原生生物(protists)是指除植物、真菌和动物外的显微级真核生物, 其细胞结构、繁殖方式和生活史与其他真核生物显著不同(宋微波, 2007; Geisen et al, 2018)。原生生物的系统发生分类通常被认为是并系或多系群, 而非单系群(宋微波, 2007; Geisen et al, 2018)。1830年, 德国生物学家格奥尔格·奥古斯特·戈德弗斯第一次使用“protozoa” (希腊语“proto”代表“初始的, 最初的”, “zoa”代表“动物”)来指代诸如纤毛虫(ciliates)等生物, 意为最初级的动物(宋微波, 2007)。1866年, 德国生物学家恩斯特·海克尔首次将原生生物命名为“protista”, 意为“包括原生植物和动物在内的原生生物”, 将其与植物界和动物界进行区分(宋微波, 2007)。现代生物分类学已不再使用“protista”和“protozoa”这两个词指代原生生物类群, 更多用protists指代, 而protozoa则用于指代原生动物。
原生生物类群庞大, 早期有关原生生物的研究主要集中在水环境中, 近些年通过分子生物学技术的应用, 发现原生生物广泛分布在自然界的各种生境中, 包括土壤、冰川、火山沉积物等(Geisen et al, 2018)。据估计, 原生生物的物种数量为1.46 × 105 -1.66 × 106种, 但目前已知的物种仅约4万余种(Moon-van der Staay et al, 2001; Adl et al, 2005; Not et al, 2009; Geisen et al, 2018), 大量的原生生物还未被认知。对原生生物的研究迄今已有300多年历史, 研究方法也从早期的直接观察法和培养方法, 发展到BIOLOG微平板、磷脂脂肪酸(phospholipid fatty acid analysis, PLFA)、流动细胞仪、显微技术和第二代高通量测序技术(high-throughput sequencing, HTS)等(Zelles, 1999; Stefanowicz, 2006; Geisen et al, 2017; 韦中等, 2021), 极大促进了对原生生物的分类、多样性、分布特征及其生态功能等的认识。本文对近年来有关土壤原生生物的研究进展进行了总结和论述, 回顾了原生生物分类系统的发展, 概述了生物、非生物因素对原生生物群落组成及群落构建的影响, 总结了原生生物在生态系统中的功能作用及其提供的服务, 并对未来研究方向和应用潜力进行了展望。
1 原生生物分类系统和营养功能类群
原生生物的分类系统一直存在争议, 迄今仍没有统一的分类体系。Butschli是第一位建立原生动物分类系统框架的学者, 其在1889年首次将原生动物分为4纲8个亚纲, 即肉足纲、孢子纲、鞭毛纲和纤毛纲(宋微波, 2007)。随着对原生生物超微结构认识的增加, 1985年, 国际原生生物动物学会将原生动物亚界分为6个门, 即肉足鞭毛门、盘蜷门、顶复门、微孢子门、粘体门和纤毛门, 并进一步分为28个纲, 建立了较为系统的原生动物分类体系(宋微波, 2007)。此后, 随着对原生生物形态学、分子生物学和进化的深入认识, 原生生物界又被划分为5个亚界30多个门(包括菌藻植物超门和囊泡虫超门) 70多个纲。其中, 5个亚界指: (1)原生动物亚界, 如根足门、鞭毛虫门、孢子虫门等; (2)原生植物亚界, 如硅藻门、绿藻门、褐藻门等; (3)原生菌亚界, 如黏菌门、卵菌门等; (4)囊泡藻亚界, 如纤毛虫门、顶复门、有孔虫门等; (5)古虫亚界, 如眼虫门、后滴门等(宋微波, 2007; Geisen et al, 2018)。基于近年不断增加的DNA序列和电子显微镜超微结构信息, 有学者提出了新的“超群”分类系统, 建议将原生生物划分为泛植物超群、不等鞭藻超群、囊泡虫超群、有孔虫超群、Hacrobia超群、后鞭毛生物超群、皮胆虫超群、变形虫超群、陷摄虫超群和无根虫超群等十余个超群。其中, 不等鞭藻超群目前已知的物种约有25,000种, 泛植物超群、囊泡虫超群和有孔虫超群均有10,000余种, 变形虫超群(2,400余种)、陷摄虫超群(2,300余种)和后鞭毛生物超群(300余种)相对较少(Caron et al, 2017)。尽管该分类系统更好地反映了原生生物的系统进化关系, 但由于很多超群可能同时包含不同营养类型或不同生活方式的原生生物类群, 如不等鞭藻超群既包含自养型的硅藻、褐藻等, 也包含异养型原生生物卵菌、太阳虫(actinophryds)等(Caron et al, 2017), 增加了原生生物分类复杂性。因此现阶段原生生物分类系统的划分仍在不断发展和修正中。
原生生物无论是体型和细胞结构, 还是生活方式和营养类型等都异常丰富, 几乎涵盖了所有类型, 因此很难描述其群落的共同特征并使用统一的分类标准。如原生生物体型大小可以跨越6个数量级, 从比许多细菌小的微米级微孢子虫(microsporidia)到厘米级大的有孔虫, 甚至到超过1 m的黏菌(Geisen et al, 2017, 2018)。其细胞结构也有较大差异, 如变形虫(amoeba)只含原生质膜, 而硅藻和放射虫(radiolaria)等有坚硬的细胞壁(宋微波, 2007; Geisen et al, 2018)。根据运动方式不同, 又可将原生生物分为不动的孢子虫、有限运动的卵菌和黏菌以及可以自由运动的鞭毛虫(flagellate)等(宋微波, 2007; Geisen et al, 2018)。
原生生物的营养方式多样, 包括自养型、腐生型、共生型和吞噬型, 不同营养型的原生生物在土壤食物网中扮演着不同的生态功能“角色” (Geisen et al, 2018)。因此, Geisen等(2018)基于原生生物的营养类型将其划分为异养型原生生物和光合自养型原生生物。其中, 异养型原生生物在原生生物中占有绝对优势, 根据生活方式不同又可进一步划分为: 异养吞噬型原生生物(heterotrophic phagotrophic protists)、异养寄生型原生生物(heterotrophic parasitic protists)和异养腐生型原生生物(heterotrophic saprophytic protists)三类(表1)。其中, 异养吞噬型原生生物主要有鞭毛虫、纤毛虫和变形虫三大类。鞭毛虫顾名思义是指细胞周围存在鞭毛的一类原生动物, 其鞭毛不仅是运动的细胞器, 也是感觉细胞器, 并有助于将食物颗粒引导到细胞体内进行摄取, 通常为1-4个鞭毛(大多为2个) (Mitchell, 2007)。纤毛虫是唯一被证明是单系的原生动物(Foissner, 1998), 隶属于囊泡虫超群。纤毛虫的细胞特征在于具有两种类型的核(大核营养、小核生殖), 其纤毛具有一定的刚性和柔性, 可作为运动器, 通常沿细胞体成排排列数百个短纤毛或棘毛(Foissner, 1998; Dunthorn et al, 2015)。变形虫是具有柔性细胞形状的生物, 多数物种靠细胞内原生质的流动形成瞬时延伸的伪足来移动和摄取食物(Smirnov et al, 2011)。异养寄生型原生生物主要寄生于动植物等真核生物的细胞内部, 对动植物造成健康风险。孢子虫门是异养寄生型原生生物最主要的类群, 如隐孢子虫(Cryptomycota)常寄生于原生生物藻类、变形虫等细胞内, 也可引起人体感染(Corsaro et al, 2014)。异养腐生型原生生物被认为是低等的真菌或者是真菌的祖先, 主要有卵菌和黏菌两大类, 可以行使类似于腐生真菌的生态功能, 对土壤有机质的分解具有重要作用(Neuhauser et al, 2014)。此外, 一些绿藻失去了光合作用能力, 也会演变成腐生菌(Figueroa-Martinez et al, 2015)。光合自养型原生生物通常具有光合色素, 通过光合作用合成有机物供其生命活动所需, 如硅藻、褐藻、绿藻、鞭毛藻和黄藻等(表1) (Zancan et al, 2006)。尽管光合自养型原生生物仅占原生生物的一小部分, 但据估计海洋和陆地上约1/4的光合作用来自自养型原生生物(Falkowski, 2002; Geisen et al, 2020; 韦中等, 2021)。
