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Cross-inoculation of Andropogon virginicus rhizobiome enhances fungal diversity and network complexity in maize (Zea mays) rhizosphere under drought
Abstract
Rhizosphere soil microbes are increasingly recognized for their significant roles in enhancing plant resilience to
abiotic stress and stimulating plant growth. Rhizobiome adapted to dry conditions can enhance drought tolerance
in crops by cross-inoculation. However, changes in the rhizobiome that help in conferring drought tolerance
remain poorly understood. Here, by conducting a drought-manipulating greenhouse experiment, we characterized
changes in the rhizobiome of maize (Zea mays) after cross-inoculation of rhizosphere soil collected from droughtadapted
Andropogon virginicus (Andropogon rhizobiome). Results showed that maize inoculated with Andropogon
rhizobiome reduced oxidative damage of leaves under drought. Drought stress increased the species richness and
Shannon diversity of the fungal community. Additionally, the inoculation of Andropogon rhizobiome induced a
more significant increase in fungal diversity than the inoculation of organic rhizobiome. The increase of fungal
diversity was positively correlated with the increased drought resistance of maize. Bacterial richness and diversity
under the inoculation of Andropogon rhizobiome were negatively affected by drought stress. In addition,
increased positive links in the fungal network in the Andropogon inoculation under drought conditions as
compared with the ambient controls suggests more cooperation between fungal taxa to cope with drought stress.
Collectively, our findings indicate that the fungal but not bacterial community diversity and network complexity
stimulates drought tolerance in maize by cross-inoculation of the rhizobiome from A. virginicus. This study provides
important insights that will enhance theoretical understanding and applications of plant–rhizobiome associations
to promote drought resilience in agricultural crops.
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Drought is a significant global issue affecting agricultural production, and the utilization of beneficial rhizosphere microorganisms is one of the effective ways to increase the productivity of crops and forest under drought. In this study, we characterized a novel growth-promoting dark septate endophytes (DSE) fungus R16 derived from the blueberry roots. Hyphae or microsclerotia were visible within the epidermal or cortical cells of R16-colonized blueberry roots, which was consistent with the typical characteristics of DSE fungi. Inoculation with R16 promoted the growth of blueberry seedlings and the advantage over the control group was more significant under PEG-induced drought. Comparison of physiological indicators related to drought resistance between the inoculated and control groups was performed on the potted blueberry plants, including the chlorophyll content, net photosynthetic rate, root activities, MDA and H2O2 content, which indicated that R16 colonization mitigated drought injury in blueberry plants. We further analyzed the effects of R16 on phytohormones and non-structural carbohydrates (NSCs) to explore the mechanism of increased drought tolerance by R16 in blueberry seedlings. The results showed that except for the GA content, IAA, ZT and ABA varied significantly between the inoculated and control groups. SPS and S6PDH activities in mature leaves, the key enzymes responsible for sucrose and sorbitol synthesis, respectively, as well as SDH, SuSy, CWINV, HXK and FRK in roots, the key enzymes involved in the NSCs metabolism, showed significant differences between the inoculated and control groups before and after drought treatment. These results suggested that the positive effects of R16 colonization on the drought tolerance of blueberry seedlings are partially attributable to the regulation of phytohormone and sugar metabolism. This study provided valuable information for the research on the interaction between DSE fungi and host plants as well as the application of DSE preparations in agriculture.
Plant growth‐promoting rhizobacteria (PGPR) can help plants to resist drought stress. However, the mechanisms of how PGPR inoculation affect plant status under drought remain incompletely understood. We performed a meta‐analysis of plant response to PGPR inoculation by compiling data from 57 PGPR‐inoculation studies, including 2, 387 paired observations on morphological, physiological and biochemical parameters under drought and well‐watered conditions. We compare the PGPR effect on plants performances among different groups of controls and treatments. Our results reveal that PGPR enables plants to restore themselves from drought‐stressed to near a well‐watered state, and that C4 plants recover better from drought stress than C3 plants. Furthermore, PGPR is more effective underdrought than well‐watered conditions in increasing plant biomass, enhancing photosynthesis and inhibiting oxidant damage, and the responses of C4 plants to the PGPR effect was stronger than that of C3 plants under drought conditions. Additionally, PGPR belonging to different taxa and PGPR with different functional traits have varying degrees of drought‐resistance effects on plants. These results are important to improve our understanding of the PGPR beneficial effects on enhanced drought‐resistance of plants.
Food insecurity early warning can provide time to mitigate unfolding crises; however, drought remains a large source of uncertainty. The challenge is to filter unclear or conflicting signals from various climatic and socio-economic variables and link them to food security outcomes. Integrating lag-1 autocorrelation diagnostics into remotely sensed observations from the Soil Moisture Active Passive (SMAP) mission and food prices, we found dramatic improvement in anticipating the timing and intensity of food crises, except in conflict settings. We analysed drought-induced food crises globally in the SMAP record (since 2015; approximately five per year). The change in soil moisture autocorrelation, which we term the Soil Moisture Auto-Regressive Threshold (SMART), signalled an accurate food security transition for all cases studied here (P < 0.05; n = 212), including lead time of up to three to six months for every case. The SMART trigger anticipates the timing of the transition and the magnitude of the food security change among small to large transitions, both into and out of crises (R2 = 0.80–0.83). While we do not evaluate out-of-sample forecast accuracy using our model, our findings suggest a significant advancement in the capabilities of food security early-warning diagnostics and could save lives and resources. Early warnings of impending food crises can provide valuable time to mitigate their worst impacts, but droughts have proven difficult to predict. Soil moisture autocorrelation measured by remote sensing satellites advances our ability to anticipate food security crises resulting from drought.
Plant response to drought stress involves fungi and bacteria that live on and in plants and in the rhizosphere, yet the stability of these myco- and micro-biomes remains poorly understood. We investigate the resistance and resilience of fungi and bacteria to drought in an agricultural system using both community composition and microbial associations. Here we show that tests of the fundamental hypotheses that fungi, as compared to bacteria, are (i) more resistant to drought stress but (ii) less resilient when rewetting relieves the stress, found robust support at the level of community composition. Results were more complex using all-correlations and co-occurrence networks. In general, drought disrupts microbial networks based on significant positive correlations among bacteria, among fungi, and between bacteria and fungi. Surprisingly, co-occurrence networks among functional guilds of rhizosphere fungi and leaf bacteria were strengthened by drought, and the same was seen for networks involving arbuscular mycorrhizal fungi in the rhizosphere. We also found support for the stress gradient hypothesis because drought increased the relative frequency of positive correlations. Fungi are expected to be more resistant and less resilient than bacteria to environmental disturbances. Here, the authors report complex responses by microbial co-occurrence networks to drought in an agricultural system, challenging simple predictions of fungal and bacterial drought responses.
