Methane-derived carbon flows into host-virus networks at different trophic levels in soil
Methane-derived carbon flows into host-virus networks at different trophic levels in soil
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DOI：
10.1073/pnas.2105124118
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发表时间：
2021-08-10
影响因子：
11.1
通讯作者：
Nicol, Graeme W.
中科院分区：
文献类型：
--
作者：
Lee, Sungeun;Sieradzki, Ella T.;Nicol, Graeme W.
大气甲烷（CH 4）浓度持续增加，微生物群落控制土壤-大气通量。虽然对调节甲烷生产和消耗的原核生物的多样性和功能有大量的了解，但尚未确定它们与土壤中病毒的积极相互作用。土壤微生物群落的宏基因组测序能够识别病毒和宿主之间的联系。然而，这并不能确定这些是否代表当前或历史的相互作用，也不能确定病毒或宿主是否活跃。在这项研究中，我们确定了积极的相互作用，个别主机和病毒种群在原位以下的转移同化碳。使用DNA稳定同位素探测结合宏基因组分析，我们的特点是甲烷燃料的微生物网络在酸性和中性pH值的土壤，特别是初级和二级利用，以及最近的转移甲烷衍生的碳病毒。来自复制的土壤孵育物的病毒重叠群中共有63%含有已知甲基营养细菌中存在的基因的同源物。富含C-13的病毒的基因组序列在多个密切相关的甲基孢囊菌种群的CRISPR阵列中超过三分之一的间隔区中表现出来，并揭示了它们之间病毒相互作用历史的差异。感染非甲烷营养型甲基营养菌和异养捕食性细菌的病毒也通过分析共享的同源基因进行了鉴定，表明碳被转移到与CH 4燃料的微生物食物网络相关的各种病毒中。
The concentration of atmospheric methane (CH4) continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH4 production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active. In this study, we identified active interactions between individual host and virus populations in situ by following the transfer of assimilated carbon. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized CH4-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers, together with the recent transfer of CH4-derived carbon to viruses. A total of 63% of viral contigs from replicated soil incubations contained homologs of genes present in known methylotrophic bacteria. Genomic sequences of C-13-enriched viruses were represented in over one-third of spacers in CRISPR arrays of multiple closely related Methylocystis populations and revealed differences in their history of viral interaction. Viruses infecting nonmethanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with CH4-fueled microbial food networks.