表1 土壤原生生物的主要类群及其特征(改自Geisen等, 2018)
Table 1
| 分类 Classification | 主要类群 Main groups | 主要类群特征 Main groups characteristics |
|---|---|---|
| 异养型原生生物 Heterotrophy protists | ||
| 异养吞噬型原生生物 Heterotrophic phagotrophic protists | 变形虫: 大多单细胞; 无永久运动器, 靠伪足运动。 Amoeba: Mostly unicellular; without permanent motile organelles, and rely on pseudopodia for movement. | |
| 纤毛虫: 单细胞, 具有双核; 靠纤毛运动器运动。 Ciliophora: Unicellular, dual-nucleated; moved by cilia. | ||
| 鞭毛虫: 单细胞; 鞭毛既是运动器也是感应器, 一般1-4个, 大多2个。 Flagellate: Unicellular; flagella are both motor organs and sensing organs, generally 1-4, mostly 2. | ||
| 异养寄生型原生生物 Heterotrophic parasitic protists | 簇虫: 寄生于各类无脊椎动物, 包括节肢动物和环节动物的消化道内。 Gregarine: Parasitic in the digestive tract of various invertebrates, including arthropods and annelids. | |
| 孢子虫: 单细胞; 不移动; 孢子的顶端包含一个复杂的细胞器复合体。 Apicomplexa: Unicellular; don’t move; the apex of the spore contains a complex organelle complex. | ||
| 异养腐生型 Heterotrophic saprophytic protists | 卵菌: 能有限运动, 多为植物专性腐生菌, 有菌丝体, 既可进行有性生殖也可以无性生殖。 Oomycetes: Capable of limited movement, most of them are plant obligate saprophytes with mycelium, which can reproduce both sexually and asexually. | |
| 黏菌: 能有限运动, 沿着多核原生质团流动, 运动摄食方式类似变形虫。 Eumycetozoa: It has limited movement, flows along multinucleated protoplasm, and feeds in a similar way to amoeba. | ||
| 自养型原生生物 Photoautotrophy protist | ||
| 光合自养型原生生物 Photoautotrophy protists | 硅藻: 单细胞; 特有的二氧化硅双层外壳, 含叶绿素a和c。 Diatom: Unicellular; characteristic silica double-layered shell, contains chlorophyll a and c. | |
| 海藻: 多细胞; 含叶绿素a和c。 Trebouxiophyceae: Multicellular; containing chlorophyll a and c. | ||
| 绿藻: 单细胞或多细胞; 含叶绿素a和b。 Green algae: Unicellular or multicellular; containing chlorophyll a and b. | ||
2 土壤原生生物群落分布的影响因子
原生生物在不同环境条件下广泛分布, 其分布除受环境因素如水分、温度、pH值以及土壤养分等的影响外, 也受土壤生物因素诸如生物间的竞争、捕食者-被捕食者以及腐生食物、寄生宿主等影响, 具体如下。
2.1 环境因子
2.1.1 水分
土壤水分是控制土壤中原生生物多样性、密度和种群构成的关键因素。在大尺度范围上, 土壤原生生物的群落结构主要由土壤水分含量决定(Oliverio et al, 2020), 这与全球尺度上细菌群落主要由pH值驱动有所不同(Delgado-Baquerizo et al, 2018)。土壤水分不但给原生生物创造了摄食和生存的良好环境, 而且还是原生生物完成生长繁殖和能量物质转换的重要载体媒介。有研究表明, 异养型原生生物多样性随着土壤水分含量(田间持水量的30%、50%、70%)的增加而增加, 在持续潮湿的土壤环境中多样性最高(Geisen & Cornelia, 2014), 但某些类群(例如, 双叶细胞黏菌)的多样性在湿季和干季的交替变化下更高(Cavender et al, 2016)。具有不同生活方式和体型的原生生物分类群对土壤水分的耐受性明显不同, 体型大的变形虫通常比体型小的鞭毛虫更易受到干旱的影响(Geisen & Cornelia, 2014)。在干旱胁迫下, 多数原生生物会因为细胞失水、体积逐渐缩小、细胞质的粘性逐渐增强、流动性逐渐减弱而产生自噬行为, 从而使得诸如线粒体、核糖体等细胞器及质膜被逐步降解和同化, 并进而形成具有保护性功能的胞囊(宋微波, 2007; Geisen et al, 2018)。胞囊具有降低生命活动代谢的作用, 可以有效抵抗干旱、极端温度和高盐度等造成的细胞严重缺水, 并且当水分再次充足时, 原生生物可以在短短数小时内进行脱胞囊、摄食、生长和繁殖, 因而胞囊的形成是原生生物应对极端缺水环境的一种自我保护机制(宋微波, 2007)。
此外, 过量的水分会导致土壤处于缺氧状态, 而在缺氧条件下, 土壤中的原生生物增长率不到有氧条件下的25% (Fenchel & Finaly, 1990)。不同原生生物类群对缺氧的耐受性不同, 某些物种需要氧气, 但可以通过渗入承受暂时的缺氧, 例如, 榴弹虫(Coleps)、滴虫(Monas)、多核变形虫(Pelomyxa)和喇叭虫(Stentor)等可以在较低溶氧量的土壤中生存,但其代谢速率、繁殖能力会下降(Schwarz & Frenzel, 2003)。也有少量的原生生物可耐受缺氧条件并对O2敏感, 例如, 轲氏异毛虫(Allotricha curdsi)多营厌氧生活, 也可耐受低氧条件, 但寄生型原生生物则为严格厌氧生活(Foissner, 1998)。另一方面, 过量的水分还会导致土壤中CO2含量增加, 有研究发现鞭毛虫的相对丰度与CO2含量呈显著的正相关关系, 而变形虫与CO2含量呈负相关关系(田佳玉, 2012)。
2.1.2 温度
