Phosphate-Solubilizing Bacteria Nullify the Antagonistic Effect of Soil Calcification on Bioavailability of Phosphorus in Alkaline Soils

Cultural techniques capture diverse phosphate-solubilizing bacteria in rock phosphate-enriched habitats

Phosphorus (P) deficiency is a common problem in croplands where phosphate-based fertilizers are regularly used to maintain bioavailable P for plants. However, due to their limited mobility in the soil, there has been an increased interest in microorganisms that can convert insoluble P into a bioavailable form, and their use to develop phosphate-solubilizing bioinoculants as an alternative to the conventional use of P fertilizers. In this study, we proposed two independent experiments and explored two entirely different habitats to trap phosphate-solubilizing bacteria (PSBs). In the first experiment, PSBs were isolated from the rhizoplane of native plant species grown in a rock-phosphate (RP) mining area. A subset of 24 bacterial isolates from 210 rhizoplane morphotypes was selected for the inorganic phosphate solubilizing activities using tricalcium phosphate (TCP) as the sole P source. In the second experiment, we proposed an innovative experimental setup to select mycohyphospheric bacteria associated to arbuscular mycorrhizal fungal hyphae, indigenous of soils where agronomic plant have been grown and trapped in membrane bag filled with RP. A subset of 25 bacterial isolates from 44 mycohyphospheric morphotypes was tested for P solubilizing activities. These two bacterial subsets were then screened for additional plant growth-promoting (PGP) traits, and 16S rDNA sequencing was performed for their identification. Overall, the two isolation experiments resulted in diverse phylogenetic affiliations of the PSB collection, showing only 4 genera (24%) and 5 species (17%) shared between the two communities, thus underlining the value of the two protocols, including the innovative mycohyphospheric isolate selection method, for selecting a greater biodiversity of cultivable PSB. All the rhizoplane and mycohyphospheric PSB were positive for ammonia production. Indol-3-acetic acid (IAA) production was observed for 13 and 20 isolates, respectively among rhizoplane and mycohyphospheric PSB, ranging, respectively, from 32.52 to 330.27 μg mL-1 and from 41.4 to 963.9 μg mL-1. Only five rhizoplane and 12 mycohyphospheric isolates were positively screened for N2 fixation. Four rhizoplane PSB were identified as siderophore producers, while none of the mycohyphospheric isolates were. The phenotype of one PSB rhizoplane isolate, assigned to Pseudomonas, showed four additive PGP activities. Some bacterial strains belonging to the dominant genera Bacillus and Pseudomonas could be considered potential candidates for further formulation of biofertilizer in order to develop bioinoculant consortia that promote plant P nutrition and growth in RP-enriched soils.

Chryseobacterium pyrolae sp. nov., isolated from the rhizosphere soil of Pyrola calliantha H

A novel Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated pc2-12T, was isolated from the rhizosphere soil of the herb Pyrola calliantha collected from arid areas of Tibet. The strain grew most vigorously with 1 % (w/v) NaCl, at pH 7.0 and at 25 °C. According to the results of 16S rRNA gene sequence analysis, pc2-12T was closely related to the members of the genus Chryseobacterium, with highest levels of sequence similarity to Chryseobacterium viscerum 687B-08T (98.42 %), Chryseobacterium oncorhynchi 701B-08T (98.11 %) and Chryseobacterium ureilyticum DSM 18017T (97.98 %). The average nucleotide identity values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 79.71, 79.49 and 79.26 %, respectively. The in silico DNA-DNA hybridisation values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 23.30, 23.00 and 22.90 %, respectively. The draft genome sequence of pc2-12T was 4.64 Mb long, with DNA G+C content of 37.0 mol%. The fatty acids contained in the cells of pc2-12T were mainly composed of iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipid was phosphatidylethanolamine. MK-6 was the sole respiratory quinone. On the basis of the results of analysis of all the data described, pc2-12T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium pyrolae sp. nov., is proposed. The type strain is pc2-12T (=GDMCC 1.3256T= JCM 35712T).

Application of Bacillus spp. Phosphate-Solubilizing Bacteria Improves Common Bean Production Compared to Conventional Fertilization

The use of phosphate-solubilizing bacteria (PSB) can be a sustainable strategy to increase phosphorus availability and promote satisfactory crop yields. The objective of this study was to evaluate whether inoculation with PSB in common bean increases (i) growth, (ii) nutrition, (iii) yield, and (iv) grain quality, and (v) reduces the chemical phosphorus application dose to obtain maximum yields. The experiment was conducted in an Oxisol using a randomized block design in a 4 × 4 factorial scheme, with four replicates, using the cultivar IAC 2051. The first factor was four doses of P2O5 (0, 20, 40 and 60 kg ha-1), and the second factor was four doses of PSB (0, 100, 200 and 300 mL ha-1). For leaf area and leaf chlorophyll content, the association of PSB inoculation with a P2O5 dose of 40 kg ha-1 promoted the best conditions for the common bean. P2O5 application increased yield by 79 kg ha-1 for each 10 kg ha-1 added. PSB inoculation at a dose of 192 mL ha-1 promoted P export of 15.3 kg ha-1, and the PSB dose of 159 mL ha-1 increased yield by 389 kg ha-1 (12%) compared to the control. Grain quality remained within the standards required by the consumer market, being little affected by the treatments. Improvements in common bean growth and nutritional and physiological status promoted by P2O5 application and PSB were essential in increasing yield, so these are sustainable production strategies.

Antagonistic and plant growth promotion of rhizobacteria against Phytophthora colocasiae in taro

Taro leaf blight caused by Phytophthora colocasiae adversely affects the growth and yield of taro. The management of this disease depends heavily on synthetic fungicides. These compounds, however, pose potential hazards to human health and the environment. The present study aimed to investigate an alternative approach for plant growth promotion and disease control by evaluating seven different bacterial strains (viz., Serratia plymuthica, S412; S. plymuthica, S414; S. plymuthica, AS13; S. proteamaculans, S4; S. rubidaea, EV23; S. rubidaea, AV10; Pseudomonas fluorescens, SLU-99) and their different combinations as consortia against P. colocasiae. Antagonistic tests were performed in in vitro plate assays and the effective strains were selected for detached leaf assays and greenhouse trials. Plant growth-promoting and disease prevention traits of selected bacterial strains were also investigated in vitro. Our results indicated that some of these strains used singly (AV10, AS13, S4, and S414) and in combinations (S4+S414, AS13+AV10) reduced the growth of P. colocasiae (30-50%) in vitro and showed disease reduction ability when used singly or in combinations as consortia in greenhouse trials (88.75-99.37%). The disease-suppressing ability of these strains may be related to the production of enzymes such as chitinase, protease, cellulase, and amylase. Furthermore, all strains tested possessed plant growth-promoting traits such as indole-3-acetic acid production, siderophore formation, and phosphate solubilization. Overall, the present study revealed that bacterial strains significantly suppressed P. colocasiae disease development using in vitro, detached leaf, and greenhouse assays. Therefore, these bacterial strains can be used as an alternative strategy to minimize the use of synthetic fungicides and fertilizers to control taro blight and improve sustainable taro production.

