LIU Run-Jin, Tel: 86-532-88030113; E-mail:
所谓互惠共生微生物(mutualistic symbiotic microbes,MSM)是指能定殖其他生物构建互惠共生体系的微生物,主要包括互惠共生细菌、互惠共生放线菌和互惠共生真菌等。MSM种类繁多、分布广泛、物种多样性丰富,涉及原核生物界和真菌界等。MSM定殖人体、动物、植物、藻类或其他真菌,可构建各自相应的互惠共生体系,进而形成范围更加巨大的共生网络,发挥不可替代的生理生态功能。本文在介绍MSM概念的基础上,重点总结了MSM多样性研究进展,指出了目前研究中尚存在的问题,探讨了今后应该开展的工作,MSM多样性研究成果可望为研发MSM应用技术提供依据和材料。
The so-called mutualistic symbiotic microbes (MSM) can colonize other organisms to build a mutual symbiotic system. MSM mainly include mutualistic symbiotic bacteria, mutualistic symbiotic actinomycetes and mutualistic symbiotic fungi. MSM are diverse, with a wide distribution and rich in species diversity, involving those in procaryotae and kingdom fungi. MSM colonize human body, animals, plants, algae, or other fungi, and can build their respective reciprocal symbiotic systems, and then form a wider symbiotic network to play irreplaceable physiological and ecological functions. On the basis of introducing the concept of MSM, this paper summarizes the progress of MSM diversity research, problems existing in the current research, and the work in the future. The results of MSM diversity research are expected to provide basis for the development of MSM application.
生态系统中,物种间长期的互作与进化形成了稳定、动态平衡的种间关系,进而构建共生网络,有效地发挥生理生态效能。开展生物共生学研究,对于农林牧渔产业发展、动植物与人类健康、环境与食品安全等具有重大意义。当前,互惠共生微生物(mutualistic symbiotic microbes,MSM)已成为诸多国家竞相占有和发掘的战略资源以及生命科学研究的重点之一。关于昆虫共生细菌、昆虫共生真菌、植物共生放线菌、菌根真菌、暗隔内生真菌(dark septate endophytes,DSE)和禾草共生真菌等前人已分别给予综述[
微生物与人类、动物、植物、藻类、地衣和其他微生物关系密切,共同发展、协同进化,形成了普遍的共生关系。由于“共生”是生物间“共同生活”(living together)的广义概念,包括了互惠共生(mutualistic symbiosis)、偏利共生(commensalistic symbiosis)、竞争共生(competitive symbiosis)和寄生共生(parasitic symbiosis)等种间关系[
MSM种类繁多,涉及原核生物界和真菌界的大多数物种,同时其宿主则涉及整个动物界,其寄主则涉及整个植物界。因此,MSM及其宿主和寄主均具有丰富的物种多样性。从南极到北极、从高山到平原、从河流到海洋、从湖泊到盆地、从荒漠到湿地、从农田到林地、从城市到农村等生活的人类、动物、植物、藻类和地衣等均定殖着MSM。其中以人体和动物的肠道MSM、昆虫MSM、植物根系MSM分布最为广泛,社会、经济与生态意义最为重要[
