Adaptation

Aspergillus flavus, the primary causal agent for aflatoxin contamination on crops, consists of isolates with two distinct morphologies: isolates of the S morphotype produce numerous small sclerotia and lower numbers of conidia while isolates of the L morphotype produce fewer large sclerotia and abundant conidia. The morphotypes also differ in aflatoxin production with S isolates consistently producing high concentrations of aflatoxin, whereas L isolates range from atoxigenic to highly toxigenic. The production of abundant sclerotia by the S morphotype suggests adaptation for long-term survival in the soil, whereas the production of abundant conidia by the L morphotype suggests adaptation for aerial dispersal to the phyllosphere. To identify genomic changes that support differential niche adaption, the sequences of three S and three L morphotype isolates were compared. Differences in genome structure and gene content were identified between the morphotypes. A >530 kb inversion between the morphotypes affect a secondary metabolite gene cluster and a cutinase gene. The morphotypes also differed in proteins predicted to be involved in carbon/nitrogen metabolism, iron acquisition, antimicrobial defense, and evasion of host immunity. The S morphotype genomes contained more intact secondary metabolite clusters indicating there is higher selection pressure to maintain secondary metabolism in the soil and that it is not limited to aflatoxin production. The L morphotype genomes were enriched in amino acid transporters, suggesting efficient nitrogen transport may be critical in the nutrient limited phyllosphere. These findings indicate the genomes of the two morphotypes differ beyond developmental genes and have diverged as they adapted to their respective niches.

Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa

Rhizobacteria play an important role in bridging the soil and plant microbiomes and improving the health and growth of plants. In this study, the bacterial community structures and compositions of rhizosphere microbiomes associated with six plant species, representing two orders and three families of wild plants grown in the same field, were evaluated. The six plant species examined harbored a core and similar bacterial communities of the rhizosphere microbiome, which was dominated by members of Rhizobiales, Sphingomonadales, Burkholderiales, and Xanthomonadales of Proteobacteria, Subgroup 4 of Acidobacteria, and Sphingobacteriales of Bacteroidetes. Plant species had a significant effect on the microbial composition and Operational Taxonomic Unit (OTU) abundance of the rhizosphere microbiome. Statistical analysis indicated a significant differential OTU richness (Chao1, p < 0.05) and bacterial diversity (Shannon index, p < 0.0001) of the rhizosphere microbiome at the plant species, genus, or families levels. The paralleled samples from the same plant species in the PCoA and hierarchical cluster analysis demonstrated a clear tendency to group together, although the samples were not strictly separated according to their taxonomic divergence at the family or order level. The CAP analysis revealed a great proportion (44.85%) of the variations on bacterial communities could be attributed to the plant species. The results demonstrated that largely conserved and taxonomically narrow bacterial communities of the rhizosphere microbiome existed around the plant root. The bacterial communities and diversity of the rhizosphere microbiome were significantly related to the plant taxa, at least at the species levels.

The structure and function of the global citrus rhizosphere microbiome

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.

Plant Phenotypic Traits Eventually Shape Its Microbiota: A Common Garden Test

Plant genotype drives the development of plant phenotypes and the assembly of plant microbiota. The potential influence of the plant phenotypic characters on its microbiota is not well characterized and the co-occurrence interrelations for specific microbial taxa and plant phenotypic characters are poorly understood. We established a common garden experiment, which quantifies prokaryotic and fungal communities in the phyllosphere and rhizosphere of six spruce (Picea spp.) tree species, through Illumina amplicon sequencing. We tested for relationships between bacterial/archaeal and fungal communities and for the phenotypic characters of their plant hosts. Host phenotypic characters including leaf length, leaf water content, leaf water storage capacity, leaf dry mass per area, leaf nitrogen content, leaf phosphorous content, leaf potassium content, leaf δ¹³C values, stomatal conductance, net photosynthetic rate, intercellular carbon dioxide concentration, and transpiration rate were significantly correlated with the diversity and composition of the bacterial/archaeal and fungal communities. These correlations between plant microbiota and suites of host plant phenotypic characters suggest that plant genotype shape its microbiota by driving the development of plant phenotypes. This will advance our understanding of plant-microbe associations and the drivers of variation in plant and ecosystem function.

Influence of Light on Plant-Phyllosphere Interaction

Plant-phyllosphere interactions depend on microbial diversity, the plant host and environmental factors. Light is perceived by plants and by microorganisms and is used as a cue for their interaction. Photoreceptors respond to narrow-bandwidth wavelengths and activate specific internal responses. Light-induced plant responses include changes in hormonal levels, production of secondary metabolites, and release of volatile compounds, which ultimately influence plant-phyllosphere interactions. On the other hand, microorganisms contribute making some essential elements (N, P, and Fe) biologically available for plants and producing growth regulators that promote plant growth and fitness. Therefore, light directly or indirectly influences plant-microbe interactions. The usage of light-emitting diodes in plant growth facilities is helping increasing knowledge in the field. This progress will help define light recipes to optimize outputs on plant-phyllosphere communications. This review describes research advancements on light-regulated plant-phyllosphere interactions. The effects of full light spectra and narrow bandwidth-wavelengths from UV to far-red light are discussed.

How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture

All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.