土壤温度是影响土壤中原生生物群落多样性和丰度的关键因子之一。一般而言, 大多数原生生物能在0-40℃的范围内生活, 最适温度一般在15-25℃ (田佳玉, 2012)。但不同的原生生物群落对土壤温度的响应不同, 如Opperman等(1989)研究表明, 在5℃时土壤中异养鞭毛虫占优势, 而在23℃时变形虫占主导地位。对大多数原生生物来说, 温度超过40℃会导致其死亡, 而低温危害不大。但也有一些原生生物能在冰点生活, 例如腰鞭虫的几个属(如Amphidinium、Gymnodinium和Glenodininum)、纤毛虫(如Antarcticus)以及一些金藻可以在0℃或-2℃左右的环境中生存, 而放射太阳虫(Actinophrys sol)、伪尖毛虫(Oxytricha fallax)、斜管虫(Chilodonella sp.)和纤毛虫中的Trimyema minutum等可以在35-50℃的高温环境中生存, 并有较高的生长繁殖速率(宋微波, 2007)。
水分是影响原生生物群落大尺度分布的决定性因素(Oliverio et al, 2020), 温度则可通过调节土壤水分含量进而影响原生生物的群落组成(Geisen et al, 2018)。在全球尺度上, 温度较高的热带和干旱地区主要以寄生型(如棘阿米巴属(Acanthamoeba sp.))和光合自养型(如原生生物藻类)原生生物为主(Stefan et al, 2014; Oliverio et al, 2020)。而在温度适宜的森林和中纬度地区土壤中, 节肢动物寄生虫、纤毛虫、孢子虫和变形虫等类群丰度较高(Stefan et al, 2014; Seppey et al, 2017)。此外, 基于增温模拟气候变暖的研究表明, 气候变暖带来的土壤水分减少会使原生生物的丰度降低7.5% (Wu et al, 2022)。这些研究表明, 未来气候变暖是导致原生生物多样性丧失的一个主要驱动力。未来气候变化对土壤原生生物群落的影响及其引起的土壤生物食物网结构和功能的级联变化值得关注。
2.1.3 土壤pH值
土壤pH值作为土壤中微生物生命活动的重要化学指标, 会显著影响原生生物维持生命活动所需底物的化学形态、浓度和可利用性(Kemmitt et al, 2006), 并进一步影响原生生物的密度、多样性、物种组成以及群落分布等(Dupont et al, 2016; Lara et al, 2016)。在一定范围内, 多数原生生物的丰度通常会随着土壤pH值的降低而下降(宁应之和沈韫芬, 1998)。也有研究发现光合自养型原生生物多样性会随着pH值的升高而下降(Antonelli et al, 2017)。如纤毛虫和孢子虫丰度会随着pH值的升高而升高, 而不等鞭藻的丰度则会随着pH值的升高而降低(Oliverio et al, 2020), 有壳肉足虫在pH值较低的高腐殖质土壤中具有更高的丰度(Dupont et al, 2016)。此外, 不同类群的土壤原生生物对pH值的耐受范围也有所不同, 多数原生生物可以在相对较宽的pH值范围(4.0-9.0)内生存, 而在过酸(pH < 4.0)或过碱(pH > 9.0)环境中, 其生命活动会受到严重抑制甚至难以存活, 比如僧帽肾形虫(Colpoda cucullus)最低耐受pH值是3.3, 鞭毛虫类为3.5, 变形虫类为3.9 (田佳玉, 2012)。然而在全球尺度上, 土壤原生生物群落的丰度和多样性受土壤pH值的影响较小(Bates et al, 2013; Oliverio et al, 2020), 与细菌群落主要受pH值影响不同(Delgado-Baquerizo et al, 2018), 这可能与多数原生生物具有较宽的pH值适应范围有关。
2.1.4 土壤养分
土壤原生生物丰富的物种多样性与其生存土壤的高度异质性紧密相关。土壤的各种团粒结构、孔隙、植物凋落物的有机残体以及植物根系等为土壤原生生物提供了适宜的栖息地、丰富的养分资源和生存繁殖必需的微环境(Geisen et al, 2018)。氮、磷是原生生物维持生命活动所必需的营养元素(Acosta-Mercado & Lynn, 2004; Antonelli et al, 2017)。在一定范围内, 土壤有机质、总氮和总磷含量越高, 原生生物的多样性和丰度也越高(宁应之和沈韫芬, 1998; Acosta-Mercado & Lynn, 2004; Bernasconi et al, 2011)。另有研究表明, 土壤有机碳含量与土壤原生生物功能多样性存在明显的正相关关系, 土壤高有机碳含量对维持原生生物高功能多样性至关重要(Yang et al, 2000)。农田秸秆还田也可通过提高土壤有机碳含量来增加原生生物的多样性(胡菏等, 2022)。但是, 变形虫的多样性和密度也会随着碳和磷含量的降低而降低, 这种现象在泥炭地等营养贫乏的环境中更明显(Mitchell, 2004; Krashevska et al, 2014)。
土壤氮素对原生生物的影响较为复杂。有研究表明纤毛虫、变形虫和藻类的多样性与丰度会随着土壤总氮含量的增加而增加(Acosta-Mercado & Lynn, 2004; Bernasconi et al, 2011)。Singh (1949)也证实在施用厩肥的农田中土壤变形虫的丰度显著高于施用化肥的农田, 在不施肥的土壤中最少, 表明土壤越肥沃原生生物丰度越高。然而, 由于原生生物群落极其庞杂, 以及土壤的空间异质性和不同土壤的性质差异较大, 原生生物对土壤养分变化的响应可能不敏感或者表现出不一致规律。如有研究发现, 施用氮肥后, 不同类型的农田土壤中原生生物的alpha多样性显著降低并改变了其群落组成, 表明原生生物对施肥的响应比细菌和真菌更加敏感(Zhao et al, 2019)。胡菏等(2022)发现不同原生生物类群对氮肥施用梯度(100-300 kg/ha)响应不同, 锥足亚门和丝足虫门的相对丰度会随着施氮量的增加而增加, 而绿藻门的相对丰度会随着施氮量的增加而减少, 且氮肥施用降低了农田土壤中原生生物的整体多样性。而Stapleton等(2005)在苔原土壤的氮添加实验中发现, 氮的添加(30 g/m2)并未改变土壤原生生物数量。
除以上因素外, 土壤中的农药和重金属污染对原生生物群落的组成和分布也有显著影响, 如肾形虫在重金属Ni、Cu和Zn污染的土壤中难以生存(Campbell et al, 1997), 土壤中高含量的Pb、Zn、Cu、Cd等重金属也会对土壤原生生物产生极大的危害, 使得原生生物丰度锐减(冯伟松等, 2004)。对土壤盘基网柄菌(Dictyostelium discoideum)的农药浓度测试以及纤毛虫的抗重金属测试结果显示, 当农药和重金属浓度逐渐升高时, 原生生物死亡率逐步提高(Díaz et al, 2006; Amaroli, 2015)。因此原生生物可作为土壤农药和重金属污染的指示生物(杨再超等, 2010)。
2.2 生物因子
2.2.1 植被
土壤原生生物的生长与繁殖在很大程度上要依赖于植物提供的栖息地和基质, 植物多样性不仅可以改变局部地区小气候(如森林对土壤水分的涵养以及土壤地表温度的影响), 并通过凋落物或根系分泌物影响土壤微环境中的养分、pH值、水分、含氧量和温度等(Acosta-Mercado & Lynn, 2004)。不同植被下的原生生物群落组成和数量差异极大。如Bamforth (1980)的研究发现, 在没有植被覆盖的荒漠土壤中, 原生生物数量极少, 相对丰度最高的变形虫也只有100个/g湿土, 而森林土壤中的变形虫和鞭毛虫数量则可达到105-106个/g湿土, 纤毛虫达5,000个/g湿土; 草地土壤中的纤毛虫数量多但种类少, 而同区域相邻的苔藓植被下的纤毛虫则是数量少种类多。另有研究报道不同泥炭藓类型如泥炭地、泥炭藓和棕色苔藓根际的变形虫群落也有着明显不同, 且变形虫的物种丰度随着植被功能多样性的增加而增加(Ledeganck, 2003; Scherber et al, 2010; Jassey et al, 2014)。孙焱鑫等(2003)的研究则发现在玉米根际土壤中的肾形虫、变形虫、波豆虫(Bodo)和尾滴虫(Cercomonas)显著高于非根际土壤。这些研究表明植被对原生生物的组成和相对丰度具有重要影响。
