The Root-Associated Microbial Community of the World's Highest Growing Vascular Plants

Soil microbial communities' contributions to soil ecosystem multifunctionality in the natural restoration of abandoned metal mines

On a global scale, the restoration of metal mine ecosystem functions is urgently required, and soil microorganisms play an important role in this process. Conventional studies frequently focused on the relationship between individual functions and their drivers; however, ecosystem functions are multidimensional, and considering any given function in isolation ignores the trade-offs and interconnectedness between functions, which complicates obtaining a comprehensive understanding of ecosystem functions. To elucidate the relationships between soil microorganisms and the ecosystem multifunctionality (EMF) of metal mines, this study investigated natural restoration of metal mines, evaluated the EMF, and used high-throughput sequencing to explore the bacterial and fungal communities as well as their influence on EMF. Bacterial community diversity and composition were more sensitive to mine restoration than fungal community. Bacterial diversity exhibited redundancy in improving N-P-K-S multifunctionality; however, rare bacterial taxa including Dependentiae, Spirochaetes, and WPS-2 were important for metal multifunctionality. Although no clear relationship between fungal diversity and EMF was observed, the abundance of Glomeromycota had a significant effect on the three EMF categories (N-P-K-S, carbon, and metal multifunctionality). Previous studies confirmed a pronounced positive association between microbial diversity and multifunctionality; however, the relationship between microbial diversity and multifunctionality differs among functions' categories. In contrast, the presence of critical microbial taxa exerted stronger effects on mine multifunctionality.

Himalayan alpine ecohydrology: An urgent scientific concern in a changing climate

Climate change is projected to have important impacts on snow and vegetation distribution in global mountains. Despite this, the coupling of ecological shifts and hydrological processes within alpine zones has not attracted significant scientific attention. As the largest and one of the most climatically sensitive mountain systems, we argue that Himalayan alpine ecohydrological processes require urgent scientific attention because up to 1.6 billion people rely on water supplies from the mountains. We review studies from global mountain systems to highlight the importance of considering ecohydrological impacts within Himalayan alpine zones (4100-6000 m.a.s.l), explaining mechanisms for interactions between snow and dwarf plants. Our findings highlight the paucity of monitoring stations within Himalayan alpine systems. We suggest that it is likely that alpine ecological shifts will impact hydrological processes, but we found that specific mechanisms and functional relationships are missing for Himalayan systems, so the strength and direction of ecohydrological relationships is currently unknown. We advocate for more purposeful and widespread monitoring efforts below glaciers and above the treeline, calling for new experiments to query the role of small plants within the Himalayan alpine hydrological system. We outline the need for community engagement with alpine ecohydrological experiments, and we explain how new snow and vegetation products derived from remote sensing observations have the potential to improve scientific understanding of the interacting effects of warming and ecohydrological factors in this sensitive region.

Response of the wheat mycobiota to flooding revealed substantial shifts towards plant pathogens

Rainfall extremes are intensifying as a result of climate change, leading to increased flood risk. Flooding affects above- and belowground ecosystem processes, representing a substantial threat to crop productivity under climate change. Plant-associated fungi play important roles in plant performance, but their response to abnormal rain events is unresolved. Here, we established a glasshouse experiment to determine the effects of flooding stress on the spring wheat-mycobiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages, such as tillering, booting and flowering. We assessed the wheat mycobiota response to flooding in three soil-plant compartments (phyllosphere, roots and rhizosphere) using metabarcoding. Key soil and plant traits were measured to correlate physiological plant and edaphic changes with shifts in mycobiota structure and functional guilds. Flooding reduced plant fitness, and caused dramatic shifts in mycobiota assembly across the entire plant. Notably, we observed a functional transition consisting of a decline in mutualist abundance and richness with a concomitant increase in plant pathogens. Indeed, fungal pathogens associated with important cereal diseases, such as Gibberella intricans, Mycosphaerella graminicola, Typhula incarnata and Olpidium brassicae significantly increased their abundance under flooding. Overall, our study demonstrate the detrimental effect of flooding on the wheat mycobiota complex, highlighting the urgent need to understand how climate change-associated abiotic stressors alter plant-microbe interactions in cereal crops.

Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.)

Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.