Proteomics and the microbiome: pitfalls and potential

Introduction: Human symbiotic microbiota are now known to play important roles in human health and disease. Significant progress in our understanding of the human microbiome has been driven by recent technological advances in the fields of genomics, transcriptomics, and proteomics. As a complementary method to metagenomics, proteomics is enabling detailed protein profiling of the microbiome to decipher its structure and function and to analyze its relationship with the human body. Fecal proteomics is being increasingly applied to discover and validate potential health and disease biomarkers, and Therapeutic Goods Administration (TGA)-approved instrumentation and a range of clinical assays are being developed that will collectively play key roles in advancing personalized medicine. Areas covered: This review will introduce the complexity of the microbiome and its role in health and disease (in particular the gastrointestinal tract or gut microbiome), discuss current genomic and proteomic methods for studying this system, including the discovery of potential biomarkers, and outline the development of clinically accepted protocols leading to personalized medicine. Expert commentary: Recognition of the important role the microbiome plays in both health and disease is driving current research in this key area. A proteogenomics approach will be essential to unravel the biologies underlying this complex network.

Chloromethane formation and degradation in the fern phyllosphere

Chloromethane (CH₃Cl) is the most abundant halogenated trace gas in the atmosphere. It plays an important role in natural stratospheric ozone destruction. Current estimates of the global CH₃Cl budget are approximate. The strength of the CH₃Cl global sink by microbial degradation in soils and plants is under discussion. Some plants, particularly ferns, have been identified as substantial emitters of CH₃Cl. Their ability to degrade CH₃Cl remains uncertain. In this study, we investigated the potential of leaves from 3 abundant ferns (Osmunda regalis, Cyathea cooperi, Dryopteris filix-mas) to produce and degrade CH₃Cl by measuring their production and consumption rates and their stable carbon and hydrogen isotope signatures. Investigated ferns are able to degrade CH₃Cl at rates from 2.1 to 17 and 0.3 to 0.9μgg_dw^-1day^-1 for C. cooperi and D. filix-mas respectively, depending on CH₃Cl supplementation and temperature. The stable carbon isotope enrichment factor of remaining CH₃Cl was -39±13‰, whereas negligible isotope fractionation was observed for hydrogen (-8±19‰). In contrast, O. regalis did not consume CH₃Cl, but produced it at rates ranging from 0.6 to 128μgg_dw^-1day^-1, with stable isotope values of -97±8‰ for carbon and -202±10‰ for hydrogen, respectively. Even though the 3 ferns showed clearly different formation and consumption patterns, their leaf-associated bacterial diversity was not notably different. Moreover, we did not detect genes associated with the only known chloromethane utilization pathway "cmu" in the microbial phyllosphere of the investigated ferns. Our study suggests that still unknown CH₃Cl biodegradation processes on plants play an important role in global cycling of atmospheric CH₃Cl.

Nitrogen Fixation in Cereals

Cereals such as maize, rice, wheat and sorghum are the most important crops for human nutrition. Like other plants, cereals associate with diverse bacteria (including nitrogen-fixing bacteria called diazotrophs) and fungi. As large amounts of chemical fertilizers are used in cereals, it has always been desirable to promote biological nitrogen fixation in such crops. The quest for nitrogen fixation in cereals started long ago with the isolation of nitrogen-fixing bacteria from different plants. The sources of diazotrophs in cereals may be seeds, soils, and even irrigation water and diazotrophs have been found on roots or as endophytes. Recently, culture-independent molecular approaches have revealed that some rhizobia are found in cereal plants and that bacterial nitrogenase genes are expressed in plants. Since the levels of nitrogen-fixation attained with nitrogen-fixing bacteria in cereals are not high enough to support the plant’s needs and never as good as those obtained with chemical fertilizers or with rhizobium in symbiosis with legumes, it has been the aim of different studies to increase nitrogen-fixation in cereals. In many cases, these efforts have not been successful. However, new diazotroph mutants with enhanced capabilities to excrete ammonium are being successfully used to promote plant growth as commensal bacteria. In addition, there are ambitious projects supported by different funding agencies that are trying to genetically modify maize and other cereals to enhance diazotroph colonization or to fix nitrogen or to form nodules with nitrogen-fixing symbiotic rhizobia.

Diversity of Bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola), and characterization of osmoregulatory genes in halophilic Bacilli

Salinity is one of the major abiotic stresses; a total of 3% of the world’s land mass is affected by salinity. Approximately 6.3 million hectares of land in Pakistan is affected by salinity to varying degrees, and most of the areas are arid to semiarid with low annual precipitation. The aim of the present study is to identify and characterize Bacillus and Bacillus-derived bacterial genera from the rhizospheric and non-rhizospheric soil samples from the Khewra Salt Mine, Pakistan, by using culture-independent and -dependent methods. Seven Bacillus-like bacterial genera, Bacillus, Halobacillus, Virgibacillus, Brevibacillus, Paenibacillus, Tumebacillus, and Lysinibacillus, were detected by using pyrosequencing analysis, whereas only four genera, Bacillus, Halobacillus, Oceanobacillus, and Virgibacillus, were identified by culture-dependent methods. Most of the Bacillus-like isolates identified in this study were moderately halophilic, alkaliphilic, and mesophilic bacteria and were considered a good source of hydrolytic enzymes because of their ability to degrade proteins, carbohydrates, and lipids. Eight Bacillus-like strains from the genera Bacillus, Halobacillus, Oceanobacillus, and Virgibacillus showed positive results for the presence of ectABC gene cluster (ectoine), six strains could synthesize betaine from choline, and six strains tested positive for the synthesis of proline from either glutamate or ornithine by using proline dehydrogenase enzyme.

Below-ground-above-ground Plant-microbial Interactions: Focusing on Soybean, Rhizobacteria and Mycorrhizal Fungi

INTRODUCTION

Organisms seldom exist in isolation and are usually involved in interactions with several hosts and these interactions in conjunction with the physicochemical parameters of the soil affect plant growth and development. Researches into below and aboveground microbial community are unveiling a myriad of intriguing interactions within the rhizosphere, and many of the interactions are facilitated by exudates that are secreted by plants roots. These interactions can be harnessed for beneficial use in agriculture to enhance crop productivity especially in semi-arid and arid environments.

