Analysis of Nitrification in Agricultural Soil and Improvement of Nitrogen Circulation with Autotrophic Ammonia-Oxidizing Bacteria

Unveiling the dual role of heterotrophic ammonia-oxidizing bacteria: enhancing plant regrowth through modulating cytokinin delivery

This study aims to investigate the dual impacts of heterotrophic ammonia-oxidizing bacteria (HAOB) strains on the regrowth of Italian ryegrass by studying cytokinin delivery from roots to leaves. The dual impacts encompass both the "soil-inside-role" and "soil-outside-role," which refer to the HAOB operating inside and outside the rhizosphere soil within the rhizosphere microenvironment. The experimental design consisted of two sets of experiments, Exp-1 and Exp-2, involving different treatments. In Exp-1, various concentrations of NO3- were added to the roots to observe the soil-inside-role on cytokinin delivery from roots to leaves. In Exp-2, NO3- addition was combined with HAOB inoculation to observe the combined effects of the root-outside-role and root-inside-role on cytokinin synthesis and transport. The results indicated that NO3- concentrations ranging from 30 to 40 mmol L-1 had the most optimal effect on increasing leaf cytokinin content and delivery from roots to leaves, consequently promoting greater leaf regrowth biomass. When inoculated, the HAOB strain significantly increased rhizosphere soil nitrification rates under the soil-inside-role, leading to increased NO3- release from the soil and a subsequent boost in cytokinin delivery from roots to leaves. Additionally, the HAOB strain independently enhanced cytokinin delivery from roots to leaves outside the rhizosphere soil within the rhizosphere microenvironment, demonstrating its soil-outside-role. The combined effects of the soil-inside-role and soil-outside-role substantially increased leaf cytokinin content, playing a crucial role in promoting Italian ryegrass regrowth. The study's findings shed light on the mechanisms through which HAOB can enhance plant growth by performing dual roles in the rhizosphere, offering potential applications in agriculture. Understanding the interaction between HAOB, cytokinins, and plant growth could lead to more effective strategies for improving crop productivity and promoting sustainable agriculture.

Effect of Ammonia-Oxidizing Bacterial Strains That Coexist in Rhizosphere Soil on Italian Ryegrass Regrowth

Potted Italian ryegrasses (Lolium multiflorum L.) were used to investigate the effect of ammonia-oxidizing bacterial (AOB) strain that coexisted in rhizosphere soil on Italian ryegrass regrowth. The results showed that the isolated and screened AOB strain (S2_8_1) had 100% similarity to Ensifer sesbaniae. The inoculation of S2_8_1 on day 44 before defoliation caused its copy number in rhizosphere soils to increase by 83-157% from day 34 before defoliation to day 14 after defoliation compared with that in Italian ryegrass without S2_8_1 inoculation, indicating that S2_8_1 coexisted permanently with Italian ryegrass. The coexistence promoted the delivery of root-derived cytokinin to leaves and to increase its cytokinin concentrations; thus, the Italian ryegrass regrowth accelerated. During the 14-day regrowth period, the S2_8_1 coexistence with Italian ryegrass caused its leaf and xylem sap cytokinin concentrations, rhizosphere soil nitrification rates, net photosynthetic rates, and total biomass to increase by 38%, 58%, 105%, 18%, and 39% on day 14 after defoliation, respectively. The inoculation of S2_8_1 on day 2 before defoliation also increased the regrowth of Italian ryegrass. Thus, the coexistence of AOB with Italian ryegrass increased its regrowth by regulating the delivery of cytokinins from roots to leaves.