Rhizobiome confer stress tolerance to ruderal plants, yet their ability to alleviate stress in crops is widely debated, and the associated mechanisms are poorly understood. We monitored the drought tolerance of maize (Zea mays) as influenced by the cross‐inoculation of rhizobiota from a congeneric ruderal grass Andropogon virginicus (andropogon‐inoculum), and rhizobiota from organic farm maintained under mesic condition (organic‐inoculum). Across drought treatments (40% field capacity), maize that received andropogon‐inoculum produced two‐fold greater biomass. This drought tolerance translated to a similar leaf metabolomic composition as that of the well‐watered control (80% field capacity) and reduced oxidative damage, despite a lower activity of antioxidant enzymes. At a morphological‐level, drought tolerance was associated with an increase in specific root length and surface area facilitated by the homeostasis of phytohormones promoting root branching. At a proteome‐level, the drought tolerance was associated with upregulation of proteins related to glutathione metabolism and endoplasmic reticulum‐associated degradation process. Fungal taxa belonging to Ascomycota, Mortierellomycota, Archaeorhizomycetes, Dothideomycetes, and Agaricomycetes in andropogon‐inoculum were identified as potential indicators of drought tolerance. Our study provides a mechanistic understanding of the rhizobiome‐facilitated drought tolerance and demonstrates a better path to utilize plant–rhizobiome associations to enhance drought tolerance in crops.
In the past and present, human activities have been involved in triggering global warming, causing drought stresses that affect animals and plants. Plants are more defenseless against drought stress; and therefore, plant development and productive output are decreased. To decrease the effect of drought stress on plants, it is crucial to establish a plant feedback mechanism of resistance to drought. The drought reflex mechanisms include the physical stature physiology and biochemical, cellular, and molecular-based processes. Briefly, improving the root system, leaf structure, osmotic-balance, comparative water contents and stomatal adjustment are considered as most prominent features against drought resistance in crop plants. In addition, the signal transduction pathway and reactive clearance of oxygen are crucial mechanisms for coping with drought stress via calcium and phytohormones such as abscisic acid, salicylic acid, jasmonic acid, auxin, gibberellin, ethylene, brassinosteroids and peptide molecules. Furthermore, microorganisms, such as fungal and bacterial organisms, play a vital role in increasing resistance against drought stress in plants. The number of characteristic loci, transgenic methods and the application of exogenous substances [nitric oxide, (C28H48O6) 24-epibrassinolide, proline, and glycine betaine] are also equally important for enhancing the drought resistance of plants. In a nutshell, the current review will mainly focus on the role of phytohormones and related mechanisms involved in drought tolerance in various crop plants.
Increasing temperature leads to intensive water evaporation, contributing to global warming and consequently leading to drought stress. These events are likely to trigger modifications in plant physiology and microbial functioning due to the altered availability of nutrients. Plants exposed to drought have developed different strategies to cope with stress by morphological, physiological, anatomical, and biochemical responses. First, visible changes influence plant biomass and consequently limit the yield of crops. The presented review was undertaken to discuss the impact of climate change with respect to drought stress and its impact on the performance of plants inoculated with plant growth-promoting microorganisms (PGPM). The main challenge for optimal performance of horticultural plants is the application of selected, beneficial microorganisms which actively support plants during drought stress. The most frequently described biochemical mechanisms for plant protection against drought by microorganisms are the production of phytohormones, antioxidants and xeroprotectants, and the induction of plant resistance. Rhizospheric or plant surface-colonizing (rhizoplane) and interior (endophytic) bacteria and fungi appear to be a suitable alternative for drought-stress management. Application of various biopreparations containing PGPM seems to provide hope for a relatively cheap, easy to apply and efficient way of alleviating drought stress in plants, with implications in productivity and food condition.
Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.
The ever-growing human population globally has resulted in the quest for solutions to the problem of hunger by providing food security. The importance of plant-root-associated microorganisms cannot be overlooked, plants rely on them. These root colonizers dominate the rhizosphere due to the abundance of available nutrients, relying on their host plant for nutrients and other essential requirements. The relationships between microbial communities and plants are controlled by the type of plant and microorganism involved. Advances in modern molecular techniques have led to the evolution of omic technology using nucleic acid molecules to study plant-microorganism associations capable of stimulating plant growth, improve yield, and induce disease suppression. This review elucidates the activities of microbial communities, especially nitrogen-fixing rhizobacteria associated with plant roots, nitrogen fixation as a mechanism of promoting plant growth, their importance, and the challenges employing bioinoculants. Prospecting plant growth promoters using omic technology will advance sustainable agriculture globally.
Drylands are stressful environment for plants growth and production. Plant growth-promoting rhizobacteria (PGPR) acts as a rampart against the adverse impacts of drought stress in drylands and enhances plant growth and is helpful in agricultural sustainability. PGPR improves drought tolerance by implicating physio-chemical modifications called rhizobacterial-induced drought endurance and resilience (RIDER). The RIDER response includes; alterations of phytohormonal levels, metabolic adjustments, production of bacterial exopolysaccharides (EPS), biofilm formation, and antioxidant resistance, including the accumulation of many suitable organic solutes such as carbohydrates, amino acids, and polyamines. Modulation of moisture status by these PGPRs is one of the primary mechanisms regulating plant growth, but studies on their effect on plant survival are scarce in sandy/desert soil. It was found that inoculated plants showed high tolerance to water-deficient conditions by delaying dehydration and maintaining the plant’s water status at an optimal level. PGPR inoculated plants had a high recovery rate after rewatering interms of similar biomass at flowering compared to non-stressed plants. These rhizobacteria enhance plant tolerance and also elicit induced systemic resistance of plants to water scarcity. PGPR also improves the root growth and root architecture, thereby improving nutrient and water uptake. PGPR promoted accumulation of stress-responsive plant metabolites such as amino acids, sugars, and sugar alcohols. These metabolites play a substantial role in regulating plant growth and development and strengthen the plant’s defensive system against various biotic and abiotic stresses, in particular drought stress.