THE RHIZOSPHERE

The rhizosphere is the region of soil close to plants roots that contain large number of diverse organisms. Examples of microbial candidates that are found in the rhizosphere include the Arbuscular Mycorrhizal Fungi (AMF) and rhizobacteria. These rhizosphere microorganisms use plant root secretions such as mucilage and flavonoids which are able to influence their diversity and function and also enhance their potential to colonize plants root.

NATURAL INTERACTIONS BETWEEN MICROORGANISMS AND PLANT

In the natural environments, plants live in interactions with different microorganisms, which thrive belowground in the rhizosphere and aboveground in the phyllosphere. Some of the plant-microbial interactions (which can be in the form of antagonism, amensalism, parasitism and symbiosis) protect the host plants against detrimental microbial and non-microbial invaders and provide nutrients for plants while others negatively affect plants. These interactions can influence below-ground-above-ground plants' biomass development thereby playing significant role in sustaining plants. Therefore, understanding microbial interactions within the rhizosphere and phyllosphere is urgent towards farming practices that are less dependent on conventional chemical fertilizers, which have known negative impacts on the environments.

BELOW GROUND RHIZOBACTERIA INTERACTIONS ALLEVIATE DROUGHT STRESS

Drought stress is one of the major factors militating against agricultural productivity globally and is likely to further increase. Belowground rhizobacteria interactions could play important role in alleviating drought stress in plants. These beneficial rhizobacterial colonize the rhizosphere of plants and impart drought tolerance by up regulation or down regulation of drought responsive genes such as ascorbate peroxidase, S-adenosyl-methionine synthetase, and heat shock protein.

INSIGHTS INTO BELOW AND ABOVE THE GROUND MICROBIAL INTERACTIONS VIA OMIC STUDIES

Investigating complex microbial community in the environment is a big challenge. Therefore, omic studies of microorganisms that inhabit the rhizosphere are important since this is where most plant-microbial interactions occur. One of the aims of this review is not to give detailed account of all the present omic techniques, but instead to highlight the current omic techniques that can possibly lead to detection of novel genes and their respective proteins within the rhizosphere which may be of significance in enhancing crop plants (such as soybean) productivity especially in semi-arid and arid environments.

FUTURE PROSPECTS AND CONCLUSIONS

Plant-microbial interactions are not totally understood, and there is, therefore, the need for further studies on these interactions in order to get more insights that may be useful in sustainable agricultural development. With the emergence of omic techniques, it is now possible to effectively monitor transformations in rhizosphere microbial community together with their effects on plant development. This may pave way for scientists to discover new microbial species that will interact effectively with plants. Such microbial species can be used as biofertilizers and/or bio-pesticides to increase crop yield and enhance global food security.

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars

Severity of plant diseases is often influenced by the availability of nutrients, particularly N; however, its effect on the phyllosphere microbiome in foliar pathogen challenged plants is less investigated in rice. The tripartite interaction among the fungal pathogen (Magnaporthe oryzae), rice cultivars (basmati and non-basmati, blast resistant or susceptible) and nitrogen (N) fertilization (0, 120 and 180 N) was investigated. Plant growth, elicitation of defense responses and abundance of microbial members in the rice phyllosphere were monitored using biochemical and molecular methods. In general, photosynthetic pigments were distinct for each cultivar, and optimal N doses led to higher values. The susceptible var. CO-39 and resistant CO-39I exhibited higher contents of photosynthetic pigments and micronutrients such as zinc in leaves in response to N doses. Elicitation of defense and hydrolytic enzymes was significantly influenced by pathogen inoculation and modulated by N doses, but varietal effects were distinct. Scoring indices emphasized the pathogen susceptibility of var. CO-39 and PB-1, which showed almost 40-60% higher values than the resistant cultivars; the interactions of cultivars and N doses was also significant. Characteristic changes were recorded in the abundances of the gene copies, particularly, with an overall increase in the number of cyanobacterial 16S rRNA, and bacterial amoA in pathogen-challenged treatments, while nifH gene copies exhibited a reducing trend with increasing N doses, in the presence or absence of pathogen. The varietal differences in the cause and effect relationships can be valuable in crop protection for more effective foliar application of pesticides or biocontrol agents.

Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays

Rice is one of the most important nourishments and its cultivation binds large agricultural areas in the world. Its cultivation leads to huge water consumption and high methane emissions. To diminish these problems, crop rotation between paddy rice and maize is introduced in Asia, but can lead to losses of carbon and water by the formation of desiccation cracks. To counteract these problems rice straw can be applied. We analyzed soil microbial responses to different crop rotation systems [rice–rice (RR), maize–maize (MM), maize–rice (MR)] and to rice straw application in the soil and rhizosphere of maize. Zea mays was grown in microcosms using soils from different field locations, each including different crop rotation regimes. The bacterial and fungal community composition was analyzed by 16S rRNA gene and ITS based amplicon sequencing in the bulk soil and rhizosphere. The microbiota was clearly different in soils from the different field locations (analysis of similarity, ANOSIM: R = 0.516 for the bacterial community; R = 0.817 for the fungal community). Within the field locations, crop rotation contributed differently to the variation in microbial community composition. Strong differences were observed in communities inhabiting soils under monosuccession (RR vs. MM) (ANOSIM: R = 0.923 for the bacterial and R = 0.714 for the fungal community), while the communities in soils undergoing MR crop rotation were more similar to those of the corresponding RR soils (ANOSIM: R = 0.111–0.175). The observed differences could be explained by altered oxygen availabilities in RR and MR soils, resulting in an enrichment of anaerobic bacteria in the soils, and the presence of the different crops, leading to the enrichment of host-plant specific microbial communities. The responses of the microbial communities to the application of rice straw in the microcosms were rather weak compared to the other factors. The taxa responding in bulk soil and rhizosphere were mostly distinct. In conclusion, this study revealed that the different agricultural management practices affect microbial community composition to different extent, not only in the bulk soil but also in the rhizosphere, and that the microbial responses in bulk soil and rhizosphere are distinct.