An oxygen-sensing mechanism for angiosperm adaptation to altitude

Flowering plants (angiosperms) can grow at extreme altitudes, and have been observed growing as high as 6,400 metres above sea level^1,2; however, the molecular mechanisms that enable plant adaptation specifically to altitude are unknown. One distinguishing feature of increasing altitude is a reduction in the partial pressure of oxygen (pO₂). Here we investigated the relationship between altitude and oxygen sensing in relation to chlorophyll biosynthesis—which requires molecular oxygen³—and hypoxia-related gene expression. We show that in etiolated seedlings of angiosperm species, steady-state levels of the phototoxic chlorophyll precursor protochlorophyllide are influenced by sensing of atmospheric oxygen concentration. In Arabidopsis thaliana, this is mediated by the PLANT CYSTEINE OXIDASE (PCO) N-degron pathway substrates GROUP VII ETHYLENE RESPONSE FACTOR transcription factors (ERFVIIs). ERFVIIs positively regulate expression of FLUORESCENT IN BLUE LIGHT (FLU), which represses the first committed step of chlorophyll biosynthesis, forming an inactivation complex with tetrapyrrole synthesis enzymes that are negatively regulated by ERFVIIs, thereby suppressing protochlorophyllide. In natural populations representing diverse angiosperm clades, we find oxygen-dependent altitudinal clines for steady-state levels of protochlorophyllide, expression of inactivation complex components and hypoxia-related genes. Finally, A. thaliana accessions from contrasting altitudes display altitude-dependent ERFVII activity and accumulation. We thus identify a mechanism for genetic adaptation to absolute altitude through alteration of the sensitivity of the oxygen-sensing system.

Plants have adapted to grow at specific altitudes by regulating chlorophyll synthesis in response to ambient oxygen concentration, calibrated by altitude-dependent activity of GROUP VII ETHYLENE RESPONSE FACTOR.

Ecology and potential functions of plant-associated microbial communities in cold environments

Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.

Flooding Causes Dramatic Compositional Shifts and Depletion of Putative Beneficial Bacteria on the Spring Wheat Microbiota

Flooding affects both above- and below-ground ecosystem processes, and it represents a substantial threat for crop and cereal productivity under climate change. Plant-associated microbiota play a crucial role in plant growth and fitness, but we still have a limited understanding of the response of the crop-microbiota complex under extreme weather events, such as flooding. Soil microbes are highly sensitive to abiotic disturbance, and shifts in microbial community composition, structure and functions are expected when soil conditions are altered due to flooding events (e.g., anoxia, pH alteration, changes in nutrient concentration). Here, we established a pot experiment to determine the effects of flooding stress on the spring wheat-microbiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages (PGSs), such as tillering, booting and flowering. After each flooding event, we measured in the control and flooded pots several edaphic and plant properties and characterized the bacterial community associated to the rhizosphere and roots of wheat plant using a metabarcoding approach. In our study, flooding caused a significant reduction in plant development and we observed dramatic shifts in bacterial community composition at each PGS in which the hydrological stress was induced. However, a more pronounced disruption in community assembly was always shown in younger plants. Generally, flooding caused a (i) significant increase of bacterial taxa with anaerobic respiratory capabilities, such as members of Firmicutes and Desulfobacterota, (ii) a significant reduction in Actinobacteria and Proteobacteria, (iii) depletion of several putative plant-beneficial taxa, and (iv) increases of the abundance of potential detrimental bacteria. These significant differences in community composition between flooded and control samples were correlated with changes in soil conditions and plant properties caused by the hydrological stress, with pH and total N as the soil, and S, Na, Mn, and Ca concentrations as the root properties most influencing microbial assemblage in the wheat mircobiota under flooding stress. Collectively, our findings demonstrated the role of flooding on restructuring the spring wheat microbiota, and highlighted the detrimental effect of this hydrological stress on plant fitness and performance.

