Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

BACKGROUND

Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities.

RESULTS

Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless, all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula, and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere.

CONCLUSIONS

Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis toward a more mechanistic understanding of plant microbiomes. Video Abstract.

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

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

Field Exploitation of Multiple Functions of Beneficial Microorganisms for Plant Nutrition and Protection: Real Possibility or Just a Hope?

Bioproducts, i.e., microbial based pesticides or fertilizers (biopesticides and biofertilizers), should be expected to play an ever-increasing role and application in agricultural practices world-wide in the effort to implement policies concerned with sustainable agriculture. However, several microbial strains have proven the capacity to augment plant productivity by enhancing crop nutrition and functioning as biopesticides, or vice-versa. This multifunctionality is an issue that is still not included as a concept and possibility in any legal provision regarding the placing on the market of bioproducts, and indicates difficulties in clearly classifying the purpose of their suitability. In this review, we overview the current understanding of the mechanisms in plant-microbe interactions underlining the dual function of microbial strains toward plant nutrition and protection. The prospects of market development for multifunctional bioproducts are then considered in view of the current regulatory approach in the European Union, in an effort that wants to stimulate a wider adoption of the new knowledge on the role played by microorganisms in crop production.

Tripartite mutualisms as models for understanding plant-microbial interactions

All plants host diverse microbial assemblages that shape plant health, productivity, and function. While some microbial effects are attributable to particular symbionts, interactions among plant-associated microbes can nonadditively affect plant fitness and traits in ways that cannot be predicted from pairwise interactions. Recent research into tripartite plant-microbe mutualisms has provided crucial insight into this nonadditivity and the mechanisms underlying plant interactions with multiple microbes. Here, we discuss how interactions among microbial mutualists affect plant performance, highlight consequences of biotic and abiotic context-dependency for nonadditive outcomes, and summarize burgeoning efforts to determine the molecular bases of how plants regulate establishment, resource exchange, and maintenance of tripartite interactions. We conclude with four goals for future tripartite studies that will advance our overall understanding of complex plant-microbial interactions.

Mutualistic Outcomes Across Plant Populations, Microbes, and Environments in the Duckweed Lemna minor

The picture emerging from the rapidly growing literature on host-associated microbiota is that host traits and fitness often depend on interactive effects of host genotype, microbiota, and abiotic environment. However, testing interactive effects typically requires large, multi-factorial experiments and thus remains challenging in many systems. Furthermore, most studies of plant microbiomes focus on terrestrial hosts and microbes. Aquatic habitats may confer unique properties to microbiomes. We grew different populations of duckweed (Lemna minor), a floating aquatic plant, in three microbial treatments (adding no, "home", or "away" microbes) at two levels of zinc, a common water contaminant in urban areas, and measured both plant and microbial performance. Thus, we simultaneously manipulated plant source population, microbial community, and abiotic environment. We found strong effects of plant source, microbial treatment, and zinc on duckweed and microbial growth, with significant variation among duckweed genotypes and microbial communities. However, we found little evidence of interactive effects: zinc did not alter effects of host genotype or microbial community, and host genotype did not alter effects of microbial communities. Despite strong positive correlations between duckweed and microbe growth, zinc consistently decreased plant growth, but increased microbial growth. Furthermore, as in recent studies of terrestrial plants, microbial interactions altered a duckweed phenotype (frond aggregation). Our results suggest that duckweed source population, associated microbiome, and contaminant environment should all be considered for duckweed applications, such as phytoremediation. Lastly, we propose that duckweed microbes offer a robust experimental system for study of host-microbiota interactions under a range of environmental stresses.

Endophytes: Colonization, Behaviour, and Their Role in Defense Mechanism

Biotic and abiotic factors cause an enormous amount of yield and economical loss. However, endophytes can play a significant role in enhancing the tolerance of plants. Endophytes systematically colonize different parts of the host, but plants use a variety of defense mechanisms towards microbial infection. However, they have to survive the oxidative environments, and endophytes like Enterobacter sp. encode superoxide dismutases, catalases, and hydroperoxide reductases to cope up the oxidative stress during colonization. On the contrary, others produce subtilomycin which binds with flagella to affect flg22-induced plant defense. The behavior of endophytes can be affected by different genes in hydrolase activity when they come into contact with the host plant. The lifestyle of endophytes is influenced by environmental factors, the host, and microbial genotypes, as well as an imbalance in nutrient exchange between the microbe and the host. For instance, induction of PiAMT1 in root endophyte Piriformospora indica indicates depletion of nitrogen which plays as a triggering factor for activation of the saprotrophic program. Microbes enhance disease resistance through induced systemic resistance (ISR), and Bacillus cereus triggers ISR against Botrytis cinerea through an accumulation of the PR1 protein and activates MAPK signaling and WRKY53 gene expression by the JA/ET signaling pathway. Similarly, Trichoderma arundinaceum produces trichodiene that affects Botrytis cinerea through induction of defense-related genes encoding salicylic acid (SA) and jasmonate (JA). Overall, endophytes can play a vital role in disease management.