Plant Growth Promotion Under Water: Decrease of Waterlogging-Induced ACC and Ethylene Levels by ACC Deaminase-Producing Bacteria

Some plant growth-promoting bacteria encode for 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which facilitates plant growth and development by lowering the level of stress ethylene under waterlogged conditions. The substrate ACC is the immediate precursor for ethylene synthesis in plants; while bacterial ACC deaminase hydrolyzes this compound into α-ketobutyrate and ammonia to mitigate the adverse effects of the stress caused by ethylene exposure. Here, the structure and function of ACC deaminase, ethylene biosynthesis and waterlogging response, waterlogging and its consequences, role of bacterial ACC deaminase under waterlogged conditions, and effect of this enzyme on terrestrial and riparian plants are discussed.

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves

Coffee is one of the most valuable agricultural commodities and the plants’ leaves are the primary site of infection for most coffee diseases, such as the devastating coffee leaf rust. Therefore, the use of bacterial microbiota that inhabits coffee leaves to fight infections could be an alternative agricultural method to protect against coffee diseases. Here, we report the leaf-associated bacteria in three coffee genotypes over the course of a year, with the aim to determine the diversity of bacterial microbiota. The results indicate a prevalence of Enterobacteriales in Coffea canephora, Pseudomonadales in C. arabica ‘Obatã’, and an intriguing lack of bacterial dominance in C. arabica ‘Catuaí’. Using PERMANOVA analyses, we assessed the association between bacterial abundance in the coffee genotypes and environmental parameters such as temperature, precipitation, and mineral nutrients in the leaves. We detected a close relationship between the amount of Mn and the abundance of Pseudomonadales in ‘Obatã’ and the amount of Ca and the abundance of Enterobacteriales in C. canephora. We suggest that mineral nutrients can be key drivers that shape leaf microbial communities.

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

Archaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.

The Archaea represent a significant component of the plant microbiome, whereas their function is still unclear. Different plant species representing the natural vegetation of alpine bogs harbor a substantial archaeal community originating from five phyla, 60 genera, and 334 operational taxonomic units (OTUs). We identified a core archaeome for all bog plants and ecosystem-specific, so far unclassified Archaea. In the metagenomic data set, Archaea were found to have the potential to interact with plants by (i) possible plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic (especially oxidative and osmotic) stress. The unexpectedly high degree of plant specificity supports plant-archaeon interactions. Moreover, functional signatures of Archaea reveal genetic capacity for the interplay with fungi and an important role in the carbon and nitrogen cycle: e.g., CO₂ and N₂ fixation. These facts reveal an important, yet unobserved role of the Archaea for plants as well as for the bog ecosystem.

IMPORTANCEArchaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.

Bacterial diversity associated with poplar trees grown on a Hg-contaminated site: Community characterization and isolation of Hg-resistant plant growth-promoting bacteria

Industrial waste dumps are rarely colonized by vegetation after they have been abandoned, indicating biological infertility. Revegetation of industrial tailings dumps is thus necessary to prevent wind erosion, metal leaching and has been shown to restore soil functions and ecosystem services. However, little is known about the microbial colonization and community structure of vegetated tailings following the application of restoration technologies. In this study, we investigated the rhizosphere and phyllosphere bacterial communities of a poplar tree plantation within a phytomanagement-based restoration program of a Hg-contaminated site. We used Illumina-based sequencing combined with culture-dependent approaches to describe plant-associated bacterial communities and to isolate growth-promoting bacteria (PGPB) and Hg-resistant bacteria. The genus Streptomyces was highly specific to the root community, accounting for 24.4% of the relative abundance but only representing 0.8% of the soil community, whereas OTUs from the Chloroflexi phylum were essentially detected in the soil community. Aboveground habitats were dominated by bacteria from the Deinococcus-Thermus phylum, which were not detected in belowground habitats. Leaf and stem habitats were characterized by several dominant OTUs, such as those from the phylum Firmicutes in the stems or from the genera Methylobacterium, Kineococcus, Sphingomonas and Hymenobacter in the leaves. Belowground habitats hosted more cultivable Hg-resistant bacteria than aboveground habitats and more Hg-resistant bacteria were found on the episphere than in endospheric habitats. Hg-resistant isolates exhibiting plant growth-promoting (PGP) traits, when used as inoculants of Capsicum annuum, were shown to increase its root dry biomass but not Hg concentration. The N₂-fixing and Hg-resistant species Pseudomonas graminis, observed in the poplar phyllosphere, may be a key microorganism for the restoration of industrial tailings dumps.

Chemical signaling involved in plant-microbe interactions

Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.

Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants

Plant leaves (phyllosphere) have a great potential for colonization and microbial growth, consisting of a dynamic environment in which several factors can interfere with the microbial population structure. The use of genetically modified (GM) plants has introduced several traits in agriculture, such as the improvement of plant drought tolerance, as observed in the AtAREB1 transcription factor overexpression in soybean (Glycine max L. Merrill). The present study aimed at investigating the taxonomic and functional profile of the leaf microbial community of bacteria found in GM (drought-tolerant event 1Ea2939) and conventional (BR 16) soybean plants. Bacterial DNA was extracted from leaf samples collected from each genotype and used for microbial diversity and richness analysis through the MiSeq Illumina platform. Functional prediction was performed using the PICRUSt tool and the STAMP v 2.1.3 software. The obtainment of the GM event 1Ea2939 showed minimum effects on the microbial community and in the potential for chemical-genetic communication, i.e. in the potential for symbiotic and/or mutualistic interaction between plants and their natural microbiota.

Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture

Rhizosphere microbiome which has been shown to enhance plant growth and yield are modulated or influenced by a few environmental factors such as soil type, plant cultivar, climate change and anthropogenic activities. In particular, anthropogenic activity, such as the use of nitrogen-based chemical fertilizers, is associated with environmental destruction and this calls for a more ecofriendly strategy to increase nitrogen levels in agricultural land. This feat is attainable by harnessing nitrogen-fixing endophytic and free-living rhizobacteria. Rhizobium, Pseudomonas, Azospirillum and Bacillus, have been found to have positive impacts on crops by enhancing both above and belowground biomass and could therefore play positive roles in achieving sustainable agriculture outcomes. Thus, it is necessary to study this rhizosphere microbiome with more sophisticated culture-independent techniques such as next generation sequencing (NGS) with the prospect of discovering novel bacteria with plant growth promoting traits. This review is therefore aimed at discussing factors that can modulate rhizosphere microbiome with focus on the contributions of nitrogen fixing bacteria towards sustainable agricultural development and the techniques that can be used for their study.

Long-Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field-Experiment

Global warming is currently a much discussed topic with as yet largely unexplored consequences for agro-ecosystems. Little is known about the warming effect on the bacterial microbiota inhabiting the plant surface (phyllosphere), which can have a strong impact on plant growth and health, as well as on plant diseases and colonization by human pathogens. The aim of this study was to investigate the effect of moderate surface warming on the diversity and composition of the bacterial leaf microbiota of the herbaceous plant Galium album. Leaves were collected from four control and four surface warmed (+2°C) plots located at the field site of the Environmental Monitoring and Climate Impact Research Station Linden in Germany over a 6-year period. Warming had no effect on the concentration of total number of cells attached to the leaf surface as counted by Sybr Green I staining after detachment, but changes in the diversity and phylogenetic composition of the bacterial leaf microbiota analyzed by bacterial 16S rRNA gene Illumina amplicon sequencing were observed. The bacterial phyllosphere microbiota were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Warming caused a significant higher relative abundance of members of the Gammaproteobacteria, Actinobacteria, and Firmicutes, and a lower relative abundance of members of the Alphaproteobacteria and Bacteroidetes. Plant beneficial bacteria like Sphingomonas spp. and Rhizobium spp. occurred in significantly lower relative abundance in leaf samples of warmed plots. In contrast, several members of the Enterobacteriaceae, especially Enterobacter and Erwinia, and other potential plant or human pathogenic genera such as Acinetobacter and insect-associated Buchnera and Wolbachia spp. occurred in higher relative abundances in the phyllosphere samples from warmed plots. This study showed for the first time the long-term impact of moderate (+2°C) surface warming on the phyllosphere microbiota on plants. A reduction of beneficial bacteria and an enhancement of potential pathogenic bacteria in the phyllosphere of plants may indicate that this aspect of the ecosystem which has been largely neglected up till now, can be a potential risk for pathogen transmission in agro-ecosystems in the near future.

The Divergence in Bacterial Components Associated with Bactrocera dorsalis across Developmental Stages

Eco-evolutionary dynamics of microbiotas at the macroscale level are largely driven by ecological variables. The diet and living environment of the oriental fruit fly, Bactrocera dorsalis, diversify during development, providing a natural system to explore convergence, divergence, and repeatability in patterns of microbiota dynamics as a function of the host diet, phylogeny, and environment. Here, we characterized the microbiotas of 47 B. dorsalis individuals from three distinct populations by 16S rRNA amplicon sequencing. A significant deviation was found within the larvae, pupae, and adults of each population. Pupae were characterized by an increased bacterial taxonomic and functional diversity. Principal components analysis showed that the microbiotas of larvae, pupae, and adults clearly separated into three clusters. Acetobacteraceae, Lactobacillaceae, and Enterobacteriaceae were the predominant families in larval and adult samples, and PICRUSt analysis indicated that phosphoglycerate mutases and transketolases were significantly enriched in larvae, while phosphoglycerate mutases, transketolases, and proteases were significantly enriched in adults, which may support the digestive function of the microbiotas in larvae and adults. The abundances of Intrasporangiaceae, Dermabacteraceae (mainly Brachybacterium) and Brevibacteriaceae (mainly Brevibacterium) were significantly higher in pupae, and the antibiotic transport system ATP-binding protein and antibiotic transport system permease protein pathways were significantly enriched there as well, indicating the defensive function of microbiotas in pupae. Overall, differences in the microbiotas of the larvae, pupae, and adults are likely to contribute to differences in nutrient assimilation and living environments.

Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere

Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents.

The Role of Host Genetic Signatures on Root-Microbe Interactions in the Rhizosphere and Endosphere

Microbiomes inhabiting plants are crucial for plant productivity and well-being. A plethora of interactions between roots, microbiomes, and soil shapes the self-organization of the microbial community associated with the root system. The rhizosphere (i.e., the soil close to the root surface) and endosphere (i.e., all inner root tissues) are critical interfaces for the exchange of resources between roots and the soil environment. In recent years, next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes in the endosphere and interactions between roots and microbes at the root-soil interfaces. Genetic factors such as species and genotype of host plants are the driving force of microbial community differentiation and composition. In this mini-review, we will survey the role of these factors on plant-microbe interactions by highlighting the results of next-generation genomic and transcriptomic studies in the rhizosphere and endosphere of land plants. Moreover, environmental factors such as geography and soil type shape the microbiome. Relationships between the root-associated microbiome, architectural variations and functional switches within the root system determine the health and fitness of the whole plant system. A detailed understanding of plant-microbe interactions is of fundamental agricultural importance and significance for crop improvement by plant breeding.