Contributions of Beneficial Microorganisms in Soil Remediation and Quality Improvement of Medicinal Plants

Medicinal plants (MPs) are important resources widely used in the treatment and prevention of diseases and have attracted much attention owing to their significant antiviral, anti-inflammatory, antioxidant and other activities. However, soil degradation, caused by continuous cropping, excessive chemical fertilizers and pesticide residues and heavy metal contamination, seriously restricts the growth and quality formation of MPs. Microorganisms, as the major biota in soil, play a critical role in the restoration of the land ecosystem. Rhizosphere microecology directly or indirectly affects the growth and development, metabolic regulation and active ingredient accumulation of MPs. Microbial resources, with the advantages of economic efficiency, harmless to environment and non-toxic to organisms, have been recommended as a promising alternative to conventional fertilizers and pesticides. The introduction of beneficial microbes promotes the adaptability of MPs to adversity stress by enhancing soil fertility, inhibiting pathogens and inducing systemic resistance. On the other hand, it can improve the medicinal quality by removing soil pollutants, reducing the absorption and accumulation of harmful substances and regulating the synthesis of secondary metabolites. The ecological and economic benefits of the soil microbiome in agricultural practices are increasingly recognized, but the current understanding of the interaction between soil conditions, root exudates and microbial communities and the mechanism of rhizosphere microecology affecting the secondary metabolism of MPs is still quite limited. More research is needed to investigate the effects of the microbiome on the growth and quality of different medicinal species. Therefore, the present review summarizes the main soil issues in medicinal plant cultivation, the functions of microbes in soil remediation and plant growth promotion and the potential mechanism to further guide the use of microbial resources to promote the ecological cultivation and sustainable development of MPs.

Seed priming with calcium chloride enhances stress tolerance in rice seedlings

Calcium is a crucial second messenger in plant cells and contributes to plant resistance against biotic and abiotic stress. Plant defense priming with natural or synthetic compounds leads to quicker and stronger resistance responses. However, whether pretreatment of plant seeds with calcium could improve their resistance to stress remains poorly understood. In this study, we showed that rice seedlings grown from calcium chloride (CaCl₂)-pretreated seeds displayed enhanced resistance to the rice blast fungus Magnaporthe oryzae and the rice bacterial pathogen Xanthomonas oryzae pv. Oryzae (Xoo). Seed priming with CaCl₂ also led to enhanced rice tolerance to salt and cold. Furthermore, the reactive oxygen species (ROS) burst increased significantly upon immunity activation in the leaves of rice seedlings grown from CaCl₂-pretreated seeds. Additionally, we analyzed the rice calmodulin-binding protein 60 (OsCBP60) family and found that there were 19 OsCBP60s in rice cultivar Zhonghua 11 (ZH11). The transcripts of several OsCBP60s were chitin- and M. oryzae-inducible, suggesting that they may contribute to rice resistance. Taken together, these data indicate that seed priming with CaCl₂ can effectively enhance rice tolerance to multiple stresses, perhaps by boosting the burst of ROS, and OsCBP60 family members may also play an essential role in this process.

Local Wisdom of West Timorese Farmers in Land Management

This paper’s working hypothesis is that the indigenous farming practices of Timorese farmers are those most suitable and adaptable with regard to these farmers’ circumstances. Intensive farming and the acceleration of land conversion in Java lead to a reduction in favorable cropland and the degradation of soil biology. To meet the demand for food production, unfavorable areas outside Java, including marginal semi-arid areas on Timor Island, East Nusa Tenggara province, have become an important option. Unfortunately, the national crop production policy has paid less attention to the specific biophysical characteristics of the region and how local people have adapted to the diverse marginal environment. We review the literature in the areas of soil nutrition retention and soil biology, vegetation/crop diversity, and farming practices/management, including local wisdom on soil management. This paper highlights that the values of the chemical parameters of the soils in question are varied, but generally range from low to high. The existence of beneficial micro-organisms is important both for improving soil fertility and due to their association with local vegetation/crops. Traditional farming practices, such as the local agroforestry of Mamar, have effectively preserved the existence of micro-organisms that promote conservation practices, crop/vegetation diversity, and sustainable agriculture. We recommend that the expansion of croplands and crop production into marginal semi-arid areas needs to be considered and adapted while taking into consideration sustainability and environmentally sound traditional practices.

Desert truffle mycorrhizosphere harbors organic acid releasing plant growth-promoting rhizobacteria, essentially during the truffle fruiting season

Desert truffle is becoming a new crop in semiarid areas. Climatic parameters and the presence of microorganisms influence the host plant physiology and alter desert truffle production. Desert truffle plants present a typical summer deciduous plant phenology divided into four stages: summer dormancy, autumn bud break, winter photosynthetic activity, and spring fruiting. We hypothesize that the bacterial community associated with desert truffle plants will show a seasonal trend linked to their plant growth-promoting rhizobacteria (PGPR) traits. This information will provide us with a better understanding about its potential role in this symbiosis and possible management implementations. Bacteria were isolated from root-adhering soil at the four described seasons. A total of 417 isolated bacteria were phenotypically and biochemically characterized and gathered by molecular analysis into 68 operational taxonomic units (OTUs). They were further characterized for PGPR traits such as indole acetic acid production, siderophore production, calcium phosphate solubilization, and ACCD (1-amino-cyclopropane-1-carboxilatedeaminase) activity. These PGPR traits were used to infer functional PGPR diversity and cultivable bacterial OTU composition at different phenological moments. The different seasons induced shifts in the OTU composition linked to their PGPR traits. Summer was the phenological stage with the lowest microbial diversity and PGPR functions, whereas spring was the most active one. Among the PGPR traits analyzed, P-solubilizing rhizobacteria were harbored in the mycorrhizosphere during desert truffle fruiting in spring.

Effects of Low Temperature Stress on Source-Sink Organs in Wheat and Phosphorus Mitigation Strategies

The 21st century presents many challenges to mankind, including climate change, fast growing human population, and serious concerns over food security. Wheat is a leading cereal crop that largely fulfills the global food needs. Low temperature stress accompanied by nutrient-starved soils is badly disrupting the source-sink relationship of wheat, thus causing an acute decline in final yield and deteriorating the grain quality. This review paper aimed to understand how low temperature stress affects wheat source-sink organs (i.e., leaves, roots, and spikes) and how phosphorus application reliefs in alleviating its harmful consequences. Also, we discussed mitigation strategies to enhance wheat capacity to adapt to varying temperature extremes and made rational recommendations based on modern agronomic and breeding approaches. Therefore, this study is likely to establish a solid foundation for improving the tolerance to low temperature stress and to improve its phosphorus utilization efficiency in wheat.

Interaction Between Halotolerant Phosphate-Solubilizing Bacteria (Providencia rettgeri Strain TPM23) and Rock Phosphate Improves Soil Biochemical Properties and Peanut Growth in Saline Soil

Soil salinity has adverse effects on soil microbial activity and nutrient cycles and therefore limits crop growth and yield. Amendments with halotolerant phosphate-solubilizing bacteria (PSB) and rock phosphate (RP) may improve properties of saline soil. In this study, we investigated the effects of RP either alone or in combination with PSB (Providencia rettgeri strain TPM23) on peanut growth and soil quality in a saline soil. With the combined application of RP and PSB, plant length and biomass (roots and shoots) and uptake of phosphorus (P), nitrogen (N), and potassium (K) increased significantly. Soil Na+ and Cl- contents decreased in the PR alone or PR combined with PSB treatment groups. There were strongly synergistic effects of RP and PSB on soil quality, including a decrease in pH. The soil available N, P, and K contents were significantly affected by the PSB treatments. In addition, the alkaline phosphomonoesterases, urease, and dehydrogenase activities increased significantly compared with the untreated group; highest alkaline phosphomonoesterases activity was observed in the RP and PSB treatment groups. The composition of rhizosphere soil bacterial communities was determined using 454-pyrosequencing of the 16S rRNA gene. In the PR alone or PR combined with PSB treatment groups, the structure of the soil bacterial community improved with increasing richness and diversity. With PSB inoculation, the relative abundance of Acidobacteria, Chloroflexi, and Planctomycetes increased. The three phyla were also positively correlated with soil available N and root dry weight. These results suggested microbiological mechanisms by which the combined use of RP and PSB improved saline soil and promoted plant growth. Overall, the study indicates the combined use of RP and PSB can be an economical and sustainable strategy to increase plant growth in P-deficient and salt-affected soils.

