Showing papers in "Plant and Soil in 2018"

The seed microbiome: Origins, interactions, and impacts

Abstract: The development and dispersal of seeds as well as their transition to seedlings represent perhaps the most critical stages of a plant’s life cycle The endophytic and epiphytic microbial interactions that take place in, on, and around seeds during these stages of the plant’s life cycle may have profound impacts on plant ecology, health, and productivity While our understanding of the seed microbiota has lagged far behind that of the rhizosphere and phyllosphere, many advances are now being made This review explores the microbial associations with seeds through various stages of the plant life cycle, beginning with the earliest stages of seed development on the parent plant and continuing through the development and establishment of seedlings in soil This review represents a broad synthesis of the ecological and agricultural literature focused on seed-microbe interactions as a means of better understanding how these interactions may ultimately influence plant ecology, health, and productivity in both natural and agricultural systems Our current understanding of seed-microbe associations will be discussed, with an emphasis on recent findings that specifically highlight the emerging contemporary understanding of how seed-microbe associations may ultimately impact plant health and productivity The diversity and dynamics of seed microbiomes represent the culmination of complex interactions with microbes throughout the plant life cycle The richness and dynamics of seed microbiomes is revealing exciting new opportunities for research into plant-microbe interactions Often neglected in plant microbiome studies, the renaissance of inquiry into seed microbiomes is offering exciting new insights into how the diversity and dynamics of the seed microbiome with plant and soil microbiomes as well as the microbiomes of dispersers and pollinators It is clear that the interactions taking place in and around seeds indeed have significant impacts on plant health and productivity in both agricultural and natural ecosystems

It is not all about sodium: revealing tissue specificity and signalling roles of potassium in plant responses to salt stress

Abstract: Salinity is a global issue threatening agricultural production systems across the globe. While the major focus of plant salinity stress tolerance research has been on sodium, the transport and physiological roles of K+ in plant salt stress response has received less attention. This review attempts to bridge this knowledge gap. The major emphasis is on newly proposed K+ signalling roles and plant salt tolerance cell- and tissuespecificity. In addition to summarizing the importance of K+ retention for plant salt tolerance, we focus onaspects that were not the subject of previous reviews including (1) the importance of HAK/KUP family of transporters in K+ uptake in salt stressed plants and its possible linkage with Ca2+ and ROS signalling; (2) control of xylem K+ loading in salt stressed plants, control of phloem K+ recirculation in salt stressed plants and the potential importance of plant’s ability to efficiently coordinate K+ signals between root and shoot; (3) the buffering capacity of the vacuolar K+ pool; and (4) mechanisms of restoring the basal cytosolic K+ levels by coordinated activity of tonoplast K+-permeable channels. Overall, this review emphasises the need to fully understand the newly emerging roles of K+ and regulation of its transport for improving salinity stress tolerance in plants.

How does biochar influence soil N cycle? A meta-analysis

Abstract: Modern agriculture is driving the release of excessive amounts of reactive nitrogen (N) from the soils to the environment, thereby threatening ecological balances and functions. The amendment of soils with biochar has been suggested as a promising solution to regulate the soil N cycle and reduce N effluxes. However, a comprehensive and quantitative understanding of biochar impacts on soil N cycle remains elusive. A meta-analysis was conducted to assess the influence of biochar on different variables involved in soil N cycle using data compiled across 208 peer-reviewed studies. On average, biochar beneficially increases symbiotic biological N2 fixation (63%), improves plant N uptake (11%), reduces soil N2O emissions (32%), and decreases soil N leaching (26%), but it poses a risk of increased soil NH3 volatilization (19%). Biochar-induced increase in soil NH3 volatilization commonly occurs in studies with soils of low buffering capacity (soil pH ≤ 5, organic carbon≤10 g kg−1, or clay texture), the application of high alkaline biochar (straw- or manure-derived biochar), or biochar at high application rate (>40 t ha−1). Besides, if the pyrolytic syngas is not purified, the biochar production process may be a potential source of N2O and NOx emissions which correspond to 2–4% and 3–24% of the feedstock-N, respectively. This study suggests that to make biochar beneficial for decreasing soil N effluxes, clean advanced pyrolysis technique and adapted use of biochar are of great importance.

Opportunities for mobilizing recalcitrant phosphorus from agricultural soils: a review

Abstract: Phosphorus (P) fertilizer is usually applied in excess of plant requirement and accumulates in soils due to its strong adsorption, rapid precipitation and immobilisation into unavailable forms including organic moieties. As soils are complex and diverse chemical, biochemical and biological systems, strategies to access recalcitrant soil P are often inefficient, case specific and inconsistently applicable in different soils. Finding a near-universal or at least widely applicable solution to the inefficiency in agricultural P use by plants is an important unsolved problem that has been under investigation for more than half a century. In this paper we critically review the strategies proposed for the remobilization of recalcitrant soil phosphorus for crops and pastures worldwide. We have additionally performed a meta-analysis of available soil 31P–NMR data to establish the potential agronomic value of different stored P forms in agricultural soils. Soil inorganic P stocks accounted on average for 1006 ± 115 kg ha−1 (57 ± 7%), while the monoester P pool accounted for 587 ± 32 kg ha−1 (33 ± 2%), indicating the huge potential for the future agronomic use of the soil legacy P. New impact driven research is needed in order to create solutions for the sustainable management of soil P stocks.

Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities

Abstract: Background: The dynamics of phosphorus (P) in the environment is important for regulating nutrient cycles in natural and managed ecosystems and an integral part in assessing biological resilience against environmental change. Organic P (Po) compounds play key roles in biological and ecosystems function in the terrestrial environment being critical to cell function, growth and reproduction. Scope: We asked a group of experts to consider the global issues associated with Po in the terrestrial environment, methodological strengths and weaknesses, benefits to be gained from understanding the Po cycle, and to set priorities for Po research. Conclusions: We identified seven key opportunities for Po research including: the need for integrated, quality controlled and functionally based methodologies; assessment of stoichiometry with other elements in organic matter; understanding the dynamics of Po in natural and managed systems; the role of microorganisms in controlling Po cycles; the implications of nanoparticles in the environment and the need for better modelling and communication of the research. Each priority is discussed and a statement of intent for the Po research community is made that highlights there are key contributions to be made toward understanding biogeochemical cycles, dynamics and function of natural ecosystems and the management of agricultural systems.

Defining plant growth promoting rhizobacteria molecular and biochemical networks in beneficial plant-microbe interactions

Abstract: Our knowledge of plant beneficial bacteria in the rhizosphere is rapidly expanding due to intense interest in utilizing these types of microbes in agriculture. Laboratory and field studies consistently document the growth, health and protective benefits conferred to plants by applying plant growth promoting rhizobacteria (PGPR). PGPR exert their influence on other species, including plants, in the rhizosphere by producing a wide array of extracellular molecules for communication and defense. The types of PGPR molecular products are characteristically diverse, and the mechanisms by which they are acting on the plant are only beginning to be understood. While plants may contribute to shape their microbiome, it is these bacterial products which induce beneficial responses in plants. PGPR extracellular products can directly stimulate plant genetic and molecular pathways, leading to increases in plant growth and induction of plant resistance and tolerance. This review will discuss known PGPR-derived molecules, and how these products are implicated in inducing plant beneficial outcomes through complex plant response mechanisms. In order to move PGPR research to the next level, it will be important to describe and document the genetic and molecular mechanisms employed in these interactions. In this way, we will be able to restructure and harness these mechanisms in a way that allows for broad-based applications in agriculture. A greater depth of understanding of how these PGPR molecules are acting on the plant will allow more effective development of rhizobacterial applications in the field.

Zinc nutrition in wheat-based cropping systems

Abstract: Zinc (Zn) deficiency is one of the most important micronutrient disorders affecting human health. Wheat is the staple food for 35% of the world’s population and is inherently low in Zn, which increases the incidence of Zn deficiency in humans. Major wheat-based cropping systems viz. rice–wheat, cotton–wheat and maize–wheat are prone to Zn deficiency due to the high Zn demand of these crops. This review highlights the role of Zn in plant biology and its effect on wheat-based cropping systems. Agronomic, breeding and molecular approaches to improve Zn nutrition and biofortification of wheat grain are discussed. Zinc is most often applied to crops through soil and foliar methods. The application of Zn through seed treatments has improved grain yield and grain Zn status in wheat. In cropping systems where legumes are cultivated in rotation with wheat, microorganisms can improve the available Zn pool in soil for the wheat crop. Breeding and molecular approaches have been used to develop wheat genotypes with high grain Zn density. Options for improving grain yield and grain Zn concentration in wheat include screening wheat genotypes for higher root Zn uptake and grain translocation efficiency, the inclusion of these Zn-efficient genotypes in breeding programs, and Zn fertilization through soil, foliar and seed treatments.

How belowground interactions contribute to the coexistence of mycorrhizal and non-mycorrhizal species in severely phosphorus-impoverished hyperdiverse ecosystems

Abstract: Mycorrhizal strategies are very effective in enhancing plant acquisition of poorly-mobile nutrients, particularly phosphorus (P) from infertile soil. However, on very old and severely P-impoverished soils, a carboxylate-releasing and P-mobilising cluster-root strategy is more effective at acquiring this growth-limiting resource. Carboxylates are released during a period of only a few days from ephemeral cluster roots. Despite the cluster-root strategy being superior for P acquisition in such environments, these species coexist with a wide range of mycorrhizal species, raising questions about the mechanisms contributing to their coexistence. We surmise that the coexistence of mycorrhizal and non-mycorrhizal strategies is primarily accounted for by a combination of belowground mechanisms, namely (i) facilitation of P acquisition by mycorrhizal plants from neighbouring cluster-rooted plants, and (ii) interactions between roots, pathogens and mycorrhizal fungi, which enhance the plants’ defence against pathogens. Facilitation of nutrient acquisition by cluster-rooted plants involves carboxylate exudation, making more P available for both themselves and their mycorrhizal neighbours. Belowground nutrient exchanges between carboxylate-exuding plants and mycorrhizal N2-fixing plants appear likely, but require further experimental testing to determine their nutritional and ecological relevance. Anatomical studies of roots of cluster-rooted Proteaceae species show that they do not form a complete suberised exodermis. The absence of an exodermis may well be important to rapidly release carboxylates, but likely lowers root structural defences against pathogens, particularly oomycetes. Conversely, roots of mycorrhizal plants may not be as effective at acquiring P when P availability is very low, but they are better defended against pathogens, and this superior defence likely involves mycorrhizal fungi. Taken together, we are beginning to understand how an exceptionally large number of plant species and P-acquisition strategies coexist on the most severely P-impoverished soils.