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.
Global climate change is expected to further raise the frequency and severity of extreme events, such as droughts. The effects of extreme droughts on trees are difficult to disentangle given the inherent complexity of drought events (frequency, severity, duration, and timing during the growing season). Besides, drought effects might be modulated by trees’ phenotypic variability, which is, in turn, affected by long‐term local selective pressures and management legacies. Here we investigated the magnitude and the temporal changes of tree‐level resilience (i.e., resistance, recovery, and resilience) to extreme droughts. Moreover, we assessed the tree‐, site‐, and drought‐related factors and their interactions driving the tree‐level resilience to extreme droughts. We used a tree‐ring network of the widely distributed Scots pine (Pinus sylvestris) along a 2,800 km latitudinal gradient from southern Spain to northern Germany. We found that the resilience to extreme drought decreased in mid‐elevation and low productivity sites from 1980–1999 to 2000–2011 likely due to more frequent and severe droughts in the later period. Our study showed that the impact of drought on tree‐level resilience was not dependent on its latitudinal location, but rather on the type of sites trees were growing at and on their growth performances (i.e., magnitude and variability of growth) during the predrought period. We found significant interactive effects between drought duration and tree growth prior to drought, suggesting that Scots pine trees with higher magnitude and variability of growth in the long term are more vulnerable to long and severe droughts. Moreover, our results indicate that Scots pine trees that experienced more frequent droughts over the long‐term were less resistant to extreme droughts. We, therefore, conclude that the physiological resilience to extreme droughts might be constrained by their growth prior to drought, and that more frequent and longer drought periods may overstrain their potential for acclimation.
Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim to establish sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we also suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the field of microbial inoculant application.
Early-childhood caries is one of the most prevalent diseases in children worldwide and, while preventable, remains a global public health concern. Untreated cavities are painful and expensive and can lead to tooth loss and a lower quality of life. Caries are driven by acid production via microbial fermentation of dietary carbohydrates, resulting in enamel erosion. While caries is a well-studied disease, most research has focused on bacterial impacts, even though fungi are commensal organisms living within the plaque biofilm. There is very little known about how fungi impact caries pathogenicity. The elucidation of fungal taxa involved in caries disease progression is necessary for a more holistic view of the human oral microbiome. Data from this study will improve our understanding of how the fungal community changes as disease progresses and provide insight into the complex etiology of dental caries, which is necessary for the development of treatment plans and preventative measures.
Turgor loss point (πtlp) has been suggested to be a key trait for drought resistance in woody species. In herbaceous grassland species, the role of πtlp for species drought survival has not yet been tested, although grasslands are projected to experience more frequent and intense droughts with climate change.
To gain insights into the role of πtlp for drought resistance of temperate perennial grassland species, we assessed πtlp of 41 species common in Germany (20 forbs, 21 grasses). We directly related them to the species’ comparative whole‐plant drought survival and midday leaf water potentials under drought (ΨMD) assessed in a common garden drought experiment, and to species moisture association.
Species drought survival increased with increasing πtlp across all species as well as within forbs or grasses separately. ΨMD was positively related to πtlp and drought survival. Our results imply that high πtlp promotes drought survival of common perennial European temperate mesic grassland species by enabling them to maintain high leaf water potentials under drought, that is, a desiccation avoidance strategy. However, πtlp was not related to species moisture association.
The positive relationship between πtlp and drought survival in herbaceous grassland species was opposite to the negative relationship previously established in woody plants, implying that mechanisms of drought resistance differ between woody and herbaceous species. Our results highlight the necessity of directly testing the relationship of functional traits to whole‐plant drought survival in different plant life forms, before using trait assessments for predicting plant responses to drought.
A free plain language summary can be found within the Supporting Information of this article.
Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes — collectively termed the root microbiome — are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.
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.
This study reports the application of a novel bioprospecting procedure designed to screen plant growth-promoting rhizobacteria (PGPR) capable of rapidly colonizing the rhizosphere and mitigating drought stress in multiple hosts. Two PGPR strains were isolated by this bioprospecting screening assay and identified as Bacillus sp. (12D6) and Enterobacter sp. (16i). When inoculated into the rhizospheres of wheat (Triticum aestivum) and maize (Zea mays) seedlings, these PGPR resulted in delays in the onset of plant drought symptoms. The plant phenotype responding to drought stress was associated with alterations in root system architecture. In wheat, both PGPR isolates significantly increased root branching, and Bacillus sp. (12D6), in particular, increased root length, when compared to the control. In maize, both PGPR isolates significantly increased root length, root surface area and number of tips when compared to the control. Enterobacter sp. (16i) exhibited greater effects in root length, diameter and branching when compared to Bacillus sp. (12D6) or the control. In vitro phytohormone profiling of PGPR pellets and filtrates using LC/MS demonstrated that both PGPR strains produced and excreted indole-3-acetic acid (IAA) and salicylic acid (SA) when compared to other phytohormones. The positive effects of PGPR inoculation occurred concurrently with the onset of water deficit, demonstrating the potential of the PGPR identified from this bioprospecting pipeline for use in crop production systems under drought stress.
Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harbored a much more complex fungal network with significantly higher connectivity than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. We also found a strong negative association (R2 = 0.366; P < 0.0001) between agricultural intensification and root fungal network connectivity. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH, and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome.
Understanding soil nutrient distributions and the factors affecting them are crucial for fertilizer management and environmental protection in vulnerable ecological regions. Based on 555 soil samples collected in 2012 in Renshou County, located in the purple soil hilly area of Sichuan Basin, China, the spatial variability of soil total nitrogen (TN), total phosphorus (TP) and total potassium (TK) was studied with geostatistical analysis and the relative roles of the affecting factors were quantified using regression analysis. The means of TN, TP and TK contents were 1.12, 0.82 and 9.64 g kg⁻¹, respectively. The coefficients of variation ranged from 30.56 to 38.75% and the nugget/sill ratios ranged from 0.45 to 0.61, indicating that the three soil nutrients had moderate variability and spatial dependence. Two distribution patterns were observed. TP and TK were associated with patterns of obvious spatial distribution trends while the spatial distribution of TN was characterized by higher variability. Soil group, land use type and topographic factors explained 26.5, 35.6 and 8.4% of TN variability, respectively, with land use being the dominant factor. Parent material, soil group, land use type and topographic factors explained 17.5, 10.7, 12.0 and 5.0% of TP variability, respectively, and both parent material and land use type played important roles. Only parent material and soil type contributed to TK variability and could explain 25.1 and 13.7% of TK variability, respectively. More attention should focus on adopting reasonable land use types for the purposes of fertilizer management and consider the different roles of the affecting factors at the landscape scale in this purple soil hilly area.