Stage-dependent concomitant microbial fortification improves soil nutrient status, plant growth, antioxidative defense system and gene expression in rice

Stage-dependent concomitant fortification of rice (Oryza sativa L.) varieties PB1612 and CO51 with microbial inoculants Trichoderma asperellum and Pseudomonas fluorescens as seed coating, seedling root inoculation and soil application enhanced growth, activated antioxidant enzymes and modulated defence-related genes in plants. Microbial inoculants improved shoot height, tiller numbers, fresh weight and dry biomass. Co-inoculation was more impactful in enhancing plant growth and development as compared to single inoculation. Single and co-inoculation improved organic carbon (OC) and N, P and K content in the soil substantially. Mean values between control and co-inoculation varied significantly for OC in PB1612 (p0.001) and CO51 (p0.019) and phosphorus content in PB1612 (p0.044) and CO51 (p0.021). Microbial inoculation enhanced soil nutrients and increased their bioavailability for the plants. Total polyphenolics, flavonoids and protein content increased in the leaves following microbial inoculation. Enhanced non-enzymatic antioxidant parameters (ABTS, DPPH, Fe-ion reducing power and Fe-ion chelation) was found in microbe inoculated rice reflecting high free radical scavenging activity in polyphenolics-rich leaf extracts. Increased enzyme activity of superoxide dismutase (SOD), glutathione reductase (GR), phenylalanine ammonia-lyase (PAL), peroxidase (PO), glutathione peroxidase (GPX), ascorbate peroxidase (APX) and catalase (CAT) showed improved ROS scavenging in rice plants having co-inoculation. Over-expression of PAL, cCuZn-SOD and CAT genes in microbial inoculated rice plants was recorded. The study concludes that plant stage-wise concomitant fortification by microbial inoculants could play multi-pronged manifestations at physiological, biochemical and molecular level in rice to positively influence growth, development and defense attributes in plants.

Metabolomics of Myrcia bella Populations in Brazilian Savanna Reveals Strong Influence of Environmental Factors on Its Specialized Metabolism

Environmental conditions influence specialized plant metabolism. However, many studies aiming to understand these modulations have been conducted with model plants and/or under controlled conditions, thus not reflecting the complex interaction between plants and environment. To fully grasp these interactions, we investigated the specialized metabolism and genetic diversity of a native plant in its natural environment. We chose Myrcia bella due to its medicinal interest and occurrence in Brazilian savanna regions with diverse climate and soil conditions. An LC-HRMS-based metabolomics approach was applied to analyze 271 samples harvested across seven regions during the dry and rainy season. Genetic diversity was assessed in a subset of 40 samples using amplified fragment length polymorphism. Meteorological factors including rainfall, temperature, radiation, humidity, and soil nutrient and mineral composition were recorded in each region and correlated with chemical variation through multivariate analysis (MVDA). Marker compounds were selected using a statistically informed molecular network and annotated by dereplication against an in silico database of natural products. The integrated results evidenced different chemotypes, with variation in flavonoid and tannin content mainly linked to soil conditions. Different levels of genetic diversity and distance of populations were found to be correlated with the identified chemotypes. These observations and the proposed analytical workflow contribute to the global understanding of the impact of abiotic factors and genotype on the accumulation of given metabolites and, therefore, could be valuable to guide further medicinal exploration of native species.

Microbe-mediated local adaptation to limestone barrens is context dependent

Plant-root-associated microbes influence plant phenotype and tolerance to environmental stress, and thus have been hypothesized to play a role in plant local adaptation. Here, we test this hypothesis with factorial experiments addressing the role of microbes in local adaptation of Hypericum perforatum (St. John's wort) to stressful limestone barrens (alvars) compared to neighboring old-fields. Alvar plants benefited more from microbes in early life history stages, while at later growth stages, alvar and old-field plants benefited equally from microbes but only in the old-field habitat. Patterns of local adaptation were changed by the presence of microbes. Alvar plants grown in association with alvar microbes outperformed old-field plants in the alvar habitat, whereas old-field plants showed patterns of maladaptation when grown with microbes. In this demonstration of microbe-mediated adaptation, we show that rhizosphere microbes can be important for plant fitness and patterns of local adaptation but that those effects are dependent on life-history stage and habitat.

Microbial symbionts and ecological divergence of Caribbean sponges: A new perspective on an ancient association

Marine sponges host diverse communities of microbial symbionts that expand the metabolic capabilities of their host, but the abundance and structure of these communities is highly variable across sponge species. Specificity in these interactions may fuel host niche partitioning on crowded coral reefs by allowing individual sponge species to exploit unique sources of carbon and nitrogen, but this hypothesis is yet to be tested. Given the presence of high sponge biomass and the coexistence of diverse sponge species, the Caribbean Sea provides a unique system in which to investigate this hypothesis. To test for ecological divergence among sympatric Caribbean sponges and investigate whether these trends are mediated by microbial symbionts, we measured stable isotope (δ13C and δ15N) ratios and characterized the microbial community structure of sponge species at sites within four regions spanning a 1700 km latitudinal gradient. There was a low (median of 8.2 %) overlap in the isotopic niches of sympatric species; in addition, host identity accounted for over 75% of the dissimilarity in both δ13C and δ15N values and microbiome community structure among individual samples within a site. There was also a strong phylogenetic signal in both δ15N values and microbial community diversity across host phylogeny, as well as a correlation between microbial community structure and variation in δ13C and δ15N values across samples. Together, this evidence supports a hypothesis of strong evolutionary selection for ecological divergence across sponge lineages and suggests that this divergence is at least partially mediated by associations with microbial symbionts.

