The relative importance of rapid evolution for plant-microbe interactions depends on ecological context

Multi-Generation Ecosystem Selection of Rhizosphere Microbial Communities Associated with Plant Genotype and Biomass in Arabidopsis thaliana

The role of the microbiome in shaping the host's phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres' microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet it remains challenging. Here, we conducted an artificial ecosystem selection experiment for eight generations of Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with a higher or lower biomass of the host. This resulted in divergent microbial communities shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment had modest but significant impacts. Over time, the plant genotype and biomass treatments gained more influence, explaining ~40% of the variation in the microbial community's composition. Furthermore, a genotype-specific association of plant-growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, was observed under selection for high biomass.

Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction

BACKGROUND

Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants.

RESULTS

We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla.

CONCLUSION

Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.

Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response

While a plant's microbiome can facilitate adaptive phenotypes, the plant's role in selecting for these microbes is unclear. Do plants actively recruit microbes beneficial to their current environment, or are beneficial microbes only an incidental by-product of microbial adaptation? We addressed these questions through a multigeneration greenhouse experiment, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After three plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants. We found that plants generally benefited from soil microbes, and this benefit was greater whenever their current watering conditions matched the microbes' historical watering conditions. Principally, the plant's presence was not necessary in the historical treatments for this environmental matching benefit to emerge. Moreover, we found microbes from droughted soils could better tolerate drought stress. Taken together, these results suggest that the moisture environment selects for microbes that benefit plants under those specific moisture conditions, and that these beneficial properties arise as a by-product of microbial adaptation to the watering environment and not as a co-adapting plant-microbe system. This work highlights that understanding the selective agents on these plant-associated microbes will lead to a better understanding of plant adaptation.

Symbiont genotype influences holobiont response to increased temperature

As coral reefs face warming oceans and increased coral bleaching, a whitening of the coral due to loss of microalgal endosymbionts, the possibility of evolutionary rescue offers some hope for reef persistence. In tightly linked mutualisms, evolutionary rescue may occur through evolution of the host and/or endosymbionts. Many obligate mutualisms are composed of relatively small, fast-growing symbionts with greater potential to evolve on ecologically relevant time scales than their relatively large, slower growing hosts. Numerous jellyfish species harbor closely related endosymbiont taxa to other cnidarian species such as coral, and are commonly used as a model system for investigating cnidarian mutualisms. We examined the potential for adaptation of the upside-down jellyfish Cassiopea xamachana to increased temperature via evolution of its microalgal endosymbiont, Symbiodinium microadriaticum. We quantified trait variation among five algal genotypes in response to three temperatures (26 °C, 30 °C, and 32 °C) and fitness of hosts infected with each genotype. All genotypes showed positive growth rates at each temperature, but rates of respiration and photosynthesis decreased with increased temperature. Responses varied among genotypes but were unrelated to genetic similarity. The effect of temperature on asexual reproduction and the timing of development in the host also depended on the genotype of the symbiont. Natural selection could favor different algal genotypes at different temperatures, affecting host fitness. This eco-evolutionary interaction may be a critical component of understanding species resilience in increasingly stressful environments.

Phytomicrobiome communications: Novel implications for stress resistance in plants

The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.

Contemporary evolution rivals the effects of rhizobium presence on community and ecosystem properties in experimental mesocosms

Because genotypes within a species commonly differ in traits that influence other species, whole communities, or even ecosystem functions, evolutionary change within one key species may affect the community and ecosystem processes. Here we use experimental mesocosms to test how the evolution of reduced cooperation in rhizobium mutualists in response to 20 years of nitrogen fertilization compares to the effects of rhizobium presence on soil nitrogen availability and plant community composition and diversity. The evolution of reduced rhizobium cooperation caused reductions in soil nitrogen, biological nitrogen fixation, and leaf nitrogen concentrations that were as strong as, or even stronger than, experimental rhizobium inoculation (presence/absence) treatments. Effects of both rhizobium evolution and rhizobium inoculation on legume dominance, plant community composition, and plant species diversity were often smaller in magnitude, but suggest that rhizobium evolution can alter the relative abundance of plant functional groups. Our findings indicate that the consequences of rapid microbial evolution for ecosystems and communities can rival the effects resulting from the presence or abundance of keystone mutualists.

