Selection and Characterization of Burkholderia spp. for Their Plant-Growth Promoting Effects and Influence on Maize Seed Germination

Burkholderia sp. is a bacterial genus extremely versatile in the environment and has been reported for a great potential to promote plant growth via different mechanisms. Here we evaluate the plant growth-promoting mechanisms in twenty-six Burkholderia strains. Strains were evaluated for their ability to promote plant growth by means of: indole-3-acetic acid (IAA) production under different conditions of pH, salt stress and the presence or absence of L-tryptophan; exopolysaccharides (EPS) production and quorum sensing (ALH). The strains were also characterized in terms of their genetic variability and species identification through Sanger sequencing. Then, the bacteria most responsive in the greatest number of plant-growth promotion mechanisms were selected for a corn seed germination test. All bacteria synthesized IAA in medium with 0.0 or 5.0 mM of L-tryptophan in combination with either 1 or 5% of NaCl, and pH values of either 4.5 or 7.2. The EPS production was confirmed for 61.54% of the bacterial strains. Quorum sensing also occurred in 92.3% of the selected bacteria. The Jaccard similarity coefficient revealed 16 clusters with high genetic variability between bacterial strains. Bacterial strains were assigned to seven species: B. anthina, B. cepacia, B. gladioli, B. ambifaria, B. graminis, B. heleia, and Burkholderia spp. The corn seed bacterization did not affect the germination velocity index (GSI), as well as the first count of germinated seeds (FC). However, inoculations formulated with B. heleia strain G28, B. gladioli strain UAGC723, and B. graminis strain UAGC348 promoted significant increases in root length, seedling height and fresh and dry seedling phytomass, respectively. These results indicate the high biotechnological potential of several strains in the genus Burkholderia sp. as seed inoculants, favoring germination and seedling initial development.

Cross Talk Between Zinc-Solubilizing Bacteria and Plants: A Short Tale of Bacterial-Assisted Zinc Biofortification

A contemporary approach to bacterially mediated zinc (Zn) biofortification offers a new dimension in the crop improvement program with better Zn uptake in plants to curb Zn malnutrition. The implication of Zn solubilizing bacteria (ZSB) represents an inexpensive and optional strategy for Zn biofortification, with an ultimate green solution to enlivening sustainable agriculture. ZSB dwelling in the rhizospheric hub or internal plant tissues shows their competence to solubilize Zn via a variety of strategies. The admirable method is the deposition of organic acids (OAs), which acidify the surrounding soil environment. The secretion of siderophores as a metal chelating molecule, chelating ligands, and the manifestation of an oxidative–reductive system on the bacterial cell membrane are further tactics of bacterially mediated Zn solubilization. The inoculation of plants with ZSB is probably a more effective tactic for enhanced Zn translocation in various comestible plant parts. ZSB with plant growth-enhancing properties can be used as bioelicitors for sustainable plant growth via the different approaches that are crucial for plant health and its productivity. This article provides an overview of the functional properties of ZSB-mediated Zn localization in the edible portions of food crops and provides an impetus to explore such plant probiotics as natural biofortification agents.

Appropriate Use of Local Phosphate Rock Increases Phosphorus Use Efficiency and Grain Yield of Sorghum and Cowpea in the Sudan Savanna

Development of local P fertilizers using low-grade phosphate rock (PR) is expected to overcome the low-stagnated crop yield in Sub-Saharan Africa. Calcination and partial acidulation methods have been proposed to increase the phosphate (P) solubility of PRs. However, the effects of fertilization with calcinated PR (CPR) and partially acidulated PR (PAPR) on sorghum [Sorghum bicolor (L.)] and cowpea [Vigna unguiculata (L.) Walp.] cultivation are poorly understood. Therefore, we conducted a 2-year field experiment in Burkina Faso to identify the differences in sorghum and cowpea responses to CPR and PAPR application. The following eight treatments were applied with six replicates using a complete randomized block design: control without P fertilization, two types of CP (CPs), triple superphosphate (TSP) as a positive control for CPs, three types of PAPR with different degrees of acidulation (PAPRs), and single superphosphate (SSP) as a positive control for PAPRs. SSP mostly comprised of water-soluble P fraction (WP), TSP and PAPRs of WP and alkaline ammonium citrate-soluble P fraction (SP), and CPRs of SP and 2% citric acid-soluble P fraction (CP). Their solubility was in the order WP > SP > CP. The fertilization effects were evaluated by P use efficiency (PUE). In 2019, the biomass and P uptake of sorghum was decreased by the low available soil water at the early growth stage. On the contrary, cowpea survived the low available soil water because of its shorter growing period compared to sorghum. P fertilization significantly increased the grain yields. However, the effect size differed according to the crop and fertilizer types. The SP, along with WP, significantly contributed to the PUE and grain yield of sorghum, whereas only WP contributed to the PUE of cowpea. Therefore, CPs, mainly consisting of SP and CP, had a disadvantage compared to TSP, especially for cowpea. We thus concluded that PAPRs are effective for sorghum and would be effective for cowpea when the acidulation level is sufficiently high. We also conclude that the long growing period of sorghum is favorable for absorbing slow-release P, but is unfavorable for the variable rainfall often observed in this region.