Soil microbial communities play a crucial role in ecosystem functioning, but it is unknown
how co-occurrence networks within these communities respond to disturbances such as
climate extremes. This represents an important knowledge gap because changes in microbial
networks could have implications for their functioning and vulnerability to future disturbances.
Here, we show in grassland mesocosms that drought promotes destabilising
properties in soil bacterial, but not fungal, co-occurrence networks, and that changes in
bacterial communities link more strongly to soil functioning during recovery than do changes
in fungal communities. Moreover, we reveal that drought has a prolonged effect on bacterial
communities and their co-occurrence networks via changes in vegetation composition and
resultant reductions in soil moisture. Our results provide new insight in the mechanisms
through which drought alters soil microbial communities with potential long-term consequences,
including future plant community composition and the ability of aboveground and
belowground communities to withstand future disturbances.
Plant and soil microbiome studies are becoming increasingly important for understanding the roles microorganisms play in agricultural productivity. The purpose of this manuscript is to provide detail on how to rapidly sample soil, rhizosphere, and endosphere of replicated field trials and analyze changes that may occur in the microbial communities due to sample type, treatment, and plant genotype. The experiment used to demonstrate these methods consists of replicated field plots containing two, pure, warm-season grasses (Panicum virgatum and Andropogon gerardii) and a low-diversity grass mixture (A. gerardii, Sorghastrum nutans, and Bouteloua curtipendula). Briefly, plants are excavated, a variety of roots are cut and placed in phosphate buffer, and then shaken to collect the rhizosphere. Roots are brought to the laboratory on ice and surface sterilized with bleach and ethanol (EtOH). The rhizosphere is filtered and concentrated by centrifugation. Excavated soil from around the root ball is placed into plastic bags and brought to the lab where a small amount of soil is taken for DNA extractions. DNA is extracted from roots, soil, and rhizosphere and then amplified with primers for the V4 region of the 16S rRNA gene. Amplicons are sequenced, then analyzed with open access bioinformatics tools. These methods allow researchers to test how the microbial community diversity and composition varies due to sample type, treatment, and plant genotype. Using these methods along with statistical models, the representative results demonstrate there are significant differences in microbial communities of roots, rhizosphere, and soil. Methods presented here provide a complete set of steps for how to collect field samples, isolate, extract, quantify, amplify, and sequence DNA, and analyze microbial community diversity and composition in replicated field trials.
Significance
The development of high-throughput technologies has allowed mapping a significant proportion of interactions between biochemical entities in the cell. However, it is unclear how much information is lost given the lack of measurements on the kinetic parameters governing the dynamics of these interactions. Using biochemical networks with experimentally measured kinetic parameters, we show that a knowledge of the network topology offers 65–80% accuracy in predicting the impact of perturbation patterns. In other words, we can use the increasingly accurate topological models to approximate perturbation patterns, bypassing expensive kinetic constant measurement. These results could open new avenues in modeling drug action and in identifying drug targets relying on the human interactome only.
Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have shown that microbial communities harbour keystone taxa, which drive community composition and function irrespective of their abundance. In this Opinion article, we propose a definition of keystone taxa in microbial ecology and summarize over 200 microbial keystone taxa that have been identified in soil, plant and marine ecosystems, as well as in the human microbiome. We explore the importance of keystone taxa and keystone guilds for microbiome structure and functioning and discuss the factors that determine their distribution and activities.
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.
The elevational pattern of soil microbial diversity along mountain slopes has received considerable interest over the last decade. An increasing amount of taxonomic data on soil microbial community composition along elevation gradients have been collected, however the trophic patterns and environmental drivers of elevational changes remain largely unclear. Here, we examined the distribution patterns of major soil bacterial and fungal taxa along the northern slope of Changbai Mountain, Northeast China, at five typical vegetation types located between 740 and 2,691 m above sea level. Elevational patterns of the relative abundance of specific microbial taxa could be partially explained by the oligotrophic-copiotrophic theory. Specifically, two dark-coniferous forests, located at mid-elevation sites, were considered to be oligotrophic habitats, with relatively higher soil C/N ratio and NH4+-N concentrations. As expected, oligotrophic microbial taxa, belonging to the bacterial phyla Acidobacteria and Gemmatimonadetes, and fungal phylum Basidiomycota, were predominant in the two dark-coniferous forests, exhibiting a mid-elevation maximum pattern. In contrast, the broad leaf-Korean pine mixed forest located at the foot of the mountain, Betula ermanii-dominated forest located below the tree line, and alpine tundra at the highest elevation were considered more copiotrophic habitats, characterized by higher substrate-induced-respiration rates and NO3--N concentrations. Microbial taxa considered to be so called copiotrophic members, such as bacterial phyla Proteobacteria and Actinobacteria, and fungal phylum Ascomycota, were relatively abundant in these locations, resulting in a mid-elevation minimum pattern. At finer taxonomic levels, the two most abundant proteobacterial classes, alpha- and beta-Proteobacteria, along with Acidobacteria Gp1, 2, 3, 15, and the Basidiomycotal class of Tremellomycetes were classified with the copiotrophic group. Gamma- and delta-Proteobacteria, Acidobacteria Gp4, 6, 7, 16, and Basidiomycotal class of Agaricomycetes were classified as oligotrophic taxa. This work uses the oligotrophic-copiotrophic theory to explain the elevational distribution pattern of the relative abundance of specific microbial taxa, confirming some of the existing trophic classifications of microbial taxa and expanding on the theory to include a broader range of taxonomic levels.