Impacts of global change on the phyllosphere microbiome

Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.

Management of abiotic stresses by microbiome-based engineering of the rhizosphere

Abiotic stresses detrimentally affect both plant and soil health, threatening food security in an ever-increasing world population. Sustainable agriculture is necessary to augment crop yield with simultaneous management of stresses. Limitations of conventional bioinoculants has shifted the focus on more effective alternatives. With the realisation of the potential of rhizospheric microbiome engineering in enhancing plant's fitness under stresses, efforts have accelerated in this direction. Though still in its infancy, microbiome-based engineering has gained popularity because of its advantages over microbe-based approach. This review briefly presents major abiotic stresses afflicting arable land, followed by introduction to the conventional approach of microbe-based enhancement of plant attributes and stress mitigation with its inherent limitations. It then focusses on the significance of rhizospheric microbiome, and harnessing its potential by its strategic engineering for stress management. Further, success stories related to two major approaches of microbiome engineering (generation of synthetic microbial community/consortium, and host-mediated artificial selection) pertaining to stress management have been critically presented. Together with bringing forth the challenges associated with wide application of rhizospheric microbiome engineering in agriculture, the review proposes the adoption of combinatorial scheme for the same, bringing together ecological and reductionist approaches for improvised sustainable agricultural practices.

Storage of soil microbiome for application in sustainable agriculture: prospects and challenges

Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as "next-generation biologicals" for future applications via soil transplantation. The challenge, therefore, is to devise a strategy for the storage of soil microbiome such that its "functionality" is preserved for later application. This review discusses the current endeavours made towards storage of the soil microbiome. The methods for assessing the integrity of soil microbiome by targeting the structural diversity and functional potential of the preserved microbiomes have also been discussed. Further, the success stories related to the storage of fecal microbiome for application in transplants have also been highlighted. This is done primarily with the objective of learning lessons, and parallel application of the knowledge gained, in bringing about improvement in the research domain of soil microbiome storage. Subsequently, the limitations of current techniques of preservation have also been delineated. Further, the open questions in the area have been critically discussed. In conclusion, possible alternatives for storage, comprehensive analyses of the composition of the stored microbiome and their potential have been presented.

Competition alters species' plastic and genetic response to environmental change

Species react to environmental change via plastic and evolutionary responses. While both of them determine species' survival, most studies quantify these responses individually. As species occur in communities, competing species may further influence their respective response to environmental change. Yet, how environmental change and competing species combined shape plastic and genetic responses to environmental change remains unclear. Quantifying how competition alters plastic and genetic responses of species to environmental change requires a trait-based, community and evolutionary ecological approach. We exposed unicellular aquatic organisms to long-term selection of increasing salinity-representing a common and relevant environmental change. We assessed plastic and genetic contributions to phenotypic change in biomass, cell shape, and dispersal ability along increasing levels of salinity in the presence and absence of competition. Trait changes in response to salinity were mainly due to mean trait evolution, and differed whether species evolved in the presence or absence of competition. Our results show that species' evolutionary and plastic responses to environmental change depended both on competition and the magnitude of environmental change, ultimately determining species persistence. Our results suggest that understanding plastic and genetic responses to environmental change within a community will improve predictions of species' persistence to environmental change.