In Vitro Study of Biocontrol Potential of Rhizospheric Pseudomonas aeruginosa against Pathogenic Fungi of Saffron (Crocus sativus L.)

Plant rhizosphere soil contains a large number of plant-growth promoting rhizobacteria, which can not only resist the invasion of pathogenic microorganisms and protect plants from damage, but also promote the growth and development of plants. In this study, Pseudomonas aeruginosa strain YY322, isolated and screened from the rhizosphere soil of saffron (Crocus sativus L.), was found through a plate confrontation experiment to show highly effectual and obvious antagonistic activity against the pathogens of saffron, including Fusarium oxysporum, Fusarium solani, Penicillium citreosulfuratum, Penicillium citrinum and Stromatinia gladioli. In addition, the volatile organic compounds of strain YY322 had great antagonistic activity against these pathogens. Observation under a scanning electron microscope and transmission electron microscope reflected that strain YY322 had a significant effect on the hyphae and conidia of F. oxysporum and F. solani. Through the detection of degrading enzymes, it was found that P. aeruginosa can secrete protease and glucanase. The plant growth promoting performance was evaluated, finding that strain YY322 had the functions of dissolving phosphorus, fixing nitrogen, producing siderophore and producing NH3. In addition, whole genome sequencing analysis indicated that the YY322 genome is comprised of a 6,382,345-bp circular chromosome, containing 5809 protein-coding genes and 151 RNA genes. The P. aeruginosa YY322 genome encodes genes related to phenazine (phzABDEFGIMRS), hydrogen cyanide(HCN) (hcnABC), surfactin (srfAA), salicylate (pchA), biofilm formation (flgBCDEFGHIJKL, motAB, efp, hfq), and colonization (minCDE, yjbB, lysC). These results collectively indicated the role of P. aeruginosa YY322 in plant growth enhancement and biocontrol mechanisms. All in all, this study provides a theoretical basis for P. aeruginosa as the PGPR of saffron, paving the way for the subsequent development and utilization of microbial fertilizer.

Rhizosphere Microbial Communities Are Significantly Affected by Optimized Phosphorus Management in a Slope Farming System

Soil rhizosphere microorganisms play crucial roles in promoting plant nutrient absorption and maintaining soil health. However, the effects of different phosphorus (P) managements on soil microbial communities in a slope farming system are poorly understood. Here, rhizosphere microbial communities under two P fertilization levels-conventional (125 kg P2O5 ha-1, P125) and optimal (90 kg P2O5 ha-1, P90)-were compared at four growth stages of maize in a typical sloped farming system. The richness and diversity of rhizosphere bacterial communities showed significant dynamic changes throughout the growth period of maize, while different results were observed in fungal communities. However, both the P fertilization levels and the growth stages influenced the structure and composition of the maize rhizosphere microbiota. Notably, compared to P125, Pseudomonas, Conexibacter, Mycobacterium, Acidothermus, Glomeromycota, and Talaromyces were significantly enriched in the different growth stages of maize under P90, while the relative abundance of Fusarium was significantly decreased during maize harvest. Soil total nitrogen (TN) and pH are the first environmental drivers of change in bacterial and fungal community structures, respectively. The abundance of Gemmatimonadota, Proteobacteria, and Cyanobacteria showed significant correlations with soil TN, while that of Basidiomycota and Mortierellomycota was significantly related to pH. Additionally, P90 strengthened the connection between bacteria, but reduced the links between fungi at the genus level. Our work helps in understanding the role of P fertilization levels in shaping the rhizosphere microbiota and may manipulate beneficial microorganisms for better P use efficiency.

Accentuating the Role of Nitrogen to Phosphorus Ratio on the Growth and Yield of Wheat Crop

Nitrogen (N) and Phosphorus (P) deficiency is a major yield limiting factor across the globe and their proper management plays a vital role in optimizing crop yield. This field experiment was conducted to assess the impact of soil and plant nitrogen N and P ratio on the growth and yield of wheat (Triticum aestivum L.) in alkaline calcareous soil. The study consisted of various levels of nitrogen (0, 40, 80, and 160 kg ha−1 as urea) and phosphorus (0, 30, 60, and 90 kg P2O5 ha−1 as diammonium phosphate), and was carried out in randomized complete block design (RCBD) with factorial arrangement having three replications. The result showed that the addition of 160 kg N ha−1 significantly improved biological yield (10,052 kg ha−1), grain weight (3120 kg ha−1), chlorophyll content at tillering stage soil plant analysis development (SPAD) value (35.38), N uptake in straw (33.42 kg ha−1), and K uptake in straw (192 kg ha−1) compared to other N levels. In case of P, 90 kg P2O5 ha−1 had resulted maximum biological yield (9852 kg ha−1), grain yield (3663 kg ha−1), chlorophyll content at tillering stage (SPAD value 34.36), P (6.68 mg kg−1) and K (171 kg ha−1) uptake in straw. The sole use of N and P have positively influenced the biological and grain yield but their interaction didn’t response to biological yield. The present study reveals that SPAD value (chlorophyll meter) is the better choice for determining plant N and P concentrations to estimate the yield potential.

Alcaligenes aquatilis GTE53: Phosphate solubilising and bioremediation bacterium isolated from new biotope "phosphate sludge enriched-compost"

The isolation and identification of beneficial bacteria from the active phase of composting is considered to be a key bio-quality parameter for the assessment of the process. The aim of this work was the selection and identification of beneficial bacteria from a co-composting experiment of vegetable waste (VW), olive oil mill waste (O₂MW), and phosphate sludge (PS). Phosphate-solubilizing strains were isolated from the thermophilic phase using Pikovskaya (PVK) solid medium supplemented with tricalcium phosphate Ca3(PO4) (TCP) as the sole source of phosphorus (P). Therefore, the selected isolate Alcaligenes aquatilis GTE53 was tested to tolerate abiotic stresses (different levels of temperature, variable pH, high salinity and water stress). The isolate was also assessed for indole acetic acid (IAA) and siderophores synthesis, nitrogen fixation, phenol degradation and pathogens inactivation. The quality of the co-composting process was also investigated by monitoring the physico-chemical parameters. The obtained results showed that A. aquatilis GTE53 displayed a higher solubilization index of 2.4 and was efficiently dissolved, up to 162.8 and 247.4 mg·mL^-1 of inorganic phosphate from PS and phosphate rock (PR), respectively. A. aquatilis GTE53 exhibited siderophores and IAA release, along with atmospheric nitrogen fixation. In addition to that, A. aquatilis GTE53 showed a high resistance to heat and tolerance to acidic and alkaline pH, high salinity and water stress. Moreover, A. aquatilis GTE53 could degrade 99.2% of phenol from a high-concentrated medium (1100 mg·L^-1 of phenol) and can inactivate the most abundant pathogens in industrial wastes: Escherichia coli, Streptococcus sp., Salmonella sp., and Fusarium oxysporum albedinis. Analysis of temperature, pH, electrical conductivity, carbon/nitrogen (C/N) ratio, indicated successful co-composting. An efficient transformation of P to the available form and a great abatement of polyphenols, were also recorded during the process. The findings of this study will help to advance the understanding of A. aquatilis GTE53 functions and will facilitate its application to promote beneficial microbial organisms during composting, thus obtaining a high-quality product.

