Core Metabolic Features and Hot Origin of Bathyarchaeota

The archaeal phylum Bathyarchaeota comprises highly diversified subgroups and is considered to be one of the most abundant microorganisms on earth. The metabolic features and evolution of this phylum still remain largely unknown. In this article, a comparative metabolic analysis of 15 newly reconstructed and 36 published metagenomic assembled genomes (MAGs) spanning 10 subgroups was performed, revealing the core metabolic features of Bathyarchaeota—namely, protein, lipid, and benzoate degradation;glycolysis;and the Wood–Ljungdahl (WL) pathway, indicating an acetyl-CoA-centralized metabolism within this phylum. Furthermore, a partial tricarboxylic acid (TCA) cycle, acetogenesis, and sulfur-related metabolic pathways were found in specific subgroups, suggesting versatile metabolic capabilities and ecological functions of different subgroups. Intriguingly, most of the MAGs from the Bathy-21 and -22 subgroups, which are placed at the phylogenetic root of all bathyarchaeotal lineages and likely represent the ancient Bathyarchaeota types, were found in hydrothermal environments and encoded reverse gyrase, suggesting a hyperthermophilic feature. This work reveals the core metabolic features of Bathyarchaeota, and indicates a hot origin of this archaeal phylum.

Determination of carbon-fixing potential of Bathyarchaeota in marine sediment by DNA stable isotope probing analysis

Bathyarchaeota is believed to play a crucial role in the global carbon cycle due to its vast biomass,broad distribution,and diverse habitat.However,its physiological and metabolic features are hard to determine without pure culture.While metagenomic analyses have shown that Bathyarchaeota has a complete inorganic carbon fixation(Wood-Ljungdahl,WL)pathway,no direct functional confirmation has been reported.To explore the inorganic carbon fixation ability of Bathyarchaeota,we used lignin and sodium bicarbonate-^(13)C(NaH^(13)CO_(3))in the long-term incubation of marine sediment samples.We found that Bathyarchaeota grew continuously in the cultivation system with lignin,and its abundance increased up to 15.3 times after10 months,increasing its fraction of all archaea from 30%to 80%.We monitored theδ^(13)C of total organic carbon to identify microbial carbon fixation in the cultivation systems,finding that it increased in the first month while NaH^(13)CO_(3)was present but only increased continuously afterward when lignin was also present.Furthermore,ultracentrifugation was performed on DNA extracted from samples at different cultivation stages to separate DNA of different buoyant densities,and bathyarchaeotal and bacterial 16S ribosomal RNA(r RNA)gene abundance were quantified using qPCR.Compared to bacteria,bathyarchaeotal 16S rRNA tended to be concentrated in heavy layers after 4 months of incubation with lignin and NaH^(13)CO_(3),indicating that Bathyarchaeota DNA contained^(13)C through proliferation based on lignin utilization and NaH^(13)CO_(3)assimilation,proving the carbon fixation capacity of Bathyarchaeota.

宏基因组学分析揭示深古菌Bathyarchaeota B242的代谢特征

【背景】海洋沉积物中蕴含着丰富的微生物资源,估算约2.9×1029个细胞,与海水中的微生物总量相当。但是由于缺少可培养物,大部分的微生物缺乏生理特征、代谢方式以及生态功能的相关研究。深古菌(Bathyarchaeota)是一类典型的未培养微生物,在全球海洋沉积物中普遍存在,并且具有很高的丰度。【目的】对深古菌代谢潜能及其在海洋沉积物中发挥的生态功能进行更加深入的研究。【方法】应用宏基因组学的技术手段,对采集自瓜伊马斯盆地的深海热液沉积物样本进行了分析,获得了一个接近完整的深古菌基因组Bathyarchaeota B242。【结果】对Bathyarchaeota B242基因组的分析发现,其具有以降解蛋白质和多种碳水化合物为主的异养代谢途径,同时还具有通过还原型乙酰辅酶A途径实现的自养途径。【结论】同时具有自养和异养代谢途径对Bathyarchaeota B242适应低物质能量供给环境下的生存起到重要作用。