Drought stress is one of the key abiotic stresses restraining the crop growth and production worldwide. Drought stress can also influence the structure and function of rhizosphere microbiome. The main objective of current investigation was to explore the effects of drought stress on shaping bacterial and fungal community structure in the wild and cultivated-type soybean genotypes. The results revealed that under drought, higher accumulation of osmolytes (sugar and proline) contents and NCED1 transcript were found in wild soybean (Glycine soja) as compared to the cultivated soybean (Glycine max), which elucidate that wild soybean genotype was more drought tolerant. Moreover, dehydration stress significantly suppressed the fungal diversity of the two host plants,though the diversity of the bacterial community in G. soja was significantly increased.Sulfitobacter sp. was only found in wild soybean. There was an increase in the proportion of Bradyrhizobium sp. under drought in two soybean genotypes whereas Sphingomonas sp. significantly enhanced in wild genotype. Our results indicated that G. soja a wild soybean genotype was highly drought tolerant than G. max, and established more microbial association by increasing the number of bacterial community and diversity than G. max. Therefore, this study provides a new evidence for improving soybean drought tolerant genotypes by studying the mechanism of plant-microbe interaction.
In the United Arab Emirates (UAE), about 34 percent of the area is affected with different levels of salinity, where growth of normal plants is almost impossible. The extremely low rainfall and occurrence of brackish groundwater for irrigation further complicates the crop production issues. In the hyper-arid environment of UAE, integrating trees and shrubs with other farm enterprises could be a useful strategy to increase system’s productivity. Field studies conducted on UAE soils have shown that Acacia ampliceps can fix nitrogen under different salinity levels ranging from 10 to 30 dSm-1, thus supporting the nutrient requirements for the two grasses i.e. Sporobolus arabicus and Paspalum vaginatum. These grasses produced up to 28 tons ha-1yr-1
of dry matter. When harvested at 2 m from the ground surface, these trees additionally provided ~ 10 tons ha-1yr-1 of foliage. The nitrogen fixation by the Acacia trees increases soil nitrogen to support forages. In the (Sabkha) coastal areas, growing halophytic plants such as Atriplex species can be beneficial due to low annual maintenance costs and their ability to survive high salt contents in the soil. Once the soil improves, non-halophytic trees, shrubs and grasses can also be planted. Until now 76 halophyte species have been identified for the UAE, which include 14 seawater tolerant halophytes, 29 halophytes, 31 semi-halophytes, and two parasitic plants belonging to Chenopodaceae and Zygophyllaceae family. The transformation of these saline lands into productive lands through large-scale adoption of halophytes and salt-tolerant plant species can have a significant impact on the livelihood and food security of rural pastoral communities of the dry regions.
The ability to predict microbial community dynamics lags behind the quantity of data available in these systems. Most predictive models use only environmental parameters, although a long history of ecological literature suggests that community complexity should also be an informative parameter. Thus, we hypothesize that incorporating information about a community’s complexity might improve predictive power in microbial models. Here, we present a new metric, called community ‘cohesion,’ that quantifies the degree of connectivity of a microbial community. We analyze six long-term (10+ years) microbial data sets using the cohesion metrics and validate our approach using data sets where absolute abundances of taxa are available. As a case study of our metrics’ utility, we show that community cohesion is a strong predictor of Bray–Curtis dissimilarity (R²=0.47) between phytoplankton communities in Lake Mendota, WI, USA. Our cohesion metrics outperform a model built using all available environmental data collected during a long-term sampling program. The result that cohesion corresponds strongly to Bray–Curtis dissimilarity is consistent across the six long-term time series, including five phytoplankton data sets and one bacterial 16S rRNA gene sequencing data set. We explain here the calculation of our cohesion metrics and their potential uses in microbial ecology.
Drought is a major environmental factor that limits crop growth and productivity. Flue-cured tobacco (Nicotiana tabacum) is one of the most important commercial crops worldwide and its productivity is vulnerable to drought. However, comparative analyses of physiological, biochemical and gene expression changes in flue-cured tobacco varieties differing in drought tolerance under long-term drought stress are scarce. In this study, drought stress responses of two flue-cured tobacco varieties, LJ851 and JX6007, were comparatively studied at the physiological and transcriptional levels. After exposing to progressive drought stress, the drought-tolerant LJ851 showed less growth inhibition and chlorophyll reduction than the drought-sensitive JX6007. Moreover, higher antioxidant enzyme activities and lower levels of H2O2, Malondialdehyde (MDA), and electrolyte leakage after drought stress were found in LJ851 when compared with JX6007. Further analysis showed that LJ851 plants had much less reductions than the JX6007 in the net photosynthesis rate and stomatal conductance during drought stress; indicating that LJ851 had better photosynthetic performance than JX6007 during drought. In addition, transcriptional expression analysis revealed that LJ851 exhibited significantly increased transcripts of several categories of drought-responsive genes in leaves and roots under drought conditions. Together, these results indicated that LJ851 was more drought-tolerant than JX6007 as evidenced by better photosynthetic performance, more powerful antioxidant system, and higher expression of stress defense genes during drought stress. This study will be valuable for the development of novel flue-cured tobacco varieties with improved drought tolerance by exploitation of natural genetic variations in the future.
Phospholipid fatty acids (PLFAs) are key components of microbial cell membranes. The analysis of PLFAs extracted from soils can provide information about the overall structure of terrestrial microbial communities. PLFA profiling has been extensively used in a range of ecosystems as a biological index of overall soil quality, and as a quantitative indicator of soil response to land management and other environmental stressors.
The standard method presented here outlines four key steps: 1. lipid extraction from soil samples with a single-phase chloroform mixture, 2. fractionation using solid phase extraction columns to isolate phospholipids from other extracted lipids, 3. methanolysis of phospholipids to produce fatty acid methyl esters (FAMEs), and 4. FAME analysis by capillary gas chromatography using a flame ionization detector (GC-FID). Two standards are used, including 1,2-dinonadecanoyl-sn-glycero-3-phosphocholine (PC(19:0/19:0)) to assess the overall recovery of the extraction method, and methyl decanoate (MeC10:0) as an internal standard (ISTD) for the GC analysis.