健康人体的皮肤、毛发、口腔、鼻腔、眼睛、肺部、生殖器及胃肠道等定殖着数以万亿计的微生物,可称为人体共生微生物,即人体微生物组,这些共生微生物所编码的数百万个基因被称为人体第二基因组[
与肠道共生细菌相比,肠道共生真菌的物种丰富度和多样性要低得多,而且随时间推移其组成也不稳定[
越来越多的研究表明,肠道MSM具有一系列的共生功能,即发酵不消化的食物、提取饮食中的养分和能量、诱导宿主机体免疫系统、防御条件致病菌、介导心理健康和稳定体内平衡等[
健康的肺通常定殖着与小鼠中相似的厚壁菌门、变形杆菌门、拟杆菌门和放线菌门的细菌群落,最丰富的门是拟杆菌门和厚壁菌门;优势属为普氏菌属(
皮肤共生微生物有1 000多种,其中,细菌包括放线菌门、硬壁菌门、变形菌门和拟杆菌门等;优势属为棒杆菌属(
眼部共生微生物群落较少,主要分布在结膜和角膜上,而定殖于眼睑和睫毛的则被认为是皮肤微生物的一部分。眼睛表面主要定殖葡萄球菌、链球菌、丙酸杆菌(
健康女性阴道共生微生物主要为细菌,优势属为乳酸杆菌属,其中,卷曲乳酸杆菌(
与人类相比,动物共生微生物具有更为丰富的物种多样性,特别是一些反刍动物和昆虫能长期与细菌、放线菌和真菌等共同进化,建立多样的共生关系,进而影响宿主的营养、代谢、生长、发育、寿命和演化等[
近10年来人们应用高通量测序技术广泛探索了包括人类在内的灵长类动物、食肉动物、啮齿类动物、反刍动物、鸟和海洋动物的MSM[
Le等[
作为陆地物种多样性最丰富的昆虫,其MSM倍受关注。众多研究表明,食叶甲虫、白蚁、蚜虫、蝗虫、烟粉虱、叶蝉、粉蚧和木虱等植食性昆虫的体表、体腔、消化道、肠道、中肠、后肠、淋巴、脂肪体和储菌器等定殖着大量的细菌和放线菌[
动物MSM在宿主的营养、代谢、生长、发育、免疫和健康中发挥关键作用。反刍动物可利用肠道MSM通过发酵难消化的纤维素和半纤维素而产生养分、抗生素、维生素和能量,以有助于其自身的营养与健康[
然而,动物MSM群落与物种多样性及其功能受宿主、环境、食物和季节等因素的影响。反刍动物瘤胃MSM多样性在宿主个体间存在差异,这可能是营养成分、pH、转运速率、宿主生理和免疫细胞群的局部变化以及宿主上皮细胞与共生细菌之间的不同相互作用造成的[
与动物共生细菌相比,动物共生真菌的研究尚不够全面、系统和深入。尽管我们对反刍动物瘤胃共生真菌物种多样性、群落结构与功能的认识远不如对瘤胃共生细菌的了解,对厌氧真菌的大部分活动和代谢仍然未知,但这种状况正在悄然改变。与动物共生细菌类似,当前动物共生真菌的研究多集中于反刍动物和昆虫的肠道共生真菌。已确定10余属和许多未培养类群的共生真菌,其中,棘孢霉属(
动物胃肠道共生真菌能高效降解食物中的纤维素。厌氧真菌是已知的生物界中最有效的纤维降解菌之一,瘤胃共生真菌还具有淀粉和蛋白水解活性,这些共生厌氧真菌可提高饲料摄入量、饲料消化率、饲料效率、日增重和乳汁产量[
关于昆虫共生真菌的研究多集中于植食性昆虫和植菌昆虫。经ITS1 rDNA MiSeq鉴定,定殖卷叶象甲(
早在19世纪人们就开始研究植物共生微生物,甚至开始施用根瘤菌肥。进入21世纪以来,植物共生微生物研究与应用进展更加迅猛,特别是在共生固氮微生物与菌根真菌等领域。
植物共生细菌具有丰富的物种多样性,定殖于几乎所有已测定的植物体内,一种植物可分离数种至数百种,包括共生固氮细菌、联合固氮细菌、自生固氮细菌、光合细菌、根围促生细菌(plant growth-promoting rhizobacteria,PGPR)、叶围细菌、花围细菌、果围细菌和种围细菌等共生细菌及共生固氮放线菌、其他共生放线菌等。已报道的植物共生细菌90余属1 000余种。其中,根瘤菌150余种,这些根瘤菌不仅是豆科植物的专性共生细菌,有时也是其他非豆科植物的体内或根围的共生细菌[
柑橘根围细菌具有较高的多样性,尽管样地不同,蜡样芽孢杆菌(
弗兰克氏菌属(
Gohain等[
[
角担菌属(
DSE大多属于子囊菌。然而关于DSE的分类地位、系统发育和演化尚需深入研究。谢玲[
属于子囊菌的哈茨木霉、绿色木霉(
隶属于子囊菌的多种白僵菌(
印度梨形孢为担子菌门层菌纲腊壳耳目梨形孢属的一种丝状植物共生真菌,目前仅1种,可与蕨类植物、苔藓植物、裸子植物和被子植物等建立共生关系[
麝香霉属于子囊菌,已分离麝香霉属(
香柱菌即子囊菌门核菌纲肉座菌目麦角菌科香柱菌属(
树状多节孢(
分子数据表明,即使在一株植物中也能定殖着数百种真菌[
在生物形成与演化的早期,真菌与真菌、真菌与细菌、真菌与病毒等可能就已营共生生活,这些共生关系的建立事实上比动植物与微生物的共生早得多,直至各生物演化至今,仍有相对数量的真菌与其他微生物共生,在人类与动植物健康、农林牧渔业生产和生态系统过程中发挥作用。