岩溶环境古菌的研究进展

岩溶环境是一类具有特殊水文和水质特征的环境,蕴含着丰富的水资源同时具有重要的生态功能。微生物对岩溶环境水质具有重要的影响,然而作为地球微生物群体重要组成的古菌,相关研究报道十分有限。本文综述了近20年有关岩溶环境古菌的研究论文,总结了已报道的岩溶环境中古菌的群落组成和数量分布特征,探讨了当前岩溶环境古菌研究的现状和存在的问题,并对将来岩溶环境古菌的研究方向进行了展望。

Towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods

The archaea that can be readily cultivated in the laboratory are only a small fraction of the total diversity that exists in nature.Although molecular ecology methods,such as metagenomic sequencing,can provide valuable information independent of cell cultivation,it is only through cultivation-based experiments that they may be fully characterized,both for their physiological and ecological properties.Here,we report our efforts towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods.Initially,cells were retrieved from the sediment samples through a cell extraction procedure and the sediment-free mixed cells were then divided into different size-range fractions by successive filtration through 0.8µm,0.6µm and 0.2µm membranes.Archaeal 16S rRNA gene analyses indicated noticeable retention of different archaeal groups in different fractions.For each fraction,supplementation with a variety of defined substrates(e.g.,methane,sulfate,and lignin)and stepwise dilutions led to highly active enrichment cultures of several archaeal groups with Bathyarchaeota most prominently enriched.Finally,using a roll-bottle technique,three co-cultures consisting of Bathyarchaeota(subgroup-8)and a bacterial species affiliated with either Pseudomonas or Glutamicibacter were obtained.Our results demonstrate that a combination of cell extraction,size fractionation,and roll-bottle isolation methods could be a useful protocol for the successful enrichment and isolation of numerous slow-growing archaeal groups from marine sediments.

滨海深古菌的研究进展

深古菌(Bathyarchaeota),原名MCG(Miscellaneous Crenarchaeotal Group)古菌,是一类至今未被分离培养的古菌,普遍存在于海洋和陆地环境中。深古菌具有极高的种群多样性,目前已发现多达23个亚群。深古菌具有多种生理生化功能,能降解蛋白质、多聚碳水化合物、脂肪酸、芳香族化合物和甲基化合物等有机质,参与甲烷代谢循环,产乙酸,异化还原亚硝酸盐和硫酸盐,很可能是地球碳元素循环的重要驱动力之一。本文简要概述了深古菌的研究发展历史,阐述了深古菌的分子系统发育分析、分布和基于基因组的生理特征研究的最新进展,总结了滨海深古菌的研究现状,并对滨海深古菌研究的发展方向进行了分析和展望。

中国南海北部陆坡沉积物古菌多样性及丰度分析

【目的】海洋沉积物中的古菌在全球生物地球化学循环中充当重要的角色,深入了解沉积物中古菌群落的结构及功能特征是探究海洋沉积物中古菌参与生物地球化学循环和生态学功能的基础。【方法】采用高通量测序技术,分别对南海北部陆坡不同海域(东部,西部和神狐海域的7个站位)沉积物中古菌16SrRNA基因进行Illumina Mi Seq测序。【结果】中国南海北部陆坡沉积物中古菌的主要门类是Bathyarchaeota、Thermoplasmata、Woesearchaeota(DHVEG-6)、Thaumarchaeota(Marine Group I)、Lokiarchaeota和Marine Hydrothermal Vent Group(MHVG),还存在少量的AK8、Marine Benthic Group A和Terrestrial Hot Spring Crenarchaeota Group(THSCG)等。在潜在水合物区沉积物中还发现了甲烷代谢相关古菌(Anaerobic methanotrophic archaea,ANME)类群,主要为ANME-1、ANME-2ab和ANME-2c等。甲烷代谢古菌的分布特征也从甲烷代谢保守功能基因mcr A(Methyl coenzyme-Mreductase A)的扩增中得到了验证。利用定量PCR对南海沉积物中的细菌、古菌的16SrRNA基因和mcrA基因进行了定量,发现细菌16SrRNA基因拷贝数为10~5-10~7 copies/g(湿重),古菌16SrRNA基因拷贝数为10~5-10~6 copies/g(湿重),潜在水合物区mcrA基因拷贝数为10~3-10~5 copies/g(湿重)。【结论】揭示了中国南海北部陆坡沉积物中具有丰富的微生物资源,其中古菌种类多样且丰度较高,同时发现冷泉特征古菌群落,为深入认识和理解南海沉积物中微生物丰度和古菌多样性,以及解析古菌地球化学功能奠定基础。