Adaptation and competition in deteriorating environments

Evolution might rescue populations from extinction in changing environments. Using experimental evolution with microalgae, we investigated if competition influences adaptation to an abiotic stressor, and vice versa, if adaptation to abiotic change influences competition. In a first set of experiments, we propagated monocultures of five species with and without increasing salt stress for approximately 180 generations. When assayed in monoculture, two of the five species showed signatures of adaptation, that is, lines with a history of salt stress had higher population growth rates at high salt than lines without prior exposure to salt. When assayed in mixtures of species, however, only one of these two species had increased population size at high salt, indicating that competition can alter how adaptation to abiotic change influences population dynamics. In a second experiment, we cultivated two species in monocultures and in pairs, with and without increasing salt. While we found no effect of competition on adaptation to salt, our experiment revealed that evolutionary responses to salt can influence competition. Specifically, one of the two species had reduced competitive ability in the no-salt environment after long-term exposure to salt stress. Collectively, our results highlight the complex interplay of adaptation to abiotic change and competitive interactions.

Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit

Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit regardless of vegetation density, showing a greater relative abundance of Hypocrea sp. Tailings deposit fungal communities were distinct from those found in boreal forest soils. Alder rhizosphere had greater relative abundances of Hypocrea sp. and Thelephora sp., while birch rhizosphere were more often associated with Mollisia sp. Our results indicate that, with increasing vegetation density on the mine site, the bacterial communities associated with the individual deciduous or coniferous species studied were increasingly similar to the bacterial communities found in the adjacent forest. In order to properly assess and restore disturbed sites, it is important to characterize and understand the plant-microbe associations that occur since they likely improve plant fitness in these harsh environments.

Soil precipitation legacies influence intraspecific plant-soil feedback

Feedbacks between plants and soil microbial communities can play an important role in structuring plant communities. However, little is known about how soil legacies caused by environmental disturbances such as drought and extreme precipitation events may affect plant-soil feedback or whether plant-soil feedback operates within species as it does between species. If soil legacies alter plant-soil feedback among genotypes within a plant species, then soil legacies may alter the diversity within plant populations. We conducted a fully factorial pairwise plant-soil feedback experiment to test how precipitation legacies influenced intraspecific plant-soil feedbacks among three genotypes of a dominant grass species, Panicum virgatum. Panicum virgatum experienced negative intraspecific plant-soil feedback, i.e., genotypes generally performed worse on soil from the same genotype than different genotypes. Soil precipitation legacies reversed the rank order of the strength of negative feedback among the genotypes. Feedback is often positively correlated with plant relative abundance. Therefore, our results suggest that soil precipitation legacies may alter the genotypic composition of P. virgatum populations, favoring genotypes that develop less negative feedback. Changes in intraspecific diversity will likely further affect community structure and ecosystem functioning, and may constrain the ability of populations to respond to future changes in climate.

Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities

In spite of the growing interest in the role of the gut microbiome (GM) in host physiology and health, the mechanisms governing its assembly and its effects on the environment are poorly understood. In this article, we show that the host genotype and the GM of Daphnia influence the community structure of the surrounding bacterioplankton (BPK). When Daphnia genotypes were placed in an identical environment, both the GM and BPK showed a genotype and diet-dependent taxonomic composition. Overall, the GM strongly differed from the BPK in taxonomic composition and was characterized by a lower α-diversity, suggesting a selective rejecting of bacteria from the regional species pool. In a microbiome transplant experiment, the assembly of both the GM and BPK was strongly affected by the host genotype and the inoculum to which germ-free Daphnia were exposed. The combination of these results suggests a strong interaction between the host genotype, its GM and free-living microbial communities. Currently, it is generally assumed that an animal’s diet has a strong effect on the animal’s GM, but only a negligible (if any) effect on the surrounding environment. However, our results indicate that the diet/microbiome inocula have a small effect on the gut community and a large effect on the community in the surrounding environment. This structuring genotype × microbiome × environment effect is an essential prerequisite that could indicate that microbiomes play an important role in eco-evolutionary processes.