Complex role of the polymeric matrix in biological soil crusts

Abstract: Extracellular polymeric matrix (EPM) is a complex component of the organo-mineral assemblages created by biological soil crusts (BSCs). Mainly of polysaccharidic origin, it embeds soil and sediments and provides key benefits to the crust community. Services provided include: sediment cohesion and resistance to erosion, moisture provision, protection from external harmful factors, as well as support to plant establishment and growth. EPM is the product of BSC microbial community, and it is constituted by exopolysaccharides (EPS) associated to other substances, organized in a three-dimensional structure having different levels of gelation, and degrees of condensation. This review aims at focusing scientific attention, for the first time, on the characteristics and the roles of three operationally defined EPM fractions, one water soluble, one more adherent to cells and sediments, and one firmly attached to microbial cells. The latest results obtained by analyzing EPM of natural and induced (i.e, the result of cyanobacteria inoculation) BSCs are outlined, and the optimized extraction methodology is described in details. The review underlines the complexity of investigating the characteristics and the role of microbial EPS, and its supra-structure (EPM), in natural conditions (as opposed to cultures in laboratory conditions), where the matrix is subjected to continuous microbial rearrangement due to biosynthetic, self- and cross-feeding processes, and where microbial activity affected by environmental parameters.

The Cucurbita pepo seed microbiome: genotype-specific composition and implications for breeding

Abstract: Plant breeding activities shape the rhizosphere microbiome but less is known about the relationship of both with the seed microbiome. We analyzed the composition of bacterial communities of seeds and rhizospheres of Styrian oil pumpkin genotypes in comparison to bulk soil to elucidate specific microbial signatures to support a concept involving plant-microbe interactions in breeding strategies. The seed and rhizosphere microbiomes of 14 genotypes of oilseed pumpkin and relatives were analyzed using a 16S rRNA gene amplicon sequencing approach, which was assessed by bioinformatics and statistical methods. All analyzed microhabitats were characterized by diverse bacterial communities, but the relative proportions of phyla and the overall diversity was different. Seed microbiomes were characterized by the lowest diversity and dominant members of Enterobacteriaceae including potential pathogens (Erwinia, Pectobacterium). Potential plant-beneficial bacteria like Lysobacter, Paenibacillus and Lactococcus contributed to the microbial communities in significant abundances. Interestingly, strong genotype-specific microbiomes were detected for seeds but not for the rhizospheres. Our study indicates a strong impact of the Cucurbita pepo genotype on the composition of the seed microbiome. This should be considered in breeding of new cultivars that are more capable of exploiting beneficial indigenous microbial communities.

Nramp5 expression and functionality likely explain higher cadmium uptake in rice than in wheat and maize

Abstract: Cereals are the main dietary source of cadmium (Cd). Rice grains often contain higher levels of Cd than other cereals, but the reasons are unknown. The aims of this study were to compare Cd uptake, translocation and influx kinetics between rice, wheat and maize and to investigate whether the expression and functionality of Nramp5 genes differ between the three crop species. Two cultivars each of rice, wheat and maize were grown hydroponically and exposed to a range of Cd concentrations. Nramp5 genes were cloned from the three plants and their expression levels determined. The Cd transport activities of Nramp5 proteins were tested in yeast. Under hydroponic conditions, Cd uptake in rice was 2.5–8.1 and 1.1–3.6 times that of wheat and maize, respectively. The maximum Cd influx velocity of rice was 6.5 and 2.2 times that in wheat and maize, respectively. Wheat showed the lowest Cd uptake but the highest Cd root-to-shoot translocation. The absolute expression level of OsNramp5 in rice roots was 4–5 times that of TaNramp5A and TaNramp5D in wheat or ZmNramp5 in maize. All Nramp5 proteins were localized to the plasma membrane. When expressed in yeast, OsNramp5 showed a greater Cd transport activity than wheat or maize Nramp5. Rice has a greater Cd uptake ability than wheat or maize, likely because OsNramp5 is more highly expressed and the protein has a higher Cd transport activity than wheat or maize Nramp5.