2.2.2 土壤生物
除植被外, 土壤中的其他生物, 包括细菌、真菌、古菌和原生生物不同类群间的捕食、竞争以及捕食者-被捕食者的关系也是影响土壤原生生物群落组成的重要因子(图1)。由于原生生物种类繁多, 体型、生活习性和营养类型差异较大, 在土壤食物网中占据着不同的生态位。作为被捕食者, 原生生物也会被土壤中的其他高等动物捕食, 因而受到自上而下(top-down)的影响。如一些线虫和小的节肢动物等会捕食土壤中的原生生物, 导致其丰度下降(Geisen et al, 2018)。同时, 一些小的鞭毛虫和肉足虫也会被大型肉足虫和纤毛虫所捕食(宋微波, 2007)。作为捕食者, 原生生物的群落组成和多样性受其他低等生物如细菌、真菌和古菌等自下而上(bottom-up)的影响。如有研究表明, 在食源性细菌丰度低时, 原生生物的生长和繁殖速率也较慢, 随着细菌丰度的升高, 原生生物的繁殖速率也逐渐加快, 但当食物浓度达到一定程度后, 其繁殖速率则不再增加(Beaver & Crisman, 1989)。在由真菌导致的小麦全蚀病发病土壤中, 嗜真菌的肉足虫数量要显著高于未发病土壤(Chakraborty & Waecup, 1984)。而原生生物对细菌、真菌和古菌等微生物的捕食也是有选择性的, 如向土壤中加入球形节杆菌(Arthrobacter globiformis)和苏云金芽孢杆菌(Bacillus thuringiensis)并不会增加土壤原生生物数量, 只有加入蕈状芽孢杆菌(B. mycoides)孢子和大肠杆菌(Escherichia coli)后, 土壤原生生物数量才显著增加(高云超等, 2000)。有趣的是, 除了经典的自上而下的食物链, 原生生物还存在着自下而上的捕食行为, 如一种非常常见的有壳变形虫可以通过群体协作主动捕食更大的线虫来生长繁殖(Geisen et al, 2020)。可见, 土壤原生生物与不同营养级食物网成员之间, 以及原生生物不同类群间存在着复杂的相互作用, 这种相互作用深刻地影响着原生生物群落的组成和多样性。
图1
图1
原生生物群落在土壤食物网和能量流动中扮演着重要角色
Fig. 1
Protists community plays an important role in soil food webs and energy flow
3 土壤原生生物的生态功能及其应用潜能
3.1 广泛参与土壤生态系统养分和物质循环
土壤中原生生物种类众多、功能多样, 它们可以促进动植物残体分解、土壤有机物矿化以及碳、氮、磷等营养元素的释放, 对提高土壤生物代谢活性, 维持土壤生物多样性和生态系统稳定等方面都有着积极的作用(图1) (朱永官等, 2021, 2022)。光合自养型藻类原生生物作为生产者, 在土壤碳的固定中起着重要作用, 而异养型原生生物在碳的矿化作用中起着重要作用(Oliverio et al, 2020)。有研究表明, 原生生物的异养呼吸占土壤异养呼吸的6%左右(细菌、真菌是主要贡献者, 占91%) (陈素芬和徐润林, 2003), 但当细菌和原生生物一起培养时, 总呼吸效率比二者单独培养更高, 表明原生生物和细菌的相互作用会增加矿化作用(Stefan et al, 2014; Seppey et al, 2017)。与异养微生物类似, 原生生物通过对氮的同化吸收和矿化释放而对其循环转化具有重要意义(Peng et al, 2022)。但原生生物对土壤氮的矿化作用有别于细菌通过细胞生理代谢将有机氮转化成无机氮, 它们会排出通过捕食细菌或真菌获得的多余的氮, 供给其他微生物或宿主植物利用(Geisen et al, 2020)。有研究表明, 土壤中原生生物的存在可以增加65%氮的矿化, 并促进植被对氮的吸收(Kuikman & Van Veen, 1989), 如Woods等(1982)的研究表明, 当土壤中有原生动物后, 植物吸氮量增加了75%。此外, 原生生物对硫和磷也有一定的矿化作用, 可见其广泛参与着土壤中的物质能量循环过程, 在土壤生态系统中具有至关重要的作用(Geisen et al, 2018, 2020; Gao et al, 2019)。
3.2 维持土壤和植物健康
作为土壤食物网的重要组成部分, 原生生物对细菌、真菌和古菌等微生物的选择性捕食有利于稀有微生物类群的增加, 提高微生物组的均匀性和互补性, 进一步影响土壤微生物群落的组成和功能多样性(Saleem et al, 2012; 朱永官等, 2022)。如鞭毛虫对特定细菌的捕食有利于螺旋状及丝状细菌数量的增加(Geisen et al, 2018), 而纤毛虫对棒状细菌的捕食有利于长方形细菌的生殖(Foissner, 1998; Dunthorn et al, 2015)。同时, 原生生物对某些病原性细菌和真菌的选择性捕食可直接控制病原体的增殖, 减少病原菌在土壤中的存活, 对维持土壤健康具有重要意义(孙新等, 2021; 韦中等, 2021)。如变形虫对病原青枯菌(Ralstonia solanacearum)的捕食、肉足虫对全蚀病病原真菌的捕食, 可显著降低土传病害的发病率(Xiong et al, 2020; 韦中等, 2021)。除直接捕食外, 原生生物也可通过生态位竞争或分泌拮抗性的代谢产物抑制病原性细菌和真菌的生长, 从而减少土传病害的发生(宋微波, 2007; Geisen et al, 2018)。如变形虫和肾形虫可通过代谢产物抑制水稻黄单胞菌(Xanthomonas oryzae)和棉花黄萎病菌(Vertieillium dahiiae)的生长, 使得土壤更加健康, 更加有利于水稻和棉花健康生长(棉花产量可提高30%) (韦中等, 2021)。基于控制实验的研究也发现, 拟南芥(Arabidopsis thaliana)在含有细菌、真菌和卵菌的土壤中的生长状况要明显好于没有卵菌的土壤, 这表明微生物之间的相互作用更有利于土壤健康, 而不是单一微生物类群(Durán et al, 2018)。
另一方面, 原生生物可以通过改变根际微生物的丰度和活性影响微生物与植物的相互作用。如有研究表明, 原生生物不仅可以促进产生生长素的细菌生长, 刺激侧根分枝(Brazelton et al, 2008; Krome et al, 2010); 也能够增加土壤微生物对养分的矿化, 为宿主植物提供营养(Gao et al, 2019)。此外, 原生生物还可以通过对根际细菌的捕食影响植物激素的释放, 如原生生物摄食的细菌生物量中的氮约1/3以铵态氮的形式释放到土壤中并被转化为硝态氮, 增加的氮素可促进植物细胞分裂素浓度增加, 进而促进植物生长(Bonkowski & Brandt, 2002; Krome et al, 2010)。但有些原生生物也会导致植物病害的发生, 例如, 锥虫属(Trypanosoma)原生动物会导致咖啡、椰子等植物韧皮部坏死病(Yang et al, 2000; Zancan et al, 2006), 疟原虫则可导致植物根腐病等(Neuhauser et al, 2014)。一些原生生物则会通过自身细胞中携带的病原体、共生体以及病原性细菌等导致植物病害发生(Xiong et al, 2020)。总之, 原生生物可以直接或间接通过改变微生物组组成来影响植物的感病性和抗病能力, 对原生生物与植物互作机理的深入认识, 有望为土传病害的防控和土壤健康的评价提供新的思路和技术方案。
4 展望