Increased severity of droughts, due to anthropogenic activities and global warming, has imposed a severe threat on agricultural productivity. This has escalated the need for environmentally sustainable solutions to secure global food security. In this context, the application of plant growth-promoting rhizobacteria (PGPR) can be beneficial. PGPR through various mechanisms viz. osmotic adjustments, increased antioxidant activity, phytohormone production, etc., not only ensure the plant’s survival during drought but also augment its growth. Further, due to recent advances in omics technologies, better insights are emerging for PGPR, which facilitates the exploration of genes that are responsible for plant tissue colonization. This review extensively discusses the various mechanisms of PGPR in drought stress resistance; we have also summarized the recent molecular and omics-based approaches for elucidating the role of drought-responsive genes. The manuscript comprises the in-depth mechanistic approach along with designing the PGPR-based bioinoculants to combat drought stress and a possible flowchart for increasing their efficacy.
Plant litter decomposition in the soil is governed by microorganisms such as bacteria and fungi that colonize lignocellulose residues during the decomposition process, and thus, the interplay of bacterial and fungal communities can yield insight into the lignocellulose decomposition dynamics. Previous studies have mainly investigated litter decomposing communities in microcosms or ex-situ conditions or at a single soil ecosystem. Here we conducted a 12 week-long litter decomposition experiment to explore how the temporal dynamics of soil enzyme activities and microbial communities are linked to litter decomposition under three different land use sites (forestland, farmland, and abandoned farmland) in Nanjing, China. We found that litter decomposition in the forestland was the highest among the three land use sites. Then, using a multifactorial approach, we showed that this higher decomposition rate in forest soils is determined by microbial communities with higher ligninolytic enzyme activities, higher diversity, and a less complex but more specialized network. Chryseobacterium in bacteria, and Fusarium, Aspergillus and Penicillium in fungi were the keystone taxa in networks across three land use types. We conducted subsequent culturing that further confirmed the strong decomposition ability and enzyme activities of these taxa, indicating their importance for microbial litter decomposition. As such, this is one of the first studies to validate the role of keystone taxa for litter decomposition, and it demonstrates that co-occurrence network scores can be used for statistical identification of putative keystone taxa for further screening and linking to microbiome functioning. Overall, we show that land-use alters the composition and network structure of soil microbiota that determine the litter decomposition. Our study also reveals that specialized keystone taxa are involved in the decomposition dynamics, and highlights an opportunity of harnessing such taxa for manipulating lignocellulose decomposition in soil ecosystems.
Plant invasion can dramatically impact soil carbon (C) cycling and sequestration while, other global change factors, such as nitrogen (N) deposition, are predicted to promote plant invasion. However, questions remain as to whether the chemical composition of soil organic C (SOC) may alter with plant invasion and how N availability modulates the invasion effects on SOC. In this study, we conducted a 10-year mesocosm experiment simulating the invasion of Japanese knotweed (Polygonum cuspidatum) into a fallow soil, coupled with a simultaneous mineral fertilizer application scheme for the invasive plants. We investigated the invasion effects on the chemical composition of various SOC components at the molecular level, and examined how these effects responded to changes in soil N availability. Compared with the noninvaded soils, the knotweed-invaded soils exhibited a 17% increase in the microbial-derived C, mainly through the accumulation of fungal residue in the form of amino sugars. Despite receiving leaf litter which was abundant in polyphenolic compounds (40% and 3-times higher in lignin and tannins per unit biomass, respectively), the knotweed-invaded soils did not differ in the concentration of plant lipids and lignin monomers compared to the noninvaded soils inhabited by grasses. However, the concentrations of phytosterol in the knotweed-invaded soils were 1.5-fold as that in the noninvaded soils. Fertilizer application significantly increased the retention of plant-derived compounds in the knotweed-invaded soils, but also induced 45% greater degradation of lignin. Moreover, under fertilizer application, the knotweed-invaded soils accumulated 46% more microbial-derived C, primarily due to the altered microbial biomass and community composition. Collectively, our findings suggest that plant invasion has the potential to influence SOC chemical composition through changes in plant-derived and microbial-derived C. Furthermore, N deposition could reinforce the invasion effects on the molecular composition and accrual of SOC. Our results also highlight the need to understand the impacts of biological invasion in the context of other global change drivers that both affect invasion and modulate their effects.
Microorganisms interact in complex communities, affecting microbially-mediated processes in the environment. Particularly, aerobic methanotrophs showed significantly stimulated growth and activity in the presence of accompanying microorganisms in an interaction network (interactome). Yet, little is known of how the interactome responds to disturbances, and how community functioning is affected by the disturbance-induced structuring of the interaction network. Here, we employed a time-series stable isotope probing (SIP) approach using 13C-CH4 coupled to a co-occurrence network analysis after Illumina MiSeq sequencing of the 13C-enriched 16S rRNA gene to directly relate the response in methanotrophic activity to the network structure of the interactome after desiccation-rewetting of a paddy soil. Methane uptake rate decreased immediately (< 5 days) after short-term desiccation-rewetting. Although the methanotroph subgroups differentially responded to desiccation-rewetting, the metabolically active bacterial community composition, including the methanotrophs, recovered after the disturbance. However, the interaction network was profoundly altered, becoming more complex but, less modular after desiccation-rewetting, despite the recovery in the methanotrophic activity and community composition/abundances. This suggests that the legacy of the disturbance persists in the interaction network. The change in the network structure may have consequences for community functioning with recurring desiccation-rewetting.
Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant-associated microbiomes confer fitness advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment. We also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits, such as nutrient acquisition and plant health, in addition to highlighting knowledge gaps and future directions. In this Review, Trivedi and colleagues explore the interactions between plants, their associated microbial communities and the environment, and also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.
Anaerobic co-digestion of fats, oils and grease (FOG) with municipal wastewater sludge offers the opportunity to increase methane yields; yet the impact of FOG on overall process dynamics and the associated microbial communities is not well understood. This study employed lab-scale batch anaerobic co-digestion assays to advance the understanding of the co-digestion process through studying the dynamics of formation and consumption of intermediates along the anaerobic digestion pathway and correlating these to temporal analysis of methanogenic activity as well as end-point microbial community structure. Methane production was delayed during sludge co-digestion with FOG, but not during digestion of sludge alone. Palmitic acid, a long-chain fatty acid (LCFA), accumulated during co-digestion to concentrations above 16 mM, resulting in a lag in methane production. Acetate, hydrogen, and formate, carbon and/or energy sources for methanogens during methane production, did not accumulate during the lag-phase. Expression of the mcrA gene, which encodes the methyl coenzyme M reductase alpha subunit necessary for catalyzing the final step of methanogenesis, increased when co-digesters were spiked with acetate during the lag-phase, indicating no direct total inhibition from palmitic acid to methanogenic activity in assays with a 23% FOG loading (based on total g VS). End-point microbial community analyses revealed distinct community structure and composition differences between co-digestion assays and controls, and between biological replicates with variable responses. The hydrogenotrophic methanogen genus Methanoculleus dominated adapted co-digesters, but not inhibited co-digesters suggesting its importance for adapting to FOG loadings. Palmitic acid accumulation resulting from distinct microbial community composition and structure thus characterizes stalled or inhibited FOG co-digesters.