The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here?

The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ~600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the 17 biomes encompassed by our survey, 7 were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.

Cover Crop Diversity as a Tool to Mitigate Vine Decline and Reduce Pathogens in Vineyard Soils

Wine grape production is an important economic asset in many nations; however, a significant proportion of vines succumb to grapevine trunk pathogens, reducing yields and causing economic losses. Cover crops, plants that are grown in addition to main crops in order to maintain and enhance soil composition, may also serve as a line of defense against these fungal pathogens by producing volatile root exudates and/or harboring suppressive microbes. We tested whether cover crop diversity reduced disease symptoms and pathogen abundance. In two greenhouse experiments, we inoculated soil with a 106 conidia suspension of Ilyonectria liriodendri, a pathogenic fungus, then conditioned soil with cover crops for several months to investigate changes in pathogen abundance and fungal communities. After removal of cover crops, Chardonnay cuttings were grown in the same soil to assess disease symptoms. When grown alone, white mustard was the only cover crop associated with reductions in necrotic root damage and abundance of Ilyonectria. The suppressive effects of white mustard largely disappeared when paired with other cover crops. In this study, plant identity was more important than diversity when controlling for fungal pathogens in vineyards. This research aligns with other literature describing the suppressive potential of white mustard in vineyards.

Do Foliar Endophytes Matter in Litter Decomposition?

Litter decomposition rates are affected by a variety of abiotic and biotic factors, including the presence of fungal endophytes in host plant tissues. This review broadly analyzes the findings of 67 studies on the roles of foliar endophytes in litter decomposition, and their effects on decomposition rates. From 29 studies and 1 review, we compiled a comprehensive table of 710 leaf-associated fungal taxa, including the type of tissue these taxa were associated with and isolated from, whether they were reported as endo- or epiphytic, and whether they had reported saprophytic abilities. Aquatic (i.e., in-stream) decomposition studies of endophyte-affected litter were significantly under-represented in the search results (p < 0.0001). Indicator species analyses revealed that different groups of fungal endophytes were significantly associated with cool or tropical climates, as well as specific plant host genera (p < 0.05). Finally, we argue that host plant and endophyte interactions can significantly influence litter decomposition rates and should be considered when interpreting results from both terrestrial and in-stream litter decomposition experiments.

Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

BACKGROUND

The shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing.

RESULTS

OJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO₃^--N, NH₄⁺-N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions.

CONCLUSION

Soil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.

A potential antifungal and growth-promoting bacterium Bacillus sp. KTMA4 from tomato rhizosphere

Plant growth-promoting rhizobacteria are indigenous beneficial bacteria that will enhance plant growth as well as suppress phytopathogens. In the present study, the isolate KTMA4 showed the highest inhibition against major phytopathogens of tomato; Fusarium oxysporum (66%) and Alternaria solani (54%) after seven days of incubation. Analysis of the 16S rRNA gene sequence revealed that the isolate KTMA4 is Bacillus cereus (MG547975). The isolate produced in vitro plants growth-promoting factors such as Indole-3-acetic acid, ammonia, catalase, siderophore and 1-aminocyclopropane-1-carboxylate deaminase and it has nitrogen fixation ability. The bacterial strain has also produced lytic enzymes such as amylase, cellulase, xylanase, lipase, and protease. Moreover, the bacterium Bacillus cereus KTMA4 effectively produced biofilm, biosurfactants and salt-tolerant (5% NaCl). The bacterium exhibited intrinsic antibiotic resistance. The in vivo studies using tomato plants grown from seeds treated with the bacterial strain KTMA4 demonstrated an enhancement in seed germination percentage (86.66 ± 2.88) and vigour index (637.5 ± 21.65) over the uninoculated control (germination percentage- 28.33 ± 2.88 and vigour index- 42.5 ± 4.33). 60 days of greenhouse study revealed that the bacterial isolate enhanced the plant growth significantly (P ≤ 0.05) compared to the uninoculated control and the treated plants. Therefore the study suggests that the newly isolated rhizosphere bacterial strain can be used as a potential biocontrol agent against a multitude of fungal pathogens as well as a biofertilizer inoculant for tomato cultivation.

Recurrent mutualism breakdown events in a legume rhizobia metapopulation

Bacterial mutualists generate major fitness benefits for eukaryotes, reshaping the host phenotype and its interactions with the environment. Yet, microbial mutualist populations are predicted to generate mutants that defect from providing costly services to hosts while maintaining the capacity to exploit host resources. Here, we examined the mutualist service of symbiotic nitrogen fixation in a metapopulation of root-nodulating Bradyrhizobium spp. that associate with the native legume Acmispon strigosus. We quantified mutualism traits of 85 Bradyrhizobium isolates gathered from a 700 km transect in California spanning 10 sampled A. strigosus populations. We clonally inoculated each Bradyrhizobium isolate onto A. strigosus hosts and quantified nodulation capacity and net effects of infection, including host growth and isotopic nitrogen concentration. Six Bradyrhizobium isolates from five populations were categorized as ineffective because they formed nodules but did not enhance host growth via nitrogen fixation. Six additional isolates from three populations failed to form root nodules. Phylogenetic reconstruction inferred two types of mutualism breakdown, including three to four independent losses of effectiveness and five losses of nodulation capacity on A. strigosus. The evolutionary and genomic drivers of these mutualism breakdown events remain poorly understood.