Topsoil Texture Regionalization for Agricultural Soils in Germany—An Iterative Approach to Advance Model Interpretation

Site-specific spatially continuous soil texture data is required for many purposes such as the simulation of carbon dynamics, the estimation of drought impact on agriculture, or the modeling of water erosion rates. At large scales, there are often only conventional polygon-based soil texture maps, which are hardly reproducible, contain abrupt changes at polygon borders, and therefore are not suitable for most quantitative applications. Digital soil mapping methods can provide the required soil texture information in form of reproducible site-specific predictions with associated uncertainties. Machine learning models were trained in a nested cross-validation approach to predict the spatial distribution of the topsoil (0–30 cm) clay, silt, and sand contents in 100 m resolution. The differential evolution algorithm was applied to optimize the model parameters. High-quality nation-wide soil texture data of 2,991 soil profiles was obtained from the first German agricultural soil inventory. We tested an iterative approach by training models on predictor datasets of increasing size, which contained up to 50 variables. The best results were achieved when training the models on the complete predictor dataset. They explained about 59% of the variance in clay, 75% of the variance in silt, and 77% of the variance in sand content. The RMSE values ranged between approximately 8.2 wt.% (clay), 11.8 wt.% (silt), and 15.0 wt.% (sand). Due to their high performance, models were able to predict the spatial texture distribution. They captured the high importance of the soil forming factors parent material and relief. Our results demonstrate the high predictive power of machine learning in predicting soil texture at large scales. The iterative approach enhanced model interpretability. It revealed that the incorporated soil maps partly substituted the relief and parent material predictors. Overall, the spatially continuous soil texture predictions provide valuable input for many quantitative applications on agricultural topsoils in Germany.

Does the Introduction of N2-Fixing Trees in Forest Plantations on Tropical Soils Ameliorate Low Fertility and Enhance Carbon Sequestration via Interactions Between Biota and Nutrient Availability? Case Studies From Central Africa and South America

Plant and/or crop growth rely on nutrient dynamics driven by specific soil biota in different environments. This mini-review aims to provide an overview of interactions between soil organisms, nutrient dynamics, and C sequestration. To this end, we investigated published results from three forest plantations (eucalyptus monocultures and mixed plantations with N2-fixing acacia) on tropical nutrient-poor soils. One case study is located in Central Africa (Congolese coastal plains) and two others in South America (Southeastern Brazil). Overall, the studies showed that soil biota activity exerted positive effects on (i) C accretion, as both soil carbon and belowground and aboveground biomass are driven and enhanced by soil biota; and (ii) on nutrient dynamics and biogeochemical cycles in nutrient-poor soil of tropical ecosystems, which are boosted following C accumulation. On the other hand, the pedoclimatic environment may potentially impact soil functioning of mixed-species plantations through its influence on the composition and activity of bacterial communities. Regardless of the potential risk of acacia invasiveness, benefits such as pulp, fuelwood, electric pole and non-timber products supply, have been reported in Central Africa. We, therefore, conclude that including N2 fixing trees in forestry plantations as reported in this mini-review helps strengthen the links between soil biota, nutrient and SOC dynamics in mixed-species plantations on tropical nutrient-poor soils.