Bacterial endophytes from rice cut grass (Leersia oryzoides L.) increase growth, promote root gravitropic response, stimulate root hair formation, and protect rice seedlings from disease

Abstract: Leersia oryzoides, a wild relative of rice (Oryza sativa), may carry potential seed-borne bacterial endophytes which could be used to enhance growth of rice. We hypothesized that seed-associated bacteria from L. oryzoides would be compatible with rice and promote seedling growth, development, and survival. We isolated bacteria from seed of L. oryzoides and checked compatibility with rice as well as Bermuda grass seeds for seedling growth promotion. Internal colonisation of bacteria into root cells was observed by ROS staining and microscopic observation. Growth promoting bacteria were evaluated for IAA production, phosphate solubilization and antifungal activities. Overall, ten bacteria were found to be growth promoting in rice seedlings with effects including restoration of root gravitropic response, increased root and shoot growth, and stimulation of root hair formation. All bacteria were identified by 16S rDNA sequencing. Six bacteria were found to become intracellular in root parenchyma and root hairs in rice and in Bermuda grass seedlings. Six bacteria were able to produce IAA in LB broth with highest (47.06 ± 1.99 μg ml−1) by LTE3 (Pantoea hericii). Nine isolates solubilized phosphate and inhibited at least one soil borne fungal pathogen. Seed bacteria of L. oryzoides are compatible with rice. Many of these bacteria become intracellular, induce root gravitropic response, increase root and shoot growth, and stimulate root hair formation in both rice and Bermuda grass seedlings. Presence of bacteria protects seedlings from soil pathogens during seedling establishment. This research suggests that bioprospecting microbes on near relatives of rice and other crop plants may be a viable strategy to obtain microbes to improve cultivation of crops.

Biocrusts: the living skin of the earth

Abstract: Biological soil crusts (biocrusts) form a Bliving skin^ at the soil surface in many low-productivity ecosystems around the world including waterand cold-limited environments, and early-successional seres (Belnap et al. 2003). They may be composed of any configuration of soil surfacedwelling cyanobacteria, eukaryotic algae, lichens, mosses or liverworts, and support assemblages of decomposers and a faunal food web (Belnap et al. 2003). These soil surface communities have global relevance, as it has been recently estimated that they cover about 12% of the terrestrial surface currently (Rodríguez-Caballero et al. 2018). Biocrust communities are perhaps an ideal subject for the journal Plant and Soil, as they are simultaneously plantlike, due to their dominance by photoautotrophs, yet biocrusts are also clearly a physical feature of the soil given that component organisms are enmeshed in, adherent to, or otherwise in direct contact with the soil surface. The activity of the organisms is what engineers the wellaggregated thin layer at the soil surface that we recognize as a biocrust (Belnap et al. 2003). The contributions of biocrusts to ecosystem function has fueled much research interest, initially based on the observation of biocrusts’ soil aggregating and erosion-resisting nature. More recently biocrusts have been identified as a multifunctional, globally-relevant ecosystem element instrumental in: 1. building or otherwise altering soil nutrient stocks through N-fixation (Elbert et al. 2012), dust trapping (Reynolds et al. 2001) and nutrient cycling (Strauss et al. 2012), 2. influencing hydrological properties of soil such as the water balance (Chamizo et al. 2016), and 3. the thermal energy balance of the ecosystem (Coradeau et al. 2016; Rutherford et al. 2017). Biocrust science was sparse before the 1970s, as evidenced by few publications and little recognition of the concept; however, a series of key events in the biocrust research community has brought biocrusts from a niche interest into the mainstream. First, the initial publication in 2001 of an edited volume (Belnap and Lange 2003) served to bring together disparate threads floristic, biogeographical, physiological, functional, applied of biocrust research through an ecological lens. One effect of this publication was to demonstrate that biocrusts were a global phenomenon, and hasten the internationalization of the field from a handful of Plant Soil https://doi.org/10.1007/s11104-018-3735-1

Soil aggregate stability in Mediterranean and tropical agro-ecosystems: effect of plant roots and soil characteristics

Abstract: Our aim was to determine the effect of soil characteristics and root traits on soil aggregate stability at an inter- and intra-site scale in a range of agro-ecosystems. We also evaluated the effect of soil depth and the type of land use on aggregate stability. Soil aggregate stability, soil physicochemical properties and fine root traits were measured along land use gradients (from monocultures to agroforestry systems and forests), at two soil depths at four sites (Mediterranean and tropical climates) with contrasting soils (Andosol, Ferralsol, Leptosol and Fluvisol). Aggregate stability was much lower in deep than in surface soil layers, likely linked to lower soil organic carbon (SOC) and lower root mass density (RMD). Locally, and consistently in all sites, land use intensification degrades soil aggregate stability, mainly in surface soil layers. Soil organic carbon, cation exchange capacity and root traits: water-soluble compounds, lignin and medium root length proportion were the most important drivers of aggregate stability at the inter-site level, whereas SOC, root mass and root length densities (RMD, RLD) were the main drivers at the intra-site level. Overall, the data suggest different controls on soil aggregate stability globally (soil) and locally (roots). Conversion from forests to agricultural land will likely lead to greater C losses through a loss of aggregate stability and increased soil erosion.