The effects of a newly discovered endophytic fungus, Talaromyces omanensis, on the drought tolerance of tomato is presented in this study. The fungus was obtained from a desert plant Rhazya stricta in Oman. Drought stress was induced by a 15% solution of Polyethylene glycol-6000 (PEG-6000). Several parameters were measured including pollen sterility, pollen tube length, growth, flowering, and yield characteristics, the biochemical analysis of the leaves and fruits, as well as other physiological and anatomical parameters. The results showed that T. omanensis provided multiple advantages to tomato grown under drought stress, including improved reproductive characteristics, chlorophyll fluorescence, and some anatomical characteristics such as increased phloem and cortex width and a reduction of pith autolysis that leads to hollow stem. In addition, T. omanensis significantly increased drought-stress related characteristics such as shoot dry weight, root length, the number of flowers, and fruit weight. A significantly higher concentration of gibberellic acid (GA3) was found in tomato plants treated by T. omanensis, which may enhance their drought tolerance. These results suggest that T. omanensis is a potential biological anti-stress stimulator for important horticultural crops such as tomatoes. This study is the first to report the beneficial effects of T. omanensis in alleviating drought stress in tomatoes.
The purpose of this research was to evaluate tree species effects on quantitative and qualitative soil organic matter (SOM) properties of forest floors and mineral soil layers. Additionally, the contribution of soil microbial biomass to SOM was studied in five forest stands with different dominant tree species.
The study was conducted at the afforested spoil heap ‘Sophienhöhe’ located at the lignite open-cast mine Hambach near Jülich, Germany. The 35 year-old afforested sites consisted of monocultural stands of Douglas fir (Pseudotsuga mienziesii), pine (Pinus nigra), beech (Fagus sylvatica) and red oak (Quercus rubra) as well as a mixed deciduous stand site planted mainly with hornbeam (Carpinus betulus), lime (Tilia cordata) and common oak (Quercus robur). There, boundary conditions regarding soil, climate, topography and management were highly similar, equivalent to a common garden experiment but on landscape level. Because the parent material used for site recultivation was free from organic matter or coal material, the SOM accumulation is a result of in situ soil development.
Tree species had a significant effect on soil organic carbon (SOC) stocks, stoichiometric patterns of C, hydrogen (H), nitrogen (N), oxygen (O) and sulfur (S) and the microbial biomass carbon (MBC) content in the forest floor and the top mineral soil layers (0–5 cm, 5–10 cm, 10–30 cm). In general, forest floor SOC stocks were significantly higher in coniferous forest stands compared to deciduous tree species. Differences in SOM quantity became less pronounced with increasing depth, while stoichiometric molar ratios of SOM as indices of litter turnover and SOM composition differed also in deeper layers. Differences in H:C and O:C ratios among tree species clearly increased along the depth gradient in mineral soils, indicating that SOM turnover by oxidative processes depends on tree species. Differences in depth gradients of the microbial quotient (MBC to SOC ratio) among tree species emphasized differences in the microbial C turnover. Furthermore, the relationship between the microbial quotient and SOM stoichiometry (C:N and C:S ratio) became stronger with increasing soil depth. This suggests that N and especially S limitation determined the microbial turnover of SOM in deeper mineral soil layers.
Droughts are among the costliest natural disasters. They affect wide regions and large numbers of people worldwide by tampering with water availability and agricultural production. In this research, soil moisture drought trends are assessed for Europe using the Soil Moisture Index (SMI) estimated on Joint UK Land Environment Simulator simulations under two Representative Concentration Pathways, the RCP 2.6 and RCP 6.0 scenarios. Results show that SMI drought conditions are expected to exacerbate in Europe with substantial differences among regions. Eastern Europe and Mediterranean regions are found to be the most affected. Spatially and temporally contiguous regions that exhibit SMI of Severe and Extreme index categories are identified as distinct drought events and are assessed for their characteristics. It is shown that even under strong emissions mitigation, these events are expected to increase in occurrence (22% to 123%), while their characteristics will become more unfavorable. Results indicate increase in their spatial extend (between 23% and 46%) and their duration (between 16% and 48%) depending on the period and the scenario. Additional analysis was performed for the exceptionally wide-area (over 10⁶ km²) severe and extreme soil moisture drought events that are expected to drastically increase comparing to the recent past. Projections show that those events are expected to happen between 11 and 28 times more frequently depending on the scenario and the period with a 59% to 246% larger duration. These findings indicate that even applying strong mitigation measures, agricultural drought risk in Europe is expected to become higher than our present experience.
Drought is well known to have strong effects on the composition and activity of soil microbial communities, and may be determined by drought history and drought duration, but the characterisation and prediction of these effects remains challenging. This is because soil microbial communities that have previously been exposed to drought may change less in response to subsequent drought events, due to the selection of drought-resistant taxa. We set up a 10-level drought experiment to test the effect of water stress on the composition and diversity of soil bacterial and fungal communities. We also investigated the effect of a previous long-term drought on communities in soils with different historical precipitation regimes. Saplings of the holm oak, Quercus ilex L., were included to assess the impact of plant presence on the effects of the drought treatment. The composition and diversity of the soil microbial communities were analysed using DNA amplicon sequencing of bacterial and fungal markers and the measurement of phospholipid fatty acids. The experimental drought affected the bacterial community much more than the fungal community, decreasing alpha diversity and proportion of total biomass, whereas fungal diversity tended to increase. The experimental drought altered the relative abundances of specific taxa of both bacteria and fungi, and in many cases these effects were modified by the presence of the plant and soil origin. Soils with a history of drought had higher overall bacterial alpha diversity at the end of the experimental drought, presumably because of adaptation of the bacterial community to drought conditions. However, some bacterial taxa (e.g. Chloroflexi) and fungal functional groups (plant pathogens and saprotrophic yeasts) decreased in abundance more in the pre-droughted soils. Our results suggest that soil communities will not necessarily be able to maintain the same functions during more extreme or more frequent future droughts, when functions are influenced by community composition. Drought is likely to continue to affect community composition, even in soils that are acclimated to it, tending to increase the proportion of fungi and reduce the proportion and diversity of bacteria.
