Exploring microbial diversity responses in agricultural fields: a comparative analysis under pesticide stress and non-stress conditions

Effects of pesticide application on soil bacteria community structure in a cabbage-based agroecosystem in Ghana

Modern sustainable agriculture often relies on pesticide application, which may unintentionally affect non-target soil microorganisms. This study assessed the effects of commonly used pesticides in cabbage cultivation on bacteria diversity, composition, and abundance in soils from some farming communities in Bosome Freho District, Ghana. The pesticides included a neonicotinoid (acetamiprid), microbial agents (Pieris rapae granulosis virus+ Bacillus thuringiensis), avermectin (emamectin benzoate), and pyrrole (chlorfenapyr). Soil samples were collected from non-contaminated (NCS), abandoned pesticide-contaminated (AB-PCS) and actively pesticide-contaminated (AC-PCS) soils. Bacteria communities were analysed in the soil at phylum, class, order, family, genus, and species levels using 16S rRNA gene sequencing. The soils were also analyzed for physicochemical properties. Our results showed a decrease in bacteria diversity and abundance in pesticide-contaminated soils in the following order: NCS > AB-PCS > AC-PCS. Sorensen's coefficient of similarity indicated major shifts in bacteria taxa composition due to pesticide contamination. In NCS, Pseudomonas veronii, Bacillus sp., and Prevotella albensis were the most abundant species, while Rhodoplanes elegans and Nostocoida limicola dominated AB-PCS. In AC-PCS, R. elegans, Gemmata obscuriglobus, Nitrospira calida, and N. limicola were the most abundant species. The abundance of Bacillus sp., P. veronii, and P. albensis decreased in the contaminated soils, while the abundance of N. calida, Cystobacter sp., Pedomicrobium australicum and Byssovorax cruenta was higher in the contaminated soils. Key genera involved in nutrient cycling such as Clostridium, Bacillus, Prevotella, Pseudomonas, and Arthrobacter, declined in abundance in pesticide exposed soils. In contrast, an increase in abundance of various taxa such as Pedomicrobium, Hyphomicrobiaceae, Pirellulaceae, Comamonadaceae, Nitrospirales, Nitrospira, Anaerolineae, Planctomycetes, Acidobacteriaí and Nitrospirae was observed in the contaminated soils. These bacteria may possess bioremediation potential that could be exploited for environmental remediation. Soil physicochemical properties and nutrient levels varied across the three soil treatments, with potential implications for bacteria community structure.

Emission of CO2 enhanced by thiamethoxam and cadmium in agricultural soil

The coexistence of neonicotinoid insecticide thiamethoxam (TMX) and heavy metal cadmium (Cd) is quite common in agricultural soils, yet their effects on the emission of greenhouse gas CO2 remain insufficiently studied. To address this issue, microcosms spiked with singe or combined TMX (20 mg/kg) and Cd (20 mg/kg) in soil were studied for 90 days. It turned out that single TMX (+12.13 %) and Cd (+22.76 %) both stimulated the emission of CO2, and the combined TMX and Cd exhibited synergic effect (+51.00 %). The presence of Cd reduced the attenuation of TMX (-3.32 %), while the presence of TMX increased the attenuation of Cd (+3.11 %). The relative abundances of bacteria Sphingomonas, Devosia, Erythrobacter, Phaselicystis, Woeseia, FFCH7168, Rhizorhapis, Hamadaea and genes related to sugar metabolism, glycolysis and the TCA cycle were found positively correlated to CO2 emission in the studied microcosms (p < 0.05). Results from this study provide scientific basis for developing sound environmental policies that aim to reduce CO2 emission from agricultural soils.

Functional versus compositional tests in the risk assessment of the impacts of pesticides on the soil microbiome

The Organisation of Economic Co-operation and Development (OECD) 216 nitrogen transformation test is used to understand the impacts of plant protection products (PPPs) on the soil microbiome. However, there is significant interest in developing the European PPP risk assessment to include new technologies such as amplicon sequencing to assess impacts on soil microbial community composition and diversity. We have little understanding of how to generate endpoints from amplicon sequencing data sets, their robustness, and whether they provide an appropriate level of protection to the soil microbiome. Our study addresses this key knowledge gap. We conducted a dose-response OECD 216 study with two chemicals, nitrapyrin and streptomycin, and calculated traditional functional endpoints, in accordance with the OECD 216 guideline, and used amplicon sequencing techniques to generate a range of endpoints based on soil bacterial diversity, richness, dissimilarity from the control, species sensitivity distributions, and threshold indicator analysis. We show it is possible to generate a range of endpoints from amplicon sequencing data sets; however, these endpoints varied significantly based on the calculation method, with up to a 101-fold difference between the least and most sensitive endpoints. Additionally, the relative sensitivity of these endpoints compared to the currently used functional OECD 216 metrics was compound dependent, with many endpoint calculation methods unable to detect the impacts of nitrapyrin on the soil microbiome at concentrations deemed ecotoxicologically relevant by OECD 216. Our study shows amplicon sequencing methods to study soil microbial ecotoxicology did not perform consistently and reliably when considering both nitrapyrin and streptomycin treatments and in many cases did not consistently provide an enhanced degree of protection over the functional OECD 216 assessments already integrated into the PPP risk assessment.

Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus

During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566T, delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566T. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HST (DSM 115941T = NRRL B-65665T). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology.

IMPORTANCE

The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.