Direct effects of soil organic matter on productivity mirror those observed with organic amendments

Abstract: Organic amendments to arable soil build soil organic matter (SOM), which can increase crop yields. However, organic amendments can influence crop yields independently of SOM by providing nutrients directly to plants. The relative importance of native organic matter versus organic amendments is not well quantified. We experimentally manipulated both organic amendments and native SOM concentrations to quantify their relative importance to crop yields. We created OM concentration gradients by (1) diluting an organic-rich A-horizon with a mineral base and (2) amending compost to the same mineral base, generating OM concentrations for both treatments of approximately 2, 4 and 8%. We grew buckwheat and measured plant productivity and a range of soil fertility variables. Higher concentrations of OM, whether native or amended, were associated with higher soil water holding capacity and nutrients, and improved soil structure. Consequently, increases in both native and amended OM were associated with strong positive but saturating impacts on productivity, though amendment effects were greater. Our results suggest that native SOM can support productivity levels comparable to those observed with organic amendments. Although our quantitative findings will likely vary for different soils and amendments, our results lend support to the idea that SOM stocks directly increase productivity.

Disease protection and allelopathic interactions of seed-transmitted endophytic pseudomonads of invasive reed grass ( Phragmites australis )

Abstract: Non-native Phragmites australis (haplotype M) is an invasive grass that decreases biodiversity and produces dense stands. We hypothesized that seeds of Phragmites carry microbes that improve seedling growth, defend against pathogens and maximize capacity of seedlings to compete with other plants. We isolated bacteria from seeds of Phragmites, then evaluated representatives for their capacities to become intracellular in root cells, and their effects on: 1.) germination rates and seedling growth, 2.) susceptibility to damping-off disease, and 3.) mortality and growth of competitor plant seedlings (dandelion (Taraxacum officionale F. H. Wigg) and curly dock (Rumex crispus L.)). Ten strains (of 23 total) were identified and characterized; seven were identified as Pseudomonas spp. Strains Sandy LB4 (Pseudomonas fluorescens) and West 9 (Pseudomonas sp.) entered root meristems and became intracellular. These bacteria improved seed germination in Phragmites and increased seedling root branching in Poa annua. They increased plant growth and protected plants from damping off disease. Sandy LB4 increased mortality and reduced growth rates in seedlings of dandelion and curly dock. Phragmites plants associate with endophytes to increase growth and disease resistance, and release bacteria into the soil to create an environment that is favorable to their seedlings and less favorable to competitor plants.

Frontiers in root ecology: recent advances and future challenges

Abstract: Roots play a pivotal role in defining plant ecological success and mediating terrestrial ecosystem functioning. However, roots are difficult to study as they are hidden in the soil matrix and express a plurality of forms and functions: nutrient acquisition, anchorage, nutrient and water transport. In this special issue, we gather 20 articles from emerging topics in root ecology. We specifically focus on five frontiers that are essential to better capture plant, soil and ecosystem processes: (1) root structure and soil resource acquisition; (2) root dynamics; (3) root-root interactions; (4) root-microbe interactions and (5) the effects of roots on soil properties. For each of these sections we provide an overview of our current knowledge, highlight the contributions of this special issue, and pinpoint key remaining challenges for future work. Root resource acquisition, root dynamics, root-root and root-microbes interaction and the relative importance of root vs. soil properties on soil aggregation were shown to vary among biomes, soil and climate conditions. Such variability gives a complex but realistic picture of root functioning in real ecosystems and lays an important foundation for future work identify broad patterns of root functioning.

Abiotic and biotic factors affecting crop seed germination and seedling emergence: a conceptual framework

Abstract: Global agriculture is undergoing a phase of agroecological transition This transition will be characterized by adoption of agroecological cropping practices and by an increased diversity of soil management/tillage practices However, very little is known as to whether or not crop seed germination and seedling emergence (hereafter referred to as SGE) will be affected under these cropping practices This paper first proposes a conceptual scheme which integrates key abiotic and biotic factors affecting crop SGE Subsequently, the key mechanistic factors affecting SGE (ie intrinsic factors related to the seeds, and extrinsic factors related to the biotic and abiotic conditions of the seedbed), and how crop management practices can influence SGE through alterations of these direct mechanistic factors are discussed This is done with special emphasis on how agricultural practices, particularly those related to agro-ecology, may impact SGE Crop SGE are affected by five major groups of drivers, namely seed and seedling characteristics, seedbed physical components, seedbed chemical components, seedbed biological components, and cropping systems Although the crop SGE failure frequently occurs under field conditions, very little quantitative information is available in the literature on the real economic impact, the precise cause/s and ranking of factors associated with this failure Re-seeding is often practiced for a number of crops to compensate the lack of SGE with significant direct and indirect costs for farmers Little information exists in the literature concerning how SGE will be affected under agroecological cropping systems, such as conservation agriculture, or organic farming, or under climate-driven changes Field observation, experimental and modeling studies are needed to fill the current knowledge gaps on the economic impact, precise cause/s and ranking of different stress factors associated with SGE failure

