微生物学报  2021, Vol. 61 Issue (6): 1441-1462   DOI: 10.13343/j.cnki.wsxb.20210230.
http://dx.doi.org/10.13343/j.cnki.wsxb.20210230
中国科学院微生物研究所,中国微生物学会,中国菌物学会
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文章信息

林喜铮, 谢伟. 2021
Xizheng Lin, Wei Xie. 2021
深部生物圈古菌的研究进展与展望
Research progresses and prospects of archaea in deep biosphere
微生物学报, 61(6): 1441-1462
Acta Microbiologica Sinica, 61(6): 1441-1462

文章历史

收稿日期:2021-04-16
修回日期:2021-05-17
网络出版日期:2021-05-21
深部生物圈古菌的研究进展与展望
林喜铮1,2 , 谢伟1,2     
1. 中山大学海洋科学学院, 广东 珠海 519082;
2. 南方海洋科学与工程广东省实验室(珠海), 广东 珠海 519082
摘要:古菌作为深部生物圈中常见的原核生物,广泛分布于各类海洋沉积生境中,在沉积物生物地球化学循环中发挥着重要作用。由于不同的古菌类群对环境条件存在生理适应性差异,它们分别在近岸沿海和开阔大洋沉积物中构成了厌氧微生物生态系统和好氧微生物生态系统。本文通过对近岸与远洋、沉积物与上覆水体两个不同维度的古菌群落结构进行比较,以及对出现在深部生物圈中的常见古菌(奇古菌门(Thaumarchaeota)、深古菌门(Bathyarchaeota)、底栖古菌目(Thermoprofundales)、Asgard古菌超级门、乌斯古菌门(Woesearchaeota))的分布、代谢和环境适应机制进行论述,总结了深部生物圈中古菌的研究进展,并在此基础上展望了几个未来研究的方向与重点。
关键词古菌    深部生物圈    海洋沉积物    分布    代谢    
Research progresses and prospects of archaea in deep biosphere
Xizheng Lin1,2 , Wei Xie1,2     
1. College of Marine Science, Sun Yat-Sen University, Zhuhai 519082, Guangdong Province, China;
2. Southern Laboratory of Ocean Science and Engineering(Guangdong, Zhuhai), Zhuhai 519082, Guangdong Province, China
Abstract: As a common prokaryote in the deep subsurface biosphere, archaea are widely distributed in various marine sedimentary habitats and play important roles in the biogeochemical cycles. Due to the differences in physiological adaptabilities of different archaeal groups to environmental conditions, they constitute anaerobic microbial ecosystem and aerobic microbial ecosystem in coastal and open ocean sediments, respectively. In this paper, we compare the archaeal community structure in two different dimensions: nearshore and ocean, sediment and overlying water, and discuss the distribution, metabolism and environmental adaptation mechanism of common archaea (Thaumarchaeota, Bathyarchaeota, Thermoprofundales, Asgard, Woesearchaeota) in deep subsurface biosphere. We summary the research progresses of archaea in the deep subsurface biosphere. We also put forward several future research directions and key points of archaea for references.
Keywords: archaea    deep subsurface biosphere    marine sediment    distribution    metabolism    

自1977年Woese和Fox运用核糖体RNAs的分子系统发育分析,将古菌确定为细菌和真核生物之外的第三种生命形式以来,古菌逐渐成为学术界研究的热点[1]。最初的几十年里,古菌一直被认为是专性嗜极微生物,只存在于高温、高压、高盐和厌氧[2-4]等极端环境中,并被划分为两个主要门类:广古菌门(Euryarchaeota)和泉古菌门(Crenarchaeota)[3, 5-6]。后来,温带富氧海水中泉古菌的发现[3, 5]颠覆了以前关于古菌专性嗜极端环境的观点。基于16S rRNA序列比对以及基因组学分析,将中温泉古菌划分为一个新门——奇古菌门(Thaumarchaeota)[7]。近年来,随着高通量测序技术的发展,自然界大量未培养的古菌被发现。大量研究表明,古菌广泛存在于淡水[8]、土壤[9]、河口[10-11]、海洋[3, 5, 12]等常规生境,以及盐湖[13]、热泉[14]、海底热液[15]等极端生境中,其参与甚至主导了生物圈生源元素循环的关键过程[16]。古菌作为海洋微生物的重要组成部分,是海洋生态系统中物质与能量传递的重要贡献者,在全球生物地球化学循环中扮演着不可或缺的角色。

目前,古菌家族主要包含约30个门,隶属于四个超级门:广古菌、TACK、DPANN和Asgard。其中,TACK包括奇古菌门、泉古菌门、深古菌门(Bathyarchaeota)[17]、初古菌门(Korarchaeota)[18]Geothermarchaeota[19]Marsarchaeota[20]Nezharchaeota[21]、韦斯特古菌门(Verstraetearchaeota)[19, 22]和曙古菌门(Aigarchaeota)[23]。DAPNN主要包括Diapherotrites[24]Aenigmarchaeota[24]、微古菌门(Parvarchaeota)[25-26]、纳古菌门(Nanoarchaeota)[27-28]、盐纳古菌门(Nanohaloarchaeota)[29]、佩斯古菌门(Pacearchaeota)[25]、乌斯古菌门(Woesearchaeota)[25]Micrarchaeota[25-26]Altiarchaeota[27]Huberarchaeota[27]。Asgard则包括洛基古菌门(Lokiarchaeota)[30]、索尔古菌门(Thorarchaeota)[31]、海拉古菌门(Helarchaeota)[32]、奥丁古菌门(Odinarchaeota)[33]、海姆达尔古菌门(Heimdallarchaeota)[33]和葛德古菌门(Gerdarchaeota)[34]。TACK的不同门之间的代谢功能差异很大。DAPNN的一些成员被假设为具有共生或寄生的生活方式。Asgard超级门的成员被认为是与真核生物关系最密切的原核生物。例如,Asgard古菌成员含有编码真核生物特征蛋白的基因,而这些基因曾被认为是真核生物所特有[30, 32-34]。尽管迄今为止只获得了极少的纯培养古菌菌株,但包括宏基因组学和单细胞基因组学在内的非培养技术能够极大地帮助我们拓宽对古菌多样性和功能的理解[24]。此外,组学数据结果也可为未培养古菌的富集培养提供指导[35]