A large area of Iran is located in arid and semi-arid regions; as a result, drought stress is a major problem for the growth of plants. Therefore, it is very important in crop productivity to increase plant tolerance to drought stress. Plant growth promoting rhizobacteria such as Azotobacter may enhance plant growth under drought stress conditions by different mechanisms. In this study, a total of 20 Azotobacter strains were isolated and characterized from 77 rhizosphere soil samples collected from semi-arid regions. The strains were screened for the production of siderophore and IAA, solubilization of phosphate and potassium and growth under drought stress in PEG 6000. The strains were identified by 16S rRNA gene sequencing. The efficient strains were tested on the growth of maize (Zea mays) under drought stress by using three levels of irrigation, including 80, 60 and 40 percent of field capacity in greenhouse conditions. The laboratory results revealed that Az63, Az69 and Az70 were the most effective strains in terms of phosphate and potassium solubilisation, siderophore producion and maximum growth in PEG 6000. At 40 percent of field capacity, the inoculation increased shoot dry weight, plant height, chlorophyll content, nitrogen, phosphorous and iron concentration compared to the control. Az63 and Az70 increased shoot dry weight significantly at 60 percent of field capacity.
The effects of short-term drought on soil microbial communities remain largely unexplored, particularly at large scales and under field conditions. We used seven experimental sites from two continents (North America and Australia) to evaluate the impacts of imposed extreme drought on the abundance, community composition, richness and function of soil bacterial and fungal communities. The sites encompassed different grassland ecosystems spanning a wide range of climatic and soil properties. Drought significantly altered the community composition of soil bacteria and, to a lesser extent, fungi in grasslands from two continents. The magnitude of the fungal community change was directly proportional to the precipitation gradient. This greater fungal sensitivity to drought at more mesic sites contrasts with the generally observed pattern of greater drought sensitivity of plant communities in more arid grasslands, suggesting that plant and microbial communities may respond differently along precipitation gradients. Actinobateria, and Chloroflexi, bacterial phyla typically dominant in dry environments, increased their relative abundance in response to drought, whereas Glomeromycetes, a fungal class regarded as widely symbiotic, decreased in relative abundance. The response of Chlamydiae and Tenericutes, two phyla of mostly pathogenic species, decreased and increased along the precipitation gradient, respectively. Soil enzyme activity consistently increased under drought, a response that was attributed to drought-induced changes in microbial community structure rather than to changes in abundance and diversity. Our results provide evidence that drought has a widespread effect on the assembly of microbial communities, one of the major drivers of soil function in terrestrial ecosystems. Such responses may have important implications for the provision of key ecosystem services, including nutrient cycling, and may result in the weakening of plant-microbial interactions and a greater incidence of certain soil-borne diseases. This article is protected by copyright. All rights reserved.
The underground root–soil–microbe interactions are extremely complex, but vitally important for aboveground plant growth, health and fitness. The pressure to reduce our reliance on agrochemicals, and sustainable efforts to develop agriculture makes rhizosphere interactions’ research a hotspot. Recent advances provide new insights about the signals, pathways, functions and mechanisms of these interactions. In this review, we provide an overview about recent progress in rhizosphere interaction networks in crops. We also discuss a holistic view of the root–soil–rhizomicrobiome interactions achieved through the advances of omics and bioinformatics technologies, and the potential strategies to manage the complex rhizosphere interactions for enhancing crop production.
Dark septate endophytes (DSE) protect host plants against a variety of environmental stresses, however our knowledge about the roles of DSE in improving drought tolerance of crops is poor. In this study, sorghum (Sorghum bicolor L. Moench) was inoculated with a DSE strain (Exophiala pisciphila GM25) under two different soil water conditions (well-watered (WW), -0.11 MPa; drought-stressed (DS), -0.69 MPa) for one month. At the end of this experiment, sorghum roots were obviously colonized by DSE with 50.5%-62.5% colonization rate. When compared with non-inoculated seedlings under both WW and DS conditions, E. pisciphila-inoculated sorghum had greater plant height, collar diameter, shoot dry weight, net photosynthetic rate (Pn), stomatal conductance (gs), transpiration rate (E), maximal photochemical efficiency of PSII photochemistry (Fv/Fm) and actual quantum yield (φPSII), and lower intercellular CO2 concentration (Ci). In addition, in comparison to non-inoculation under DS conditions, E. pisciphila inoculation also improved the root dry weight, non-photochemical quenching values (NPQ), photochemical quenching values (qP), increased the content of related secondary metabolites including anthocyanin, polyphenol and flavonoid and enhanced the enzymatic activities related to secondary metabolism, such as cinnamyl alcohol dehydrogenase (CAD), phenylalanine ammonia-lyase (PAL), guaiacol peroxidase (G-POD) in sorghum seedlings. Our results demonstrated that the drought resistance of sorghum seedlings were positively improved by E. pisciphila inoculation with better plant growth, gas exchange, photosynthesis, chlorophyll fluorescence, secondary metabolites and enzyme activities related to secondary metabolism. Inoculation with E. pisciphila is an efficient strategy to survive for sorghum in drought environment.
Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes. In this review, we first focus on microbe-mediated plant salt tolerance, in particular on the physiological and molecular mechanisms underlying root-microbe symbiosis. Unfortunately, when introducing such microbes as single strains to soils, they are often ineffective in improving plant growth and stress tolerance, largely due to competition with native soil microbial communities and limited colonization efficiency. Rapid progress in rhizosphere microbiome research has revived the belief that plants may benefit more from association with interacting, diverse microbial communities (microbiome) than from individual members in a community. Understanding how a microbiome assembles in the continuous compartments (endosphere, rhizoplane, and rhizosphere) will assist in predicting a subset of core or minimal microbiome and thus facilitate synthetic re-construction of microbial communities and their functional complementarity and synergistic effects. These developments will open a new avenue for capitalizing on the cultivable microbiome to strengthen plant salt tolerance and thus to refine agricultural practices and production under saline conditions.