The application of biomodified fertilizers as a way to increase the effective fertility of orchard soils

The crucial trend in the intensification of gardening is the use of agrochemicals, including the systematic application of mineral fertilizers, regulated by the production flow chart of fruit products. Technological pressure on the soil causes aggravating the ecological problem of loss of the fertility level in the conditions of the orchard monoculture. The search for sustainable and environmentally effective approaches to solving the problem of managing fertility factors is aimed at studying the effects of biological and biomodified fertilizers. The changes in the main indicators of the effective fertility of the structural-metamorphic agrosem in the conditions of the orchard monoculture with the application of biomodified organo-mineral fertilizer were studied in dynamics. The prolonged effect of organo-mineral fertilizer on increasing the content of the main indicators of effective fertility in the soil was determined six years after application. The use of biomodified organo-mineral fertilizer in the orchard fertilization system is considered as an element of an integrated strategy for the management of orchard soil fertility.

Beneficiary of nitrifying bacteria for enhancing lettuce (Lactuca sativa) and vetiver grass (Chrysopogon zizanioides L.) growths align with carp (Cyprinus carpio) cultivation in an aquaponic system

The aquaponic system is an alternative strategy to treat aquaculture waste and achieve food independence. Bacteria play vital roles in the aquaponic system as they can transform ammonia or ammonium into nitrite and then into nitrate, which is more favorable for bacteria, fish, and plants. The objective of this study was to determine the effect of nitrifying bacteria (Nitrosomonas europaea Winogradsky and Nitrobacter winogradskyi Winslow) on the aquaponic system in terms of water quality, nutrient availability, and productivity of carp (Cyprinus carpio), lettuce (Lactuca sativa var. crispa), and vetiver grass (Chrysopogon zizanioides L.). The experiment consisted of four treatments: aquaculture of carp as a control for fish (A), hydroponic of lettuce and vetiver grass without nutrient addition as a control for plants (B), aquaponic (carp, lettuce, vetiver grass) (C), and aquaponic with nitrifying bacteria addition (D). The results showed nitrifying bacteria addition had a significant effect on daily growth rate (DGR) and relative growth rate (RGR) of lettuce within a treatment; on the other hand, the nitrifying bacteria did not give a significant effect to RGR of vetiver grass. The growth rate, specific growth rate, and survival rate of the carp in aquaculture treatment (A) were lower than in both aquaponic treatments (C and D). Nitrifying bacteria addition in the aquaponics system had a significant effect of increasing the orthophosphate concentration. Water quality was also indicated to be better in the aquaponic system than in the aquaculture system. The integration of aquaculture and hydroponics with the addition of nitrifying bacteria enables the formation of microorganism communities, nitrate, and orthophosphate, which lead to the improvement of water quality, nutrient availability, and plant growth.

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.

Industrial polluted soil borne fungi decolorize the recalcitrant azo dyes Synozol red HF-6BN and Synozol black B

Today's world needs to control the industrial pollution through smarter ways. Presently, we observed the capacity of soil borne fungi to digest Synozol Red HF-6BN and Synozol Black B. Initially, 86 fungal strains were isolated from soil samples randomly collected from industrial sites. Among these, 31 isolates were capable of dye decolorization on solid media, with SN12f and SN13a isolates showed the highest decolorization capacity. The dye decolorization by both strains was higher (80-95%), when incubated for 120 h under optimized conditions of pH, concentration, nutrient source and temperature. The dye (Synozol red HF-6BN and Synozol black B) decolorization by SN12f isolate was maximum (˃90%) at pH7, whereas the SN13a decolorized 90% of Synozol red HF-6BN and 89% of Synozol black B at pH3. The SN13a and SN12f isolates at 40 mg/L showed de-colorization of 94.71%, 81.4% (for Synozol red HF-6BN) and 90.5%, 84.4% (Synozol black B), respectively. Our isolates also mitigated the toxic effect of azo dyes on the growth of phosphate solubilizing soil bacteria. In fact, the untreated effluent showed toxic effects on the growth of beneficial bacterial by developing zone of inhibition (16.5 mm around Aeromonas spp., 14.5 mm around Sallmonella while 14.25 mm around Citrobacter spp). However, the fungal treated dye was unable to develop zone of inhibition. Laccase activity was positive for both of fungal isolates after incubation on Bassnell Hass Medium (0.0733 U/mL for SN12f and 0.0439 U/mL SN13a). Using molecular approaches (ITS region), SN12f was identified as Aspergillus nidulans, while SN13a as Aspergillus fumigatus. The current study showed that local fungal flora can reclaim the contaminated soils and support the agro-friendly micro-flora.

Use of Mineral Weathering Bacteria to Enhance Nutrient Availability in Crops: A Review

Rock powders are low-cost potential sources of most of the nutrients required by higher plants for growth and development. However, slow dissolution rates of minerals represent an obstacle to the widespread use of rock powders in agriculture. Rhizosphere processes and biological weathering may further enhance mineral dissolution since the interaction between minerals, plants, and bacteria results in the release of macro- and micronutrients into the soil solution. Plants are important agents in this process acting directly in the mineral dissolution or sustaining a wide diversity of weathering microorganisms in the root environment. Meanwhile, root microorganisms promote mineral dissolution by producing complexing ligands (siderophores and organic acids), affecting the pH (via organic or inorganic acid production), or performing redox reactions. Besides that, a wide variety of rhizosphere bacteria and fungi could also promote plant development directly, synergistically contributing to the weathering activity performed by plants. The inoculation of weathering bacteria in soil or plants, especially combined with the use of crushed rocks, can increase soil fertility and improve crop production. This approach is more sustainable than conventional fertilization practices, which may contribute to reducing climate change linked to agricultural activity. Besides, it could decrease the dependency of developing countries on imported fertilizers, thus improving local development.

Cadmium Immobilization in the Rhizosphere and Plant Cellular Detoxification: Role of Plant-Growth-Promoting Rhizobacteria as a Sustainable Solution

Food is the major cadmium (Cd)-exposure pathway from agricultural soils to humans and other living entities and must be reduced in an effective way. A plant can select beneficial microbes, like plant-growth-promoting rhizobacteria (PGPR), depending upon the nature of root exudates in the rhizosphere, for its own benefits, such as plant growth promotion as well as protection from metal toxicity. This review intends to seek out information on the rhizo-immobilization of Cd in polluted soils using the PGPR along with plant nutrient fertilizers. This review suggests that the rhizo-immobilization of Cd by a combination of PGPR and nanohybrid-based plant nutrient fertilizers would be a potential and sustainable technology for phytoavailable Cd immobilization in the rhizosphere and plant cellular detoxification, by keeping the plant nutrition flow and green dynamics of plant nutrition and boosting the plant growth and development under Cd stress.