Variable Influences of Water Availability and Rhizobacteria on the Growth of Schizachyrium scoparium (Little Bluestem) at Different Ages

There is significant interest in understanding the role of plant growth-promoting rhizobacteria (PGPR) in alleviating different types of plant stress. Schizachyrium scoparium (little bluestem) is a moderately drought tolerant, perennial bunchgrass native to North America. The goal of this experiment was to evaluate whether the addition of a bacterial root isolate in the Pseudomonas genus promoted the growth of S. scoparium with changes in water availability. Pseudomonas are common rhizobacteria and have been shown to improve plant growth. It was hypothesized that plants inoculated with the PGPR strain would have greater growth and health, and would be less affected by shifts in water availability. Pseudomonas strains were isolated from the roots of native S. scoparium plants. After germination, S. scoparium seedlings were subjected to four treatment groups: low water; high water; low water with PGPR; and high water with PGPR. The experiment was run three times with plants at different starting ages; 14-, 28-, and 70-day-old plants. The effects of the water and PGPR treatments were variable between the experimental trials. There were no significant effects of the water treatments on plant growth in Trial 1 (14-day-old plants) or Trial 2 (28-day-old plants), however, there was a significant negative effect of the high watering treatment on the shoot length and biomass in Trial 3. High water availability was significantly associated with greater plant health in Trial 1, but appeared to reduce plant health in Trials 2 and 3. The PGPR treatment appeared to promote root growth and biomass in Trial 2, and was associated with greater plant health in all three trials, especially when paired with the low water treatment. Results from a permutational MANOVA indicate that plant growth was significantly different between the trials due to differences in the starting age of the plants and the duration of the experiments. Thus, methodological choices, such as plant life history stage and experiment duration, may affect the response of plants to PGPR in the rhizosphere. This research provides an insight into the interactions between PGPR and water availability on the growth and health of native plants.

Rhizobacterial Community Assembly Patterns Vary Between Crop Species

Currently our limited understanding of crop rhizosphere community assembly hinders attempts to manipulate it beneficially. Variation in root communities has been attributed to plant host effects, soil type, and plant condition, but it is hard to disentangle the relative importance of soil and host without experimental manipulation. To examine the effects of soil origin and host plant on root associated bacterial communities we experimentally manipulated four crop species in split-plot mesocosms and surveyed variation in bacterial diversity by Illumina amplicon sequencing. Overall, plant species had a greater impact than soil type on community composition. While plant species associated with different Operational Taxonomic Units (OTUs) in different soils, plants tended to recruit bacteria from similar, higher order, taxonomic groups in different soils. However, the effect of soil on root-associated communities varied between crop species: Onion had a relatively invariant bacterial community while other species (maize and pea) had a more variable community structure. Dynamic communities could result from environment specific recruitment, differential bacterial colonization or reflect broader symbiont host range; while invariant community assembly implies tighter evolutionary or ecological interactions between plants and root-associated bacteria. Irrespective of mechanism, it appears both communities and community assembly rules vary between crop species.

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.

Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria

Invasive species could benefit from being introduced to locations with more favorable species interactions, including the loss of enemies, the gain of mutualists, or the simplification of complex interaction networks. Microbiomes are an important source of species interactions with strong fitness effects on multicellular organisms, and these interactions are known to vary across regions. The highly invasive plant yellow starthistle (Centaurea solstitialis) has been shown to experience more favorable microbial interactions in its invasions of the Americas, but the microbiome that must contribute to this variation in interactions is unknown. We sequenced amplicons of 16S rRNA genes to characterize bacterial community compositions in the phyllosphere, ectorhizosphere, and endorhizosphere of yellow starthistle plants from seven invading populations in California, USA, and eight native populations in Europe. We tested for the differentiation of microbiomes by geography, plant compartment, and plant genotype. Bacterial communities differed significantly between native and invading plants within plant compartments, with consistently lower diversity in the microbiome of invading plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbiome differences between ranges. Our results reveal that these invading plants are experiencing either a simplified microbial environment or simplified microbial interactions as a result of the dominance of a few taxa within their microbiome. Our findings highlight several alternative hypotheses for the sources of variation that we observe in invader microbiomes and the potential for altered bacterial interactions to facilitate invasion success.IMPORTANCE Previous studies have found that introduced plants commonly experience more favorable microbial interactions in their non-native range, suggesting that changes to the microbiome could be an important contributor to invasion success. Little is known about microbiome variation across native and invading populations, however, and the potential sources of more favorable interactions are undescribed. Here, we report one of the first microbiome comparisons of plants from multiple native and invading populations, in the noxious weed yellow starthistle. We identify clear differences in composition and diversity of microbiome bacteria. Our findings raise new questions about the sources of these differences, and we outline the next generation of research that will be required to connect microbiome variation to its potential role in plant invasions.