海洋沉积物覆盖了地球表面70%的面积,代表着地球上最大的微生物栖息地之一,蕴藏着和海水一样多的生物量[36]。“大洋钻探计划”开展近半个世纪以来,最令人激动的重要成果之一是大洋“深部生物圈”的发现,即海底沉积物深处乃至岩石中仍有生命[37]。在过去的几十年里,科学家们通过在不同的海洋环境中进行科学的海洋钻探,探索了海底生命的性质和范围。目前,海洋沉积物中微生物细胞总数估计为2.9×1029–5.4×1029个,占地球总生物量的0.18%–3.6%,相当于4 Pg的生物量碳[38-39]。细胞计数和孔隙水化学分析表明,海底沉积物中的微生物呼吸速率通常极低,平均每细胞每年转移2.8×10–18至1.1×10–14摩尔电子,这取决于电子供体和受体的可用性[40-41]。单细胞靶向稳定同位素探测培养和纳米级二次离子质谱研究表明,在不同深度范围的海底沉积物样品中(包括来自2 km深的缺氧中新世沉积物[42]和距今101.5 Ma的含氧沉积物[43]),大多数微生物细胞都能将碳、氮化合物同化为细胞生物量。另外,基于沉积物中古菌膜脂计算出的TEX86指标,被广泛应用于古海水温度重建[44],这些脂类化合物最早被认为都来自生活在海洋表层的奇古菌[44],但是,近期研究表明,海洋沉积物中原位自生的各种古菌类群,也能产生这些膜脂化合物,对TEX86的计算产生了一定的影响[45]。由此可见,古菌作为海洋沉积物中微生物的重要组分,在生物地球化学研究中扮演着极为重要的角色。

尽管几十年来对各种海底沉积生境中的微生物生物量进行了广泛的探索,但古菌的丰度和分布仍然存在争议[46]。本文综述了近岸与远洋深部生物圈中古菌的水平分布,并以上覆水体古菌为比较对象,探讨了深部生物圈中古菌的独特之处,同时,对常见古菌的分布、代谢和环境适应机制进行了总结。

1 古菌在近岸与开阔大洋深部生物圈中分布的比较

海底以下沉积环境中含有数量可观的微生物,它们分别在近岸沿海和开阔海洋环流之下构成厌氧微生物生态系统[39]和好氧微生物生态系统[40]。微生物生物量、多样性和丰富度一般随着沉积物深度和埋藏时间的增加而降低[38, 47]。在沿海富含有机质的缺氧沉积物中,细胞丰度通常比在开阔大洋贫有机质的含氧沉积物中高出一个数量级[40]。最近一项研究利用基于微流控技术的数字PCR分析表明,在海洋边缘和开阔大洋,古菌16S rRNA基因占总16S rRNA基因(即古菌和细菌的16S rRNA基因)的相对丰度平均分别为22.6%和5.9%[47]。这种差异可能意味着古菌对厌氧微生物生态系统的贡献比对好氧微生物生态系统的贡献更大[47]。为了评估古菌细胞在原核生物群落中的比重,采用16S rRNA基因在古菌和细菌基因组上的平均拷贝数(分别为1.7和4.7拷贝/基因组)[48],估计古菌占海洋沉积物细胞总数的37.3%,相当于1.1×1029个细胞,其中海洋边缘沉积物中的古菌比例明显高于远洋沉积物(分别为40.0%和12.8%)[47]

到目前为止,大多数研究都集中在相对富含有机质的沉积物[49]。然而,大于2000米水深的深海沉积物覆盖的范围高达海底总面积的89%[50],与大陆边缘或沿海沉积物相比,它们通常具有贫营养、有机碳含量较低(< 1%)、沉积速率较慢等特点[50]。氧或硝酸盐等电子受体在这些贫营养沉积物中可穿透至几米[51]或几十米[52]的深度。与此形成鲜明对比的是,在富含有机物质的大陆边缘或陆架沉积物中,这些强电子受体仅在几厘米范围内就被消耗殆尽。贫营养沉积物中氧化区和硝酸盐还原区的扩大是碳沉积速度缓慢和微生物对有机碳再矿化作用的结果。在覆盖地球大部分表面的贫营养海洋沉积物中,强电子受体类型和较慢的电子供体沉积速率的综合作用,导致该环境下的微生物代谢活动受到明显的限制[53]。除了氧和有机碳浓度外,可能限制深层沉积生物圈古菌群落的因素还包括温度、盐度、压力、pH、沉积物孔隙度或渗透性等。例如,如果沉积物中没有流体传输(断层流动、泥火山活动和碳氢化合物渗漏),且质子泵驱动的鞭毛运动不太可能在如此低的能量下发生,因此微生物细胞的移动可能仅限于扩散传输[36]。在这种情况下,即使在孔隙度非常大的沉积层中,微生物在100万年内的移动距离可能仅达到6 m[41, 54]。根据能量可用性和微生物过程的数学模型,维持生存所需的能量(而非生长所需的能量)是构成沉积物中微生物群落消耗的总能量的主要部分[55]

