Core bacteria carrying the genes associated with the degradation of atrazine in different soils

Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities

The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.

Pyraclostrobin repeated treatment altered the degradation behavior in soil and negatively affected soil bacterial communities and functions

This study investigated the degradation dynamics of the fungicide pyraclostrobin in three apple orchard soils, along with the responses of soil bacterial community compositions, functions, co-occurrence patterns, and soil nitrogen cycling, under repeated treatment strategies in laboratory conditions. The degradation half-lives of pyraclostrobin varied across the soil types, ranging from 15.7 to 43.4 days, in the following order: Anyang soil > Qingdao soil > Yangling soil. Repeated pyraclostrobin treatment affected degradation behaviors across the different soils. Pyraclostrobin significantly inhibited soil microbial activity and reduced soil bacterial diversity, with more pronounced negative effects observed at high-concentration treatment. Pyraclostrobin clearly changed soil bacterial community structures, significantly enriching potentially degradative bacterial genera such as Methylibium and Nocardioides, which showed increases in the relative abundances of 3.0-181.8 % compared with control. Additionally, pyraclostrobin reduced the complexity of soil bacterial networks and modified the diversity of functional modules. Notably, repeated treatment severely disrupted soil nitrogen cycling, with the absolute abundances of amoA, amoB, nifH, nirK, and nirS in high-concentration treatment decreasing by up to 19.4-91.8 % compared with control. Collectively, pyraclostrobin repeated application altered the degradation behavior, inhibited soil microbial activities, modified soil bacterial community structures and co-occurrence patterns, and seriously disrupted soil nitrogen cycling.

A novel microbial agent reduces soil paclobutrazol residue, enhances enzyme activities and increases Ophiopogon japonicus production

Background

Ophiopogon japonicus (O. japonicus) is a versatile plant valued for its medicinal, food, and ornamental properties. Its cultivation often involves the excessive use of paclobutrazol, leading to a series of environmental and agricultural problems such as soil contamination, nutrient depletion, and safety risks. However, there is currently no effective solution.

Methods

Based on a novel microbial agent, Micrococcus yunnanensis strain HY001 (MYSH), field experiments were conducted in the main production area of O. japonicus. Soil paclobutrazol residue, soil enzyme activities, and the yield and dry matter ratio of O. japonicus were measured. Hierarchical partitioning (HP) was used to identify the relative importance of different variables, and partial least squares path modeling (PLS-PM) was applied to elucidate the mechanisms underlying MYSH's effects on soil health and crop production.

Results

MYSH significantly reduced soil paclobutrazol residue by 75.18% over five months, compared to a natural degradation rate of 50.72% over a year. Compared to the control group, the MYSH-treated group enhanced soil sucrase activity, soil urease activity, and soil alkaline phosphatase activity, with rates of 47.81%, 46.70%, and 216.66%, respectively. Additionally, MYSH improved O. japonicus productivity, with a 94.75% increase in yield and a 17.64% increase in dry matter ratio. HP revealed that MYSH was the primary factor affecting the yield and dry matter ratio of O. japonicus, with relative importance of 47.75% and 42.28%, respectively. The key mechanism was that MYSH degraded soil paclobutrazol residue, which in turn influenced soil sucrase activity, ultimately impacting the yield of O. japonicus (p < 0.05).

Conclusions

This study demonstrates the dual role of MYSH as both an environmental remediation agent and a crop productivity enhancer for the first time. By reducing paclobutrazol residue and enhancing soil health and crop production, MYSH shows great potential for broader application in sustainable agricultural practices. This research highlights the efficacy of microbial agents in addressing agrochemical contamination and promoting sustainable farming, providing a valuable contribution to the development of eco-friendly agricultural solutions.

Influence Mechanism of Vermicompost with Different Maturity on Atrazine Catabolism and Bacterial Community

Atrazine causes serious contamination of agricultural soils and groundwater. This study investigated the influence mechanism of sterilized soil (CKs), unsterilized soil (CKn), sterilized soil amended with 45 (SsV1), 60 (SsV2), 75 (SsV3) days of vermicompost (the maturity days of vermicompost), and unsterilized soil amended with 45 (SnV1), 60 (SnV2), 75 (SnV3) days of vermicompost on atrazine catabolism. The atrazine degradation experiment lasted for 40 days. The results showed that the atrazine degradation rates for CKs, CKn, SsV1, SsV2, SsV3, SnV1, SnV2, and SnV3 were 24%, 56.9%, 62.8%, 66.1%, 65.9%, 87.5%, 92.9%, and 92.3%, respectively. Indigenous microorganisms capable of degrading atrazine were present in unsterilized soil, and the addition of vermicompost enhanced atrazine degradation. The humic acid content of SnV2 was the highest, at 4.11 g/kg, which was 71.97% higher than that of CKn. The addition of the vermicompost enhanced the production of hydroxyatrazine, deethylatrazine, and deisopropylatrazine. Vermicompost increased the abundance of atrazine-degrading bacteria (Mycobacterium, Devosia, etc.), and introduced new atrazine-degrading bacteria (Mesorhizobium, Demequina). The above results showed that the best degradation of atrazine was achieved with 60 days of vermicompost addition. This study provides a new, efficient, economical, and environmentally friendly strategy for the remediation of atrazine-contaminated soil.