Role of Jasmonates in Beneficial Microbe-Root Interactions

The phytohormone jasmonate (JA) modulates various defense and developmental responses of plants, and is implied in the integration of multiple environmental signals. Given its centrality in regulating plant physiology according to external stimuli, JA influences the establishment of interactions between plant roots and beneficial bacteria or fungi. In many cases, moderate JA signaling promotes the onset of mutualism, while massive JA signaling inhibits it. The output also depends on the compatibility between microbe and host plant and on nutritional or environmental cues. Also, JA biosynthesis and perception participate in the systemic regulation of mutualistic interactions and in microbe-induced resistance to biotic and abiotic stress. Here, we review our current knowledge of the role of JA biosynthesis, signaling, and responses during mutualistic root-microbe interactions.

Drought and Salinity Stress Responses and Microbe-Induced Tolerance in Plants

Drought and salinity are among the most important environmental factors that hampered agricultural productivity worldwide. Both stresses can induce several morphological, physiological, biochemical, and metabolic alterations through various mechanisms, eventually influencing plant growth, development, and productivity. The responses of plants to these stress conditions are highly complex and depend on other factors, such as the species and genotype, plant age and size, the rate of progression as well as the intensity and duration of the stresses. These factors have a strong effect on plant response and define whether mitigation processes related to acclimation will occur or not. In this review, we summarize how drought and salinity extensively affect plant growth in agriculture ecosystems. In particular, we focus on the morphological, physiological, biochemical, and metabolic responses of plants to these stresses. Moreover, we discuss mechanisms underlying plant-microbe interactions that confer abiotic stress tolerance.

Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential

Kuwait is a semi-arid region with soils that are relatively nitrogen-poor. Thus, biological nitrogen fixation is an important natural process in which N₂-fixing bacteria (diazotrophs) convert atmospheric nitrogen into plant-usable forms such as ammonium and nitrate. Currently, there is limited information on free-living and root-associated nitrogen-fixing bacteria and their potential to fix nitrogen and aid natural plant communities in the Kuwait desert. In this study, free living N₂-fixing diazotrophs were enriched and isolated from the rhizosphere soil associated with three native keystone plant species; Rhanterium epapposum, Farsetia aegyptia, and Haloxylon salicornicum. Root-associated bacteria were isolated from the root nodules of Vachellia pachyceras. The result showed that the strains were clustered in five groups represented by class: γ-proteobacteria, and α-proteobacteria; phyla: Actinobacteria being the most dominant, followed by phyla: Firmicutes, and class: β-proteobacteria. This study initially identified 50 nitrogen-fixers by16S rRNA gene sequencing, of which 78% were confirmed to be nitrogen-fixers using the acetylene reduction assay. Among the nitrogen fixers identified, the genus Rhizobium was predominant in the rhizosphere soil of R. epapposum and H. salicornicum, whereas Pseudomonas was predominant in the rhizosphere soil of F. aegyptia, The species Agrobacterium tumefaciens was mainly found to be dominant among the root nodules of V. pachyceras and followed by Cellulomonas, Bacillus, and Pseudomonas genera as root-associated bacteria. The variety of diazotrophs revealed in this study, signifying the enormous importance of free-living and root-associated bacteria in extreme conditions and suggesting potential ecological importance of diazotrophs in arid ecosystem. To our knowledge, this study is the first to use culture-based isolation, molecular identification, and evaluation of N₂-fixing ability to detail diazotroph diversity in Kuwaiti desert soils.

Fungal functional ecology: bringing a trait-based approach to plant-associated fungi

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun^Fun ). Fun^Fun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.

Microbial Communities in Bioswale Soils and Their Relationships to Soil Properties, Plant Species, and Plant Physiology

Bioswales and other forms of green infrastructure can be effective means to reduce environmental stresses in urban ecosystems; however, few studies have evaluated the ecology of these systems, or the role that plant selection and microbial assembly play in their function. For the current study, we examined the relationship between plant transpiration rates for five commonly planted herbaceous species in three bioswales in New York City, as well as bioswale soil microbial composition and soil chemistry. Soils were sampled near individual plants, with distinction made between upper (bioswale inlet) and lower slopes (bioswale outlet). We found high variation in transpiration rates across species, and that Nepeta × faassenii was the highest conductor (13.65 mmol H2O m-2s-1), while Panicum virgatum was the lowest conductor (2.67 mmol H2O m-2s-1) (p < 0.001). There was significant variation in percent N of leaves and soil, which did not relate to the higher water conductance in bioswales. Significantly higher C, N, and water content on the high end of bioswale slopes suggest storm water run-off is mostly absorbed on the inlet side. Bacterial and fungal communities were significantly clustered by bioswale and by plant species within each bioswale implying there are micro-environmental controls on the soil microbial composition, and that plant composition matters for microbial assemblages within bioswales. Plants with higher transpiration rates were associated with greater fungal and bacterial diversity at the level of the bioswale and at scale of the individual plant, suggesting a possible link between plant physiological traits and soil microbial communities. These data suggest that the specific plant palette selected for planting bioswales can have deterministic effects on the surrounding microbial communities which may further influence functions such as transpiration and nutrient cycling. These results may have implications for bioswale management to improve urban water quality and reduce stress on sewage systems after storm events by revising plant species palette selection based on the functional consequences of plant-microbial associations in engineered green infrastructure.