Microbial Signatures in Fertile Soils Under Long-Term N Management

Long-term reliance on inorganic N to maintain and increase crop yields in overly simplified cropping systems in the U.S. Midwest region has led to soil acidification, potentially damaging biological N2 fixation and accelerating potential nitrification activities. Building on this published work, rRNA gene-based analysis via Illumina technology with QIIME 2.0 processing was used to characterize the changes in microbial communities associated with such responses. Amplicon sequence variants (ASVs) for each archaeal, bacterial, and fungal taxa were classified using the Ribosomal Database Project (RDP). Our goal was to identify bioindicators from microbes responsive to crop rotation and N fertilization rates following 34–35 years since the initiation of experiments. Research plots were established in 1981 with treatments of rotation [continuous corn (Zea mays L.) (CCC) and both the corn (Cs) and soybean (Glycine max L. Merr.) (Sc) phases of a corn-soybean rotation], and of N fertilization rates (0, 202, and 269 kg N/ha) arranged as a split-plot in a randomized complete block design with three replications. We identified a set of three archaea, and six fungal genera responding mainly to rotation; a set of three bacteria genera whose abundances were linked to N rates; and a set with the highest number of indicator genera from both bacteria (22) and fungal (12) taxa responded to N fertilizer additions only within the CCC system. Indicators associated with the N cycle were identified from each archaeal, bacterial, and fungal taxon, with a dominance of denitrifier- over nitrifier- groups. These were represented by a nitrifier archaeon Nitrososphaera, and Woesearchaeota AR15, an anaerobic denitrifier. These archaea were identified as part of the signature for CCC environments, decreasing in abundance with rotated management. The opposite response was recorded for the fungus Plectosphaerella, a potential N2O producer, less abundant under continuous corn. N fertilization in CCC or CS systems decreased the abundance of the bacteria genera Variovorax and Steroidobacter, whereas Gp22 and Nitrosospira only showed this response under CCC. In this latter system, N fertilization resulted in increased abundances of the bacterial denitrifiers Gp1, Denitratisoma, Dokdonella, and Thermomonas, along with the fungus Hypocrea, a known N2O producer. The identified signatures could help future monitoring and comparison across cropping systems as we move toward more sustainable management practices. At the same time, this is needed primary information to understand the potential for managing the soil community composition to reduce nutrient losses to the environment.

Dual Inoculation With Arbuscular Mycorrhizal Fungi and Phosphorus Solubilizing Fungi Synergistically Enhances the Mobilization and Plant Uptake of Phosphorus From Meat and Bone Meal

Phosphorus (P) is the second most important mineral nutrient for plant growth and plays a vital role in maintaining global food security. The natural phosphorus reserves [phosphate rock (PR)] are declining at an unprecedented rate, which will threaten the sustainable food supply in near future. Rendered animal byproducts such as meat and bone meal (MBM), could serve as a sustainable alternative to meet crop phosphorus demand. Even though nitrogen (N) from MBM is readily mineralized within a few days, >75% of the P in MBM is present as calcium phosphate that is sparingly available to plants. Thus, application of MBM with the aim of meeting crop N demand could result in buildup of P reserves in soil, which necessitates the need to improve the P mobilization from MBM to achieve higher plant P use efficiency. Here, we tested the potential of two microbial inoculum-arbuscular mycorrhizal fungi (AMF) and P solubilizing fungi (Penicillium bilaiae), in improving the mobilization of P from MBM and the subsequent P uptake by maize (Zea mays). Compared to the non-inoculated MBM control, the application of P. bilaiae increased the P mobilization from MBM by more than two-fold and decreased the content of calcium bound P in the soil by 26%. However, despite this mobilization, P. bilaiae did not increase the tissue content of P in maize. On the other hand, AMF inoculation with MBM increased the plant root, shoot biomass, and plant P uptake as compared to non-inoculated control, but did not decrease the calcium bound P fraction of the soil, indicating there was limited P mobilization. The simultaneous application of both AMF and P. bilaiae in association with MBM resulted in the highest tissue P uptake of maize with a concomitant decrease in the calcium bound P in the soil, indicating the complementary functional traits of AMF and P. bilaiae in plant P nutrition from MBM. Arbuscular mycorrhizal fungi inoculation with MBM also increased the plant photosynthesis rate (27%) and root phosphomonoesterase activity (40%), which signifies the AMF associated regulation of plant physiology. Collectively, our results demonstrate that P mobilization and uptake efficiency from MBM could be improved with the combined use of arbuscular mycorrhizal fungi and P. bilaiae.

Combined Use of Vinasse and Nitrogen as Fertilizers Affects Nitrification, Ammonification, and Denitrification by Prokaryotes

A common agricultural practice of combining organic fertilizer vinasse (a liquid residue from sugarcane ethanol production) with mineral nitrogen (N) fertilizer promotes N losses such as greenhouse gas emissions due to the effects of physicochemical changes in soil on the microbiota inhabiting this environment. In this study, we applied microarray GeoChip v.5.0M technology to obtain a better insight into the prokaryotic communities and identify and quantify the N functional gene families associated with the N processes in sugarcane soils without N fertilizer (N0), with urea at 60 kg ha−1 (N60), and with vinasse combined with urea (NV). Soil samples were collected at 7 (T7) and 150 (T150) days after N application, corresponding to maximum and minimum nitrous oxide (N2O) emissions, respectively, for molecular and physicochemical analysis. Additionally, the metagenomes of these DNA samples, previously deposited in the MG-RAST server, were accessed to investigate the functions and taxonomic groups associated with selected gene families. The results revealed that 87% of the select gene families were significantly responsive to the fertilizer combined treatment (NV) in the 7 days after the application. The most responsive genes and processes were nitrification [with the amoA gene from ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) and hao from Bacteria], ammonification (with gdh and ureC genes from Bacteria and Archaea), and denitrification (with p450nor from Eukarya). The AOA, Nitrosopumilus, and AOB, Nitrosomonas, were the groups with the greatest functions associated with nitrification, as well as a pathogenic Mycobacterium, with denitrification. The results also revealed that under N fertilizers and decreased O2 in soil, the increases in K and P nutrients can promote the growth of the halophile Archaea Natronomonas and the Bacteria Anaeromyxobacter, which can reduce N2O. In conclusion, this typical agricultural fertilization management may favor functional genes and archaeal and bacterial groups associated with N processes that have the potential to reduce environmental damage in tropical sugarcane soils.