Effect of ammonia-oxidizing bacterial strain that survives drought stress on corn compensatory growth upon post-drought rewatering

A pot experiment was performed under rain-shelter conditions to explore the effects of drought stress and post-drought rewatering on the abundance of an ammonia-oxidizing bacteria (AOB) strain in corn (Zea mays L.) rhizosphere soils and the relationship between the AOB strain and corn (Zea mays L.) compensatory growth after drought stress rewatering. Corn seedlings were used as test materials, and one AOB strain was isolated and screened from the soil. The experimental design included six treatments: (1) wet (WT), (2) wet with AOB strain inoculation during wetness (WI), (3) wet with AOB strain inoculation during rewatering (WR), (4) post-drought rewatering (DT), (5) post-drought rewatering with AOB strain inoculation during wetness (DI), and (6) post-drought rewatering with AOB strain inoculation during rewatering (DR). Wetness and drought stress were obtained by keeping the soil water content at 75-80% and 50-55% of the field capacities, respectively. The results showed that the isolated and screened AOB strain (S2_8_1) had 100% similarity to Ensifer sesbaniae. The inoculation of S2_8_1 during the wet period in the DI treatment caused it to colonize the rhizosphere soil. Drought stress decreased its abundance, but rewatering resulted in a great increase. The S2_8_1 in the DI treatment increased the total biomass, water use efficiencies, net photosynthetic rates, rhizosphere soil nitrification rates, leaf cytokinin concentrations, xylem sap cytokinin concentrations, copy number of S2_8_1 in rhizosphere soils, and organic carbon contents in rhizosphere soils by 23, 104, 35, 30, 18, 29, 104, and 23% on day 10 after rewatering compared with WT treatment. In the DI treatment, the increase in rhizosphere soil nitrification rates caused by S2_8_1 during wetness was closely related to the cytokinin delivery from roots to leaves and increased leaf cytokinin concentrations. The increase in leaf cytokinin concentrations improved rewatering corn growth, which caused compensatory growth and increased water use. Compensatory and over-compensatory growths occurred in DT and DR treatments, respectively. Therefore, the coexistence of the strain of AOB with corn in rhizosphere soil increased the corn compensatory growth by regulating soil nitrification and root-induced leaf cytokinin.

Polyester-based biodegradable plastics: an approach towards sustainable development

Non-degradability of conventional plastics, filling of landfill sites, raising water and land pollution and rapid depletion of fossil resources have raised the environmental issues and global concerns. The current demand and production of plastics is putting immense pressure on fossil resources, consuming about 6% of the global oil and is expected to grow up to 20%. The polyester-based biodegradable plastics (BPs) are considered as a remedy to the issue of plastics waste in the environment. BPs appear to manage the overflow of plastics by providing new means of waste management system and help in securing the non-renewable resources of nature. This review comprehensively presents the environmental burdens due to conventional plastics as well as production of polyester-based BPs as an alternative to conventional commodity plastics. The diversity of micro-organisms and their enzymes that degrade various polyester-based BPs (PLA, PCL, PHB/PHBV and PET) has also been described in detail. Moreover, the impact of plastics degradation products on soil ecology and ecosystem functions has critically been discussed. The report ends with special focus on future recommendations for the development of sustainable waste management strategies to control pollution due to plastics waste. SIGNIFICANCE AND IMPACT OF THE STUDY: Polyester-based BPs considered as a solution to current plastic waste problem as well as leading polymers in terms of biodegradability and sustainability has been critically discussed. The role of microorganisms and their enzymes involved in the biodegradation of these polymers and ecotoxicological impact of degradation products of BPs on soil microbial community and biogeochemical cycles has also been described. This report will provide an insight on the key research areas to bridge the gap for development of simulated systems as an effective and emerging strategy to divert the overflow of plastic in the environment as well as for the greener solution to the plastic waste management problems.

Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils

The recent discovery of complete ammonia oxidation (comammox) process in a single organism challenged the division of labor between two functional groups in the classical two-step nitrification model. However, the distribution and activity of comammox bacteria in various environments remain largely unknown. This study presented a large-scale investigation of the geographical distribution, phylogenetic diversity, and activity of comammox Nitrospira in typical agricultural soils. Among the 23 samples harvested across China, comammox Nitrospira clade A was ubiquitously detected at 4.14 × 10⁴-1.65 × 10⁷amoA gene copies/g dry soil, with 90% belonging to the subclade A2. The abundance of comammox Nitrospira clade B was two orders of magnitude lower than clade A. In all samples, comammox Nitrospira were 1-2 orders of magnitude less abundant than canonical nitrifiers, and soils with slightly high pH and C/N tended to enrich more comammox Nitrospira. Unlike canonical nitrifiers, comammox Nitrospira had sustained amoA gene transcription regardless of external ammonia supply, indicating their competitive advantage over other nitrifiers under low-ammonia conditions. When fed with 1 mM ammonium for 15 days, comammox Nitrospira in tested soils were enriched 2.36 times higher than those enriched by the same amount of nitrite, indicating their preference to utilizing ammonia as the substrate. DNA-SIP further confirmed the in situ nitrification activity of comammox Nitrospira. This study provided new insights into the broad distribution and diversity of comammox Nitrospira in agricultural soils, which could potentially play an important role in the microbial nitrogen cycle in soils.

Composting swine carcasses with nitrogen transformation microbial strains: Succession of microbial community and nitrogen functional genes

In this study, nitrogen transformation strains, including three ammonium transformation strains, one nitrite strain and one nitrogen fixer, were inoculated at different swine carcass composting stages to regulate the nitrogen transformation and control the nitrogen loss. The final total nitrogen content was significantly increased (p < 0.01). The bacterial communities were assessed by amplicon sequencing and association analysis. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were the four most dominant phyla.,Brevibacterium, Streptomyces and Ochrobactrum had a significant (p < 0.05) and positive correlation with total nitrogen and ammonium nitrogen content in both groups. The quantitative results of nitrogen transformation genes showed that ammonification, nitrification, denitrification and nitrogen fixation were simultaneously present in the composting process of swine carcasses, with the latter two accounting for a higher proportion. The ammonium transformation strains significantly (p < 0.05) strengthened nitrogen fixation and remarkably (p < 0.01) weakened nitrification and denitrification, which, however, were notably (p < 0.05) enhanced by the nitrite strain and nitrogen fixer. In this research, the inoculated strains changed the bacterial structure by regulating the abundance and activity of the highly connected taxa, which facilitated the growth of nitrogen transformation bacteria and regulated the balance/symbiosis of nitrogen transformation processes to accelerate the accumulation of nitrogen.

Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions

Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant establishment resulting in materials prone to wind and water dispersal. The specific objective of this study was to associate pyritic mine waste acidification, characterized through pore-water chemistry analysis, with dynamic changes in microbial community diversity and phylogenetic composition, and to evaluate the influence of different treatment strategies on the control of acidification dynamics. Samples were collected from a highly instrumented one-year mesocosm study that included the following treatments: 1) unamended tailings control; 2) tailings amended with 15% compost; and 3) the 15% compost-amended tailings planted with Atriplex lentiformis. Tailings samples were collected at 0, 3, 6 and 12months and pore water chemistry was monitored as an indicator of acidification and weathering processes. Results confirmed that the acidification process for pyritic mine tailings is associated with a temporal progression of bacterial and archaeal phylotypes from pH sensitive Thiobacillus and Thiomonas to communities dominated by Leptospirillum and Ferroplasma. Pore-water chemistry indicated that weathering rates were highest when Leptospirillum was most abundant. The planted treatment was most successful in disrupting the successional evolution of the Fe/S-oxidizing community. Plant establishment stimulated growth of plant-growth-promoting heterotrophic phylotypes and controlled the proliferation of lithoautotrophic Fe/S-oxidizers. The results suggest the potential for eco-engineering a microbial inoculum to stimulate plant establishment and inhibit proliferation of the most efficient Fe/S-oxidizing phylotypes.