缺氧海底沉积物中的古菌群落的分类组成与含氧海底沉积物中古菌群落的分类组成明显不同[36]。深古菌门、广古菌门中的底栖古菌目(Thermoprofundales)、Asgard古菌超级门已被确定为典型的、广泛存在于海洋缺氧沉积物中的古菌类群[56]。这些在富含有机质的缺氧沉积物中占据主导地位的古菌类群通常在贫营养沉积物中也会存在较低丰度[53]。与厌氧群落相反,好氧沉积物中古菌群落由奇古菌门的成员(如Nitrososphaerales)主导。奇古菌的这种优势表明海水微生物被掺入到含氧沉积物中并在那里定殖的可能性[57]。此外,在部分研究所获得的沉积物中,乌斯古菌门、Hadesarchaeaeota、纳古菌门占古菌群落总丰度的比例很高[36, 58]。研究发现,古菌16S rRNA基因的相对丰度通常随着钻探地点水深的增加而降低,表明水深是制约古菌相对丰度的关键环境因子之一,原因可能是有机物从水体光合带向下沉积到不同深度的海底时,其剩余部分在质量和数量上的差异[59]。有机物的不同可能导致不同的氧气消耗速率,从而导致沉积物中不同的氧气浓度。此外,与水深相关的任何其他因素也可能影响沉积生境中的古菌种群。

驱动贫营养沉积物中的古菌群落结构有别于富营养的因素可能是:(1)难降解有机物分布差异。在颗粒下沉过程中,有机物的组成和数量会发生显著变化,在通过深海水柱后,预计会变得更加难以降解。在对电子供体竞争激烈的贫营养沉积物中,能够代谢难降解底物的微生物比不能利用这些底物的微生物更具优势[60]。(2)沉降速率慢。贫营养沉积物的主要特征是沉积速率慢,导致微生物可利用的底物含量很低,能量也很有限。随着进入沉积物的有机碳被微生物降解,惰性的有机质变得越来越丰富起来[53]。(3)高能电子受体的深度渗透。由于沉降量和碳通量的减少导致电子受体耗尽的速度变慢,高能电子受体(氧、硝酸盐)在贫营养沉积物中渗透到更大的深度范围,而非被限制在表层沉积物中。因此,能够高效利用这些受体的特定古菌谱系在贫营养沉积物中占优势[47]

若以电子受体组成梯度划分沉积物的营养状态,氧气和硝酸盐渗透超过几十厘米至几米,并且没有硫酸盐消耗,这是贫营养沉积物的特征,甚至在部分超贫营养海区,如在南太平洋环流下的沉积物中,氧气的存在可从海底表层一直到玄武岩基底[40];显示硫酸盐下降,但在几百米深的沉积物中没有耗尽,将其认为是中度营养沉积物;富营养沉积物的氧气和硝酸盐渗透深度只有几厘米到几毫米,硫酸盐耗尽深度只有几十米甚至更少,硫酸盐的耗竭导致沉积物深层产甲烷[53]。不同氧化还原生境的定义意味着每个生境中特定的微生物活动和生理状况,因此古菌群落沿着沉积物营养状态的梯度会发生明显的变化,中度营养沉积物作为贫营养至富营养沉积物的过渡,可能同时拥有二者的部分特定古菌类群。在超贫营养海区的沉积物中,奇古菌在古菌群落中占有绝对优势。沿着沉积物营养状态梯度,深古菌、Asgard古菌、底栖古菌目等古菌类群在古菌群落中的比例逐渐升高,直至在富营养的缺氧沉积物中,这些古菌类群变得占据优势地位[61-62]

2 深部生物圈与上覆水体中古菌的比较

Tara Oceans项目估计了近表层海洋(海平面以下0至1000 m)中海洋原核生物(古菌和细菌)的全球多样性,一共包含3.75×104个基于16S rRNA的操作分类单元[63]。这些海水样品的古菌群落组成随温度变化而变化,其中以奇古菌门和广古菌门中的MG-II古菌(Candidatus Poseidoniales)在古菌群落中占优势地位。相较而言,深古菌门、广古菌门中的底栖古菌目、Asgard古菌超级门在海洋沉积物中占优势[36]。值得注意的是,在贫营养的深海好氧沉积物古菌群落中,奇古菌门占有绝对的主导地位[36]。在能量匮乏的有氧沉积环境中,奇古菌能够在长时间尺度上保持原位优势与海洋浮游AOA对营养通量较低(如氨)的贫营养环境的适应是一致的[64],在有氧海底沉积物中,氨一般低于检测阈值[65]。沉积物AOA通常代表与浮游AOA类群不同的谱系[66-67],这种分化可能由它们不同的生理适应性过程导致[68]。海水样本中,大多数氨氧化古菌(AOA)属于MG-I.1a(包括α-AOA、β-AOA、γ-AOA)的成员[69],而沉积物中占主导的是MG-I.1b中的Nitrososphaerales的成员,由于对光照、底物等环境因素的敏感性不同,各个亚群在不同的环境中可能拥有各自的生存优势。此外,海洋沉积生物圈中古菌的相对丰度与全球海洋中的估计值相似,分别为37.3%和41.9%,这表明古菌在整个海洋水体和沉积物微生物生态系统中的生物量可与细菌相媲美[47]