Comparative responses of diazotrophic abundance and community structure to the chemical composition of paddy soil

Diazotrophy is considered as one of the most crucial and dynamic phenomena in the rice field and also a major source of nitrogen input. The objective of this study was to elucidate possible interactions between diverse and dominant diazotrophic bacterial community and organic carbon composition of the paddy soil. Our results suggest that most abundantly found diazotrophs belong to a proteobacteria group and uncultured bacterial forms. A gene abundance study clearly showed significantly higher diazotrophic abundance (P < 0.01) at Chandauli (CHN) as compared to Varanasi (VNS) and Ghazipur (GHJ) districts of Eastern Uttar Pradesh, India, with nitrogenase reductase (nifH) copy number between 1.44 × 10³ and 3.34 × 10³ copy g^-1 soil. Fourier-transform infrared (FT-IR) spectroscopy data identified -CO-, C=O ([Formula: see text] and -NH-), [Formula: see text], and OH- as dominant organic functional groups in the paddy soil. Multivariate analysis was performed to get a clear and more accurate picture of interactions between free-living diazotrophs and abiotic soil factors. Regression analysis suggested a similar trend of distribution of different functional groups along each site. Relative abundance and diversity of diazotrophic population increased in response to FT-IR-based soil organic fractions. Maximum number of FT-IR spectral peak at sites in the Chandauli district augmented its bacterial diazotrophic diversity and abundance. Taken together, the present study sheds light on the substrate-driven composition of the microbial population of selected paddy areas.

Biostimulant Action of Protein Hydrolysates: Unraveling Their Effects on Plant Physiology and Microbiome

Plant-derived protein hydrolysates (PHs) have gained prominence as plant biostimulants because of their potential to increase the germination, productivity and quality of a wide range of horticultural and agronomic crops. Application of PHs can also alleviate the negative effects of abiotic plant stress due to salinity, drought and heavy metals. Recent studies aimed at uncovering the mechanisms regulating these beneficial effects indicate that PHs could be directly affecting plants by stimulating carbon and nitrogen metabolism, and interfering with hormonal activity. Indirect effects could also play a role as PHs could enhance nutrient availability in plant growth substrates, and increase nutrient uptake and nutrient-use efficiency in plants. Moreover, the beneficial effects of PHs also could be due to the stimulation of plant microbiomes. Plants are colonized by an abundant and diverse assortment of microbial taxa that can help plants acquire nutrients and water and withstand biotic and abiotic stress. The substrates provided by PHs, such as amino acids, could provide an ideal food source for these plant-associated microbes. Indeed, recent studies have provided evidence that plant microbiomes are modified by the application of PHs, supporting the hypothesis that PHs might be acting, at least in part, via changes in the composition and activity of these microbial communities. Application of PHs has great potential to meet the twin challenges of a feeding a growing population while minimizing agriculture's impact on human health and the environment. However, to fully realize the potential of PHs, further studies are required to shed light on the mechanisms conferring the beneficial effects of these products, as well as identify product formulations and application methods that optimize benefits under a range of agro-ecological conditions.

Influence of fertilizers and rice cultivation methods on the abundance and diversity of phyllosphere microbiome

Rice paddies are man-made, cross-over ecologies of aquatic and terrestrial systems, which favor the proliferation of characteristic microbial communities. Moisture regimes under flooded and different levels of irrigation such as in direct seeded rice (DSR) and system of rice intensification (SRI) lead to modulation in crop physiology, soil nutrient availability, and the soil microbiome. However, the diversity of the rice phyllosphere microbiome is less investigated in terms of the influence of fertilizer application and the method of rice cultivation (conventional-flooded, DSR and SRI). Scanning electron micrographs revealed the presence of bacteria as aggregates at microsites of the leaves. Phylogenetic analysis of the dominant culturable bacterial isolates using 16S rDNA sequences revealed that they belonged to the genera - Bacillus, Brevibacillus, Pantoea, Enterobacter, Pseudomonas, Erwinia, and Streptomyces. Fertilizer application brought about a distinct modulation in the communities belonging to phyla such as Bacteriodetes, Firmicutes, and Planctomyces, besides Proteobacteria. The cyanobacterial population was much influenced by the cultivation methods, particularly the SRI. Principal component analysis (PCA), involving the culturable phyllospheric microbial groups and leaf attributes (nutrients and pigments), illustrated the importance of leaf nitrogen and zinc. Also, the communities of the phylum Firmicutes exhibited marked changes in terms of the diversity, not only due to the cultivation method, but also the application of fertilizers. Thus, the cultivation methods and fertilizer application played important roles in modulating both the structural (taxonomical) and functional attributes of the phyllosphere microbiome.

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site

Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps.

Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree

Boswellia sacra, a frankincense producing endemic tree, has been well known for its cultural, religious and economic values. However, the tree has been least explored for the associated microsymbiota in the rhizosphere. The current study elucidates the fungal and bacterial communities of the rhizospheric regions of the wild and cultivated B. sacra tree populations through next generation sequencing. The sequence analysis showed the existence of 1006±8.9 and 60.6±3.1 operational taxonomic unit (OTUs) for bacterial and fungal communities respectively. In fungal communities, five major phyla were found with significantly higher abundance of Ascomycota (60.3%) in wild population and Basidiomycota (52%) in cultivated tree rhizospheres. Among bacterial communities, 31 major phyla were found, with significant distribution of Actinobacteria in wild tree rhizospheres, whereas Proteobacteria and Acidobacteria were highly abundant in cultivated trees. The diversity and abundance of microbiome varied significantly depending upon soil characteristics of the three different populations. In addition, significantly higher glucosidases, cellulases and indole-3-acetic acid were found in cultivated tree’s rhizospheres as compared to wild tree populations. for these plants to survive the harsh arid-land environmental conditions. The current study is a first comprehensive work and advances our knowledge about the core fungal and bacterial microbial microbiome associated with this economically important tree.