Bacterial rather than fungal community composition is associated with microbial activities and nutrient-use efficiencies in a paddy soil with short-term organic amendments

Abstract: Considering the global demands in sustaining agriculture, use of organic amendments is gradually increasing. An improved understanding of the biological process is essential to evaluate the performance of organic amendments on agro-ecosystem. Soils subjected to different fertilization regimes were collected from a field experiment. Microbial community compositions are assessed with 16S and ITS rRNA gene sequencing and subsequent bioinformatics analysis. Microbial functions are characterized with the geometric mean of the assayed enzyme activities (GMea) and the microbial carbon-use efficiency:nitrogen-use efficiency ratio (CUE:NUE). Compared with the chemically fertilized soil, the GMea significantly increased in organically amended soils. In contrast, the CUE:NUE was highest in chemically treated soil. These changes of microbial functional indicators were associated with shifts in the bacterial and not the fungal community composition, despite the fact that both the bacterial and fungal community compositions were significantly affected by the fertilization regimes. The abundances of specific soil bacterial taxa, especially the genera Luteimonas and Gemmatimona, were enriched by organic amendments. Soil organic carbon emerged as the major determinant of the bacterial community composition. Soil microbial activities and nutrient-use efficiencies were dramatically changed along with the alteration of bacterial community composition. Relatively greater abundance of Luteimonas and Gemmatimona taxa in soils might be useful indicators for soil amelioration. Our research could be helpful to provide better strategies for the maintenance of soil fertility.

Assembly of seed-associated microbial communities within and across successive plant generations

Abstract: Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations. Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model. Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota. These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.

Ground penetrating radar (GPR) detects fine roots of agricultural crops in the field

Abstract: Ground penetrating radar (GPR) as a non-invasive technique is widely used in coarse root detection. However, the applicability of the technique to detect fine roots of agricultural crops is unknown. The objective of this study was to assess the feasibility of utilizing GPR to detect fine roots in the field. This study was conducted in four locations with different soil types and soil moisture conditions in Texas. Several varieties of winter wheat and energy cane were scanned with GPR (1600 MHz). Soil cores were collected immediately after scanning to measure root parameters. Using an image analysis software, four pixel indices with or without intensity threshold were used to assess the relationships between GPR signal and root parameters. There were significant relations between GPR indices and root parameters depending on soil conditions. The accuracy of root estimation was higher in wet clay soils than in dry sandy soils. Estimated root parameters from GPR had lower variation than measured roots. Average GPR pixel intensity without intensity threshold may be better to reflect root information than pixel indices with intensity threshold. This study demonstrates that GPR has the potential to predict bulk root biomass and diameter in winter wheat and energy cane.

Response of soil microbial community dynamics to Robinia pseudoacacia L. afforestation in the loess plateau: a chronosequence approach

Abstract: The objective was to analyze soil microbial community dynamics and their responses to changes in vegetation and soil properties after Robinia pseudoacacia afforestation along a chronosequence. We investigated changes in vegetation communities, soil properties and soil microbial communities 5, 15, 25, and 35 years (Y) after R. pseudoacacia afforestation on cropland on the Loess Plateau. Soil microbial community compositions were analyzed using 16S rRNA and ITS high-throughput gene sequencing. The diversity and richness of understory vegetation community decreased with restoration stage, and available phosphorus and ammonium contents in soil were consistently low. The bacterial communities converted from Acidobacteria- to Proteobacteria-dominant communities within 25-Y but transitioned again to Acidobacteria-dominant communities at the 35-Y sites. Ascomycota and Zygomycota were the dominant fungal phyla at all sites. Compared to the cropland, fungal community composition changed at the 5-Y sites and the bacterial community composition changed at the 25-Y sites. R. pseudoacacia afforestation significantly altered soil bacteria richness rather than its diversity. The planted R. pseudoacacia rapidly altered the soil fungal community composition and altered bacterial community composition at the 25-Y. The changes in soil bacterial communities were driven by the phyla of Actinobacteria, Gemmatimonadetes and Nitrospirae and lagged behind the changes in vegetation communities. Phosphorus was a principal factor in shaping microbial community composition.

Nickel hyperaccumulation mechanisms: a review on the current state of knowledge

Abstract: Hyperaccumulator plants are unusual plants that accumulate particular metals or metalloids, such as nickel, zinc, cadmium and arsenic, in their living tissues to concentrations that are hundreds to thousands of times greater than what is normal for most plants. The hyperaccumulation phenomenon is rare (exhibited by less than 0.2% of all angiosperms), with most of the ~500 hyperaccumulator species known globally for nickel. This review highlights the contemporary understanding of nickel hyperaccumulation processes, which include root uptake and sequestration, xylem loading and transport, leaf compartmentation and phloem translocation processes. Hyperaccumulator plants have evolved highly efficient physiological mechanisms for taking up nickel in their roots followed by rapid translocation and sequestration into the aerial shoots. The uptake of nickel is mainly involved with low affinity transport systems, presumably from the ZIP family. The presence of high concentrations of histidine prevents nickel sequestration in roots. Nickel is efficiently loaded into the xylem, where it mainly presents as Ni2+. The leaf is the main storage organ, which sequestrates nickel in non-active sites, e.g. vacuoles and apoplast. Recent studies show that phloem translocates high levels of nickel, which has a strong impact on nickel accumulation in young growing tissues.