在描述生活在北大西洋超贫营养海区沉积物中的好氧微生物群落的多样性、丰富度、功能潜力和生存能力的一项研究中发现,所提取的DNA主要是来自生活在沉积物中的活细胞,大部分胞外DNA(environmental DNA)都与粘土矿物发生了化学结合而对DNA提取具有抵抗力,并且培养实验表明沉积物中的活细胞可以利用与矿物质结合的eDNA作为生长底物[70]。这些实验结果表明在该研究中所提取的DNA主要来源于沉积物中的活细胞。

3 深部生物圈中的常见古菌 3.1 奇古菌门(Thaumarchaeota)

Marine Group I(MG-I)古菌最早发现于温带海水中[3]。MG-I古菌分布广泛,在近岸水域及开阔大洋区域都十分普遍,在这些地区的微生物群落中占有相当大的比例[71]。氨氧化古菌(AOA)Nitrosopumilus maritimus SCM1的成功分离,证实了古菌具有氨氧化的能力[72]。对编码氨单加氧酶(AMO)α亚基的古菌amoA基因的分析表明,具有氨氧化潜力的古菌在自然环境中普遍存在[66, 73-74]。目前,分离得到的纯培养海洋奇古菌菌株很少,且都属于Nitrosopumilaceae科的成员[72]

然而,并不是所有的奇古菌都是氨氧化古菌,也不是所有的AOA都是专性自养氨氧化菌。前人已研究发现属于奇古菌的非AOA成员[24, 75-77],这些非AOA成员在奇古菌系统发育树上形成了基础类群(group I.1c),代表了奇古菌系统发育树中最深的谱系[76]。陆地上的非AOA成员被认为是AOA的祖先,它们在获得AOA的好氧氨氧化、钴胺和生物素生物合成途径后,将它们的栖息地扩展到海洋环境,这一过程可能主要是由氧气推动的[78]。此外,非AOA成员既可以在厌氧条件下生长,也可以在有氧条件下生长,氧气可能会影响非AOA成员群落的多样性和结构[79]

一些沿海AOA菌株能够吸收和同化有机碳化合物,被认为是营混合营养生活[80]。作为混合营养的证据,α-酮酸不仅能够增强一些AOA的活性,还在H2O2的解毒中发挥着重要作用[81]。因此,明确AOA是利用有机化合物提供生长所需的能量,还是将其用于其他生理代谢途径来改善自身的生长状况是非常重要的。奇古菌Group I.1b (Nitrososphaeraceae)的成员在污泥中过着异养的生活方式,但它们编码了amoA基因[82]。这表明,在特定条件下,并不是所有的AOA都是专性自养氨氧化菌。然而,没有明确的证据表明这些异养的AOA不能自养或实际上是混合营养。有趣的是,发现了一组与AOA关系密切的海洋奇古菌姊妹类群,它们不属于基础类群,且缺乏氧化氨和AOA特定的碳固定的能力[77, 83]。根据宏基因组学数据,这一组奇古菌广泛存在于海洋环境中,其基因组小于AOA,并且可能编码在核苷酸清除中发挥作用的III型核酮糖-二磷酸羧化酶(rubisco)[77, 83]。这一组AOA姊妹群的发现改变了人们对奇古菌代谢多样性的认识。

氨氧化古菌是地球上普遍存在的氨氧化生物之一,栖息于温和和极端环境中,也被发现是海洋无脊椎动物的共生菌[84-85]。一些AOA培养物的生长温度高达70℃以上[86],pH值范围为4.0至7.5[87]。然而,在较宽的温度(0.2℃至97℃)[88]、pH (2.5至9.0)和盐度(从0至38 psu)[89]范围,都发现了古菌amoA基因。这一发现意味着AOA或amoA编码古菌(AEA)可能会比目前所了解的更为普遍。根据许多基于amoA基因的研究,AOA或AEA的分布和丰度与环境密切相关。它们通常可以分为海洋和陆地类群[73, 90]。海洋类群的分布主要与水深有关,反映了不同生态类型对不同光照和氨浓度的响应和适应[69, 91],而陆地类群主要按pH值划分[92]

细菌amoA基因的转录随着溶解氧(DO)浓度的降低而降低,而DO的变化对古菌amoA基因的转录没有显著影响,不同的氨氧化微生物对沉积物溶解氧的变化具有不同的响应[93]。古菌amoA基因通常在海洋氧极小区或缺氧区高度丰富[94]。光线也会影响AOA的分布,古菌AMO酶比细菌AMO酶对光抑制更敏感[95],这会导致海洋次表层中AOA的富集。此外,温度对AOA的多样性和分布也有影响[96]。这是因为温度变化可能会影响底物的利用率,这对于微生物生长是至关重要的[97]。光和温度的季节性变化是控制不同AOA物种分布的重要因素[98]。AOA被认为是贫营养环境(例如贫营养海洋)中氮循环的主要参与者[66, 89]。在某些富营养化河口和湖泊,它们也被认为是主要的氨氧化者[99]。磷酸盐通常会限制近岸海区水生微生物的生长。因此,据报道,河口AOA具有许多与磷酸盐转运相关的基因以及与磷酸盐获取相关的调控系统[100]。或者,它们可以通过使用多磷酸盐酶和磷酸酶来利用各种类型的磷源[101]。在珠江口和九龙河口等富营养化河口中,AOA基因组编码参与重金属运输和调控系统以及碳水化合物代谢的额外基因,这可能是适应这些河口富营养化和重金属污染的重要策略[100-101]。这些环境参数(特别是盐度和铵盐浓度)对AOA分布的影响因物种而异[102],这表明AOA能够很好地适应同环境。