Transcriptome profiling of genes involved in nutrient uptake regulated by phosphate-solubilizing bacteria in pepper (Capsicum annuum L.)

Improving nutrient absorption in pepper has become a vital prerequisite for growth to produce a sustainable yield. In this study, transcriptome gene expression in pepper inoculated with two types of phosphate-solubilizing bacteria (PSB) and grown under low and high nutrient levels (LN and HN) was analyzed. Results showed that the root length increased when pepper was grown under LN; however, the root structure was intensively tight under HN. Our data revealed that the roots preferred horizontal growth than longitudinal growth under HN. PSB strains 'M01' and 'N3' significantly (P < 0.01) increased the P uptake by 70.44% and 98.20%, respectively, but decreased the Ca²⁺ content by 8.96% and 9.13%, respectively, compared with the control (L1). Although no remarkable difference was detected in the chlorophyll content, inoculation with the two PSB strains decreased the Fe³⁺ content in pepper under HN. The total clean sequenced data from samples ranged between 5,923,659,118 and 9,955,045,953 bp. Transcriptome profiling revealed 320 upregulated and 449 downregulated genes in L3 versus L1 and 468 upregulated and 532 downregulated genes in L4 versus L1. Gene ontology analysis revealed that the biological processes, including response to stress and secondary metabolic process, were involved. Several pathways were subordinate to glycosphingolipid biosynthesis and linoleic acid and nitrogen metabolisms. Analysis of the eukaryotic orthologous group function revealed that most differential genes were attributed to RNA processing and modification, transcription, and signal transduction. Our results provided new insights into the molecular mechanism related to nutrient uptake in pepper inoculated with PSBs.

Advances in Methods for Recovery of Ferrous, Alumina, and Silica Nanoparticles from Fly Ash Waste

Fly ash or coal fly ash causes major global pollution in the form of solid waste and is classified as a “hazardous waste”, which is a by-product of thermal power plants produced during electricity production. Si, Al, Fe Ca, and Mg alone form more than 85% of the chemical compounds and glasses of most fly ashes. Fly ash has a chemical composition of 70–90%, as well as glasses of ferrous, alumina, silica, and CaO. Therefore, fly ash could act as a reliable and alternative source for ferrous, alumina, and silica. The ferrous fractions can be recovered by a simple magnetic separation method, while alumina and silica can be extracted by chemical or biological approaches. Alumina extraction is possible using both alkali- and acid-based methods, while silica is extracted by strong alkali, such as NaOH. Chemical extraction has a higher yield than the biological approaches, but the bio-based approaches are more environmentally friendly. Fly ash can also be used for the synthesis of zeolites by NaOH treatment of variable types, as fly ash is rich in alumino-silicates. The present review work deals with the recent advances in the field of the recovery and synthesis of ferrous, alumina, and silica micro and nanoparticles from fly ash.

The Halotolerant Rhizobacterium-Pseudomonas koreensis MU2 Enhances Inorganic Silicon and Phosphorus Use Efficiency and Augments Salt Stress Tolerance in Soybean (Glycine max L.)

Optimizing nutrient usage in plants is vital for a sustainable yield under biotic and abiotic stresses. Since silicon and phosphorus are considered key elements for plant growth, this study assessed the efficient supplementation strategy of silicon and phosphorus in soybean plants under salt stress through inoculation using the rhizospheric strain—Pseudomonas koreensis MU2. The screening analysis of MU2 showed its high salt-tolerant potential, which solubilizes both silicate and phosphate. The isolate, MU2 produced gibberellic acid (GA₁, GA₃) and organic acids (malic acid, citric acid, acetic acid, and tartaric acid) in pure culture under both normal and salt-stressed conditions. The combined application of MU2, silicon, and phosphorus significantly improved silicon and phosphorus uptake, reduced Na⁺ ion influx by 70%, and enhanced K⁺ uptake by 46% in the shoots of soybean plants grown under salt-stress conditions. MU2 inoculation upregulated the salt-resistant genes GmST1, GmSALT3, and GmAKT2, which significantly reduced the endogenous hormones abscisic acid and jasmonic acid while, it enhanced the salicylic acid content of soybean. In addition, MU2 inoculation strengthened the host’s antioxidant system through the reduction of lipid peroxidation and proline while, it enhanced the reduced glutathione content. Moreover, MU2 inoculation promoted root and shoot length, plant biomass, and the chlorophyll content of soybean plants. These findings suggest that MU2 could be a potential biofertilizer catalyst for the amplification of the use efficiency of silicon and phosphorus fertilizers to mitigate salt stress.

Phosphate Solubilizing Rhizobacteria Could Have a Stronger Influence on Wheat Root Traits and Aboveground Physiology Than Rhizosphere P Solubilization

Limited P availability in several agricultural areas is one of the key challenges facing current agriculture. Exploiting P-solubilizing bacteria (PSB) has been an emerging bio-solution for a higher rhizosphere P-availability, meanwhile the above- and below-ground interactions that PSB would trigger remain unclear over plant growing stages. We hypothesized that PSB effects on plant growth may be greater on root traits that positively links with aboveground physiology more than the commonly believed rhizosphere P bio-solubilization. In this study, five contrasting PSB (Pseudomonas spp.) isolates (low "PSB1", moderate "PSB2 and PSB4" and high "PSB3 and PSB5" P-solubilizing capacity "PSC") were used to investigate above- and below-ground responses in wheat fertilized with rock P (RP) under controlled conditions. Our findings show that all PSB isolates increased wheat root traits, particularly PSB5 which increased root biomass and PSB3 that had greater effect on root diameter in 7-, 15- and 42-day old plants. The length, surface and volume of roots significantly increased along with higher rhizosphere available P in 15- and 42-day old plants inoculated with PSB4 and PSB2. Shoot biomass significantly increased with both PSB2 and PSB5. Root and shoot physiology significantly improved with PSB1 (lowest PSC) and PSB4 (moderate PSC), notably shoot total P (78.38%) and root phosphatase activity (390%). Moreover, nutrients acquisition and chlorophyll content increased in inoculated plants and was stimulated (PSB2, PSB4) more than rhizosphere P-solubilization, which was also revealed by the significant above- and below-ground inter-correlations, mainly chlorophyll and both total (R = 0.75, p = 0.001**) and intracellular (R = 0.7, p = 0.000114*) P contents. These findings demonstrate the necessity to timely monitor the plant-rhizosphere continuum responses, which may be a relevant approach to accurately evaluate PSB through considering below- and above-ground relationships; thus enabling unbiased interpretations prior to field applications.

Drought-tolerant and plant growth-promoting endophytic Staphylococcus sp. having synergistic effect with silicate supplementation

Endophytic bacteria have been reported to have symbiotic, mutualistic, commensalistic or trophobiotic relationships with various plant parts. As part of its adaptation, many endophytic organisms are known to exhibit properties with multiple beneficial effects to the plant system. Even though many bacterial genera have been identified to have endophytic association, isolation of those which were previously demonstrated well for human association is quite interesting. In the study, endophytic bacteria Ceb1 isolated from the rhizome of Curcuma longa was identified by 16S rDNA sequencing as Staphylococcus sp. Further, Ceb1 was observed to have the ability to tolerate drought stress. While screening for the plant growth-promoting traits, Ceb1 was found to be positive for IAA production both under drought-stressed and normal conditions as confirmed by HPLC. The Ceb1 priming with Vigna unguiculata was observed to enhance the growth parameters of the plant. Analysis of Ceb1-treated plants by ICP-MS further showed modulation of both macro- and micronutrients. Upon drought stress induction in Vigna unguiculata, Ceb1 was found to provide synergistic plant growth-promoting effect to the plant along with the supplemented silicate sources. Under the changing agroclimatic conditions, exploring the plant stress-alleviating effects of endophytes is highly significant.

