What role do biocontrol agents with Mg
2+
play in the fate of antibiotic resistome and pathogenic bacteria in the phyllosphere?
Authors: Zhi Qiqi , Tan Ge , Wu Shaolong , Ma Qianqian , Fan Jianqiang , Chen Yiqiang , Li Jingjing , Hu Zhengrong , Xiao Yansong , Li Liangzhi , Liu Zhenghua , Yang Zhaoyue , Yang Zhendong , Meng Delong , Yin Huaqun , Tang Qianjun , Liu Tianbo 
Published: March 2024

The contamination of the plant phyllosphere with antibiotics and antibiotic resistance genes (ARGs), caused by application of antibiotics, is a significant environmental issue in agricultural management. Alternatively, biocontrol agents are environmentally friendly and have attracted a lot of interest. However, the influence of biocontrol agents on the phyllosphere resistome remains unknown. In this study, we applied biocontrol agents to control the wildfire disease in the Solanaceae crops and investigated their effects on the resistome and the pathogen in the phyllosphere by using metagenomics. A total of 250 ARGs were detected from 15 samples, which showed a variation in distribution across treatments of biocontrol agents (BA), BA with Mg
2+
(T1), BA with Mn
2+
(T2), and kasugamycin (T3) and nontreated (CK). The results showed that the abundance of ARGs under the treatment of BA-Mg
2+
was lower than that in the CK group. The abundance of
cphA3
(carbapenem resistance),
PME-1
(carbapenem resistance),
tcr3
(tetracycline antibiotic resistance), and
AAC (3)-VIIIa
(aminoglycoside antibiotic resistance) in BA-Mg
2+
was significantly higher than that in BA-Mn
2+
(
P
< 0.05). The abundance of
cphA3
,
PME_1,
and
tcr3
was significantly negatively related to the abundance of the phyllosphere pathogen
Pseudomonas syringae
(
P
< 0.05). We also found that the upstream and downstream regions of
cphA3
were relatively conserved, in which
rpl
,
rpm,
and
rps
gene families were identified in most sequences (92%). The Ka/Ks of
cphA3
was 0 in all observed sequences, indicating that under the action of purifying selection, nonsynonymous substitutions are often gradually eliminated in the population. Overall, this study clarifies the effect of biocontrol agents with Mg
2+
on the distribution of the phyllosphere resistome and provides evolutionary insights into the biocontrol process.

IMPORTANCE

Our study applied metagenomics analysis to examine the impact of biocontrol agents (BAs) on the phyllosphere resistome and the pathogen. Irregular use of antibiotics has led to the escalating dissemination of antibiotic resistance genes (ARGs) in the environment. The majority of BA research has focused on the effect of monospecies on the plant disease control process, the role of the compound BA with nutrition elements in the phyllosphere disease, and the resistome is still unknown. We believe BAs are eco-friendly alternatives for antibiotics to combat the transfer of ARGs. Our results revealed that BA-Mg
2+
had a lower relative abundance of ARGs compared to the CK group, and the phyllosphere pathogen
Pseudomonas syringae
was negatively related to three specific ARGs,
cphA3
,
PME-1,
and
tcr3
. These three genes also present different Ka/Ks. We believe that the identification of the distribution and evolution modes of ARGs further elucidates the ecological role and facilitates the development of BAs, which will attract general interest in this field.