Soil microbes that may accompany climate warming increase alpine plant production

Climate change is causing species with non-overlapping ranges to come in contact, and a key challenge is to predict the consequences of such species re-shuffling. Experiments on plants have focused largely on novel competitive interactions; other species interactions, such as plant-microbe symbioses, while less studied, may also influence plant responses to climate change. In this greenhouse study, we evaluated interactions between soil microbes and alpine-restricted plant species, simulating a warming scenario in which low-elevation microbes migrate upslope into the distribution of alpine plants. We examined three alpine grasses from the Rocky Mountains, CO, USA (Poa alpina, Festuca brachyphylla, and Elymus scribneri). We used soil inocula from within (resident) or below (novel) the plants' current elevation range and examined responses in plant biomass, plant traits, and fungal colonization of roots. Resident soil inocula from the species' home range decreased biomass to a greater extent than novel soil inocula. The depressed growth in resident soils suggested that these soils harbor more carbon-demanding microbes, as plant biomass generally declined with greater fungal colonization of roots, especially in resident soil inocula. Although plant traits did not respond to the provenance of soil inocula, specific leaf area declined and root:shoot ratio increased when soil inocula were sterilized, indicating microbial mediation of plant trait expression. Contrary to current predictions, our findings suggest that if upwardly migrating microbes were to displace current soil microbes, alpine plants may benefit from this warming-induced microbial re-shuffling.

Towards an Integrative, Eco-Evolutionary Understanding of Ecological Novelty: Studying and Communicating Interlinked Effects of Global Change

Global change has complex eco-evolutionary consequences for organisms and ecosystems, but related concepts (e.g., novel ecosystems) do not cover their full range. Here we propose an umbrella concept of “ecological novelty” comprising (1) a site-specific and (2) an organism-centered, eco-evolutionary perspective. Under this umbrella, complementary options for studying and communicating effects of global change on organisms, ecosystems, and landscapes can be included in a toolbox. This allows researchers to address ecological novelty from different perspectives, e.g., by defining it based on (a) categorical or continuous measures, (b) reference conditions related to sites or organisms, and (c) types of human activities. We suggest striving for a descriptive, non-normative usage of the term “ecological novelty” in science. Normative evaluations and decisions about conservation policies or management are important, but require additional societal processes and engagement with multiple stakeholders.

Defence priming in Arabidopsis - a Meta-Analysis

Defence priming by organismal and non-organismal stimulants can reduce effects of biotic stress in plants. Thus, it could help efforts to enhance the sustainability of agricultural production by reducing use of agrochemicals in protection of crops from pests and diseases. We have explored effects of applying this approach to both Arabidopsis plants and seeds of various crops in meta-analyses. The results show that its effects on Arabidopsis plants depend on both the priming agent and antagonist. Fungi and vitamins can have strong priming effects, and priming is usually more effective against bacterial pathogens than against herbivores. Moreover, application of bio-stimulants (particularly vitamins and plant defence elicitors) to seeds can have promising defence priming effects. However, the published evidence is scattered, does not include Arabidopsis, and additional studies are required before we can draw general conclusions and understand the molecular mechanisms involved in priming of seeds' defences. In conclusion, defence priming of plants has clear potential and application of bio-stimulants to seeds may protect plants from an early age, promises to be both labour- and resource-efficient, poses very little environmental risk, and is thus both economically and ecologically promising.

Protective microbiomes can limit the evolution of host pathogen defense

The evolution of host immunity occurs in the context of the microbiome, but little theory exists to predict how resistance against pathogens might be influenced by the need to tolerate and regulate commensal microbiota. We present a general model to explore the optimal investment in host immunity under conditions in which the host can, versus cannot easily distinguish among commensal versus pathogenic bacteria, and when commensal microbiota can, versus cannot protect the host against the impacts of pathogen infection. We find that a loss of immune vigilance associated with innate immunity over evolutionary time can occur due to the challenge of discriminating between pathogenic and other microbe species. Further, we find the greater the protective effect of microbiome species, acting either directly or via competition with a pathogen, or the higher the costs of immunity, the more likely the loss of immune vigilance is. Conversely, this effect can be reversed when pathogens increase host mortality. Generally, the magnitude of costs of immunity required to allow evolution of decreased immune vigilance are predicted to be lowest when microbiome and pathogen species most resemble each other (in terms of host recognition), and when immune effects on the pathogen are weak. Our model framework makes explicit the core trade‐offs likely to shape the evolution of immunity in the context of microbiome/pathogen discrimination. We discuss how this informs interpretation of patterns and process in natural systems, including vulnerability to pathogen emergence.

