Holmes Dawn E, Shrestha Pravin M, Walker David J F, Dang Yan, Nevin Kelly P, Woodard Trevor L, Lovley Derek R
Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA.
Appl Environ Microbiol. 2017 Apr 17;83(9). doi: 10.1128/AEM.00223-17. Print 2017 May 1.
The possibility that (formerly ) and species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of accounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET. Most of the e-pilin genes and transcripts were affiliated with species, but sequences most closely related to putative e-pilin genes from genera such as , , , and , were also detected. Approximately 17% of all metagenomic and metatranscriptomic bacterial sequences clustered with species, and the finding that spp. were actively transcribing growth-related genes indicated that they were metabolically active in the soils. Genes coding for e-pilin were among the most highly transcribed genes. In addition, homologs of genes encoding OmcS, a -type cytochrome associated with the e-pili of and required for DIET, were also highly expressed in the soils. species in the soils highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support CO reduction in Thus, these results are consistent with a model in which species were providing electrons to species for methane production through electrical connections of e-pili. species are some of the most important microbial contributors to global methane production, but surprisingly little is known about their physiology and ecology. The possibility that DIET is a source of electrons for in methanogenic rice paddy soils is important because it demonstrates that the contribution that makes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that when species receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus, growth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason that species are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation with spp., and possibly other methanogens, via DIET.
在稻田土壤中研究了（以前的）和物种在陆地产甲烷环境中通过直接种间电子转移（DIET）进行合作的可能性。与导电菌毛（e-菌毛）的PilA菌毛单体基因具有高度序列相似性的基因，在宏基因组文库中占PilA基因序列的一半以上，在RNA测序（RNA-seq）文库中占mRNA转录本的42%。这种丰富的e-菌毛蛋白基因和转录本具有重要意义，因为e-菌毛可以作为DIET的通道。大多数e-菌毛蛋白基因和转录本与物种相关，但也检测到了与、、和等属的假定e-菌毛蛋白基因最密切相关的序列。所有宏基因组和宏转录组细菌序列中约17%与物种聚类，并且物种正在积极转录与生长相关基因这一发现表明它们在土壤中具有代谢活性。编码e-菌毛蛋白的基因是转录水平最高的基因之一。此外，编码OmcS的基因的同源物，一种与的e-菌毛相关且DIET所需的细胞色素，在土壤中也高度表达。土壤中的物种高度表达参与将二氧化碳还原为甲烷的酶的基因。DIET是已知唯一支持还原二氧化碳的电子供体。因此，这些结果与一个模型一致，即物种通过e-菌毛的电连接为物种提供电子以产生甲烷。物种是全球甲烷产生的一些最重要的微生物贡献者，但令人惊讶的是，对它们的生理学和生态学知之甚少。DIET作为产甲烷稻田土壤中物种的电子来源的可能性很重要，因为它表明在陆地环境中对甲烷产生的贡献可能超出了将乙酸盐转化为甲烷的范围。此外，明确的共培养研究表明，当物种从DIET获得一些能量时，它们比以乙酸盐为唯一能量来源时生长得更快。因此，产甲烷土壤中的生长和代谢可能比通常认为的更快、更稳健。结果还表明，物种反复被发现是产甲烷土壤中代谢活性最高的微生物之一的原因是它们通过DIET与物种以及可能的其他产甲烷菌进行共生生长。