Biocrusts enhance soil fertility and Bromus tectorum growth, and interact with warming to influence germination

Abstract: Biocrusts are communities of cyanobacteria, mosses, and/or lichens found in drylands worldwide. Biocrusts are proposed to enhance soil fertility and productivity, but simultaneously act as a barrier to the invasive grass, Bromus tectorum, in western North America. Both biocrusts and B. tectorum are sensitive to climate change drivers, yet how their responses might interact to affect dryland ecosystems is unclear. Using mesocosms with bare soil versus biocrust cover, we germinated B. tectorum seeds collected from warmed, warmed + watered, and ambient temperature plots within a long-term climate change experiment on the Colorado Plateau, USA. We characterized biocrust influences on soil fertility and grass germination, morphology, and chemistry. Biocrusts increased soil fertility and B. tectorum biomass, specific leaf area (SLA), and root:shoot ratios. Germination rates were unaffected by mesocosm cover-type. Biocrusts delayed germination timing while also interacting with the warmed treatment to advance, and with the warmed + watered treatment to delay germination. Biocrusts promoted B. tectorum growth, likely through positive influence on soil fertility which was elevated in biocrust mesocosms, and interacted with seed treatment-provenance to affect germination. Understanding how anticipated losses of biocrusts will affect invasion dynamics will require further investigation of how plant plasticity/adaptation to specific climate drivers interact with soil and biocrust properties.

Fungal endophytes from seeds of invasive, non-native Phragmites australis and their potential role in germination and seedling growth

Abstract: We characterized fungal endophytes of seeds of invasive, non-native Phragmites from three sites in the Great Lakes region to determine if fungal symbiosis could contribute to invasiveness through their effects on seed germination and seedling growth. Field-collected seeds were surface sterilized and plated on agar to culture endophytes for ITS sequencing. Prevalence of specific endophytes from germinated and non-germinated seeds, and from seedlings, was compared. One-third of 740 seeds yielded endophyte isolates. Fifteen taxa were identified with Alternaria sp. representing 54% of all isolates followed by Phoma sp. (21%) and Penicillium corylophilum (12%). Overall germination of seeds producing an isolate (36%) was significantly higher than seeds not producing an isolate (20%). Penicillium in particular was strongly associated with increased germination of seeds from one site. Sixty-three isolates and 11 taxa were also obtained from 30 seedlings where Phoma, Penicillium and Alternaria respectively were most prevalent. There was a significant effect of isolating an endophyte from the seed on seedling growth. These results suggest that many endophyte taxa are transmitted in seeds and can increase seed germination and seedling growth of invasive Phragmites. The role of fungal endophytes in host establishment, growth and invasiveness in nature requires further research.

Analyzing plant nutrient uptake and utilization efficiencies: comparison between crops and approaches

Abstract: Various indices are applied to evaluate the nutrient (mostly nitrogen, N) use efficiency of plants, but those indices have rarely been compared across different crops, and the co-limitation of growth by nutrients other than N is usually not considered. To conceptually and quantitatively compare the indices of a plant-level, a plant-soil-level and a field-level (difference) method for the assessment of N use across a set of different annual and perennial crops; and to use some plant-level indices for exploring the co-limitation of growth by nutrients other than N in wheat. Data sets from previously published studies on wheat (grain), maize (feed), potato (starch), grassland ley (feed) and Salix (bio-energy) field-grown in Sweden were re-analyzed. This study is first in conceptually and quantitatively comparing various popular N use indices across a wide range of annual and perennial crops; and also proposes a methodology for exploring the co-limitation of growth by nutrients other than N. When comparing the plant-level and plant-soil-level methods, the indices relating crop yields to the amounts of plant-internal N were correlated, while the N-uptake indices were not. Only few of the field-level (difference-method) indices were correlated with indices of the two other methods.

Continuous application of different organic additives can suppress tomato disease by inducing the healthy rhizospheric microbiota through alterations to the bulk soil microflora