Influence of shrub willow buffers strategically integrated in an Illinois corn-soybean field on soil health and microbial community composition

Soil serves many important ecological functions and is an integral part of our existence as a society. However, concerns for soil health are growing globally, in part due to the negative impacts of agricultural management on soil resources. The production of perennial bioenergy crops on marginal land in row-crop production systems is one solution that could improve land-use efficiency and address the sustainability of cropland management. Because the relationship between crop management and the environment is complex, more research is needed to evaluate the potential benefits perennial bioenergy crop production has on soil health, as well as other ecosystem services. In this study, shrub willow buffers were strategically integrated into a corn-soybean cropping system with the main objective of reducing nitrate-N leaching from grain crop production while producing biomass for bioenergy. Two buffer systems (defined by landscape positions) were included for comparison, one on marginal land with exposure to nitrate-N leaching from upslope grain (southern plots) and one on fertile soils with less nitrate-N leaching potential (northern plots). Evaluation of soil (chemistry, bulk density, microbial community) and shrub willow vegetation properties (fine roots, leaf litter decomposition, and nutrient uptake dynamics), showed that landscape position plays an important role in (1) the dynamics of soil chemical properties, (2) shrub willow's influence and productivity, and (3) the provision of additional ecosystem services such as reductions in nitrous oxide emissions and nitrate-N leaching. In addition, the combination of crop type and landscape position (N-grain, N-willow, S-grain, and S-willow) influenced the species composition of the soil microbial community, resulting in unique and identifiable communities. These results highlight the potential application of shrub willow buffers for ecosystem service provision and support of ecosystem processes; however, understanding the relationship between the microbial community, crop type, and landscape is important for understanding the sustainability of the design.

High Altitude Limits of Living Things

West, John B. High altitude limits of living things. High Alt Med Biol. 22:342-345, 2021.-The tolerance of animals to high altitude is generally limited by the low partial pressure of oxygen (PO₂) in the air. Plant growth at high altitude is also limited but by different mechanisms. This article is a brief survey of the limiting factors of all living things. By a curious coincidence, the highest point on earth, that is Mt. Everest at 8,848 m, appears to be right at the limit of human tolerance to hypoxia. The altitude of the highest permanent human habitation, that is a town, is 5,100 m. This altitude is partly determined by the hypoxia, but also by economic factors. For other terrestrial mammals, birds, and insects, the highest altitudes for permanent habitation apparently belong to field mice (Phyllotis xanthopygus rupestris) and jumping spiders (Euophrys omnisuperstes) at about 6,700 m. Birds have been known to fly as high as 11,000 m although how much they are elevated by atmospheric updrafts is not clear. The record for animals for survival in extreme hypoxia is arguably held by the primitive invertebrate, the tardigrade (Hypsibius dujardini). This has been shown to tolerate the hard vacuum of space where the PO₂ is essentially zero for many days. Less is known about the tolerance of plants to extreme altitude. However, vascular plants have been collected at >6,000 m in the Himalayas, and moss grows even higher. Lichens are very tolerant of severe hypoxia. There is evidence that global warming is increasing the highest altitudes at which plants can survive.

Alexander von Humboldt (1769-1859): early high-altitude explorer and renowned plant naturalist

Alexander von Humboldt (1769-1859) was one of the most distinguished German scientists of the late 18th and early 19th centuries. His fame came chiefly from his extensive explorations in South America and his eminence as a plant naturalist. He attempted to climb the inactive volcano Chimborazo in Ecuador, which was thought to be the highest mountain in the world at the time, and he reached an altitude of about 5,543 m, which was a record height for humans. During the climb, he had typical symptoms of acute mountain sickness, which he correctly attributed to the low level of oxygen, and he was apparently the first person to make this connection. His ability as a naturalist enabled him to recognize the effect of high altitude on the distribution of plants, and by comparing his observations on Chimborazo with those in the European Alps and elsewhere, he inferred that the deleterious effects of high altitude were universal. During his return trip to Europe, he called on President Thomas Jefferson in Washington, where he was given a warm reception, and discussed conservation issues. He then returned to Paris, where he produced 29 volumes over a period of 31 years describing his travels. Here the effects of high altitude on the distribution of plants compared with animals are briefly reviewed. Following Humboldt's death in 1859, there was extensive coverage of his contributions, but curiously, his fame has diminished over the years, and inexplicably, he now has a lower profile in North America.

Living Lithic and Sublithic Bacterial Communities in Namibian Drylands

Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities.

