Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS
Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS
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DOI：
10.1128/aem.00496-21
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发表时间：
2021-08-01
影响因子：
4.4
通讯作者：
Kleindienst, Sara
中科院分区：
文献类型：
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作者：
Huang, Yu-Ming;Straub, Daniel;Kleindienst, Sara
硝酸盐还原-铁氧化（NRFO）是许多淡水生态系统中重要的微生物过程。然而，自养硝酸盐还原铁（II）氧化细菌的特点的例子是罕见的，它们的电子转移途径以及它们与侧翼社区成员的相互作用仍然在很大程度上未知。在这里，我们应用了元组学（即，宏基因组学、元转录组学和元蛋白质组学）与在自养或异养条件下生长并源自淡水沉积物的硝酸盐还原Fe（II）氧化富集培养物KS的关系。我们构建了四个宏基因组组装的基因组，估计完整性>= 95%，包括培养物KS中NRFO的关键参与者，鉴定为Gallionellaceae sp.和Rhodanopsis sp.。Gallionellaceae sp.和Rhodanopsis sp.转录物和蛋白质可能参与Fe（II）氧化（例如，mtoAB、cyc 2和mofA），反硝化（例如，napGHI），和氧化磷酸化（例如，呼吸链复合物I至V）沿着与用于碳固定的盖菌科物种转录物和蛋白质（例如，rbcL）。总的来说，我们的结果表明，在培养KS中，Gallionellaceae sp.和Rhodanalsp.是相互依赖的：而Gallionellaceae sp.固定CO2并为Rhodanalsp.提供有机化合物，Rhodanellaceae sp.可能通过NO还原来解毒NO并完成反硝化作用，这不能由Gallionellaceae sp.单独进行。此外，cbb（3）和aa（3）型细胞色素c的转录物和部分蛋白质表明了Gallionellaceae sp.的微需氧生活方式的可能性，而培养物KS在缺氧条件下生长。我们的研究结果表明，自养NRFO是通过反硝化细菌和Fe（II）氧化细菌之间的合作进行的，这可能类似于淡水环境中的微生物相互作用。重要信息硝酸盐还原Fe（II）氧化细菌广泛存在于环境中，有助于硝酸盐的去除，并影响温室气体一氧化二氮和二氧化碳的命运。硝酸盐还原Fe（II）氧化细菌的自养生长很少被研究，也没有完全了解。这种类型的研究最突出的模型系统是富集培养KS。为了深入了解在有机碳和氧的情况下，硝酸盐还原与Fe（II）氧化的代谢，我们进行了宏基因组学，元转录组学和元蛋白质组学分析的文化KS和确定Gallionellaceae属。我们的工作表明，自养硝酸盐还原耦合Fe（II）氧化不是由单个菌株进行，但至少有两个成员的细菌群落在文化KS的合作。这些发现为我们了解环境中硝酸盐还原Fe（II）氧化细菌奠定了基础。
Nitrate reduction coupled to Fe(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing Fe(II)oxidizing bacteria are rare, and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics, and metaproteomics) to the nitrate-reducing Fe(II)-oxidizing enrichment culture KS growing under autotrophic or heterotrophic conditions and originating from freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of >= 95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in Fe(II) oxidation (e.g., mtoAB, cyc2, and mofA), denitrification (e.g., napGHI), and oxidative phosphorylation (e.g., respiratory chain complexes I to V) along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be performed by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb(3)- and aa(3)-type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and Fe(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments.IMPORTANCE Nitrate-reducing Fe(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing Fe(II)oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of study is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to Fe(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic, and metaproteomic analyses of culture KS and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key Fe(II) oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to Fe(II) oxidation is not performed by an individual strain but is a cooperation of at least two members of the bacterial community in culture KS. These findings serve as a foundation for our understanding of nitrate-reducing Fe(II)-oxidizing bacteria in the environment.