Impact of superabsorbent hydrogels on microbial community and atrazine fate in soils by 14C-labeling techniques

The accumulation of atrazine in soils can create environmental challenges, potentially posing risks to human health. Superabsorbent hydrogel (SH)-based formulations offer an eco-friendly approach to accelerate herbicide degradation. However, the impact of SHs on soil microbial community structure, and thus on the fate of atrazine, remains uncertain. In this study, a radioactive tracer was employed to investigate the influence of SHs on microbial communities and atrazine transformation in soils. The results revealed that the mineralization of atrazine in active soils was considerably greater than that in sterilized soils. Atrazine degradation proceeded rapidly under SH treatment, indicating the potential of SH to accelerate atrazine degradation. Furthermore, SH addition did not alter the atrazine degradation pathway in soils, which included dealkylation, dechlorination and hydroxylation. The relative abundance of dominant microbial population was influenced by the presence of SHs in the soil. Additionally, SH application led to an increased relative abundance of Lysobacter, suggesting its potential involvement in atrazine degradation. These findings reveal the significance of soil microorganisms and SH in atrazine degradation, offering crucial insights for the development of effective strategies for atrazine remediation and environmental sustainability.

Biodegradation of atrazine and nicosulfuron by Streptomyces nigra LM01: Performance, degradative pathway, and possible genes involved

Microbial herbicide degradation is an efficient bioremediation method. In this study, a strain of Streptomyces nigra, LM01, which efficiently degrades atrazine and nicosulfuron, was isolated from a corn field using a direct isolation method. The degradation effects of the identified strain on two herbicides were investigated and optimized using an artificial neural network. The maximum degradation rates of S. nigra LM01 were 58.09 % and 42.97 % for atrazine and nicosulfuron, respectively. The degradation rate of atrazine in the soil reached 67.94 % when the concentration was 108 CFU/g after 5 d and was less effective than that of nicosulfuron. Whole genome sequencing of strain LM01 helped elucidate the possible degradation pathways of atrazine and nicosulfuron. The protein sequences of strain LM01 were aligned with the sequences of the degraded proteins of the two herbicides by using the National Center for Biotechnology Information platform. The sequence (GE005358, GE001556, GE004212, GE005218, GE004846, GE002487) with the highest query cover was retained and docked with the small-molecule ligands of the herbicides. The results revealed a binding energy of - 6.23 kcal/mol between GE005358 and the atrazine ligand and - 6.66 kcal/mol between GE002487 and the nicosulfuron ligand.

Impacts of farming activities on carbon deposition based on fine soil subtype classification

Introduction

Soil has the highest carbon sink storage in terrestrial ecosystems but human farming activities affect soil carbon deposition. In this study, land cultivated for 70 years was selected. The premise of the experiment was that the soil could be finely categorized by subtype classification. We consider that farming activities affect the soil bacterial community and soil organic carbon (SOC) deposition differently in the three subtypes of albic black soils.

Methods

Ninety soil samples were collected and the soil bacterial community structure was analysed by high-throughput sequencing. Relative changes in SOC were explored and SOC content was analysed in association with bacterial concentrations.

Results

The results showed that the effects of farming activities on SOC deposition and soil bacterial communities differed among the soil subtypes. Carbohydrate organic carbon (COC) concentrations were significantly higher in the gleying subtype than in the typical and meadow subtypes. RB41, Candidatus-Omnitrophus and Ahniella were positively correlated with total organic carbon (TOC) in gleying shallow albic black soil. Corn soybean rotation have a positive effect on the deposition of soil carbon sinks in terrestrial ecosystems.

Discussion

The results of the present study provide a reference for rational land use to maintain sustainable development and also for the carbon cycle of the earth.

Coinoculation of arbuscular mycorrhizal fungi and rhizobia stimulates atrazine dissipation by changing the atrazine-degrading bacterial community at the soil aggregate scale

As a potential low-cost and environmentally friendly strategy, bioremediation of herbicide polluted soil has attracted increasing attention. However, there is a lack of knowledge regarding the response of the atrazine-degrading bacterial community to coinoculation of arbuscular mycorrhizal (AM) fungi and rhizobia for atrazine dissipation. In this study, a pot experiment was conducted with AM fungi Glomus mosseae (AM), rhizobia Rhizobium trifolii TA-1 (R) and their coinoculation (AMR) with atrazine. In each treatment, the atrazine-degrading bacterial community of four soil size aggregates, namely large macroaggregates (LMa), small macroaggregates (SMa), microaggregates (Mia) and primary particles (P) were investigated. The results showed that the atrazine residue concentration was lowest in AMR, and that in LMa was also significantly lower than that in the other smaller aggregate sizes. Overall, inoculation, the aggregate fraction and their interaction had significant effects on soil TN, SOC, AP and pH. For the atrazine-degrading bacterial community, the Chao1 index increased with decreasing particle size, but the Shannon index decreased. Moreover, the abundances of the dominant atrazine-degrading bacterial genera Arthrobacter, Bacillus, Marmoricola and Nocardioides in the Mia and P particle size groups were greater than those in the LMa and SMa groups in each treatment. The bacterial communities in the Mia and P particle sizes in each treatment group were more complex. Therefore, coinoculation of AM fungi and rhizobia stimulated atrazine dissipation by changing the atrazine-degrading bacterial community, and the response of the atrazine-degrading bacterial community to each aggregate size varied depending on its distinct soil physicochemical properties.