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest

AIMS

The soil microbial community plays a critical role in increasing phosphorus (P) availability in low-P, weathered soils by "mining" recalcitrant organic P through the production of phosphatase enzymes. However, there is a lack of data on the fungal and bacterial taxa which are directly involved in P mining, which could also serve as potential microbial bioindicators of low P availability.

METHODS AND RESULTS

Leveraging a 5-year P enrichment experiment on low-P forest soils, high-throughput sequencing was used to profile the microbial community to determine which taxa associate closely with P availability. We hypothesized that there would be a specialized group of soil micro-organisms that could access recalcitrant P and whose presence could serve as a bioindicator of P mining. Community profiling revealed several candidate bioindicators of P mining (Russulales, Acidobacteria Subgroup 2, Acidobacteriales, Obscuribacterales and Solibacterales), whose relative abundance declined with elevated P and had a significant, positive association with phosphatase production. In addition, we identified candidate bioindicators of high P availability (Mytilinidales, Sebacinales, Chitinophagales, Cytophagales, Saccharimonadales, Opitulales and Gemmatales).

CONCLUSIONS

This research provides evidence that mitigating P limitation in this ecosystem may be a specialized trait and is mediated by a few microbial taxa.

SIGNIFICANCE AND IMPACT OF THE STUDY

Here, we characterize Orders of soil microbes associated with manipulated phosphorus availability in forest soils to determine bioindicator candidates for phosphorus. Likewise, we provide evidence that the microbial trait to utilize recalcitrant organic forms of P (e.g. P mining) is likely a specialized trait and not common to all members of the soil microbial community. This work further elucidates the role that a complex microbial community plays in the cycling of P in low-P soils, and provides evidence for future studies on microbial linkages to human-induced ecosystem changes.

Unique bacterial assembly, composition, and interactions in a parasitic plant and its host

How plant-associated microbiota are shaped by, and potentially contribute to, the unique ecology and heterotrophic life history of parasitic plants is relatively unknown. Here, we investigate the leaf and root bacterial communities of the root holoparasite Orobanche hederae and its host Hedera spp. from natural populations. Root bacteria inhabiting Orobanche were less diverse, had fewer co-associations, and displayed increased compositional similarity to leaf bacteria relative to Hedera. Overall, Orobanche bacteria exhibited significant congruency with Hedera root bacteria across sites, but not the surrounding soil. Infection had localized and systemic effects on Hedera bacteria, which included effects on the abundance of individual taxa and root network properties. Collectively, our results indicate that the parasitic plant microbiome is derived but distinct from the host plant microbiota, exhibits increased homogenization between shoot and root tissues, and displays far fewer co-associations among individual bacterial members. Host plant infection is accompanied by modest changes of associated microbiota at both local and systemic scales compared with uninfected individuals. Our results are a first step towards extending the growing insight into the assembly and function of the plant microbiome to include the ecologically unique but often overlooked guild of heterotrophic plants.

How do vascular plants perform photosynthesis in extreme environments? An integrative ecophysiological and biochemical story

In this work, we review the physiological and molecular mechanisms that allow vascular plants to perform photosynthesis in extreme environments, such as deserts, polar and alpine ecosystems. Specifically, we discuss the morpho/anatomical, photochemical and metabolic adaptive processes that enable a positive carbon balance in photosynthetic tissues under extreme temperatures and/or severe water-limiting conditions in C₃ species. Nevertheless, only a few studies have described the in situ functioning of photoprotection in plants from extreme environments, given the intrinsic difficulties of fieldwork in remote places. However, they cover a substantial geographical and functional range, which allowed us to describe some general trends. In general, photoprotection relies on the same mechanisms as those operating in the remaining plant species, ranging from enhanced morphological photoprotection to increased scavenging of oxidative products such as reactive oxygen species. Much less information is available about the main physiological and biochemical drivers of photosynthesis: stomatal conductance (g_s ), mesophyll conductance (g_m ) and carbon fixation, mostly driven by RuBisCO carboxylation. Extreme environments shape adaptations in structures, such as cell wall and membrane composition, the concentration and activation state of Calvin-Benson cycle enzymes, and RuBisCO evolution, optimizing kinetic traits to ensure functionality. Altogether, these species display a combination of rearrangements, from the whole-plant level to the molecular scale, to sustain a positive carbon balance in some of the most hostile environments on Earth.