Spatiotemporal Variation Characteristics and Driving Factors of Nitrogen Use Efficiency of Wheat–Rice Rotation Systems in the Taihu Lake Region

During the past three decades, a large amount of nitrogen (N) fertilizers has been applied in the rice and wheat rotation system in the Taihu Lake region of southern China to achieve high yield, resulting in low N use efficiency (NUE). China is implementing the national strategy “fertilizer reduction with efficiency increase” to solve the serious ecological problems caused by excessive fertilization. However, the effects of N fertilizer reduction on soil fertility and their integrated effect on NUE of rice–wheat rotation systems in the Taihu Lake region are not fully understood. In this study, test fields with different soil-fertility qualities were selected in typical rice–wheat areas in the Taihu Lake region to perform a 2-year rice–wheat N fertilizer effect test to obtain the comprehensive quantitative relationship among the integrated fertility index (IFI), nitrogen application level (NA), and NUE. Through the investigation and spatial analysis of NA and IFI in the study area in 2003 and 2017, the spatial and temporal variation characteristics of NA and IFI in the study area in the past 15-year period were obtained, and this information was spatially coupled with the comprehensive quantitative relationship model of NUE to reveal the variation characteristics and driving factors of NUE in the study area. The result shows that the wheat and rice NA in the study area in 2017 increased by 35.5 and 8.4%, respectively, compared with 2003. Due to excessive fertilization, the soil nitrogen, phosphorus, and potassium content of cultivated land in the study area in 2017 was greater than that in 2003, especially soil-available phosphorus and potassium contents, whereas soil organic matter (SOM) content was reduced. The cultivated land IFI of the study area as a whole increased by 7.2% in the 15-year period. The NUE of rice and wheat rotation increased by 5.8% in 2017 compared with that of 2003 due to the improvement in crop varieties and N fertilizer yield benefits. The increases of NA and IFI both have negative correlations with the NUE improvement, and the NA increase has a greater impact. In addition, the terrain, soil type, texture, and parent material also affect the soil nutrient-preserving capability and, thus, affect the spatial variation of IFI and NUE improvement. These factors have greater influence on NUE improvement of wheat than rice. This study provides a novel and effective method for analyzing the spatial-temporal variation characteristics of NUE in the rice–wheat system and is conducive to guide precise fertilization and N fertilizer reduction based on the spatial analysis of NA with IFI and NUE.

Soil Phosphorus Exchange as Affected by Drying-Rewetting of Three Soils From a Hawaiian Climatic Gradient

Current understanding of phosphorus (P) dynamics is mostly based on experiments carried out under steady-state conditions. However, drying-rewetting is an inherent feature of soil behavior, and as such also impacts P cycling. While several studies have looked at net changes in P pool sizes with drying-rewetting, few studies have dynamically tracked P exchange using isotopes, which would give insights on P mean residence times in a given pool, and thus P availability. Here, we subjected three soils from a climatic gradient on the Kohala peninsula from Hawaii to 5-month drying-rewetting treatments. The hypotheses were that physico-chemical and biotic processes would be differently affected by repeated drying-rewetting cycles, and that response would depend on climatic history of the soils. Soils were labeled with 33P and 18O enriched water. At select time intervals, we carried out a sequential extraction and measured P concentration, 33P recovery (only first 3 months), and incorporation of 18O from water into phosphate. This allowed tracing P dynamics in sequentially extracted pools as well as O dynamics in phosphate, which are driven by biological processes. Results showed that P concentration and 33P recovery were predominantly driven by soil type. However, across all soils we observed faster dilution of 33P from resin-P into less mobile inorganic pools under drying-rewetting. On the other hand, O dynamics in phosphate were mostly governed by drying-rewetting treatment. Under drying-rewetting, considerably less O was incorporated from water into phosphate of resin-P, microbial-P and HCl-P, suggesting that drying-rewetting reduced biological P cycling. Hence, our results suggest that repeated drying-rewetting increases inorganic P exchange while reducing biological P cycling due to reduced microbial activity, independent of climatic history of the soils. This needs to be considered in P management in ecosystems as well as model representations of the terrestrial P cycle.