Soil microorganisms surviving in mining sites have developed metal‐resistance mechanisms to biotransform metals. Their use as biofertilizers can improve phytoremediation efficiency in contaminated soils by reducing metal toxicity while promoting plant growth. We analysed through whole‐metagenome shotgun sequencing the composition, diversity and function of microbial communities present in a contaminated mine soil along a gradient of metals (As, Cu, Fe, Mn, Pb, Zn) to identify tolerant species carrying metal‐resistance functional genes that can be used in association with plants for phytoremediation. Soil samples were collected from an abandoned copper mine, across three areas with different levels of metal contamination (unaffected, moderately contaminated and highly contaminated). The relative abundance of Proteobacteria, especially genus Bradyrhizobium, increased in the highly contaminated area, whereas Actinobacteria dominated in the unaffected area. Archaea (Euryarchaeota) predominated in the moderately contaminated area, Haloarcula, Halobacterium and Halorubrum being the most abundant genera. The fungi Basidiomycota did not exhibit differences among the areas, whereas Ascomycota, especially the genus Aspergillus, increased in areas with low metal concentrations. Metal‐resistance genes associated with Fe (acn, furA, dpsA), Cu (cop‐unnamed, copF, actP, copA, mmco, cutO) and As (arsT, arsC, aioA/aoxB) metabolism were the most abundant and were affected by the gradient of soil contamination. Those associated with Cu predominated in the most contaminated area, whereas As and Fe genes were more abundant in the least contaminated. Among the carriers of these metal‐resistance genes, Bradyrhizobium diazoefficiens, Pseudomonas aeruginosa, Halorubrum trapanicum, Aspergillus fumigatus and A. fischeri were dominant in the most contaminated area. These species could give rise to promising biofertilizers to be used in association with suitable plants for the phytoremediation of contaminated mining sites.

中文翻译：

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金属（胶体）污染梯度下矿区土壤微生物群落的分类和功能分析

在采矿现场幸存的土壤微生物已开发出抗金属机制以生物转化金属。它们用作生物肥料可通过降低金属毒性同时促进植物生长来提高被污染土壤的植物修复效率。我们通过全基因组shot弹枪测序，分析了沿金属梯度（As，Cu，Fe，Mn，Pb，Zn）存在于受污染矿山土壤中的微生物群落的组成，多样性和功能，从而确定了具有抗金属功能的耐性物种可与植物结合用于植物修复的基因。土壤样品是从一个废弃的铜矿中采集的，分布在三个金属污染程度不同的地区（未受影响，中度污染和高度污染）。变形杆菌，尤其是属的相对丰度缓生根瘤菌在高度污染的地区增加，而放线菌在未受影响的地区占主导地位。在中度污染的区域为主古（广古菌门），Haloarcula，嗜盐杆菌和Halorubrum是最丰富的属。真菌担子菌在各区域之间没有差异，而在金属浓度低的地区，子囊菌，尤其是曲霉属，有所增加。以Fe（相关联金属抗性基因ACN，的furA，DPSA），铜（COP-无名，copF，ACTP，COPA，mmco，cutO）和As（arsT，arsC，aioA / aoxB）代谢最丰富，并且受到土壤污染梯度的影响。与铜有关的那些在受污染最严重的地区占主导地位，而砷和铁的基因在受污染最少的地区更为丰富。在这些金属抗性基因的载体，慢生根瘤菌diazoefficiens，绿脓杆菌，Halorubrum trapanicum，烟曲霉和A.鲵在污染最严重的地区占主导地位。这些物种可能会产生有前途的生物肥料，与合适的植物结合使用，以对受污染的采矿场进行植物修复。