The Value of a Comparative Approach to Understand the Complex Interplay between Microbiota and Host Immunity

The eukaryote immune system evolved and continues to evolve within a microbial world, and as such is critically shaped by-and in some cases even reliant upon-the presence of host-associated microbial species. There are clear examples of adaptations that allow the host to simultaneously tolerate and/or promote growth of symbiotic microbiota while protecting itself against pathogens, but the relationship between immunity and the microbiome reaches far beyond simple recognition and includes complex cross talk between host and microbe as well as direct microbiome-mediated protection against pathogens. Here, we present a broad but brief overview of how the microbiome is controlled by and interacts with diverse immune systems, with the goal of identifying questions that can be better addressed by taking a comparative approach across plants and animals and different types of immunity. As two key examples of such an approach, we focus on data examining the importance of early exposure on microbiome tolerance and immune system development and function, and the importance of transmission among hosts in shaping the potential coevolution between, and long-term stability of, host-microbiome associations. Then, by comparing existing evidence across short-lived plants, mouse model systems and humans, and insects, we highlight areas of microbiome research that are strong in some systems and absent in others with the hope of guiding future research that will allow for broad-scale comparisons moving forward. We argue that such an approach will not only help with identification of generalities in host-microbiome-immune interactions but also improve our understanding of the role of the microbiome in host health.

Culturable Facultative Methylotrophic Bacteria from the Cactus Neobuxbaumia macrocephala Possess the Locus xoxF and Consume Methanol in the Presence of Ce3+ and Ca2

Methanol-consuming culturable bacteria were isolated from the plant surface, rhizosphere, and inside the stem of Neobuxbaumia macrocephala. All 38 isolates were facultative methylotrophic microorganisms. Their classification included the Classes Actinobacteria, Sphingobacteriia, Alpha-, Beta-, and Gammaproteobacteria. The deduced amino acid sequences of methanol dehydrogenase obtained by PCR belonging to Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria showed high similarity to rare-earth element (REE)-dependent XoxF methanol dehydrogenases, particularly the group XoxF5. The sequences included Asp³⁰¹, the REE-coordinating amino acid, present in all known XoxF dehydrogenases and absent in MxaF methanol dehydrogenases. The quantity of the isolates showed positive hybridization with a xoxF probe, but not with a mxaF probe. Isolates of all taxonomic groups showed methylotrophic growth in the presence of Ce³⁺ or Ca²⁺. The presence of xoxF-like sequences in methylotrophic bacteria from N. macrocephala and its potential relationship with their adaptability to xerophytic plants are discussed.

Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes

Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O3), sulfur dioxide (SO2), nitrogen dioxides (NO2), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption. Various policies, regulations, and technologies have been brought together for remediation of air pollution, but the air still remains polluted. In this review, we direct attention to bioremediation of air pollutants by exploiting the potentials of plant leaves and leaf-associated microbes. The aerial surfaces of plants, particularly leaves, are estimated to sum up to 4 × 108 km2 on the earth and are also home for up to 1026 bacterial cells. Plant leaves are able to adsorb or absorb air pollutants, and habituated microbes on leaf surface and in leaves (endophytes) are reported to be able to biodegrade or transform pollutants into less or nontoxic molecules, but their potentials for air remediation has been largely unexplored. With advances in omics technologies, molecular mechanisms underlying plant leaves and leaf associated microbes in reduction of air pollutants will be deeply examined, which will provide theoretical bases for developing leaf-based remediation technologies or phylloremediation for mitigating pollutants in the air.

Application of Struvite Alters the Antibiotic Resistome in Soil, Rhizosphere, and Phyllosphere

Struvite recovered from wastewater is a renewable source of phosphorus and nitrogen and can be used as fertilizer for plant growth. However, antibiotics and resistome can be enriched in the struvite derived from wastewater. Robust understanding of the potential risks after struvite application to soils has remained elusive. Here, we profiled antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in struvite, soil, rhizosphere and phyllosphere of Brassica using high-throughput quantitative PCR. A total of 165 ARGs and 10 MGEs were detected. Application of struvite was found to increase both the abundance and diversity of ARGs in soil, rhizosphere and phyllosphere. In addition, ARGs shared exclusively between Brassica phyllosphere and struvite were identified, indicating that struvite was an important source of ARGs found in phyllosphere. Furthermore, OTUs shared between rhizosphere and phyllosphere were found to significantly correlate with ARGs, suggesting that microbiota in leaf and root could interconnect and ARGs might transfer from struvite to the surface of plants via rhizosphere using bacteria as spreading medium. These findings demonstrated that struvite as an organic fertilizer can facilitate the spread of antibiotic resistance into human food chain and this environment-acquired antibiotic resistance should be put into human health risk assessment system.

