Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan

Soil Amendments and Slow-Release Urea Improved Growth, Physiological Characteristics, and Yield of Salt-Tolerant Rice Under Salt Stress Conditions

The present study aimed to investigate the effects of different soil amendments coupled with nitrogen fertilizer on the morpho-physiological characteristics and yield of salt-tolerant rice under saline conditions. The soil amendments, i.e., S1: zeolite amendment, S2: coconut coir amendment, S3: humic acid amendment, and S0: no amendment, and fertilizer treatments, i.e., N1: urea, N2: slow-release urea, and N0: no N fertilizer, were kept in main plots and sub-plots, respectively, in a split-plot design. The salt-tolerant variety 'Shuangliangyou 138' was exposed to 0.3% salt irrigation water. The results showed that during the entire growth period, compared to S0, the S1 and S3 treatments increased the SPAD values by an average of 6.3%and 5.5%, respectively, the leaf area index by an average of 24.5% and 19.8%, the canopy interception rate by an average of 11.5% and 4.1%, and the aboveground biomass by an average of 36.8% and 13.9%, respectively. Moreover, under S1 and S3 conditions, the tiller number per square meter, leaf water potential, leaf water content, and chlorophyll contents were also improved under the slow-release urea than urea. Moreover, slow-release urea promoted root vitality and nutrient absorption as well as enhanced the activity of antioxidant and nitrogen metabolism enzymes than urea under the S1 and S3 conditions. In sum, the rational application of soil amendments and slow-release urea could improve the rice productivity on saline-alkali land.

Diversity and functional traits based indigenous rhizosphere associated phosphate solubilizing bacteria for sustainable production of rice

Introduction

Rice, particularly Basmati rice, holds significant global importance as a staple food. The indiscriminate use of phosphate-based fertilizers during rice production has led to high residual levels of these chemicals in soil, impacting soil health and fertility. This study aimed to address this challenge by investigating the potential of phosphate solubilizing bacteria (PSB) in improving soil fertility and boosting the growth of Basmati rice.

Methods

Using amplicon-based 16S rDNA sequencing, bacterial isolation and cultivation, conducting greenhouse and field experiments, and PSB localization, we optimized the search for PSB inoculants to enhance Basmati rice growth.

Results and discussion

Rice rhizosphere prokaryote communities showed significant differences in microbial diversity and composition between between basmati and non-basmati rice cultivated areas. Dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Firmicutes, with Actinobacteria and Proteobacteria playing a crucial role in nutrient recycling. Isolation and optimization of PSB strains, including Acinetobacter sp. MR5 and Pseudomonas sp. R7, were carried out and soil microcosm studies confirmed their efficacy in increasing soil available phosphorus concentration. Response surface methodology revealed the relative importance of factors such as pH, inoculum density and incubation temperature in maximising phosphate solubilization. Microplot experiments demonstrated the effectiveness of optimized PSB inoculants in promoting Basmati rice growth, with significant increases in plant height, tiller number, biomass, and grain yield compared to uninoculated controls. A consortium of PSB proved superior to single-strain inoculants, even with reduced chemical fertilizer application. Field trials at several rice growing sites confirmed the positive impact of the PSB consortium on grain yield, soil phosphorus availability, and plant phosphorus uptake. The competence and persistence of the inoculated strains in the rhizosphere was confirmed by FISH and BOX Polymerase Chain Reaction (BOX-PCR). This work highlights the potential of PSB-based biofertilizers to improve soil fertility, promote sustainable rice production and reduce the negative environmental impacts of chemical fertilizers. Future research would focus on scaling up these findings for widespread adoption in agriculture and exploring their applicability to other crops and agroecosystems.

Halotolerant Microorganism-Based Soil Conditioner Application Improved the Soil Properties, Yield, Quality and Starch Characteristics of Hybrid Rice under Higher Saline Conditions

Soil salinity represents a significant factor affecting agricultural productivity and crop quality. The present study was conducted to investigate the effects of soil conditioner (SC) comprising halotolerant microorganisms on the soil fertility, yield, rice quality, and the physicochemical and structural properties of starch in hybrid rice under saline conditions. The experimental treatments were composed of two high-quality hybrid rice varieties, i.e., 'Y Liangyou 957' (YLY957) and Jing Liangyou 534 (JLY534), and two soil amendment treatments, i.e., the application of SC at control levels and 2250 kg hm-2, or 'CK and SC', respectively. The crop was subjected to a mixture of fresh and sea water (EC 11 dS/m). The results demonstrated that the application of SC significantly enhanced the rice yield under salt stress conditions owing to an increase in the number of grains per panicle. Furthermore, SC was found to be effective in improving the organic matter and soil nutrient content. Furthermore, the application of SC resulted in an improvement in antioxidant defense, higher leaf SPAD values, and greater crop biomass, as well as the translocation of photo-assimilates at the heading stage. The application of SC not only improved the milling and appearance quality but also enhanced the taste value of rice by increasing the amylose and reducing the protein content. Furthermore, the application of SC also decreased the indentations on the surfaces of starch granules and cracks on the edges of the granules. The rice varieties subjected to SC exhibited excellent pasting properties, characterized by reduced proportions of amylopectin short chains and a lower gelatinization temperature and enthalpy of gelatinization. Overall, these findings serve to reinforce the efficacy of soil conditioner as a valuable tool to improve rice productivity and sustainability with improved rice grain quality under saline conditions.