Interactions and Coadaptation in Plant Metaorganisms

Plants associate with a wide diversity of microorganisms. Some microorganisms engage in intimate associations with the plant host, collectively forming a metaorganism. Such close coexistence with plants requires specific adaptations that allow microorganisms to overcome plant defenses and inhabit plant tissues during growth and reproduction. New data suggest that the plant immune system has a broader role beyond pathogen recognition and also plays an important role in the community assembly of the associated microorganism. We propose that core microorganisms undergo coadaptation with their plant host, notably in response to the plant immune system allowing them to persist and propagate in their host. Microorganisms, which are vertically transmitted from generation to generation via plant seeds, putatively compose highly adapted species and may have plant-beneficial functions. The extent to which plant domestication has impacted the underlying genetics of plant-microbe associations remains poorly understood. We propose that the ability of domesticated plants to select and maintain advantageous microbial partners may have been affected. In this review, we discuss factors that impact plant metaorganism assembly and function. We underline the importance of microbe-microbe interactions in plant tissues, as they are still poorly studied but may have a great impact on plant health.

Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location

Previous studies indicate that the plant phenotypic traits eventually shape its microbiota due to the community assembly based on the functional types. If so, the distance-related variations of microbial communities are mostly only in taxonomical composition due to the different seeds pool, and there is no difference in microbial community functional structure if the location associated factors would not cause phenotypical variations in plants. We test this hypothesis by investigating the phyllospheric microbial community from five species of spruce (Picea spp.) trees that planted similarly but at three different locations. Results indicated that the geographical location affected microbial taxonomical compositions and had no effect on the community functional structure. In fact, this actually leads to a spurious difference in the microbial community. Our findings suggest that, within similar host plants, the phyllosphere microbial communities with differing taxonomical compositions might be functionally similar.

Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes

Background

Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and soil microorganisms to reduce the salt concentrations is believed to be environmentally-friendly. However, little is known about the change of bacterial community during salt pond restoration in the context of phytoremediation. In the present study, we used 16S metagenomics to compare seasonal changes of bacterial communities between the revegetated and barren salterns at Sicao, Taiwan.

Results

In both saltern types, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes were predominant at the phylum level. In the revegetated salterns, the soil microbiomes displayed high species diversities and underwent a stepwise transition across seasons. In the barren salterns, the soil microbiomes fluctuated greatly, indicating that mangroves tended to stabilize the soil microorganism communities over the succession. Bacteria in the order Halanaerobiaceae and archaea in the family Halobacteriaceae that were adapted to high salinity exclusively occurred in the barren salterns. Among the 441 persistent operational taxonomic units detected in the revegetated salterns, 387 (87.5%) were present as transient species in the barren salterns. Only 32 persistent bacteria were exclusively detected in the revegetated salterns. Possibly, salt-tolerant plants provided shelters for those new colonizers.

Conclusions

The collective data indicate that revegetation tended to stabilize the microbiome across seasons and enriched the microbial diversity in the salterns, especially species of Planctomycetes and Acidobacteria.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5875-y) contains supplementary material, which is available to authorized users.

Sphingomonas sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis thaliana Under Drought Stress

The rhizosphere is colonized by a mass of microbes, including bacteria capable of promoting plant growth that carry out complex interactions. Here, by using a sterile experimental system, we demonstrate that Sphingomonas sp. Cra20 promotes the growth of Arabidopsis thaliana by driving developmental plasticity in the roots, thus stimulating the growth of lateral roots and root hairs. By investigating the growth dynamics of A. thaliana in soil with different water-content, we demonstrate that Cra20 increases the growth rate of plants, but does not change the time of reproductive transition under well-water condition. The results further show that the application of Cra20 changes the rhizosphere indigenous bacterial community, which may be due to the change in root structure. Our findings provide new insights into the complex mechanisms of plant and bacterial interactions. The ability to promote the growth of plants under water-deficit can contribute to the development of sustainable agriculture.

Environmental factors affect the distribution of two Epichloë fungal endophyte species inhabiting a common host grove bluegrass (Poa alsodes)

AIM

The endophyte Epichloë alsodes, with known insecticidal properties, is found in a majority of Poa alsodes populations across a latitudinal gradient from North Carolina to New York. A second endophyte, E. schardlii var. pennsylvanica, with known insect-deterring effects, is limited to a few populations in Pennsylvania. We explored whether such disparate differences in distributions could be explained by selection from biotic and abiotic environmental factors.

LOCATION

Along the Appalachian Mountains from North Carolina to New York, USA.

TAXON

Fungi.

METHODS

Studied correlations of infection frequencies with abiotic and biotic environmental factors. Checked endophyte vertical transmission rates and effects on overwintering survival. With artificial inoculations for two host populations with two isolates per endophyte species, tested endophyte-host compatibility. Studied effects of isolates on host performances in greenhouse experiment with four water-nutrients treatments.

RESULTS

Correlation analysis revealed positive associations of E. alsodes frequency with July Max temperatures, July precipitation, and soil nitrogen and phosphorous and negative associations with insect damage and soil magnesium and potassium. Plants infected with E. alsodes had increased overwintering survival compared to plants infected with E. schardlii or uninfected (E-) plants. Artificial inoculations indicated that E. alsodes had better compatibility with a variety of host genotypes than did E. schardlii. The experiment with reciprocally inoculated plants grown under different treatments revealed a complexity of interactions among hosts, endophyte species, isolate within species, host plant origin, and environmental factors. Neither of the endophyte species increased plant biomass, but some of the isolates within each species had other effects on plant growth such as increased root:shoot ratio, number of tillers, and changes in plant height that might affect host fitness.