Nutrients and host attributes modulate the abundance and functional traits of phyllosphere microbiome in rice

The abundance of phyllosphere bacterial communities of seven genotypes of rice ADT- 38, ADT-43, CR-1009, PB-1, PS-5, P-44, and PB-1509 was investigated, in relation to nutrient dynamics of rhizosphere and leaves. P-44 genotype recorded highest pigment accumulation, while genotypes CR-1009 and P-44 exhibited most number of different bacterial morphotypes, Colony forming units in two media (Nutrient agar and R2A) varied significantly and ranged from 10⁶-10⁷ per g plant tissues. Among the selected 60 distinct morphotypes, IAA and siderophore producers were the dominant functional types. Biocontrol activity against Drechslera oryzae was shown by 38 isolates, while 17 and 9 isolates were potent against Rhizoctonia solani and Magnaporthe oryzae respectively. Principal Component Analysis (PCA) illustrated the significant effects of selected soil and leaf nutrients of seven rice varieties on the culturable phyllospheric population (log CFU), particularly in the R2A medium. Eigen values revealed that 83% of the variance observed could be assigned to Leaf-Fe, Leaf-Mn, chlorophyll b and soil organic carbon (OC). Quantitative PCR analyses of abundance of bacteria, cyanobacteria and archaebacteria revealed a host-specific response, with CR-1009 showing highest number of 16S rRNA copies of bacterial members, while both P-44 and PS-5 had higher cyanobacterial abundance, but lowest number of those belonging to archaebacteria. Nutritional aspects of leaf and soil influenced the abundance of bacteria and their functional attributes; this is of interest for enhancing the efficacy of foliar inoculants, thereby, improving plant growth and disease tolerance.

Application of the entomogenous fungus, Metarhizium anisopliae, for leafroller (Cnaphalocrocis medinalis) control and its effect on rice phyllosphere microbial diversity

Microbial pesticides form critical components of integrated pest management (IPM) practices. Little, however, is known regarding the impacts of these organisms on the indigenous microbial community. We show that Metarhizium anisopliae strain CQMa421 was highly effective in controlling the rice leafroller, Cnaphalocrocis medinalis Guenee. In addition, M. anisopliae distribution and its effects on phyllosphere microbial diversity after application in field trials were investigated. Phylloplane specific distribution of the fungus was observed over time, with more rapid declines of M. anisopliae CFUs (colony-forming units) seen in the top leaf layer as compared to lower layers. Application of the fungus resulted in transient changes in the endogenous microbial diversity with variations seen in the bacterial observed species and Shannon index. Notable increases in both parameters were seen at 6-day post-application of M. anisopliae, although significant variation within sample replicates for bacteria and fungi were noted. Application of M. anisopliae increased the relative distribution of bacterial species implicated in plant growth promotion and organic pollutant degradation, e.g., Methylobacterium, Sphingobium, and Deinococcus. These data show minimal impact of M. anisopliae on endogenous microbial diversity with transient changes in bacterial abundance/diversity that may result in added benefits to crops.

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships

Research on biodiversity and ecosystem functioning has demonstrated links between plant diversity and ecosystem functions such as productivity. At other trophic levels, the plant microbiome has been shown to influence host plant fitness and function, and host-associated microbes have been proposed to influence ecosystem function through their role in defining the extended phenotype of host organisms However, the importance of the plant microbiome for ecosystem function has not been quantified in the context of the known importance of plant diversity and traits. Here, using a tree biodiversity-ecosystem functioning experiment, we provide strong support for the hypothesis that leaf bacterial diversity is positively linked to ecosystem productivity, even after accounting for the role of plant diversity. Our results also show that host species identity, functional identity and functional diversity are the main determinants of leaf bacterial community structure and diversity. Our study provides evidence of a positive correlation between plant-associated microbial diversity and terrestrial ecosystem productivity, and a new mechanism by which models of biodiversity-ecosystem functioning relationships can be improved.

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬

Knowledge of bacterial community host-specificity has increased greatly in recent years. However, the intermicrobiome relationships of unrelated but spatially close organisms remain little understood. Trunks of trees covered by epiphytes represent complex habitats with a mosaic of ecological niches. In this context, we investigated the structure, diversity and interactions of microbiota associated with lichens, mosses and the bare tree bark. Comparative analysis revealed significant differences in the habitat-associated community structures. Corresponding co-occurrence analysis indicated that the lichen microbial network is less complex and less densely interconnected than the moss- and bark-associated networks. Several potential generalists and specialists were identified for the selected habitats. Generalists belonged mainly to Proteobacteria, with Sphingomonas as the most abundant genus. The generalists comprise microorganisms with generally beneficial features, such as nitrogen fixation or other supporting functions, according to a metagenomic analysis. We argue that beneficial strains shared among hosts contribute to ecological stability of the host biocoenoses.

Research priorities for harnessing plant microbiomes in sustainable agriculture

Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host-microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.

Carbon source regulation of gene expression in Methylosinus trichosporium OB3b

Gene expression in methanotrophs has been shown to be affected by the availability of a variety of metals, most notably copper regulating expression of alternative forms of methane monooxygenase. Here, we show that growth substrate also affects expression of genes encoding for enzymes responsible for the oxidation of methane to formaldehyde and the assimilation of carbon. Specifically, in Methylosinus trichosporium OB3b, expression of genes involved in the conversion of methane to methanol (pmoA and mmoX) and methanol to formaldehyde (mxaF, xoxF1, and xoxF2) as well as in carbon assimilation (fae1, fae2, metF, and sga) decreased when this strain was grown on methanol vs. methane, indicating that methanotrophs manipulate gene expression in response to growth substrate as well as the availability of copper. Interestingly, growth of M. trichosporium OB3b on methane vs. methanol was similar despite such large changes in gene expression. Finally, methanol-grown cultures of M. trichosporium OB3b also exhibited the "copper-switch." That is, expression of pmoA increased and mmoX decreased in the presence of copper, indicating that copper still controlled the expression of alternative forms of methane monooxygenase in M. trichosporium OB3b even though methane was not provided. Such findings indicate that methanotrophs can sense and respond to multiple environmental parameters simultaneously.