Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.
BMC Genomics. 2013 Jul 17;14:485. doi: 10.1186/1471-2164-14-485.
Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order.
We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis.
The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.
生物浸出和酸性矿山排水（AMD）形成过程中金属硫化物矿物的溶解，创造了一个对大多数生命都不友好的环境。尽管只有少数几种细菌占主导地位，但 AMD 微生物生物膜群落中仍存在着大量共存且密切相关的广古菌，其中大多数细菌都难以进行培养。基于这个原因，我们使用宏基因组学来分析可能导致共存 AMD 古菌之间生态位分化的基因内容变化。我们的分析针对的是 Thermoplasmatales 和相关古菌的成员。这些结果大大扩展了该古菌目可用的基因组信息。
我们为未培养的相对低丰度的生物体 A-、E-和 Gplasma 以及一种新型生物体 Iplasma 重建了近乎完整的基因组，这些生物体都是 Thermoplasmatales 目成员，以及 Ferroplasma 类型 I 和 II。对这些生物体以及 Ferroplasma 类型 I 和 II 的基因组分析表明，它们都是兼性需氧异养生物，具有使用许多相同碳底物的能力，包括甲醇。大多数基因组都具有有毒金属抗性和表面层产生的基因。只有 Aplasma 和 Eplasma 具有完整的鞭毛基因，而除 Ferroplasma spp. 之外的所有古菌都具有菌毛产生的基因。低温电子显微镜（cryo-EM）和断层扫描（cryo-ET）强化了这些基于宏基因组学的超微结构预测。值得注意的是，只有 Aplasma、Gplasma 和 Ferroplasma spp. 具有预测的铁氧化基因，而 Eplasma 和 Iplasma 缺乏钴胺素、缬氨酸、（异）亮氨酸和组氨酸合成的大部分基因。
AMD 古菌的 Thermoplasmatales 共享大量代谢能力。我们在这里研究的所有未培养生物体（A-、E-、G-和 Iplasma）在代谢上与已鉴定的 Ferroplasma spp. 非常相似，主要通过生物合成、运动和可能的铁氧化的遗传能力来区分自己。这些结果表明，微妙但重要的基因组差异，加上未知的基因表达差异，足以区分这些生物体，从而允许它们共存。总的来说，这项研究揭示了 Thermoplasmatales 谱系中生物体的共同特征，并为 AMD 群落的功能提供了新的见解。