MAIN CONCLUSION

In the absence of clear and consistent effects of the endophytes on host growth, the differences in endophyte-mediated protection against herbivores may be the key factor determining distribution differences of the two endophyte species.

Importance of plant- and microbe-driven metabolic pathways for plant defence

Expression of plant phenotypes can depend on both plant genomes and interactions between plants and the microbes living in, on and near their roots. We understand a growing number of the mechanistic links between plant genotypes and phenotypes, such as defence against herbivory (see brief review in Hubbard et al., ), yet the links between root microbiomes and the comprehensive swathe of plant phenotypes they affect (Friesen et al., ) remain less clear. In this issue of Molecular Ecology, Hubbard et al. () follow microbe- and plant-driven changes in plant defence against hervibory from molecular underpinnings to ecological consequences, contrasting both the metabolites affected and the magnitude of defensive impact. Naively, we might expect plant genomes to drive more variation in phenotype than the root microbiome, but Hubbard et al. () find the opposite, implying profound consequences for plant trait evolution and ecological interactions.

Climate-driven reduction of genetic variation in plant phenology alters soil communities and nutrient pools

We examined the hypothesis that climate-driven evolution of plant traits will influence associated soil microbiomes and ecosystem function across the landscape. Using a foundation tree species, Populus angustifolia, observational and common garden approaches, and a base population genetic collection that spans 17 river systems in the western United States, from AZ to MT, we show that (a) as mean annual temperature (MAT) increases, genetic and phenotypic variation for bud break phenology decline; (b) soil microbiomes, soil nitrogen (N), and soil carbon (C) vary in response to MAT and conditioning by trees; and (c) with losses of genetic variation due to warming, population-level regulation of community and ecosystem functions strengthen. These results demonstrate a relationship between the potential evolutionary response of populations and subsequent shifts in ecosystem function along a large temperature gradient.

Relating Urban Biodiversity to Human Health With the 'Holobiont' Concept

A relatively unaccounted ecosystem service from biodiversity is the benefit to human health via symbiotic microbiota from our environment. This benefit occurs because humans evolved alongside microbes and have been constantly exposed to diverse microbiota. Plants and animals, including humans, are organised as a host with symbiotic microbiota, whose collective genome and life history form a single holobiont. As such, there are interdependencies between biodiversity, holobionts, and public health which lead us to argue that human health outcomes could be improved by increasing contact with biodiversity in an urban context. We propose that humans, like all holobionts, likely require a diverse microbial habitat to appropriate resources for living healthy, long lives. We discuss how industrial urbanisation likely disrupts the symbiosis between microbiota and their hosts, leading to negative health outcomes. The industrialised urban habitat is low in macro and microbial biodiversity and discourages contact with beneficial environmental microbiota. These habitat factors, alongside diet, antibiotics, and others, are associated with the epidemic of non-communicable diseases in these societies. We suggest that restoration of urban microbial biodiversity and micro-ecological processes through microbiome rewilding can benefit holobiont health and aid in treating the urban non-communicable disease epidemic. Further, we identify research gaps and some solutions to economic and strategic hurdles in applying microbiome rewilding into daily urban life.

The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China

Few studies have investigated the effect of environment on the root-associated microbiome, especially for woody plants in their native environment. The roots and rhizosphere soils of a native woody species (Broussonetia papyrifera) sampled across four different climate types in China were used to elucidate the influence of environment on the root-associated microbiome. Our results showed that the B. papyrifera root-associated microbiome contained abundant Proteobacteria and Basidiomycota, especially Pseudomonas and Rhizobium. The root-associated microbiomes were found to be significantly different under different climate types except for the bacterial community in the rhizosphere, and the proportion of bacterial operational taxonomic units (OTUs) shared among different climate types was lower than that of fungi. More than 50% of the total variance between microbiomes could be explained by 15 environmental factors, six of which, especially soil concentration phosphate and nitrate, had a significant effect. This study provided a comprehensive understanding of the root-associated microbiome of B. papyrifera and further confirmed the effect of environment on the root-associated microbiome of B. papyrifera under different climate types, with some exceptions in the rhizobacterial community and fungal OTUs. Our findings advanced knowledge of the effect of environment through an exploration of environmental factors and found that the nitrogen and phosphorus content represented the key factors.

Protists: Puppet Masters of the Rhizosphere Microbiome

The rhizosphere microbiome is a central determinant of plant performance. Microbiome assembly has traditionally been investigated from a bottom-up perspective, assessing how resources such as root exudates drive microbiome assembly. However, the importance of predation as a driver of microbiome structure has to date largely remained overlooked. Here we review the importance of protists, a paraphyletic group of unicellular eukaryotes, as a key regulator of microbiome assembly. Protists can promote plant-beneficial functions within the microbiome, accelerate nutrient cycling, and remove pathogens. We conclude that protists form an essential component of the rhizosphere microbiome and that accounting for predator-prey interactions would greatly improve our ability to predict and manage microbiome function at the service of plant growth and health.