Plant host and drought shape the root associated fungal microbiota in rice

Background and Aim

Water is an increasingly scarce resource while some crops, such as paddy rice, require large amounts of water to maintain grain production. A better understanding of rice drought adaptation and tolerance mechanisms could help to reduce this problem. There is evidence of a possible role of root-associated fungi in drought adaptation. Here, we analyzed the endospheric fungal microbiota composition in rice and its relation to plant genotype and drought.

Methods

Fifteen rice genotypes (Oryza sativa ssp. indica) were grown in the field, under well-watered conditions or exposed to a drought period during flowering. The effect of genotype and treatment on the root fungal microbiota composition was analyzed by 18S ribosomal DNA high throughput sequencing. Grain yield was determined after plant maturation.

Results

There was a host genotype effect on the fungal community composition. Drought altered the composition of the root-associated fungal community and increased fungal biodiversity. The majority of OTUs identified belonged to the Pezizomycotina subphylum and 37 of these significantly correlated with a higher plant yield under drought, one of them being assigned to Arthrinium phaeospermum.

Conclusion

This study shows that both plant genotype and drought affect the root-associated fungal community in rice and that some fungi correlate with improved drought tolerance. This work opens new opportunities for basic research on the understanding of how the host affects microbiota recruitment as well as the possible use of specific fungi to improve drought tolerance in rice.

Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient

Serving as “natural laboratories”, altitudinal gradients can be used to study changes in the distribution of microorganisms in response to changing environmental conditions that typically occur over short geographical distances. Besides, rhizosphere zones of plants are known to be hot-spots for microbial diversity and to contain different microbial communities when compared with surrounding bulk soil. To discriminate the effects of altitude and plants, we investigated the microbial communities in the rhizosphere of Ranunculus glacialis and bulk soil along a high-alpine altitudinal gradient (2,600–3,400 m a.s.l.). The research area of this study was Mount (Mt.) “Schrankogel” in the Central Alps of Tyrol (Austria). Our results point to significantly different microbial diversities and community compositions in the different altitudinal belts. In the case of prokaryotes, environmental parameters could explain 41% of the total variation of soil communities, with pH and temperature being the strongest influencing factors. Comparing the effects derived from fraction (bulk vs. rhizosphere soil) and environmental factors, the effects of the roots of R. glacialis accounted for about one third of the explained variation. Fungal communities on the other hand were nearly exclusively influenced by environmental parameters accounting for 37.4% of the total variation. Both, for altitudinal zones as well as for bulk and rhizosphere fractions a couple of very specific biomarker taxa could be identified. Generally, the patterns of abundance of several taxa did not follow a steady increased or decreased trend along the altitudinal gradient but in many cases a maximal or minimal occurrence was established at mid-altitudes (3,000–3,100 m). This mid-altitudinal zone is a transition zone (the so-called alpine-nival ecotone) between the (lower) alpine grassland/tundra zone and the (upper) sparsely vegetated nival zone and was shown to correspond with the summer snow line. Climate change and the associated increase in temperature will shift this transition zone and thus, might also shift the described microbial patterns and biomarkers.

Functionally distinct assembly of vascular plants colonizing alpine cushions suggests their vulnerability to climate change

BACKGROUND AND AIMS

Alpine cushion plants can initially facilitate other species during ecological succession, but later on can be negatively affected by their development, especially when beneficiaries possess traits allowing them to overrun their host. This can be reinforced by accelerated warming favouring competitively strong species over cold-adapted cushion specialists. However, little empirical research has addressed the trait-based mechanisms of these interactions. The ecological strategies of plants colonizing the cushion plant Thylacospermum caespitosum (Caryophyllaceae), a dominant pioneer of subnival zones, were studied in the Western Himalayas.

METHODS

To assess whether the cushion colonizers are phylogenetically and functionally distinct, 1668 vegetation samples were collected, both in open ground outside the cushions and inside their live and dead canopies, in two mountain ranges, Karakoram and Little Tibet. More than 50 plant traits related to growth, biomass allocation and resource acquisition were measured for target species, and the phylogenetic relationships of these species were studied [or determined].