综上所述, 随着近年来研究技术的快速发展和应用, 对原生生物的生活习性、生理及遗传特性、形态结构、多样性及其生物地理分布等方面都有了更加清晰的了解和认识。尤其是近年来, 对原生生物与土壤不同营养级食物网成员的相互作用, 以及原生生物在维持土壤生态功能和促进植物健康等中的重要作用的认识也更加深入。但相比于土壤中的其他生物类群如细菌、真菌、线虫等, 对于原生生物的关注和认识仍非常少, 仍需要大量深入的研究(包括研究技术与方法的创新与开发)。在未来的研究中, 我们认为还有以下几个方面亟待解决:
(1)原生生物系统学特征及其分类。原生生物的分类体系较为复杂, 目前已有的分类体系较多, 分类标准不统一, 迫切需要建立一个被广泛认可的统一的分类体系。基于分离培养和形态学的分类工作耗时长, 对专业技能要求较高, 大大增加了分类鉴定工作的难度。因此今后的研究需更多地结合高通量测序、基因组学、宏基因组学等技术开展, 基于大数据分析和整合构建更为全面的原生生物遗传数据库, 并更系统地开展对原生生物类群的系统进化关系及其演化特征等的研究。
(2)土壤原生生物的多样性及其维持机制。虽然我们对原生生物群落多样性和分布格局的认识越来越清晰, 但对于原生生物在全球气候变化和人类活动背景下的多样性、群落结构及其大尺度上的地理分布特征和驱动因子的认识尚不够。原生生物的多样性极其庞大, 目前仍缺乏能够针对土壤全体原生生物进行PCR扩增的引物, 当前通过单一引物对原生生物多样性的研究可能存在较大偏差。因此, 需要开发利用新技术方法, 设计更完整的能够覆盖大多数原生生物分类群的PCR引物, 或者针对某些类群设计特异性引物, 深入探究关键原生生物类群的动力学、种群演替规律及驱动因子, 并揭示原生生物与其他生物之间的相互作用, 探明不同生态系统中原生生物多样性的维持机制。
(3)原生生物的生态功能。除通过高通量测序、宏基因组学等技术探索更多未知的原生生物类群外, 仍然需要结合对原生生物的分离培养、鉴定和生理代谢特性等的深入研究, 验证不同原生生物类群的重要功能, 并深入揭示原生生物与动植物以及其他微生物之间的相互作用关系, 明晰原生生物在食物网、物质循环、信息交流以及生态系统稳定等方面所起的作用, 揭示不同生态系统中原生生物所扮演的生态功能“角色”。
(4)原生生物的开发与利用。部分原生生物具有控制病原菌和提高根际免疫的功能, 利用原生生物对病原菌的选择性捕食以及产抑制病原菌物质的能力, 可实现原生生物对土传病害的防控与治疗, 维持农田可持续健康生产。此外, 原生生物因其生长繁殖速度快、世代时间短、细胞膜直接和外界环境接触以及对环境变化反应敏感等特点, 常被用作水体健康评价的指标之一, 在指示土壤肥力和环境质量方面也有着巨大的潜能(高云超等, 2000; 周可新等, 2003)。未来需进一步探明通过调控原生生物和微生物组促进土壤和根际健康的方法和途径, 并构建利用原生生物进行土壤健康和污染风险评价的方法和标准, 为土壤健康和生态系统管理提供服务。
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DOI:10.1111/j.1550-7408.1980.tb04227.x URL [本文引用: 1]
Global biogeography of highly diverse protistan communities in soil
DOI:10.1038/ismej.2012.147 URL [本文引用: 1]
The role of ciliated protozoa in pelagic freshwater ecosystems
DOI:10.1007/BF02011847
PMID:24197241
[本文引用: 1]
The abundance and biomass of ciliates are both strongly related to lake trophic status as measured by chlorophylla concentrations. Taxonomic replacements occur with increasing eutrophication such that large-bodied forms (predominantly oligotrichs) are progressively replaced by smaller-bodied ciliates (mainly scuticociliates). Highly acidic lakes display a more pronounced dominance of large-bodied forms when contrasted with less acidic lakes of comparable trophy. Community structure of ciliate populations is determined largely by lake trophy with acidic oligotrophic systems being characterized by reduced diversity and species richness compared with hypereutrophic systems. The temporal and spatial distribution of small (< 100μm) ciliate populations is ascribed to lake thermal regimes which provide localized concentrations of food resources. Likewise, in extremely productive lakes, very large (> 100μm) meroplanktonic ciliates enter the water column during midsummer after the development of thermal stratification and associated profundal deoxygenation. Laboratory studies indicate that large zooplankton (crustaceans) are capable of utilizing ciliates as a food source, but there is little direct evidence from field studies documenting this trophic link. Ciliates can be voracious grazers of both bacterioplankton and phytoplankton, and each species has a distinct range of preferred particle size which is a function of both mouth size and morphology. Myxotrophic ciliates may be important components in some plankton communities, particularly during periods of nutrient limitation or after their displacement from the benthos of eutrophic lakes. Evidence regarding the importance of planktonic ciliated protozoa in nutrient regeneration and as intermediaries in energy flow is discussed.
