Adaptive Genomic Features of Raoultella ornithinolytica LAM1 from the Geothermal Site of Los Azufres Reveal Potential for Heavy-Metal Bioremediation.

IF 2.6 3区生物学 Q3 MICROBIOLOGY

Current Microbiology Pub Date : 2025-09-28 DOI:10.1007/s00284-025-04507-4

Grisel Fierros-Romero, Mauricio Nahuam Chávez-Avilés, Mariana Hoflack-Culebro, Cassandra Orozco-Neri, Darlene A Juárez-Beltrán, Mónica M Luviano-Reyes, Ilse Macedo-Ramírez, Marcos De Donato-Capote, Hectorina Rodulfo, David Enrique Zazueta-Alvarez, Ernesto Rodríguez-Andrade, Dianella Iglesias, Ashutosh Sharma

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Abstract

Raoultella ornithinolytica strain LAM1, a facultative anaerobe isolated from a metal-rich geothermal pond in Los Azufres, Mexico, grew in sodium arsenate concentrations up to 1500 ppm (7.215 mM/L). Whole-genome sequencing yielded a 6.01-Mbp draft genome across 104 contigs, encoding 5744 predicted genes annotated using Prokka and NCBI PGAP. Among these, 99 genes were associated with resistance to arsenic, mercury, copper, zinc, cobalt, cadmium, nickel, and lead. We identified a complete ars operon (arsR-arsB-arsC-arsA-arsD) with three arsC paralogs; mer operon genes (four merA copies, merR); zntA-zntR; copA-cueO-cusA; and the metal homeostasis system nikABCDE-nikR. Functional classification assigned 27.9% of resistance genes to zinc, 20.9% to nickel, 18.6% to copper, and 16.3% to arsenic. Cluster of orthologous genes (COG) annotation revealed enrichment in ABC-type permeases (COG0601/1173/0444), metal ion efflux systems (COG1566), and redox enzymes. Growth on CHROMagar™ ESBL medium indicated β-lactamase activity. Comparative analysis with 508 publicly available R. ornithinolytica genomes confirmed conservation of core resistance operons and identified adaptations in sulfur metabolism (dsrB). These results support R. ornithinolytica strain LAM1's survival in metal-contaminated geothermal environments and indicate potential for bioremediation applications.

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来自Los azures地热遗址的鸟类溶解Raoultella ornithinolytica LAM1的适应性基因组特征揭示了重金属生物修复的潜力

Raoultella ornithinolytica菌株LAM1是一种兼性厌氧菌，从墨西哥Los Azufres富含金属的地热池中分离出来，在砷酸钠浓度高达1500 ppm （7.215 mM/L）的环境中生长。全基因组测序获得了包含104个contigs的6.01 mbp草图基因组，编码5744个使用Prokka和NCBI PGAP注释的预测基因。其中，99个基因与对砷、汞、铜、锌、钴、镉、镍和铅的抗性有关。我们发现了一个完整的ars操纵子（arsR-arsB-arsC-arsA-arsD），它有三个arsC类似子；mer操纵子基因（4个merA拷贝，merR）；zntA-zntR;copA-cueO-cusA;以及金属稳态系统nikABCDE-nikR。功能分类将27.9%的抗性基因分配给锌，20.9%的抗性基因给镍，18.6%的抗性基因给铜，16.3%的抗性基因给砷。同源基因簇（COG）注释显示在abc型透膜（COG0601/1173/0444）、金属离子外排系统（COG1566）和氧化还原酶中富集。在CHROMagar™ESBL培养基上生长表明β-内酰胺酶活性。与508个已公开的溶鸟鼠基因组的比较分析证实了核心抗性操纵子的保守性，并确定了硫代谢（dsrB）的适应性。这些结果支持了鸟毒R. ornithinolytica菌株LAM1在金属污染的地热环境中存活，并显示了生物修复应用的潜力。

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来源期刊

Current Microbiology 生物-微生物学

CiteScore

4.80

自引率

3.80%

发文量

380

审稿时长

2.5 months

期刊介绍： Current Microbiology is a well-established journal that publishes articles in all aspects of microbial cells and the interactions between the microorganisms, their hosts and the environment. Current Microbiology publishes original research articles, short communications, reviews and letters to the editor, spanning the following areas: physiology, biochemistry, genetics, genomics, biotechnology, ecology, evolution, morphology, taxonomy, diagnostic methods, medical and clinical microbiology and immunology as applied to microorganisms.