研究发现,AOA生态型之间的基因组差异与栖息地密切相关。例如,编码K+转运蛋白的基因kefA很少出现在陆地AOA类群中,而是主要由海洋AOA所拥有,这被解释为对水生环境中渗透压的适应[78]。从河口沉积物中富集的低盐度类型Candidatus Nitrosoarchaeum limnia (N. limnia)菌株SFB1优先生活在低盐度环境中,但也可以在淡水和高盐度条件下生长,其基因组编码许多机械敏感通道蛋白,这是保护微生物免受低渗性休克所必需的[103]。此外,生活于浅水区的AOA成员通常编码uvr系统和pst系统,它们分别对修复磷限制下的紫外线诱导的DNA损伤和竞争性获取磷酸盐很重要。这些基因在深水区成员的基因组中并未找到,这与深海中缺少光线以及磷酸盐不受限制的环境条件相一致[69, 78]。表层水比深层水的氧化应激更为明显,这主要是由于许多光化学和光合作用过程产生的活性氧种类较多[104]。因此,上层AOA比深层AOA编码更多与超氧化物歧化酶相关的基因[69]。此外,与中层AOA相比,上层AOA与信号转导和调控机制相关的基因更丰富[105],这可能对适应不断变化的海洋环境至关重要。

不同的奇古菌系统发育谱系在不同的水深中占主导地位:表层水体中存在的奇古菌序列非常少[106-107],这可能是由于古菌AMO酶对光抑制很敏感;在光合作用带下部和中层海洋上部区域(约50–500 m)通常是β-AOA(如Candidatus Nitrosopelagicus brevis)的成员占主导地位[106, 108-109];γ-AOA在水体中分布广泛,在中深层水体(> 2000 m)中占据明显优势[69, 107, 110];α-AOA (如Nitrosopumilus属)在全球海洋中都普遍存在,研究发现其在超深渊水体(> 8000 m)的奇古菌群落中占有优势地位[106, 111-112]。α-AOA可能由单一的系统型组成[112],由于编码类似凝血酶原蛋白的胞外结构基因的存在,α-AOA的基因组可能会经历较少的基因流动。这种结构包含5个Ca2+结合域,可以调节细胞结构的粘附性,从而导致α-AOA的发散度较小[109];而γ-AOA有多种系统型,其较大的物种多样性导致在宏基因组分析时难以获得其高质量的基因组[107, 112]

对于生活在超深渊区海水中的α-AOA,氨氧化和通过改进的3-羟基丙酸/4-羟基丁酸(3-HP/4-HB)循环固定碳被认为是化学自养生长的核心途径。其中,改进的3-HP/4-HB循环被认为是在有氧条件下固碳的最有效途径,且非常适合古菌在低能量供应下的生活方式[113]。除此之外,不完全的三羧酸循环和非氧化性戊糖磷酸途径普遍存在于海洋AOA中,包括超深渊区的α-AOA。尿素是海水中常见的一种分子,各种Nitrosopumilus菌株都能以尿素作为唯一能源生长[80, 114]

一些海洋生物通过合成渗透保护剂来适应超深渊区的极端压力,避免体内蛋白质发生变性[115-116]。基因组分析表明,一些Nitrosopumilus属的成员具有合成渗透蛋白的遗传潜力[111]。在超深渊区的α-AOA中发现了一个与肌醇-1-磷酸胞苷基转移酶(IPCT)和二肌醇-磷酸合酶(DIPPS)有关的基因组岛[107],这些基因参与一种关键的渗透保护剂——磷酸二肌醇(DIP)的生物合成,该渗透保护剂以前在许多超嗜热古菌和细菌中发现[117]。此外,在该基因组岛中还发现了负责肌醇单磷酸水解以产生磷酸盐和肌醇的肌醇-1-单磷酸酶(IMPA)基因[107],肌醇是一种常用的渗透保护剂和DIP的前体,肌醇的生成被认为是古菌适应深海的一个关键机制[109]。在深海AOA谱系中发现的甘氨酸裂解系统也可能在渗透调节中发挥作用,并且表明甘氨酸的积累或利用可能在深海古菌分支中普遍存在[107, 109]。除了渗透保护剂外,伴侣蛋白还可以帮助蛋白质正确折叠,并在高静水压下保持其功能[107]。在超深渊区AOA中发现的独特的、非典型的ATP合成酶也可能是适应压力升高的关键因素[118]