Modeling the interactions among phythopatogens and phyllosphere microorganisms for the biological disease control of Olea europaea L

In this paper we formulate a model for assessing the interaction between the phytopathogen Spilocaea oleaginea and the phyllosphere microorganisms that are present in the olive tree leaves. The model describes the evolution in time of the foliage of the olive tree and the two different microorganisms, the phytopathogen fungi, that negatively affect the plant causing spots in the leaves, and the beneficial phyllosphere microorganisms, that help in keeping in check the invasion of the former. The system possesses five equilibria that are suitably analysed for feasibility and stability. The model shows interesting features: a bistable behavior, exhibited by three different pairs of equilibria. The separatrix surface of the basins of attraction of one such pair is computed. This allows the possible assessment of human intervention for control of the disease. Persistent oscillations via Hopf bifurcation are also discovered.

Desert plant bacteria reveal host influence and beneficial plant growth properties

Deserts, such as those found in Saudi Arabia, are one of the most hostile places for plant growth. However, desert plants are able to impact their surrounding microbial community and select beneficial microbes that promote their growth under these extreme conditions. In this study, we examined the soil, rhizosphere and endosphere bacterial communities of four native desert plants Tribulus terrestris, Zygophyllum simplex, Panicum turgidum and Euphorbia granulata from the Southwest (Jizan region), two of which were also found in the Midwest (Al Wahbah area) of Saudi Arabia. While the rhizosphere bacterial community mostly resembled that of the highly different surrounding soils, the endosphere composition was strongly correlated with its host plant phylogeny. In order to assess whether any of the native bacterial endophytes might have a role in plant growth under extreme conditions, we analyzed the properties of 116 cultured bacterial isolates that represent members of the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Our analysis shows that different strains have highly different biochemical properties with respect to nutrient acquisition, hormone production and growth under stress conditions. More importantly, eleven of the isolated strains could confer salinity stress tolerance to the experimental model plant Arabidopsis thaliana suggesting some of these plant-associated bacteria might be useful for improving crop desert agriculture.

Ectomycorrhizal Fungal Communities and Their Functional Traits Mediate Plant-Soil Interactions in Trace Element Contaminated Soils

There is an increasing consensus that microbial communities have an important role in mediating ecosystem processes. Trait-based ecology predicts that the impact of the microbial communities on ecosystem functions will be mediated by the expression of their traits at community level. The link between the response of microbial community traits to environmental conditions and its effect on plant functioning is a gap in most current microbial ecology studies. In this study, we analyzed functional traits of ectomycorrhizal fungal species in order to understand the importance of their community assembly for the soil-plant relationships in holm oak trees (Quercus ilex subsp. ballota) growing in a gradient of exposure to anthropogenic trace element (TE) contamination after a metalliferous tailings spill. Particularly, we addressed how the ectomycorrhizal composition and morphological traits at community level mediate plant response to TE contamination and its capacity for phytoremediation. Ectomycorrhizal fungal taxonomy and functional diversity explained a high proportion of variance of tree functional traits, both in roots and leaves. Trees where ectomycorrhizal fungal communities were dominated by the abundant taxa Hebeloma cavipes and Thelephora terrestris showed a conservative root economics spectrum, while trees colonized by rare taxa presented a resource acquisition strategy. Conservative roots presented ectomycorrhizal functional traits characterized by high rhizomorphs formation and low melanization which may be driven by resource limitation. Soil-to-root transfer of TEs was explained substantially by the ectomycorrhizal fungal species composition, with the highest transfer found in trees whose roots were colonized by Hebeloma cavipes. Leaf phosphorus was related to ectomycorrhizal species composition, specifically higher leaf phosphorus was related to the root colonization by Thelephora terrestris. These findings support that ectomycorrhizal fungal community composition and their functional traits mediate plant performance in metal-contaminated soils, and have a high influence on plant capacity for phytoremediation of contaminants. The study also corroborates the overall effects of ectomycorrhizal fungi on ecosystem functioning through their mediation over the plant economics spectrum.

Plant-mycorrhizal interactions mediate plant community coexistence by altering resource demand

As the diversity of plants increases in an ecosystem, so does resource competition for soil nutrients, a process that mycorrhizal fungi can mediate. The influence of mycorrhizal fungi on plant biodiversity likely depends on the strength of the symbiosis between the plant and fungi, the differential plant growth responses to mycorrhizal inoculation, and the transfer rate of nutrients from the fungus to plant. However, our current understanding of how nutrient-plant-mycorrhizal interactions influence plant coexistence is conceptual and thus lacks a unified quantitative framework. To quantify the conditions of plant coexistence mediated by mycorrhizal fungi, we developed a mechanistic resource competition model that explicitly included plant-mycorrhizal symbioses. We found that plant-mycorrhizal interactions shape plant coexistence patterns by creating a tradeoff in resource competition. Especially, a tradeoff in resource competition was caused by differential payback in the carbon resources that plants invested in the fungal symbiosis and/or by the stoichiometric constraints on plants that required additional, less-beneficial, resources to sustain growth. Our results suggested that resource availability and the variation in plant-mycorrhizal interactions act in concert to drive plant coexistence patterns. Applying our framework, future empirical studies should investigate plant-mycorrhizal interactions under multiple levels of resource availability.