In situ effects of Lathyrus sativus- PGPR to remediate and restore quality and fertility of Pb and Cd polluted soils

Rehabilitation of heavy metals contaminated soils using association between legumes and beneficial rhizospheric microorganisms such as plant growth-promoting bacteria (PGPR) is a major challenge in agronomy. The present study focuses on assessing the impact of field inoculation with I1 (Rhizobium leguminosarum (M5) + Bacillus simplex + Luteibacter sp. + Variovorax sp.) and I5 (R. leguminosarum (M5) + Pseudomonas fluorescens (K23) + Luteibacter sp. + Variovorax sp.) on growth and phytoremediation potential of Lathyrus sativus plants as well as soil quality and fertility. The experimentation was carried out in mine tailings of northern Tunisia. Obtained Results indicated that the in situ inoculation with I1 and I5 significantly increased the shoots (47% and 22%) and roots dry weights (22% and 29%), as well as nodules number (48% and 31%), respectively, compared to uninoculated plants. The maximum Pb accumulation in the above-ground tissue was recorded in plants inoculated with I5 (1180.85 mg kg^-1 DW). At the same time, we noticed a reduction in total Pb and Cd in the rhizosphere of inoculated plots mainly in those inoculated with I5 reaching 46% and 61%, respectively, compared to uninoculated plots. Likewise, I5 inoculum significantly enhanced soil total nitrogen (35%) and available phosphorus (100%), as well as β-glucosidase (16%), urease (32%) and alkaline phosphatase (12%) activities. Here we demonstrate the usefulness of L. sativus inoculated with I5 inoculum formed by mixing efficient and heavy metals resistant PGPR to boost an efficient reclamation of Cd and Pb contaminated soils and, ultimately, to improve their quality and fertility.

Exploration of strategies to increase the nitrogen and phosphate content of solid waste landfill soil

Several strategies were undertaken to increase the fertility of landfill soil as rapid urbanization remarkably decreases the agricultural land, posing challenges to the fast-growing human population. Towards this direction, soil microcosms were prepared wherein the addition of nutrient or biofertilizer or the combination of both increased the soil nitrogen and phosphate content considerably. The maximum amount of nitrogen fixation and phosphate solubilization occurred in microcosm treated with biofertilizer and nutrient. To investigate the underlying cause, we observed that separate application of nutrient or biofertilizer or combined application of both increased the abundance of nitrogen-fixing and phosphate-solubilizing bacteria in the microcosms. However, the highest abundance of nitrogen-fixing and phosphate-solubilizing bacteria was spotted in a microcosm challenged with nutrient and biofertilizer together. It was detected that with increasing population of nitrogen-fixing and phosphate-solubilizing bacteria, the soil nitrogen and phosphate level also got enhanced, respectively, thus establishing a strong positive correlation between them. The microcosm treated with biofertilizer and nutrient manifested the highest degree of heterotrophic microbial growth and microbial activity than the microcosms either treated with nutrient or biofertilizer. The microcosm treated with nutrient and biofertilizer was found to exhibit the highest functional diversity compared to others. A surface plot was constructed to demonstrate the association among microbial activity, functional diversity, and the availability of soil nitrogen and phosphate content of soil. The result indicates that the combined application of nutrient and biofertilizer increases the microbial activity leading to the formation of a heterogeneous ecosystem that enhances the nitrogen and phosphate content of landfill soil considerably.

Biotransformation of struvite by Aspergillus niger: phosphate release and magnesium biomineralization as glushinskite

Struvite (magnesium ammonium phosphate-MgNH₄ PO₄ ·6H₂ O), which can extensively crystallize in wastewater treatments, is a potential source of N and P as fertilizer, as well as a means of P conservation. However, little is known of microbial interactions with struvite which would result in element release. In this work, the geoactive fungus Aspergillus niger was investigated for struvite transformation on solid and in liquid media. Aspergillus niger was capable of solubilizing natural (fragments and powder) and synthetic struvite when incorporated into solid medium, with accompanying acidification of the media, and extensive precipitation of magnesium oxalate dihydrate (glushinskite, Mg(C₂ O₄ ).2H₂ O) occurring under growing colonies. In liquid media, A. niger was able to solubilize natural and synthetic struvite releasing mobile phosphate (PO₄ ^3- ) and magnesium (Mg²⁺ ), the latter reacting with excreted oxalate resulting in precipitation of magnesium oxalate dihydrate which also accumulated within the mycelial pellets. Struvite was also found to influence the morphology of A. niger mycelial pellets. These findings contribute further understanding of struvite solubilization, element release and secondary oxalate formation, relevant to the biogeochemical cycling of phosphate minerals, and further directions utilizing these mechanisms in environmental biotechnologies such as element biorecovery and biofertilizer applications.

Deciphering the Factors for Nodulation and Symbiosis of Mesorhizobium Associated with Cicer arietinum in Northwest India

The compatibility between rhizobia and legumes for nitrogen-fixing nodules and the stages of root hair curling, formation of infection thread, and nodulation initiation have been vitally studied, but the factors for the sustainable root surface colonization and efficient symbiosis within chickpea and rhizobia have been poorly investigated. Hence, we aimed to analyze phenotypic properties and phylogenetic relationships of root-nodule bacteria associated with chickpea (Cicer arietinum) in the north-west Indo Gangetic Plains (NW-IGP) region of Uttar Pradesh, India. In this study, 54 isolates were recovered from five agricultural locations. Strains exhibited high exopolysaccharide production and were capable of survival at 15–42 °C. Assays for phosphate solubilization, catalase, oxidase, Indole acetic acid (IAA) production, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity revealed that all the tested isolates possessed plant growth-promoting potential. Metabolic profiling using Biolog plates indicated that patterns of substrate utilization differed considerably among isolates. A biofilm formation assay showed that isolates displayed a nearly four-fold range in their capacity for biofilm development. Inoculation experiments indicated that all isolates formed nodules on chickpea, but they exhibited more than a two-fold range in symbiotic efficiency. No nodules were observed on four other legumes (Phaseolus vulgaris, Pisum sativum, Lens culinaris, and Vigna mungo). Concatenated sequences from six loci (gap, edD, glnD, gnD, rpoB, and nodC) supported the assignment of all isolates to the species Mesorhizobium ciceri, with strain M. ciceri Ca181 as their closest relative.