深海沉积AOA和浮游AOA在利用有机氮进行混合营养方面表现出很大的一致性:宏基因组分析表明,它们对肽和氨基酸的代谢潜力比糖和尿素的代谢潜力大几个数量级,表明肽和氨基酸是AOA混合营养的重要碳源[70, 119];编码氨裂解酶、脱氨酶和蛋白酶的基因普遍存在于深海沉积物AOA中,氨裂解酶和脱氨酶是降解有机氮化合物(氨基酸、核苷酸和蛋白质)过程中负责产氨的主要酶类[120]。此前认为,在深海沉积物中,AOA主要利用由脱氨异养细菌产生的氨[121]。最近的研究通过宏基因组分析发现,贫营养沉积物中的AOA具有与深海浮游AOA相同的潜在的独特氨浓缩机制,以适应环境中极低的氨浓度。它们有可能通过胞内脱氨并氧化,从而显著地限制了氨的扩散损失,在能源匮乏的环境中代表着一种适应性优势[65, 70]。3-羟基丙酸/4-羟基丁酸(3-HP/4-HB)循环是仅由AOA编码的碳固定途径,是最节能的有氧固定碳途径[113]。氧化由有机氮脱氨作用产生的细胞内再生氨有可能提供额外的能量来驱动3-HP/4-HB固碳循环,从而将混合营养代谢和化学自养代谢结合起来[70]。这种新陈代谢特征可能会减少能量损失,改善AOA在能源匮乏、有氧条件下的生长状况,从而使它们在数百万年的时间里保持其在深部生物圈中的优势地位。

3.2 深古菌门(Bathyarchaeota)

深古菌是新近提出的古菌门,以前被称为Miscellaneous Crenarchaeotal Group古菌[17],广泛存在于各种环境,如红树林湿地[122]、深海沉积物[123]、热泉[124]、河口[125]等,具有高度的系统发育多样性和丰富性。深古菌作为淡水和海洋沉积物中最主要且最活跃的微生物类群之一,其相对丰度可占总古菌丰度的36%±22%[126]。然而在深渊沉积环境中,现在仅在雅浦海沟6500 m水深的表层沉积物中检测到深古菌[127]。目前,深古菌门被划分为25个亚群[128],其中亲缘关系最远的深古菌成员的16S rRNA基因序列仅有76%的相似性[123]。虽然还没有获得其成员的纯培养或富集培养,但宏基因组学和单细胞测序的数据分析在很大程度上揭示了深古菌亚群的代谢能力、生态功能、底物偏好和生态位差异。

盐度被认为是影响深古菌群落结构的最重要的环境因子之一[126, 129]。不同的深古菌亚群是不同盐度环境的生物指标类群:亚群1和亚群8是海洋指标,亚群5和亚群11是淡水指标;深古菌的进化主要发生在从咸水到淡水的方向[126, 130]。此外,亚群3、4、13和16被确定为河口的指标亚群[129]。深古菌亚群的分布被认为与环境密切相关,在谱系中具有巨大的多样性。如在南海沉积物环境中,亚群6主要分布于氧化层和表层沉积物中,而亚群8通常在还原层和深层沉积物中占优势[131-132]。亚群15和亚群17广泛存在于淡水和海洋沉积物中,随着深度和氧化还原条件的变化,亚群15的丰度相对稳定[131]。亚群5a和亚群5b主要分布于静止、缺氧、富含硫化物和还原性有机物的底层水体中,而亚群6则广泛分布于各类沉积物[8]。这些亚群的环境特异性分布突出了深古菌在特定生境中独特的代谢能力、潜在的生态功能和适应策略。

盐度和氨氮水平是影响珠江口表层沉积物中深古菌分布的主要因素[125]。另一方面,影响滨海红树林和湖泊沉积物中深古菌群落结构的主要因素是pH和氧气水平,而非盐度[122, 133-134]。此外,在黄海南部和东海北部,水深、温度和盐度是决定表层沉积物中深古菌分布的关键因素[135]。同样,水深是解释深古菌从近岸浅海到南海北部深海的分布格局的主要变量[132]。深古菌的总丰度随着沉积物深度的增加而增加,这可能是由于不同的沉积物类型产生了多种代谢方式,从而塑造了不同深度的古菌多样性[136]。在南海沉积物岩芯和滨海红树林沉积物中,深古菌的丰度还与总有机碳浓度呈正相关[122, 131, 133-134]

基因组分析表明,深古菌的代谢类型为兼性厌氧[128],它们是底栖碳循环的重要参与者,可能通过甲烷代谢或乙酰化作用,降解各种有机化合物,包括碎屑蛋白质、芳香族化合物、多聚碳水化合物、脂肪酸[17, 137-139]等。目前,还在深古菌的基因组中发现一种利用丁烷代替甲烷的独特甲基辅酶还原酶(MCR)类型[140],表明深古菌在丁烷氧化方面的潜力。

通过在不同环境中的调查分析表明,深古菌各亚群在代谢方面具有巨大的多样性。研究发现,亚群3可以利用多肽和葡萄糖,亚群8可以降解脂肪酸[137]。在对长江口缺氧区沉积物进行的富集实验还证实了亚群8具有木质素降解潜能,且通过13C同位素发现该类群能以碳酸氢盐作为碳源[141]。陆源的木质素是长江口沉积物中的重要有机质组分[142],而长江口地区的深古菌绝大部分(超过70%)属于亚群8,表明亚群8在该区域难降解有机质的降解过程中发挥重要作用,是长时间尺度的碳循环中的关键环节[141]。对来自白栎河河口沉积物的深古菌基因组的研究发现,亚群6具有水解胞外植物来源的碳水化合物的能力[139],亚群1、6、15和17都能降解碎屑蛋白质,且在这四个基因组中都检测到编码参与乙酸生成以及还原性乙酰辅酶A途径的基因[139],因此它们可能是有机异养和自养产乙酸菌。在这些基因组中还发现了与异化亚硝酸盐还原为铵有关的基因,表明对亚硝酸盐有潜在的还原能力[139]。此外,亚群13、16、21和22也被推测是乙酸菌,可以利用不同的有机底物进行发酵[138]。最近,在亚群6的基因组中发现存在视紫红质基因、钴胺生物合成基因和依赖氧的代谢途径,表明在该亚群中可能存在一种对光敏感和微好氧的生活方式[133]。在亚群6、8、15和17中发现了III型RuBisCO基因和磷酸核酮酸激酶基因,暗示深古菌可能参与Calvin-Benson- Bassham循环来固定二氧化碳[133]。此外,来自热液环境的亚群21和亚群22可能代表了深古菌的古老类型,暗示着深古菌可能起源于海底热液或陆地热泉等热环境[124]。深古菌基因组中的不断研究,扩大了已知古菌的代谢潜力,并突显了深古菌在底栖碳循环中的关键作用。