KEY RESULTS

Species-based trait-environment analysis with phylogenetic correction showed that in both mountain ranges Thylacospermum colonizers are phylogenetically diverse but functionally similar and are functionally different from species preferring bare soil outside cushions. Successful colonizers are fast-growing, clonal graminoids and forbs, penetrating the cushion by rhizomes and stolons. They have higher root-to-shoot ratios, leaf nitrogen and phosphorus concentrations, and soil moisture and nutrient demands, sharing the syndrome of competitive species with broad elevation ranges typical of the late stages of primary succession. In contrast, the species from open ground have traits typical of stress-tolerant specialists from high and dry environments.

CONCLUSION

Species colonizing tight cushions of T. caespitosum are competitively strong graminoids and herbaceous perennials from alpine grasslands. Since climate change in the Himalayas favours these species, highly specialized subnival cushion plants may face intense competition and a greater risk of decline in the future.

Endophytic bacterial communities in peels and pulp of five root vegetables

Plants contain endophytic bacteria, whose communities both influence plant growth and can be an important source of probiotics. Here we used deep sequencing of a 16S rRNA gene fragment and bacterial cultivation to independently characterize the microbiomes of five plant species from divergent taxonomic orders—potato (Solanum tuberosum), carrot (Daucus sativus), beet (Beta vulgaris), neep (Brassica napus spp. napobrassica), and topinambur (Helianthus tuberosus). We found that both species richness and diversity tend to be higher in the peel, where Alphaproteobacteria and Actinobacteria dominate, while Gammaproteobacteria and Firmicutes dominate in the pulp. A statistical analysis revealed that the main characteristic features of the microbiomes of plant species originate from the peel microbiomes. Topinambur pulp displayed an interesting characteristic feature: it contained up to 10⁸ CFUs of lactic acid bacteria, suggesting its use as a source of probiotic bacteria. We also detected Listeria sp., in topinambur pulps, however, the 16S rRNA gene fragment is unable to distinguish between pathogenic versus non-pathogenic species, so the evaluation of this potential health risk is left to a future study.

A role for ecophysiology in the 'omics' era

Plant Ecophysiology is the study on how Plant Physiology is modulated by the environment. This discipline could have benefited greatly from the development of the different 'omic' technologies (from genomics to metabolomics). Instead, the overall impression is that ecophysiology and 'omics' have developed mostly independent each other. Here we provide a literature analysis over the past 20 years which fully confirms this view. Then, we review a few examples of studies in which ecophysiology and 'omics' studies have combined to different extents to illustrate the potential benefits from their mutualistic interaction. In addition, we debate on the possibilities of working with plants other than Arabidopsis, which is illustrated with some examples of fascinating plants from extreme environments of the world, what we call the 'sherplants'. Finally, we raise a call to both communities (ecophysiology and 'omics') to integrate these disciplines to enter an 'ecophysiolomics era' to maximize our understanding about plant mechanisms from a multidisciplinary approach.

The Impacts of Soil Fertility and Salinity on Soil Nitrogen Dynamics Mediated by the Soil Microbial Community Beneath the Halophytic Shrub Tamarisk

Nitrogen (N) is one of the most common limiting nutrients for primary production in terrestrial ecosystems. Soil microbes transform organic N into inorganic N, which is available to plants, but soil microbe activity in drylands is sometimes critically suppressed by environmental factors, such as low soil substrate availability or high salinity. Tamarisk (Tamarix spp.) is a halophytic shrub species that is widely distributed in the drylands of China; it produces litter enriched in nutrients and salts that are thought to increase soil fertility and salinity under its crown. To elucidate the effects of tamarisks on the soil microbial community, and thus N dynamics, by creating "islands of fertility" and "islands of salinity," we collected soil samples from under tamarisk crowns and adjacent barren areas at three habitats in the summer and fall. We analyzed soil physicochemical properties, inorganic N dynamics, and prokaryotic community abundance and composition. In soils sampled beneath tamarisks, the N mineralization rate was significantly higher, and the prokaryotic community structure was significantly different, from soils sampled in barren areas, irrespective of site and season. Tamarisks provided suitable nutrient conditions for one of the important decomposers in the area, Verrucomicrobia, by creating "islands of fertility," but provided unsuitable salinity conditions for other important decomposers, Flavobacteria, Gammaproteobacteria, and Deltaproteobacteria, by mitigating salt accumulation. However, the quantity of these decomposers tended to be higher beneath tamarisks, because they were relatively unaffected by the small salinity gradient created by the tamarisks, which may explain the higher N mineralization rate beneath tamarisks.