2,4-Diacetylphloroglucinol alters plant root development
DOI:10.1094/MPMI-21-10-1349
PMID:18785830
[本文引用: 1]
Pseudomonas fluorescens isolates containing the phlD gene can protect crops from root pathogens, at least in part through production of the antibiotic 2,4-diacetylphloroglucinol (DAPG). However, the action mechanisms of DAPG are not fully understood, and effects of this antibiotic on host root systems have not been characterized in detail. DAPG inhibited primary root growth and stimulated lateral root production in tomato seedlings. Roots of the auxin-resistant diageotropica mutant of tomato demonstrated reduced DAPG sensitivity with regards to inhibition of primary root growth and induction of root branching. Additionally, applications of exogenous DAPG, at concentrations previously found in the rhizosphere of plants inoculated with DAPG-producing pseudomonads, inhibited the activation of an auxin-inducible GH3 promoter::luciferase reporter gene construct in transgenic tobacco hypocotyls. In this model system, supernatants of 17 phlD+ P. fluorescens isolates had inhibitory effects on luciferase activity similar to synthetic DAPG. In addition, a phlD() mutant strain, unable to produce DAPG, demonstrated delayed inhibitory effects compared with the parent wild-type strain. These results indicate that DAPG can alter crop root architecture by interacting with an auxin-dependent signaling pathway.
Direct toxicity assessment of two soils amended with sewage sludge contaminated with heavy metals using a protozoan (Colpoda steinii) bioassay
DOI:10.1016/S0045-6535(96)00389-X URL [本文引用: 1]
Probing the evolution, ecology and physiology of marine protists using transcriptomics
DOI:10.1038/nrmicro.2016.160
PMID:27867198
[本文引用: 2]
Protists, which are single-celled eukaryotes, critically influence the ecology and chemistry of marine ecosystems, but genome-based studies of these organisms have lagged behind those of other microorganisms. However, recent transcriptomic studies of cultured species, complemented by meta-omics analyses of natural communities, have increased the amount of genetic information available for poorly represented branches on the tree of eukaryotic life. This information is providing insights into the adaptations and interactions between protists and other microorganisms and macroorganisms, but many of the genes sequenced show no similarity to sequences currently available in public databases. A better understanding of these newly discovered genes will lead to a deeper appreciation of the functional diversity and metabolic processes in the ocean. In this Review, we summarize recent developments in our understanding of the ecology, physiology and evolution of protists, derived from transcriptomic studies of cultured strains and natural communities, and discuss how these novel large-scale genetic datasets will be used in the future.
New species of Polysphondylium from Madagascar
DOI:10.3852/14-313
PMID:26490703
[本文引用: 1]
Two series of samples collected for isolation of dictyostelid cellular slime molds (dictyostelids) in Madagascar yielded a relatively large number of isolates of Polysphondylium. Most of these turned out to be species new to science that show varying degrees of clustering from unclustered to coremiform as well as an ability to migrate. Migratory ability (phototaxis) is a common feature of species assigned to Group 2 of the Polysphondylia and is common in the new species from Madagascar. Another common feature, clustering, appears to be a strategy for keeping fruiting bodies erect for a longer time in a climate that is relatively dry, whereas migratory ability may function seasonally when there is more rainfall. Thirteen species are described herein. Each of these is characterized by a particular set of distinguishing features, and collectively they expand our concept of the genus Polysphondylium. © 2016 by The Mycological Society of America.
Populations of mycophagous and other amoebae in take-all suppressive and non-suppressive soils
DOI:10.1016/0038-0717(84)90113-5 URL [本文引用: 1]
Advances of the studies on the soil protozoa
土壤原生生物的研究进展
Microsporidia-like parasites of amoebae belong to the early fungal lineage Rozellomycota
DOI:10.1007/s00436-014-3838-4
PMID:24652444
[本文引用: 1]
Molecular phylogenies based on the small subunit ribosomal RNA gene (SSU or 18S ribosomal DNA (rDNA)) revealed recently the existence of a relatively large and widespread group of eukaryotes, branching at the base of the fungal tree. This group, comprising almost exclusively environmental clones, includes the endoparasitic chytrid Rozella as the unique known representative. Rozella emerged as the first fungal lineage in molecular phylogenies and as the sister group of the Microsporidia. Here we report rDNA molecular phylogenetic analyses of two endonuclear parasites of free-living naked amoebae having microsporidia-like ultrastructural features but belonging to the rozellids. Similar to microsporidia, these endoparasites form unflagellated walled spores and grow inside the host cells as unwalled nonphagotrophic meronts. Our endonuclear parasites are microsporidia-like rozellids, for which we propose the name Paramicrosporidium, appearing to be the until now lacking morphological missing link between Fungi and Microsporidia. These features contrast with the recent description of the rozellids as an intermediate wall-less lineage of organisms between protists and true Fungi. We thus reconsider the rozellid clade as the most basal fungal lineage, naming it Rozellomycota.