近年来,基因组学方面的证据表明,深古菌在底栖氮循环和硫循环中也发挥着重要作用。目前,已经在深古菌基因组中发现了多种与氮代谢相关的基因,如氨转运蛋白(amt)、羟胺还原酶(hcp)和固氮酶铁蛋白(nifH)基因[133];在亚群6、8和15中发现了潜在的尿素产生途径,包括精氨酸酶(rocF)和胍丁酶(speB)途径[133];这表明深古菌可能具备利用各种高价含氮化合物生成铵盐并转换为尿素的能力。此外,深古菌可能利用氢酶/硫还原酶(hydA)将S0还原为硫化物,而亚群15和亚群17编码与硫酸盐还原有关的基因,亚群6的基因组含有硫代硫酸盐还原基因[133]

深古菌可能通过产甲烷和产乙酸过程与其他微生物密切相互作用。例如,其他异养和乙酰碎屑微生物可能以深古菌产生的乙酸为食[138-139],而基因组分析表明深古菌可能具有厌氧甲烷氧化能力。提出了海洋细菌、硫酸盐还原菌和厌氧甲烷氧化古菌之间可能的相互作用[128, 137]。深古菌还能在不同的环境中充当“关键种”,维持古菌群落的稳定性和适应性[129]。从遗传学角度推断,深古菌和底栖古菌目之间存在潜在的共生或协同关系,因为它们具有相似的途径,包括乙酰化和蛋白质降解途径[138-139, 143]。然而,这些假说大多是基于有限的基因组信息。详细的代谢功能和相互作用需要进一步的生理探索,进行更精确和严格的实验验证。

3.3 底栖古菌目(Thermoprofundales)

底栖古菌目(以前被称为MBG-D古菌),是隶属于广古菌门热源体纲(Thermoplasmata)下的一个新目,广泛分布于海洋沉积物、海底热液口和红树林沉积物等生境[143-144]。底栖古菌目是全球海洋沉积物中发现最多的古菌谱系之一,分布广泛,丰度高,共有16个亚群[143]。其特定亚群与特定环境条件之间存在关联:亚群3与亚群4主要分布于高盐环境中,亚群8c在中盐环境中占主导地位,亚群9c和亚群9b是非盐环境中的优势类群;亚群6和亚群7是甲烷渗漏环境中的优势类群,而亚群9c在非渗漏区占主导地位[143]

通过宏基因组学、宏转录组学和单细胞基因组的分析研究,目前已经对底栖古菌目的代谢潜力和生态功能有了一定了解。底栖古菌目可能运输和同化多肽,并通过发酵产生乙酸和乙醇[145]。宏转录组的分析表明,乙酸和氨基酸利用相关基因以及肽酶基因在底栖古菌目内均有高表达。除了异养碳代谢外,底栖古菌目基因组还包括可能编码两种自养途径的基因:以四氢甲烷蝶呤和四氢叶酸为C1载体的Wood-Ljundahl (WL)途径,以及在二羧化过程中从丙酮酸到苹果酸/草酰乙酸酯交替旁路的不完全二羧酸/4-羟基丁酸循环[143]。这些发现揭示了底栖古菌目是一个重要且普遍存在的、具有特殊混合营养代谢途径的古菌类群。此外,共现性分析表明,底栖古菌目与深古菌、洛基古菌和Hadesarchaea之间存在显著的非随机关联,表明这些古菌类群之间存在潜在的相互作用[30, 143, 146]

3.4 Asgard古菌超级门

Asgard古菌,以前被称为Marine Benthic Group B(MBG-B)[147]和Deep-Sea Archaeal Group(DSAG)[148],广泛分布于深海沉积物、河口、红树林湿地沉积物、海底热液等环境中[149],主要是栖息在缺氧生境中[53, 62],其相对丰度与沉积物中的有机质含量密切相关[53]。Asgard古菌内的各个古菌门的分布各有其特点:洛基古菌和索尔古菌广泛分布于各类不同生境中[33-34, 149-150],奥丁古菌在地热环境中最为丰富[151],海姆达尔古菌通常在海洋沉积物中最为常见[152-153],海拉古菌在深海热液沉积物中有所发现[32],葛德古菌则主要分布于河流、湖泊和海洋的沉积物中[34]