Abstract: Bio-organic fertilizer and different additives are widely applied to suppress soil-borne diseases. However, how different additives alter bulk soil microflora and thereby induce the healthy rhizospheric microflora remains unclear. A 3-season field experiment containing four fertilization management programs (chemical fertilizer, organic fertilizer, amino acid organic fertilizer, and bio-organic fertilizer was conducted in a tomato production agroecosystem with high disease incidence to evaluate the induced efficacy. The bacterial and fungal microflora of bulk and rhizosphere soil influenced by different management programs were performed on the Illumina MiSeq platform. Principal coordinate analysis based on the Bray-Curtis distance metric was performed to compare the similarities and differences of the bacterial and fungal community compositions among all soil samples. Soil amended with organic fertilizer, amino acid organic fertilizer, and bio-organic fertilizer progressively and significantly suppressed tomato diseases in comparison with chemical fertilizer, and bio-organic fertilizer presented the best efficacy in all seasons. Interestingly, rhizospheric and bulk soil bacterial and fungal communities of the different fertilization management programs were separated from each other. Six bacterial and 10 fungal rhizospheric genera positively correlated with the same genera observed in bulk soil showing significant relationships with tomato disease incidence were observed, and functional strain SQR9 can be detected in the bulk and rhizosphere soils of bio-organic fertilizer treatments. Additionally, the redundancy analysis results showed the genera in treated chemical fertilizer bulk soil were dominated by Ralstonia and Fusarium, the abundances of which were highest and lowest in treated chemical fertilizer and bio-organic fertilizer rhizosphere, respectively. This study provided insights into soil-borne disease suppression by bulk soil management and confirmed that alterations to the bulk soil microbiota by different organic additives played distinct roles in the formation of rhizospheric soil microflora for the suppression of disease.

Community structure and diversity of endophytic bacteria in seeds of three consecutive generations of Crotalaria pumila growing on metal mine residues

Abstract: We investigated the possible transgenerational transfer of bacterial seed endophytes across three consecutive seed generations of Crotalaria pumila growing on a metal mining site in Mexico. Seeds were collected during three successive years in the semi-arid region of Zimapan, Mexico. Total communities of seed endophytes were investigated using DNA extraction from surface sterilized seeds and 454 pyrosequencing of the V5-V7 hypervariable regions of the 16S rRNA gene. The communities consisted of an average of 75 operational taxonomic units (OTUs); richness and diversity did not change across years. Methylobacterium, Staphylococcus, Corynebacterium, Propionibacterium and eight other OTUs constituted >60% of the community in each generation. The microbiome was dominated by Methylobacterium (present in >80% of samples). Functions associated with the microbiome were C and N fixation, oxidative phosphorylation and photosynthesis activity. The bacterial endophytic communities were similar across three consecutive seed generations. Among the core microbiome Methylobacterium strains were the most abundant and they can contribute to nutrient acquisition, plant growth promotion and stress resilience to their host in metal contaminated mine residues. Identification of the seed microbiome of C. pumila may lead to novel and more efficient inoculants for microbe-assisted phytoremediation.

Silicon accumulated in the shoots results in down-regulation of phosphorus transporter gene expression and decrease of phosphorus uptake in rice

Abstract: Silicon (Si) as a beneficial element can improve nutrient imbalance, but the molecular mechanism for this effect is poorly understood. The objective of this study is to examine the mechanism underlying Si-induced decrease of phosphorus (P) uptake in rice (Oryza sativa) at adequate/high P supply. A rice mutant (lsi1) defective in Si uptake and its wild type (cv. Oochikara) were used. The P uptake was compared in the presence and absence of Si and the expression of Pi transporter genes was quantified. Si addition in the nutrient solution significantly decreased shoot P concentration and uptake in the WT, but not in lsi1 mutant at two P levels, adequate (90 μM) and high (210 μM). Neither the root-to-shoot translocation of P nor the P distribution in different organs was altered by Si in both WT and lsi1. Heterogeneous expression of Lsi1 in Xenopus oocyte did not show transport activity for Pi. The expression of Pi transporter genes (OsPT1, 2 and 8) in the roots was hardly affected by Si in both WT and lsi1, but that of OsPT6 was down-regulated by Si in the WT roots, but not in the lsi1 roots. Furthermore, a split root experiment showed that Si accumulated in the shoots suppressed the expression of OsPT6. In rice grown in paddy field, lsi1 showed higher P concentration in the straw, husk and brown rice than the WT. Si decreased P uptake through down-regulating the expression of P transporter gene, OsPT6 in rice and Si accumulated in the shoot is required for this down-regulation.

Maximizing establishment and survivorship of field-collected and greenhouse-cultivated biocrusts in a semi-cold desert

Abstract: Biological soil crusts (biocrusts) are soil-surface communities in drylands, dominated by cyanobacteria, mosses, and lichens. They provide key ecosystem functions by increasing soil stability and influencing soil hydrologic, nutrient, and carbon cycles. Because of this, methods to reestablish biocrusts in damaged drylands are needed. Here we test the reintroduction of field-collected vs. greenhouse-cultured biocrusts for rehabilitation. We collected biocrusts for 1) direct reapplication, and 2) artificial cultivation under varying hydration regimes. We added field-collected and cultivated biocrusts (with and without hardening treatments) to bare field plots and monitored establishment. Both field-collected and cultivated cyanobacteria increased cover dramatically during the experimental period. Cultivated biocrusts established more rapidly than field-collected biocrusts, attaining ~82% cover in only one year, but addition of field-collected biocrusts led to higher species richness, biomass (as assessed by chlorophyll a) and level of development. Mosses and lichens did not establish well in either case, but late successional cover was affected by hardening and culture conditions. This study provides further evidence that it is possible to culture biocrust components from later successional materials and reestablish cultured organisms in the field. However, more research is needed into effective reclamation techniques.