红树林土壤病毒多样性和潜在的生物地球化学影响

Diversities and potential biogeochemical impacts of mangrove soil viruses11.607Microbiome . 2019 Apr 11;7(1):58. doi: 10.1186/s40168-019-0675-9.

Abstract

Background: Mangroves are ecologically and economically important forests of the tropics. As one of the most carbon-rich biomes, mangroves account for 11% of the total input of terrestrial carbon into oceans. Although viruses are considered to significantly influence local and global biogeochemical cycles, little information is available regarding the community structure, genetic diversity and ecological roles of viruses in mangrove ecosystems.   Methods: Here, we utilised viral metagenomics sequencing and virome-specific bioinformatics tools to study viral communities in six mangrove soil samples collected from different mangrove habitats in Southern China.   Results: Mangrove soil viruses were found to be largely uncharacterised. Phylogenetic analyses of the major viral groups demonstrated extensive diversity and previously unknown viral clades and suggested that global mangrove viral communities possibly comprise evolutionarily close genotypes. Comparative analysis of viral genotypes revealed that mangrove soil viromes are mainly affected by marine waters, with less influence coming from freshwaters. Notably, we identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from mangrove viruses, most of which participate in biolysis of complex polysaccharides, which are abundant in mangrove soils and organism debris. Host prediction results showed that viral CAZyme genes are diverse and probably widespread in mangrove soil phages infecting diverse bacteria of different phyla.   Conclusions: Our results showed that mangrove viruses are diverse and probably directly manipulate carbon cycling by participating in biomass recycling of complex polysaccharides, providing the knowledge essential in revealing the ecological roles of viruses in mangrove ecosystems.   Keywords: Auxiliary metabolic genes; Carbon cycling; Mangrove soil; Viromes; Viruses.

红树林是热带生态和经济上重要的森林，作为碳含量最高的生物群落之一，红树林占陆地碳输入海洋总量的11％。病毒对本地和全球生物地球化学循环有显着影响，但关于红树林生态系统中病毒的群落结构、遗传多样性和生态作用的我们仍知之甚少。

2015年10月至2017年3月，从中国南方广西和海南省的三个不同红树林栖息地（海湾、河流和港口）收集了6个土壤样本（下图）。

病毒样本富集分为两步：第一、样品制备过程中富集。将纯化的病毒颗粒通过0.22μm过滤器过筛，以确保无外源DNA污染；并用延长消化时间用DNase I处理。通用引物27F / 1492R对细菌16S rRNA基因进行PCR扩增，验证无游离和污染细菌DNA污染。第二、测序数据纯化。对高通量测序病毒体reads进行了后验计算机过滤，以识别和去除任何非病毒信号。

1、红树林土壤病毒群落的形态和分类多样性

以NCBI RefSeqVirus数据库为参考来确定病毒分类。从红树林土壤中鉴定出总共51个属，2082种病毒体。真核ssDNA Circoviridae（天然感染鸟类和哺乳动物），ssDNA噬菌体家族Microviridae和真核ssDNA家族Nanoviridae（天然感染植物）富集。 dsDNA病毒最多隶属于Caudovirales（天热感染细菌和古细菌）（下图）。

2、红树林土壤病毒群落的遗传多样性

使用不同标记基因对六种病毒体的主要病毒家族进行系统发育分析，来评估六种红树林土壤中病毒的多样性和遗传距离。

3、红树林病毒中丰富的辅助碳水化合物代谢基因

为了研究红树林病毒的功能多样性，将预测的病毒ORF与基eggNOG数据库比较，进行了6个病毒体的直系同源组（COG）注释。正如所料，大多数ORFs的注释很少，表明红树林土壤中存在大量未表征的病毒基因。与其他辅助代谢功能相比，“碳水化合物转运和代谢”在红树林病毒体中明显过多（下图a）。

此外，基于AMG系统发育树识别编码CAZymes的病毒宿主。预测了10种CAZymes的推定宿主（下表）。系统发育分析显示病毒多糖脱乙酰酶与来自不动杆菌的多糖脱乙酰酶聚集，表明该AMG可能来源于感染该细菌的噬菌体（下图）。红树林生态系统病毒CAZymes具有潜在巨大影响。

本研究首次系统地探索了红树林土壤中的病毒群落。红树林土壤中存在广泛的多样性，且主要受海水影响，来自淡水的影响较小。从红树林土壤病毒中鉴定了丰富的CAZyme基因，病毒性碳水化合物AMG在全球碳循环中的作用可能非常显着。红树林土壤病毒可能通过复合多糖的生物分解直接操纵碳循环，这意味着环境病毒具有更大的多样性和更重要的作用。