Eco-evolutionary dynamics in a disturbed world: implications for the maintenance of ecological networks

Past management of exploited species and of conservation issues has often ignored the evolutionary dynamics of species. During the 70s and 80s, evolution was mostly considered a slow process that may be safely ignored for most management issues. However, in recent years, examples of fast evolution have accumulated, suggesting that time scales of evolutionary dynamics (variations in genotype frequencies) and of ecological dynamics (variations in species densities) are often largely comparable, so that complex feedbacks commonly exist between the ecological and the evolutionary context ("eco-evolutionary dynamics"). While a first approach is of course to consider the evolution of a given species, in ecological communities, species are interlinked by interaction networks. In the present article, I discuss how species (co)evolution in such a network context may alter our understanding and predictions for species coexistence, given the disturbed world we live in. I review some concepts and examples suggesting that evolution may enhance the robustness of ecological networks and then show that, in many situations, the reverse may also happen, as evolutionary dynamics can harm diversity maintenance in various ways. I particularly focus on how evolution modifies indirect effects in ecological networks, then move to coevolution and discuss how the outcome of coevolution for species coexistence depends on the type of interaction (mutualistic or antagonistic) that is considered. I also review examples of phenotypes that are known to be important for ecological networks and shown to vary rapidly given global changes. Given all these components, evolution produces indirect eco-evolutionary effects within networks that will ultimately influence the optimal management of the current biodiversity crisis.

Root bacterial endophytes confer drought resistance and enhance expression and activity of a vacuolar H+ -pumping pyrophosphatase in pepper plants

It has been previously shown that the transgenic overexpression of the plant root vacuolar proton pumps H+ -ATPase (V-ATPase) and H+ -PPase (V-PPase) confer tolerance to drought. Since plant-root endophytic bacteria can also promote drought tolerance, we hypothesize that such promotion can be associated to the enhancement of the host vacuolar proton pumps expression and activity. To test this hypothesis, we selected two endophytic bacteria endowed with an array of in vitro plant growth promoting traits. Their genome sequences confirmed the presence of traits previously shown to confer drought resistance to plants, such as the synthesis of nitric oxide and of organic volatile organic compounds. We used the two strains on pepper (Capsicuum annuum L.) because of its high sensitivity to drought. Under drought conditions, both strains stimulated a larger root system and enhanced the leaves' photosynthetic activity. By testing the expression and activity of the vacuolar proton pumps, H+ -ATPase (V-ATPase) and H+ -PPase (V-PPase), we found that bacterial colonization enhanced V-PPase only. We conclude that the enhanced expression and activity of V-PPase can be favoured by the colonization of drought-tolerance-inducing bacterial endophytes.

Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing

Background

Fertilization as one of the measures in restoring degraded soil qualities has been introduced on arid steppes in recent decades. However, the fertilization use efficiency on arid steppes varies greatly between steppe types and years, enhancing uncertainties and risks in introducing fertilizations on such natural system to restore degraded steppes.