Impact of Elemental Sulfur on the Rhizospheric Bacteria of Durum Wheat Crop Cultivated on a Calcareous Soil

Previous experiments have shown that the application of fertilizer granules containing elemental sulfur (S0) as an ingredient (FBS0) in durum wheat crops produced a higher yield than that produced by conventional ones (F), provided that the soils of the experimental fields (F vs. FBS0) were of comparable quality and with the Olsen P content of the field's soil above 8 mg kg-1. In this experiment the FBS0 treatment took place in soil with Olsen P at 7.8 mg kg-1, compared with the F treatment's soil with Olsen P of 16.8 mg kg-1, aiming at reducing the imbalance in soil quality. To assess and evaluate the effect of FBS0 on the dynamics of the rhizospheric bacteria in relation to F, rhizospheric soil at various developmental stages of the crops was collected. The agronomic profile of the rhizospheric cultivable bacteria was characterized and monitored, in connection with the dynamics of phosphorus, iron, organic sulfur, and organic nitrogen, in both the rhizosoil and the aerial part of the plant during development. Both crops were characterized by a comparable dry mass accumulation per plant throughout development, while the yield of the FBS0 crop was 3.4% less compared to the F crop's one. The FBS0 crop's aerial part showed a transient higher P and Fe concentration, while its organic N and S concentrations followed the pattern of the F crop. The incorporation of S0 into the conventional fertilizer increased the percentage of arylsulfatase (ARS)-producing bacteria in the total bacterial population, suggesting an enhanced release of sulfate from the soil's organic S pool, which the plant could readily utilize. The proportion of identified ARS-producing bacteria possessing these traits exhibited a maximum value before and after topdressing. Phylogenetic analysis of the 68 isolated ARS-producing bacterial strains revealed that the majority of the isolates belonged to the Pseudomonas genus. A large fraction also possessed phosphate solubilization, and/or siderophore production, and/or ureolytic traits, thus improving the crop's P, Fe, S, and N balance. The aforementioned findings imply that the used FBS0 substantially improved the quality of the rhizosoil at the available phosphorus limiting level by modulating the abundance of the bacterial communities in the rhizosphere and effectively enhancing the microbially mediated nutrient mobilization towards improved plant nutritional dynamics.

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.

Future Phosphorus: Advancing New 2D Phosphorus Allotropes and Growing a Sustainable Bioeconomy

With more than 40 countries currently proposing to boost their national bioeconomies, there is no better time for a clarion call for a "new" bioeconomy, which, at its core, tackles the current disparities and inequalities in phosphorus (P) availability. Existing biofuel production systems have widened P inequalities and contributed to a linear P economy, impairing water quality and accelerating dependence on P fertilizers manufactured from finite nonrenewable phosphate rock reserves. Here, we explore how the emerging bioeconomy in novel, value-added, bio-based products offers opportunities to rethink our stewardship of P. Development of integrated value chains of new bio-based products offers opportunities for codevelopment of "P refineries" to recover P fertilizer products from organic wastes. Advances in material sciences are exploiting unique semiconductor and opto-electrical properties of new "two-dimensional" (2D) P allotropes (2D black phosphorus and blue phosphorus). These novel P materials offer the tantalizing prospect of step-change innovations in renewable energy production and storage, in biomedical applications, and in biomimetic processes, including artificial photosynthesis. They also offer a possible antidote to the P paradox that our agricultural production systems have engineered us into, as well as the potential to expand the future role of P in securing sustainability across both agroecological and technological domains of the bioeconomy. However, a myriad of social, technological, and commercialization hurdles remains to be crossed before such an advanced circular P bioeconomy can be realized. The emerging bioeconomy is just one piece of a much larger puzzle of how to achieve more sustainable and circular horizons in our future use of P.

Response of bacterial communities in rubber plantations to different fertilizer treatments

In the present study, the effects of chemical fertilizer (CF) and organic fertilizer plus chemical fertilizer application (OF-CF) on natural rubber yield, soil properties, and soil bacterial community were systematically investigated in rubber plantations. The rubber dry yield was 26.3% more in the OF treatment group than in the CF treatment group. The contents of total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AK) as well as soil organic matter (SOM) and pH value were higher following OF-CF treatment. Using Illumina sequencing, a total of 927 operational taxonomic units (OTUs) were obtained following CF treatment, while 955 OTUs were obtained after OF-CF treatment. Relative abundance analysis showed the relative abundances of four phyla (Acidobacteria, Proteobacteria, Actinobacteria, Gemmatimonadetes) were different between the two treatment groups. Correlation analysis revealed Acidobacteria, Bacteroidetes, Thaumarchaeota, Elusimicrobia, Verrucomicrobia were the key taxa that determined the soil properties. Additionally, five OTUs (OTU_506, OTU_391, OTU_189, OTU_278, OTU_1057) were thought to be related to the biodegradation of natural rubber. Taken together, these results improve our understanding of the OF-mediated improvement in soil fertility and contribute to the identification of rubber-degrading bacteria in rubber plantations.

Phosphate deficiency induced biofilm formation of Burkholderia on insoluble phosphate granules plays a pivotal role for maximum release of soluble phosphate

Involvement of biofilm formation process during phosphate (P) solubilization by rhizobacterial strains is not clearly understood. Scanning electron microscopic observations revealed prominent biofilm development on tricalcium phosphate as well as on four different rock phosphate granules by two P solubilizing rhizobacteria viz. Burkholderia tropica P4 and B. unamae P9. Variation in the biofilm developments were also observed depending on the total P content of insoluble P used. Biofilm quantification suggested a strong correlation between the amounts of available P and degrees of biofilm formation. Lower concentrations of soluble P directed both the organisms towards compact biofilm development with maximum substratum coverage. Variation in the production of extracellular polymeric substances (EPS) in the similar pattern also suggested its close relationship with biofilm formation by the isolates. Presence of BraI/R quorum sensing (QS) system in both the organisms were detected by PCR amplification and sequencing of two QS associated genes viz. braR and rsaL, which are probably responsible for biofilm formation during P solubilization process. Overall observations help to hypothesize for the first time that, biofilm on insoluble P granules creates a close environment for better functioning of organic acids secreted by Burkholderia strains for maximum P solubilization during P deficient conditions.

Functional diversity performs a key role in the isolation of nitrogen-fixing and phosphate-solubilizing bacteria from soil

Functional diversity covers diverse functional traits of microorganisms in an ecosystem. Thus, we hypothesized that it could play an important role in the isolation of nitrogen-fixing and phosphate-solubilizing bacteria. These bacteria have been considered as biofertilizer for sustainable agriculture development. Soils were collected from different sites of agricultural field and performed several microbiological tests in which we observed considerable differences in heterotrophic microbial abundance and microbial activities among the microcosms. Functional diversity depends on both microbial richness and evenness. Based on the results of metabolic fingerprinting of the carbon sources of BiOLOG-ECO plates, richness and evenness was measured by determining Shannon diversity index and Gini coefficient, respectively. The results showed significant differences in both microbial richness and evenness, suggesting considerable variation of functional diversity among the microcosms. Thereafter, nitrogen-fixing and phosphate-solubilizing bacteria were isolated on Burk's and Pikovskaya media, respectively. The results revealed considerable variation of both types of bacterial abundance among the microcosms. Microcosm (T2) showing the highest functional diversity houses the maximum numbers of nitrogen-fixing and phosphate-solubilizing bacteria. Similarly, the microcosm (T5) exhibiting the lowest functional diversity houses the minimum numbers of nitrogen-fixing and phosphate-solubilizing bacteria. Thus, a strong positive correlation was observed between functional diversity and both types of bacterial abundance among the soil samples. Higher richness and evenness lead to the development of increased functional diversity that facilitates to accommodate substantial numbers of nitrogen-fixing and phosphate-solubilizing bacteria in soil. Taken together, the results demonstrated that functional diversity plays an important role in the isolation of nitrogen-fixing and phosphate-solubilizing bacteria from soil.