尽管目前尚未获得Asgard古菌的纯培养菌株,但Imachi等于2020年获得的洛基古菌富集培养物[154]以及越来越多的基因组学研究正不断揭示Asgard古菌的代谢潜能和生态功能。基因组学分析表明,Asgard古菌可能在碳、氮、硫循环中发挥重要作用。洛基古菌被认为是氢依赖型古菌,且能够代谢卤化有机化合物[155]。索尔古菌被认为是营混合营养的,不仅能够利用卤化有机化合物、丙酮酸盐和蛋白质水解产物,还能参与固氮和发酵产乙醇过程[150, 156]。在海姆达尔古菌的基因组中发现了编码视紫红质的基因,且可能具有微好氧的代谢途径[152-153]。海拉古菌具有激活并厌氧氧化水热作用产生的短链碳氢化合物的潜力[32]。葛德古菌具有利用有机碳和无机碳的混合营养代谢潜力[34]。此外,Asgard古菌被认为是真核生物和原核生物之间的桥梁,因为它们在系统发育上与真核细胞相近,并编码许多与真核特征蛋白相关的基因,这些基因以前被认为是真核生物所特有的[33]。最近,李猛等通过比较分析了Asgard古菌的162个完整或几乎完整的基因组,包括75个未报道的宏基因组组装的基因组,发现了6个Asgard古菌新门,分别命名为霍德尔古菌(Hodarchaeota)、卡瑞古菌(Kariarchaeota)、包尔古菌(Borrarchaeota)、巴德尔古菌(Baldrarchaeota)、赫尔莫德古菌(Hermodarchaeota)和悟空古菌(Wukongarchaeota)。悟空古菌具有氨氧化的化能自养代谢潜能,显著区别于其他Asgard古菌混合营养或异养的代谢模式。并且较其他5个Asgard古菌新门而言,悟空古菌更加古老[157]。此外,该研究的结果表明,真核生物起源于Asgard古菌内部,即海姆达尔-悟空的共同祖先分支,或起源于其他更古老的未知古菌分支[157]。该研究还重构了Asgard古菌关键代谢途径的演化过程,提出了真核生物可能起源于“自养型Asgard古菌与发酵型细菌”的代谢共生模式,为解答真核生物起源这一重大科学问题提供了新的见解[157]

3.5 乌斯古菌门(Woesearchaeota)

乌斯古菌(以前被称为Deep-sea Hydrothermal Vent Euryarchaeota Group-6,DHVEG-6)是DPANN古菌超级门中最丰富且普遍的古菌门之一[25, 158],目前被划分为26个亚群[159],广泛分布于淡水、海水[160]、淤泥[161]、深海热液[30]、深渊海沟[58, 162]等环境中。氧气被认为是驱动乌斯古菌分布与进化的重要环境因素[159]。乌斯古菌在中低纬度河口的丰度与多样性均要高于高纬度河口,其群落结构主要由温度、盐度和氧气含量决定[159]。在深渊海沟沉积物中,乌斯古菌是仅次于奇古菌的高丰度古菌类群之一[58, 162]

通过宏基因组分箱技术已经构建出乌斯古菌的完整基因组,其大小仅为0.8 Mb,缺失了一些核酸合成和糖代谢相关基因,并存在一些分解肽聚糖的壁质转糖类似基因,因此乌斯古菌可能与革兰氏阴性菌存在共生或者寄生关系[25]。此外,乌斯古菌还可能与产甲烷菌存在共生关系,乌斯古菌可能通过发酵有机物产生乙酸、氢气和甲基化合物,这些发酵产物可能会支持产甲烷菌的生长,来换取一些氨基酸和其他化合物[159]。在深部生物圈中,乌斯古菌的一些成员能够进行有氧H2氧化,这是深海沉积物能量代谢的一种潜在的重要形式[25, 163]

4 展望

随着高通量测序技术的发展,越来越多的未培养古菌逐渐被人们所熟知,但由于目前所获得的纯培养古菌菌株有限且古菌分离难度较大,因而对于古菌生理特征、代谢机制、生态功能的了解大多是基于宏基因组学和单细胞基因组学的研究,仍然缺乏实质性的证据。考虑到古菌在全球生物地球化学循环中的重要作用,古菌生态学的研究仍将有很长一段路要走。这里提出几个未来研究的方向与重点以供参考。

(1) 根据宏基因组、宏转录组、单细胞基因组学等组学技术所获得的古菌的潜在生理特征和代谢机制,为古菌的纯培养和富集培养提供针对性的指导,提高古菌培养的效率,基于培养的方法必然会继续为古菌的生理学和新陈代谢提供重要的新见解。

(2) 改进和发明新的、更有效的微生物培养策略,包括培养条件的大规模平行变化,使用改进的较低培养量和低细胞密度的培养和表征策略,以及微生物组合与共培养的富集与代谢剖析。

(3) 多学科交叉合作,结合生物、化学、地质等学科方法量化古菌在全球生物地球化学循环中的贡献。

(4) 结合组学数据,在富集实验中剖析古菌与古菌、古菌与细菌、古菌与环境因子之间的关系。

(5) 关于不同海洋古菌的生理代谢、古菌蛋白质和酶的异源表达以及随后的生化特性也是非常有价值的研究方向。

(6) 古菌病毒和其他可移动元件是海洋古菌研究的另一个新兴领域。利用宏基因组学、宏转录组学、单细胞基因组学,以及最终的古菌纯培养,将为了解它们的病毒多样性、病毒-宿主相互作用和水平基因转移提供新的见解。

(7) 对海洋古菌进行平行分析,以进一步评估它们的核心基因组、泛基因组和代谢谱、它们的病毒和可移动元件,以及它们与环境和群落的相互作用。

(8) 真核生物的起源和细胞复杂性是生物学研究中的一个重大科学问题。古菌作为在系统发育上与真核生物最近并编码许多与真核特征蛋白相关的基因的原核生物,研究其与真核生命起源的关系将对整个地球生命演化的理论体系产生重大影响。

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