PGPB and/or AM Fungi Consortia Affect Tomato Native Rhizosphere Microbiota

Tomatoes are one of the most important crops worldwide and also play a central role in the human diet. Microbial consortia are microorganism associations, often employed as bioinoculants, that can interact with the native rhizosphere microbiota. The aim of this study was to evaluate the impact of a bacterial-based biostimulant (Pseudomonas fluorescens and Bacillus amyloliquefaciens) (PSBA) in combination, or not, with a commercial inoculum Micomix (Rhizoglomus irregulare, Funnelliformis mosseae, Funnelliformis caledonium, Bacillus licheniformis, Bacillus mucilaginosus) (MYC) on the native rhizosphere communities and on tomato production. The trial was carried out using Solanum lycopersicum in an open field as follows: control full NPK (CFD), control reduced NPK (CRD), MYC, PSBA, PSBA + MYC. Bacterial population in the different samples were characterized using a next generation sequencing approach. The bioinocula effect on the native rhizosphere microbiota resulted in significant variation both in alpha and beta diversity and in a specific signature associated with the presence of biostimulants, especially in the presence of co-inoculation (PSBA + MYC). In particular, the high initial biodiversity shifts in the community composition occurred and consisted in the increase in the abundance of genera correlated to the soil acidification and in an enhanced density of nitrogen-fixing microbes. The results also highlighted the well-known rhizosphere effect.

Assessment of halotolerant bacterial and fungal consortia for augmentation of wheat in saline soils

Adaptations of green technologies to counter abiotic stress, including salinity for crops like wheat by using halotolerant microbes, is a promising approach. The current study investigated 17 salt-affected agroecological zones from the Punjab and Sindh provinces of Pakistan to explore the potential of indigenous microbial flora, with their multiple biochemical characteristics in addition to plant growth promoting (PGP) traits, for enhanced wheat production in saline areas. Initially, 297 isolated pure bacterial colonies were screened for salt tolerance, biochemical, and PGP traits. Three bacterial strains belonging to Pantoea spp. and Erwinia rhaphontici with possession of multiple characteristics were selected for the development of the halotolerant bacterial consortium. Inoculation of two local wheat varieties, Faisalabad 2008 and Galaxy 2013, with the consortium for in vitro seed germination assay and sand microcosm experiments exhibited significant improvement of selected plant growth parameters like germination percentage and root structure. Two previously reported PGP fungal strains of Trichoderma harzianum and T. viridae were also used as fungal consortium separately for pot experiments and field trials. The pot experiments exhibited a positive correlation of consortia with metabolic viz. catalase, peroxidase, and proline and agronomical parameters including shoot length, dry weight, number of spikes, spike length, and 100 grain weight. To evaluate their performance under natural environmental conditions, field trials were conducted at three salt-affected sites. Agronomical attributes including days of flowering and maturity, flag leaf weight, length and width, shoot length, number of spikes, spike length, spike weight, number of seeds spike-1, 1,000 grain weight, and plot yield indicated the efficiency of these microbes to enhance wheat growth. Concisely, the bacterial consortium showed better performance and Faisalabad 2008 was a more resistant variety as compared to Galaxy 2013. Initial promising results indicate that further extensive research on indigenous microbes might lead to the development of Pakistan's first saline-specific biofertilizers and sustainable eco-friendly agriculture practices.

Biofertilizer based on halotolerant microorganisms promotes the growth of rice plants and alleviates the effects of saline stress

Long-term soil salinization easily contributes to soil hardness, soil nutrient imbalance, and soil microbial diversity reduction, resulting in low rice yields in the salinized fields, and microbial remediation is one of the important measures to improve salinized soil. To verify the effect of biofertilizer based on halotolerant microorganisms on promoting rice growth and alleviating saline stress, this study discussed the effects of biofertilizer on soil microbial diversity and community structure and analyzed the correlation between the formation of microbial community structure and soil nutrient factors in the salinized field. The result, in comparison with applying inorganic fertilizer (referred to as CK), showed that notably increased soil available nitrogen, available phosphorus, available potassium, and rice paddy yield (p < 0.05) and significantly decreased soil electrical conductivity (p < 0.05) were achieved via biofertilizer (referred to as G2). Additionally, the application of biofertilizer contributes to the increase in soil microbial diversity and reorganization of microbial community structure, and through the analysis of linear discriminant analysis effect size, a notable difference in relative abundance was found in 13 genera, 6 families, and 3 orders between the control group and experimental groups (p < 0.05), and by linear discriminant analysis, Desulfomonas was further identified as the differentiated indicator. The redundancy analysis showed that available phosphorus and cation exchange capacity were the key environmental factors that affected microbial community structure and composition. Through bacterial functional prediction, increased rhizosphere soil bacterial metabolism, enzyme activity, membrane transport, and other potential functions were achieved by applying biofertilizer. Therefore, the application of biofertilizer could significantly alleviate rice growth stress and increase nutrient supply capacity in saline soil. These findings provide theoretical support for soil microbial improvement technology in the salinized field.

Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil

There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3-28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.