A global atlas of the dominant bacteria found in soil
DOI:10.1126/science.aap9516
PMID:29348236
[本文引用: 2]
The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents and found that only 2% of bacterial phylotypes (~500 phylotypes) consistently accounted for almost half of the soil bacterial communities worldwide. Despite the overwhelming diversity of bacterial communities, relatively few bacterial taxa are abundant in soils globally. We clustered these dominant taxa into ecological groups to build the first global atlas of soil bacterial taxa. Our study narrows down the immense number of bacterial taxa to a "most wanted" list that will be fruitful targets for genomic and cultivation-based efforts aimed at improving our understanding of soil microbes and their contributions to ecosystem functioning.Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
Evaluation of heavy metal acute toxicity and bioaccumulation in soil ciliated protozoa
Laboratory toxicity tests, using ciliated protozoa, are scarce and they have been carried out usually with freshwater species. In this study, we have analysed the acute cytotoxicity of Cd, Zn and Cu in five different strains of very common soil ciliate species (Colpoda steinii, Colpoda inflata and Cyrtolophosis elongata), which were isolated from very different soil samples (polluted or not with heavy metals). Soil ciliates are quite resistant to heavy metals pollution with regard to ciliates from other habitats. The toxicity sequence was Cd>Cu>>Zn. Results from Cd+Zn mixtures indicated that Cd cytotoxicity decreases in the presence of low or moderate Zn concentrations. A broad heavy metal resistance level diversity exists among isolates of colpodid ciliates and it is seen to be a genetic feature rather than a habitat dependence. Bioaccumulation is seen to be the main mechanism involved in the metal resistance, except for Cu. For the first time in ciliates, a fluorescent method has been applied to detect Zn intracellular deposits. This methodology might be an useful tool for monitoring heavy metal pollution in soils.
Ciliates—Protists with complex morphologies and ambiguous early fossil record
DOI:10.1016/j.marmicro.2015.05.004 URL [本文引用: 2]
Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs
DOI:10.1111/1462-2920.13220
PMID:26768496
[本文引用: 2]
A recent large-scale assessment of bacterial communities across a range of UK soil types showed that bacterial community structure was strongly determined by soil pH. We analysed a data set of eukaryotic 454 sequencing 18S rDNA from the surveyed samples and showed significant differences in eukaryotic assemblages according to pH class, mostly between low pH and higher pH soils. Soil eukaryote communities (per sample) differed most at the taxonomic rank approximating to order level. Taxonomies assigned with the Protist Ribosomal Reference and the Silva 119 databases were taxonomically inconsistent, mostly due to differing 18S annotations, although general structure and composition according to pH were coherent. A relatively small number of lineages, mostly putative parasitic protists and fungi, drive most differences between pH classes, with weaker contributions from bacterivores and autotrophs. Overall, soil parasites included a large diversity of alveolates, in particular apicomplexans. Phylogenetic analysis of alveolate lineages demonstrates a large diversity of unknown gregarines, novel perkinsids, coccidians, colpodellids and uncharacterized alveolates. Other novel and/or divergent lineages were revealed across the eukaryote tree of life. Our study provides an in-depth taxonomic evaluation of micro-eukaryotic diversity, and reveals novel lineages and insights into their relationships with environmental variables across soil gradients.© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.
Microbial interkingdom interactions in roots promote Arabidopsis survival
DOI:10.1016/j.cell.2018.10.020 URL [本文引用: 1]
The ocean’s invisible forest
Anaerobic free-living protozoa: Growth efficiencies and the structure of anaeorobic communities
DOI:10.1111/j.1574-6968.1990.tb04073.x URL [本文引用: 1]
Soil protozoa in wetland treatment system of Pb-Zn mine in Fankou
凡口铅锌矿湿地处理系统的土壤原生动物
When the lights go out: The evolutionary fate of free-living colorless green algae
The endosymbiotic origin of plastids was a launching point for eukaryotic evolution. The autotrophic abilities bestowed by plastids are responsible for much of the eukaryotic diversity we observe today. But despite its many advantages, photosynthesis has been lost numerous times and in disparate lineages throughout eukaryote evolution. For example, among green algae, several groups have lost photosynthesis independently and in response to different selective pressures; these include the parasitic/pathogenic trebouxiophyte genera Helicosporidium and Prototheca, and the free-living chlamydomonadalean genera Polytomella and Polytoma. Here, we examine the published data on colorless green algae and argue that investigations into the different evolutionary routes leading to their current nonphotosynthetic lifestyles provide exceptional opportunities to understand the ecological and genomic factors involved in the loss of photosynthesis.
An updated compilation of world soil ciliates (Protozoa, Ciliophora), with ecological notes, new records, and descriptions of new species
DOI:10.1016/S0932-4739(98)80028-X URL [本文引用: 4]
Structure of the protozoan community in soil and its ecological functions
土壤原生动物群落及其生态功能
Protists: Puppet masters of the rhizosphere microbiome
DOI:S1360-1385(18)30244-9
PMID:30446306
[本文引用: 2]
The rhizosphere microbiome is a central determinant of plant performance. Microbiome assembly has traditionally been investigated from a bottom-up perspective, assessing how resources such as root exudates drive microbiome assembly. However, the importance of predation as a driver of microbiome structure has to date largely remained overlooked. Here we review the importance of protists, a paraphyletic group of unicellular eukaryotes, as a key regulator of microbiome assembly. Protists can promote plant-beneficial functions within the microbiome, accelerate nutrient cycling, and remove pathogens. We conclude that protists form an essential component of the rhizosphere microbiome and that accounting for predator-prey interactions would greatly improve our ability to predict and manage microbiome function at the service of plant growth and health.Copyright © 2018 Elsevier Ltd. All rights reserved.
Soil water availability strongly alters the community composition of soil protists
DOI:10.1016/j.pedobi.2014.10.001 URL [本文引用: 2]
Soil protists: A fertile frontier in soil biology research
DOI:10.1093/femsre/fuy006
PMID:29447350
[本文引用: 19]
Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.
Soil protistology rebooted: 30 fundamental questions to start with
DOI:10.1016/j.soilbio.2017.04.001 URL [本文引用: 2]
Plant functional diversity drives niche-size-structure of dominant microbial consumers along a poor to extremely rich fen gradient
DOI:10.1111/1365-2745.12288 URL [本文引用: 1]
pH regulation of carbon and nitrogen dynamics in two agricultural soils
DOI:10.1016/j.soilbio.2005.08.006 URL [本文引用: 1]
Moderate changes in nutrient input alter tropical microbial and protist communities and belowground linkages
DOI:10.1038/ismej.2013.209 URL [本文引用: 1]
Soil bacteria and protozoa affect root branching via effects on the auxin and cytokinin balance in plants
DOI:10.1007/s11104-009-0101-3 URL [本文引用: 2]
The impact of protozoa on the availability of bacterial nitrogen to plants
DOI:10.1007/BF00260510 URL [本文引用: 1]
Soil microorganisms behave like macroscopic organisms: Patterns in the global distribution of soil euglyphid testate amoebae
DOI:10.1111/jbi.12660 URL [本文引用: 1]
Plant functional group diversity promotes soil protist diversity
We tested whether effects of plant diversity can propagate through food webs, down to heterotrophic protists not linked directly to plants. To this end we synthesised grassland ecosystems with varying numbers of plant functional groups (FGN) and assessed corresponding changes in testate amoebae communities. The number of plant species was kept constant. When FGN was increased from 1 to 3, species number and total community density of live testate amoebae were enhanced according to a linear and a saturating function, respectively. From FGN 1 to 2, the appearance of new testate amoebae species did not affect the presence of the resident species, whereas, from FGN 2 to 3 about one quarter of the resident testate amoebae species was replaced, without altering the total species number. Overall, density by species increased, while evenness of the testate amoebae community was not affected by FGN; although Trinema lineare, one of the most common species, became more abundant. The observed relationship between plant functional group diversity and testate amoebae diversity could shed new light on the biogeographical distribution patterns of protists.