Soil Microbial Resources for Improving Fertilizers Efficiency in an Integrated Plant Nutrient Management System

Tomorrow's agriculture, challenged by increasing global demand for food, scarcity of arable lands, and resources alongside multiple environment pressures, needs to be managed smartly through sustainable and eco-efficient approaches. Modern agriculture has to be more productive, sustainable, and environmentally friendly. While macronutrients such as nitrogen (N), phosphorus (P), potassium (K), and sulfur (S) supplied by mineral fertilizers are vital to crop production, agriculturally beneficial microorganisms may also contribute directly (i.e., biological N2 fixation, P solubilization, and phytohormone production, etc.) or indirectly (i.e., antimicrobial compounds biosynthesis and elicitation of induced systemic resistance, etc.) to crop improvement and fertilizers efficiency. Microbial-based bioformulations that increase plant performance are greatly needed, and in particular bioformulations that exhibit complementary and synergistic effects with mineral fertilization. Such an integrated soil fertility management strategy has been demonstrated through several controlled and non-controlled experiments, but more efforts have to be made in order to thoroughly understand the multiple functions of beneficial microorganisms within the soil microbial community itself and in interaction with plants and mineral resources. In fact, the combined usage of microbial [i.e., beneficial microorganisms: N2-fixing (NF), P-solubilizing, and P mobilizing, etc.] and mineral resources is an emerging research area that aims to design and develop efficient microbial formulations which are highly compatible with mineral inputs, with positive impacts on both crops and environment. This novel approach is likely to be of a global interest, especially in most N- and P-deficient agro-ecosystems. In this review, we report on the importance of NF bacteria and P solubilizing/mobilizing microbes as well as their interactions with mineral P fertilization in improving crop productivity and fertilizers efficiency. In addition, we shed light on the interactive and synergistic effects that may occur within multi-trophic interactions involving those two microbial groups and positive consequences on plant mineral uptake, crop productivity, and resiliency to environmental constraints. Improving use of mineral nutrients is a must to securing higher yield and productivity in a sustainable manner, therefore continuously designing, developing and testing innovative integrated plant nutrient management systems based on relevant biological resources (crops and microorganisms) is highly required.

Use of plant growth promoting rhizobacteria (PGPRs) with multiple plant growth promoting traits in stress agriculture: Action mechanisms and future prospects

Increased incidence of abiotic stresses impacting adversely plant growth and productivity in major crops is being witnessed all over the world. Therefore, as a result of such stress factors, plant growth under the stress conditions will be less than the non-stress conditions. Growing concerns and global demand for correct, environmentally-friendly techniques exist to reduce the adverse effects of plant stress. Under such stressful conditions, the role of interactions of plant and beneficial microorganisms is of great significance. Application of plant growth promoting rhizobacteria (PGPRs) is a useful option to decrease these stresses and is now widely in practice. Plants inoculated with PGPRs induce morphological and biochemical modifications resulting in increased tolerance to abiotic stresses defined as IST (induced systemic tolerance). PGPRs increase plant growth and resistance to abiotic stresses through various mechanisms (more than one mechanism of action) such as production of ACC (1-aminocyclopropane-1-carboxylate) deaminase, reducing production of stress ethylene, modifications in phytohormonal content, induction of synthezing plant antioxidative enzymes, improvement in the uptake of essential mineral elements, extracellular polymeric substance (EPS) production, decrease in the absorbtion of excess nutrients/heavy metals, and induction of abiotic stress resistance genes. Experimental evidence also suggests that stimulated plant growth by these bacteria is the net result of various mechanisms of action that are activated simultaneously. In this review paper, we reviewed the action mechanisms through which PGPRs could alleviate abiotic stresses (salinity, drought, heavy metal toxicity, and nutritional imbalance) in plants. Use of PGPRs is predicted to become a suitable strategy and an emerging trend in sustainable enhancement of plant growth. Generally, ACC deaminase and IAA-producing bacteria can be a good option for optimal crop production and production of bio-fertilizers in the future due to having multiple potentials in alleviating stresses of salinity, drought, nutrient imbalance, and heavy metals toxicity in plants. This review paper also emphasizes future research needs about the combined utilization of stress tolerant-PGPRs with multiple plant growth promoting (PGP) characteristics under environmental stresses.

Brazilian Ironstone Plant Communities as Reservoirs of Culturable Bacteria With Diverse Biotechnological Potential

Extensive mineral extractivism in the Brazilian Iron Quadrangle (IQ) region has destroyed large areas of land, decimating plant species, and their associated microbiota. Very little is known about the microbiota of the region; hence, cultivable bacteria associated with plants of its soils were investigated for their biotechnological potential. Samples were collected from nine plant species and six soils, and 65 cultivable bacterial isolates were obtained. These represent predominantly gram-positive bacilli (70%) capable of producing amylases (55%), proteases (63%), cellulases (47%), indole acetic acid (IAA) (46%), siderophores (26%), and to solubilize phosphate (9%). In addition, 65% of these were resistant to ampicillin, 100% were sensitive to tetracycline, and 97% were tolerant to high arsenic concentrations. Three isolates were studied further: the isolate FOB3 (Rosenbergiella sp.) produced high concentrations of IAA in vitro in the absence of tryptophan – shown by the significant improvement in plant germination and growth rate where the isolate was present. For isolates C25 (Acinetobacter sp.) and FG3 (Serratia sp.), plasmids were purified and inserted into Escherichia coli cells where they modified the physiological profile of the transformed strains. The E. coli::pFG3B strain showed the highest capacity for biofilm production, as well as an increase in the replication rate, arsenic tolerance and catalase activity. Moreover, this strain increased DNA integrity in the presence of arsenic, compared to the wild-type strain. These results help to explain the importance of bacteria in maintaining plant survival in ferruginous, rocky soils, acting as plant growth promoters, and to highlight the biotechnological potential of these bacteria.

IMPORTANCE 

The Iron Quadrangle region is responsible for ∼60% of all Brazilian iron production and, at the same time, is responsible for housing a wide diversity of landscapes, and consequently, a series of endemic plant species and dozens of rare species – all of which have been poorly studied. Studies exploring the microbiota associated with these plant species are limited and in the face of the continuous pressure of extractive action, some species along with their microbiota are being decimated. To understand the potential of this microbiota, we discovered that cultivable bacterial isolates obtained from plants in the ferruginous rocky soil of the Iron Quadrangle region have diverse biotechnological potential, revealing a genetic ancestry still unknown.

Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling

Plant rhizospheres encompass a dynamic zone of interactions between microorganisms and their respective plant hosts. For decades, researchers have worked to understand how these complex interactions influence different aspects of plant growth, development, and evolution. Studies of plant-microbial interactions in the root zone have typically focused on the effect of single microbial species or strains on a plant host. These studies, however, provide only a snapshot of the complex interactions that occur in the rhizosphere, leaving researchers with a limited understanding of how the complex microbiome influences the biology of the plant host. To better understand how rhizosphere interactions influence plant growth and development, novel frameworks and research methodologies could be implemented. In this perspective, we propose applying concepts in evolutionary biology to microbiome experiments for improved understanding of group-to-group and community-level microbial interactions influencing soil nutrient cycling. We also put forth simple experimental designs utilizing -omics techniques that can reveal important changes in the rhizosphere impacting the plant host. A greater focus on the components of complexity of the microbiome and how these impact plant host biology could yield more insight into previously unexplored aspects of host-microbe biology relevant to crop production and protection.