Brazilian Cerrado soil reveals an untapped microbial potential for unpretreated polyethylene biodegradation

Discarded PE-based products pose a social and environmental threat because of their recalcitrance to degradation, a consequence of the unique set of PE's physicochemical properties. In this study we isolated nine novel PE-degrading bacteria from plastic debris found in soil of the savanna-like Brazilian Cerrado. These bacterial strains from the genera Comamonas, Delftia, and Stenotrophomonas showed metabolic activity and cellular viability after a 90-day incubation with PE as the sole carbon source. ATR/FTIR indicated that biodegraded PE undergone oxidation, vinylene formation, chain scission, among other chemical changes. Considerable nanoroughness shifts and vast damages to the micrometric surface were confirmed by AFM and SEM. Further, phase imaging revealed a 46.7% decrease in the viscous area of biodegraded PE whereas Raman spectroscopy confirmed a loss in its crystalline content, suggesting the assimilation of smaller fragments. Intriguingly, biodegraded PE chemical fingerprint suggests that these strains use novel biochemical strategies in the biodegradation process. Our results indicate that these microbes are capable of degrading unpretreated PE of very high molecular weight (191,000gmol^-1) and survive for long periods under this condition, suggesting not only practical applications in waste management and environmental decontamination, but also future directions to understand the unraveled metabolism of synthetic polymers.

Influence of Temperature and Copper on Oxalobacteraceae in Soil Enrichments

β-Proteobacteria is one of the most abundant phylum in soils, including autotrophic and heterotrophic ammonium-consumers with relevance in N circulation in soils. The effects of high-temperature events and phytosanitary treatments, such as copper amendments, on soil bacterial communities relevant to N-cycling remain to be studied. As an example, South Portugal soils are seasonally exposed to high-temperature periods, the temperature at the upper soil layers can reach over 40 °C. Here, we evaluated the dynamics of mesophilic and thermophilic bacteria from a temperate soil, in particular of heterotrophic β-Proteobacteria, regarding the ammonium equilibrium, as a function of temperature and copper treatment. Soil samples were collected from an olive orchard in southern Portugal. Selective enrichments were performed from samples under different conditions of temperature (30 and 50 °C) and copper supplementation (100 and 500 µM) in order to mime seasonal variations and phytosanitary treatments. Changes in the microbial communities under these conditions were examined by denaturing gradient gel electrophoresis, a molecular fingerprint technique. At moderate temperature--30 °C--either without or with copper addition, dominant members were identified as different strains belonging to genus Massilia, a genus of the Oxalobacteraceae (β-Proteobacteria), while at 50 °C, members of the Brevibacillus genus, phylum Firmicutes were also represented. Ammonium production during bacterial growth at moderate and high temperatures was not affected by copper addition. Results indicate that both copper and temperature selected specific tolerant bacterial strains with consequences for N-cycling in copper-treated orchards.

Isolation and identification of phytate-degrading bacteria and their contribution to phytate mineralization in soil

To better understand the phosphorus (P) cycling in an agricultural soil environment, amounts of total, organic and inorganic P in 10 agricultural soil samples were analyzed. Since a large proportion (57.8%) of the total P in the soils was in organic form, a method was developed to evaluate the mineralization rate of organic P in the soil by adding phytate to the soil and analyzing the change in water-soluble P (WSP) content after incubating it for 3 days. Moreover, the relationship between the phytate mineralization activity and bacterial biomass in 60 agricultural soils was also investigated, where the phytate mineralization activity ranged from 0 to 61.7% (average: 18.8%), and the R² value between phytate mineralization activity and indigenous bacterial biomass was 0.11 only. Phytate-degrading bacteria were isolated from the soil environment, and identified as Pseudomonas rhodesiae JT29, JT32, JT33, JT34, JT35, Pseudomonas sp. JT30, and Flavobacterium johnsoniae JT31. When P. rhodesiae JT29 and F. johnsoniae JT31 were inoculated into the agricultural soils, the phytate mineralization activities were increased up to 16 and 27 times, respectively. It was concluded that promotion of effective phytate-degrading bacterial strains could improve the sustainable P management in the agricultural soils.