自然条件下,某些种类的真菌与真菌之间也能建立共生关系。事实上,地衣是由一种子囊菌和一种担子菌与绿藻或蓝藻共生构建的最古老的互惠共生体[
地衣型真菌与蓝细菌的共生是最古老、最典型的真菌与细菌的共生体系,早在植物和动物起源之前就已存在。这些共生蓝细菌大多是念珠藻属(
菌根真菌可广泛地与多种细菌共生,其中与根瘤菌、放线菌、PGPR等在菌根围、菌丝围、真菌组织表面、细胞间隙或细胞内建立共生体系。为了从群落生态学的角度探索真菌与细菌的共生关系,对外生菌根根尖进行了为期3年的采样,并使用454个焦磷酸测序来鉴定外生菌根根尖内的细菌,结果表明,同一土壤区块内真菌群落组成对细菌群落组成的影响比样品年份或地点的影响更大,伯克霍氏菌和根瘤菌的数量最多[
自然界中其他种类的真菌也能与一定种类的细菌或放线菌共生。利用荧光原位杂交结合共聚焦激光扫描显微镜,Chen等[
如上所述,自然条件下一些细菌与细菌间也存在奇特的共生关系。水蜡虫体内存在着一种细菌定殖于另一个细菌中的共生互补关系,这种关系允许边缘基因转移,可减慢基因退化的速度[
当前,MSM的研究范围越来越广,内容越来越深入。例如,从群体、个体、共生体发育、细胞、超微结构、生理学、生物化学和基因水平等方面进行了较为深入和全面的研究[
蒺藜苜蓿(
然而,MSM研究中尚存在一定难题。例如,多数昆虫个体微小,细菌分离培养困难,研究其功能的难度更大;众多瘤胃共生厌氧真菌不仅难以培养,而且缺乏基因组信息以及分析序列数据最佳的可操作的统一标准,作为一个整体全面、系统和深入地了解瘤胃MSM仍面临诸多挑战;植物共生放线菌分离培养也比较困难;除了菌根真菌和DSE外,由于缺乏相关测定技术或统一的测定评价体系,目前很多研究并未测定MSM (对植物或动物)的侵染定殖数量,这对于评价MSM的接种效应、探究其作用机制和共生机制等研究方面缺乏数据链支撑;一些MSM类群,例如,DSE的分类地位和分类系统尚未确定,而针对MSM物种多样性与群落结构的研究,目前大多只是局限于一定条件下部分生物MSM菌种的分离、培养与鉴定,缺乏不同生态条件下,特别是景观尺度下更多生物MSM物种多样性与群落结构特征的调查等。
(1) 应加大MSM物种多样性、群落结构与功能多样性研究范围的广度和深度,在此基础上做好MSM的物种资源分离、鉴定和收集工作。
(2) 加强有关MSM系统发育、分类地位与分类系统的研究。例如,目前亟待开展有关定殖植物体内非菌根真菌共生真菌(如DSE等)的系统发育、分类地位、分类系统等分类学和系统演化等研究。
(3) 深入系统地观测不同生物共生体构建与发育特征,并在此基础上针对不同MSM的生物学特性,特别是其自身的生长发育特点与定殖特征,建立准确、方便、可行的分离与培养方法,以及其定殖数量的检测方法等。例如,Oishi等[
(4) 继续开发和完善MSM研究技术,例如,构建和完善高通量测序所获得分子种的统一标准体系,采用培养与分子生物学方法相结合的研究手段,采用组学、基因芯片、高分辨率的纳米级二次离子质谱法,以及三维荧光原位杂交-相关的光和电子显微镜法结合基因表达数据来探究生物共生与共生体系演化的机制、共生体系的营养代谢、免疫防御、抗药性、生长发育、环境适应、生理生态效应与作用机制等。Raes教授和他的团队发现,当涉及肠道细菌含量及其与健康的关系时,不仅肠道细菌的比例比较重要,而且它们的数量也比较重要,该团队还证实他们开发出的一种新方法能够快速和准确地确定粪便样品中的细菌载量,这种方法是对粪便样品中的细菌细胞平行开展微生物组测序和流式细胞计数,即以每克样品中含有的细菌细胞数量而不是它们所占的比例进行表达的定量微生物组谱(quantitative microbiome profiling)[
(5) 继续开展MSM应用基础与应用技术研究。Liu等[
针对昆虫肠道共生微生物,通过构建揭示和利用这些MSM物种多样性的发展策略,研发作为具有工业用途的酶和原料的来源,以及通过阻断其中的纤维素降解途径来开发生物杀虫剂等。针对植物与微生物共生体系,可加大AMF+DSE、AMF+PGPR以及菌根真菌+其他共生真菌+共生细菌等共生组合菌剂的筛选、生理生态效应的评价与应用技术的开发等。
可以预见,随着技术的进步与研究的深入,可从更大范围获得更多的MSM新种,挖掘出具有特殊功能或新颖代谢产物的物种,为具有更大科学价值和开发意义的研究提供材料和技术基础。
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