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

Drought remains a critical obstacle to meeting the food demands of the coming century. Understanding the interplay between drought stress, plant development, and the plant microbiome is central to meeting this challenge. Here, we demonstrate that drought causes enrichment of a distinct set of microbes in roots, composed almost entirely of monoderms, which lack outer membranes and have thick cell walls. We demonstrate that under drought, roots increase the production of many metabolites, and that monoderms inhabiting the drought-treated rhizosphere exhibit increased activity of transporters connected with some of these same compounds. The discovery of this drought-induced enrichment and associated shifts in metabolite exchange between plant and microbe reveal a potential blueprint for manipulating plant microbiomes for improved crop fitness.

Drought stress is a major obstacle to crop productivity, and the severity and frequency of drought are expected to increase in the coming century. Certain root-associated bacteria have been shown to mitigate the negative effects of drought stress on plant growth, and manipulation of the crop microbiome is an emerging strategy for overcoming drought stress in agricultural systems, yet the effect of drought on the development of the root microbiome is poorly understood. Through 16S rRNA amplicon and metatranscriptome sequencing, as well as root metabolomics, we demonstrate that drought delays the development of the early sorghum root microbiome and causes increased abundance and activity of monoderm bacteria, which lack an outer cell membrane and contain thick cell walls. Our data suggest that altered plant metabolism and increased activity of bacterial ATP-binding cassette (ABC) transporter genes are correlated with these shifts in community composition. Finally, inoculation experiments with monoderm isolates indicate that increased colonization of the root during drought can positively impact plant growth. Collectively, these results demonstrate the role that drought plays in restructuring the root microbiome and highlight the importance of temporal sampling when studying plant-associated microbiomes.

Fungal root symbionts of high-altitude vascular plants in the Himalayas

Arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) form symbiotic relationships with plants influencing their productivity, diversity and ecosystem functions. Only a few studies on these fungi, however, have been conducted in extreme elevations and none over 5500 m a.s.l., although vascular plants occur up to 6150 m a.s.l. in the Himalayas. We quantified AMF and DSE in roots of 62 plant species from contrasting habitats along an elevational gradient (3400-6150 m) in the Himalayas using a combination of optical microscopy and next generation sequencing. We linked AMF and DSE communities with host plant evolutionary history, ecological preferences (elevation and habitat type) and functional traits. We detected AMF in elevations up to 5800 m, indicating it is more constrained by extreme conditions than the host plants, which ascend up to 6150 m. In contrast, DSE were found across the entire gradient up to 6150 m. AMF diversity was unimodally related to elevation and positively related to the intensity of AMF colonization. Mid-elevation steppe and alpine plants hosted more diverse AMF communities than plants from deserts and the subnival zone. Our results bring novel insights to the abiotic and biotic filters structuring AMF and DSE communities in the Himalayas.

Soil compartment is a major determinant of the impact of simulated rainfall on desert microbiota

Although desert soils support functionally important microbial communities that affect plant growth and influence many biogeochemical processes, the impact of future changes in precipitation patterns on the microbiota and their activities is largely unknown. We performed in-situ experiments to investigate the effect of simulated rainfall on bacterial communities associated with the widespread perennial shrub, Rhazya stricta in Arabian desert soils. The bacterial community composition was distinct between three different soil compartments: surface biological crust, root-attached, and the broader rhizosphere. Simulated rainfall had no significant effect on the overall bacterial community composition, but some population-level responses were observed, especially in soil crusts where Betaproteobacteria, Sphingobacteria, and Bacilli became more abundant. Bacterial biomass in the nutrient-rich crust increased three-fold one week after watering, whereas it did not change in the rhizosphere, despite its much higher water retention. These findings indicate that between rainfall events, desert-soil microbial communities enter into stasis, with limited species turnover, and reactivate rapidly and relatively uniformly when water becomes available. However, microbiota in the crust, which was relatively enriched in nutrients and organic matter, were primarily water-limited, compared with the rhizosphere microbiota that were co-limited by nutrients and water.