Methods

The experiment was a completely randomized design with five fertilization treatments, 0 (Control), 60 kg P ha⁻¹ (P), 100 kg N ha⁻¹ (N), 100 kg N ha⁻¹ plus 60 kg P ha⁻¹ (NP), and 4,000 kg sheep manure ha⁻¹ (M, equaling 16.4 kg P ha⁻¹ and 81.2 kg N ha⁻¹). Soils were sampled from a degraded arid steppe which was consecutively applied with organic and inorganic fertilizers for three years. We analyzed the diversity and abundance of soil bacteria and fungi using high-throughput sequencing technique, measured the aboveground biomass, the soil chemical properties (organic carbon, available and total phosphorus, available and total nitrogen, and pH), and the microbial biomass nitrogen and microbial biomass carbon.

Results

In total 3,927 OTU (operational taxonomic units) for bacteria and 453 OTU for fungi were identified from the tested soils. The Ace and Chao of bacteria were all larger than 2,400, which were almost 10 times of those of fungi. Fertilizations had no significant influence on the richness and diversity of the bacteria and fungi. However, the abundance of individual bacterial or fungi phylum or species was sensitive to fertilizations. Fertilization, particularly the phosphorus fertilizer, influenced more on the abundance of the AMF species and colonization. Among the soil properties, soil pH was one of the most important soil properties influencing the abundance of soil bacteria and fungi.

Discussion

Positive relationships between the abundance of bacteria and fungi and the soil chemical properties suggested that soil bacteria and fungi communities in degraded steppes could be altered by improving the soil chemical properties through fertilizations. However, it is still not clear whether the alteration of the soil microbe community is detrimental or beneficial to the degraded arid steppes.

Evolution as an ecosystem process: insights from genomics

Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems.

Drought and host selection influence bacterial community dynamics in the grass root microbiome

Root endophytes have been shown to have important roles in determining host fitness under periods of drought stress, and yet the effect of drought on the broader root endosphere bacterial community remains largely uncharacterized. In this study, we present phylogenetic profiles of bacterial communities associated with drought-treated root and rhizosphere tissues of 18 species of plants with varying degrees of drought tolerance belonging to the Poaceae family, including important crop plants. Through 16S rRNA gene profiling across two distinct watering regimes and two developmental time points, we demonstrate that there is a strong correlation between host phylogenetic distance and the microbiome dissimilarity within root tissues, and that drought weakens this correlation by inducing conserved shifts in bacterial community composition. We identify a significant enrichment in a wide variety of Actinobacteria during drought within the roots of all hosts, and demonstrate that this enrichment is higher within the root than it is in the surrounding environments. Furthermore, we show that this observed enrichment is the result of an absolute increase in Actinobacterial abundance and that previously hypothesized mechanisms for observed enrichments in Actinobacteria in drought-treated soils are unlikely to fully account for the phenomena observed here within the plant root.

Rapid evolution leads to differential population dynamics and top-down control in resurrected Daphnia populations

There is growing evidence of rapid genetic adaptation of natural populations to environmental change, opening the perspective that evolutionary trait change may subsequently impact ecological processes such as population dynamics, community composition, and ecosystem functioning. To study such eco‐evolutionary feedbacks in natural populations, however, requires samples across time. Here, we capitalize on a resurrection ecology study that documented rapid and adaptive evolution in a natural population of the water flea Daphnia magna in response to strong changes in predation pressure by fish, and carry out a follow‐up mesocosm experiment to test whether the observed genetic changes influence population dynamics and top‐down control of phytoplankton. We inoculated populations of the water flea D. magna derived from three time periods of the same natural population known to have genetically adapted to changes in predation pressure in replicate mesocosms and monitored both Daphnia population densities and phytoplankton biomass in the presence and absence of fish. Our results revealed differences in population dynamics and top‐down control of algae between mesocosms harboring populations from the time period before, during, and after a peak in fish predation pressure caused by human fish stocking. The differences, however, deviated from our a priori expectations. An S‐map approach on time series revealed that the interactions between adults and juveniles strongly impacted the dynamics of populations and their top‐down control on algae in the mesocosms, and that the strength of these interactions was modulated by rapid evolution as it occurred in nature. Our study provides an example of an evolutionary response that fundamentally alters the processes structuring population dynamics and impacts ecosystem features.

Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi

Lateral gene transfer (LGT, also known as horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting LGT events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions, and multiple sequence alignments, requiring researchers to accept a substantial margin of error in their datasets. Using a test case comprising plant-associated genomes across the fungal kingdom, this study reveals that composition- and phylogeny-based methods have little statistical power to detect laterally transferred genes. In particular, phylogenetic methods reveal extreme levels of topological variation in fungal gene trees, the vast majority of which show departures from the canonical species tree. Therefore, it is inherently challenging to detect LGT events in typical eukaryotic genomes. This finding is in striking contrast to the large number of claims for laterally transferred genes in eukaryotic species that routinely appear in the literature, and questions how many of these proposed examples are statistically well supported.

Drought Stress and Root-Associated Bacterial Communities

Root-associated bacterial communities play a vital role in maintaining health of the plant host. These communities exist in complex relationships, where composition and abundance of community members is dependent on a number of factors such as local soil chemistry, plant genotype and phenotype, and perturbations in the surrounding abiotic environment. One common perturbation, drought, has been shown to have drastic effects on bacterial communities, yet little is understood about the underlying causes behind observed shifts in microbial abundance. As drought may affect root bacterial communities both directly by modulating moisture availability, as well as indirectly by altering soil chemistry and plant phenotypes, we provide a synthesis of observed trends in recent studies and discuss possible directions for future research that we hope will provide for more knowledgeable predictions about community responses to future drought events.

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting.

Though both the presence and traits of a species can influence the dynamics of its ecological community, the effects of these factors are difficult to disentangle. Here, Gómez et al. demonstrate in a microbial mesocosm that local adaptation of a focal species can influence the community as much as the presence of the focal species per se.

Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes

Root-associated microbes have a profound impact on plant health, yet little is known about the distribution of root-associated microbes among different root morphologies or between rhizosphere and root environments. We explore these issues here with two commercial varieties of burley tobacco (Nicotiana tabacum) using 16S rRNA gene amplicon sequencing from rhizosphere soil, as well as from primary, secondary, and fine roots. While rhizosphere soils exhibited a fairly rich and even distribution, root samples were dominated by Proteobacteria. A comparison of abundant operational taxonomic units (OTUs) between rhizosphere and root samples indicated that Nicotiana roots select for rare taxa (predominantly Proteobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Acidobacteria) from their corresponding rhizosphere environments. The majority of root-inhabiting OTUs (~80 %) exhibited habitat generalism across the different root morphological habitats, although habitat specialists were noted. These results suggest a specific process whereby roots select rare taxa from a larger community.

Spatial heterogeneity of plant-soil feedback affects root interactions and interspecific competition

Plant-soil feedback is receiving increasing interest as a factor influencing plant competition and species coexistence in grasslands. However, we do not know how spatial distribution of plant-soil feedback affects plant below-ground interactions. We investigated the way in which spatial heterogeneity of soil biota affects competitive interactions in grassland plant species. We performed a pairwise competition experiment combined with heterogeneous distribution of soil biota using four grassland plant species and their soil biota. Patches were applied as quadrants of 'own' and 'foreign' soils from all plant species in all pairwise combinations. To evaluate interspecific root responses, species-specific root biomass was quantified using real-time PCR. All plant species suffered negative soil feedback, but strength was species-specific, reflected by a decrease in root growth in own compared with foreign soil. Reduction in root growth in own patches by the superior plant competitor provided opportunities for inferior competitors to increase root biomass in these patches. These patterns did not cascade into above-ground effects during our experiment. We show that root distributions can be determined by spatial heterogeneity of soil biota, affecting plant below-ground competitive interactions. Thus, spatial heterogeneity of soil biota may contribute to plant species coexistence in species-rich grasslands.