The evolution of eukaryotic cilia and flagella as motile and sensory organelles
Response of testate amoebae (protozoa) to N and P fertilization in an Arctic wet sedge tundra
DOI:10.1657/1523-0430(2004)036[0078:ROTAPT]2.0.CO;2 URL [本文引用: 1]
Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity
DOI:10.1038/35054541 URL [本文引用: 1]
Cross-kingdom host shifts of phytomyxid parasites
DOI:10.1186/1471-2148-14-33
PMID:24559266
[本文引用: 2]
Background: Phytomyxids (plasmodiophorids and phagomyxids) are cosmopolitan, obligate biotrophic protist parasites of plants, diatoms, oomycetes and brown algae. Plasmodiophorids are best known as pathogens or vectors for viruses of arable crops (e. g. clubroot in brassicas, powdery potato scab, and rhizomania in sugar beet). Some phytomyxid parasites are of considerable economic and ecologic importance globally, and their hosts include important species in marine and terrestrial environments. However most phytomyxid diversity remains uncharacterised and knowledge of their relationships with host taxa is very fragmentary. Results: Our molecular and morphological analyses of phytomyxid isolates-including for the first time oomycete and sea-grass parasites-demonstrate two cross-kingdom host shifts between closely related parasite species: between angiosperms and oomycetes, and from diatoms/brown algae to angiosperms. Switching between such phylogenetically distant hosts is generally unknown in host-dependent eukaryote parasites. We reveal novel plasmodiophorid lineages in soils, suggesting a much higher diversity than previously known, and also present the most comprehensive phytomyxid phylogeny to date. Conclusion: Such large-scale host shifts between closely related obligate biotrophic eukaryote parasites is to our knowledge unique to phytomyxids. Phytomyxids may readily adapt to a wide diversity of new hosts because they have retained the ability to covertly infect alternative hosts. A high cryptic diversity and ubiquitous distribution in agricultural and natural habitats implies that in a changing environment phytomyxids could threaten the productivity of key species in marine and terrestrial environments alike via host shift speciation.
Soil protozoa in typical regions of China. II. Ecological study
中国典型地带土壤原生动物. II. 生态学研究
Changes in microbial populations following the application of cattle slurry to soil at two temperatures
DOI:10.1016/0038-0717(89)90103-X URL [本文引用: 1]
Opportunities and approaches for manipulating soil-plant microbiomes for effective crop nitrogen use in agroecosystems
DOI:10.15302/J-FASE-2022450
[本文引用: 1]
<p><List> <ListItem><ItemContent><p>● Matching nitrification inhibitors with soil properties and nitrifiers is vital to achieve a higher NUE.</p></ItemContent></ListItem> <ListItem><ItemContent><p>● Enhancing BNF, DNRA and microbial N immobilization processes via soil amendments can greatly contribute to less chemical N fertilizer input.</p></ItemContent></ListItem> <ListItem><ItemContent><p>● Plant-associated microbiomes are critical for plant nutrient uptake, growth and fitness.</p></ItemContent></ListItem> <ListItem><ItemContent><p>● Coevolutionary trophic relationships among soil biota need to be considered for improving crop NUE.</p></ItemContent></ListItem></List></p> <p>Soil microbiomes drive the biogeochemical cycling of nitrogen and regulate soil N supply and loss, thus, pivotal nitrogen use efficiency (NUE). Meanwhile, there is an increasing awareness that plant associated microbiomes and soil food web interactions is vital for modulating crop productivity and N uptake. The rapid advances in modern omics-based techniques and biotechnologies make it possible to manipulate soil-plant microbiomes for improving NUE and reducing N environmental impacts. This paper summarizes current progress in research on regulating soil microbial N cycle processes for NUE improvement, plant-microbe interactions benefiting plant N uptake, and the importance of soil microbiomes in promoting soil health and crop productivity. We also proposes a potential holistic (rhizosphere-root-phyllosphere) microbe-based approach to improve NUE and reduce dependence on mineral N fertilizer in agroecosystems, toward nature-based solution for nutrient management in intensive cropping systems.</p>
Predator richness increases the effect of prey diversity on prey yield
DOI:10.1038/ncomms2287
PMID:23250435
[本文引用: 1]
Positive biodiversity-ecosystem functioning relationships are generally attributed to two mechanisms: complementarity and selection. These mechanisms have been primarily examined using plant communities, whereas bacterial communities remain largely unexplored. Moreover, it remains uncertain how predation by single or multiple predators affects these mechanisms. Here using 465 bacterial microcosms, we show that multiple predation by protists results in positive bacterial diversity effects on bacterial yields (colony-forming units) possibly due to an increased complementarity and evenness among bacterial species. By mathematically partitioning the biodiversity effects, we demonstrate that competitive interactions in diverse communities are reduced and the growth of subdominant species is enhanced. We envisage that, including diversity gradients at other trophic levels, in biodiversity-ecosystem functioning research is a key to understanding and managing ecosystem processes. Such level of manipulation can be achieved best in microbial model systems, which are powerful tools for fundamental hypothesis-driven experiments and the investigation of general ecological theories.
Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment
DOI:10.1038/nature09492 URL [本文引用: 1]
Population dynamics and ecology of ciliates (Protozoa, Ciliophora) in an anoxic rice field soil
DOI:10.1007/s00374-003-0644-z URL [本文引用: 1]
Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling
DOI:10.1016/j.soilbio.2017.05.002 URL [本文引用: 2]
The effect of artificial fertilizers and dung on the members of amoebae in Rothamsted soils
A revised classification of naked lobose amoebae (Amoebozoa: Lobosa)
DOI:10.1016/j.protis.2011.04.004 PMID:21798804 [本文引用: 1]
Microbial carbon dynamics in nitrogen amended Arctic tundra soil: Measurement and model testing
DOI:10.1016/j.soilbio.2005.03.016 URL [本文引用: 1]
Soil water availability strongly alters the community composition of soil protists
DOI:10.1016/j.pedobi.2014.10.001 URL [本文引用: 3]
The biolog plates technique as a tool in ecological studies of microbial communities
Soil fauna and soil health
土壤动物与土壤健康
Distribution of four protozoan genera in rhizosphere and non-rhizosphere soil of corn
玉米根际与非根际土壤中4种原生动物分布特征
Inpact factor of growth and distribution of protozoa
原生动物生长和分布的影响因子
Soil protozoa: Research methods and roles in the biocontrol of soil-borne diseases
土壤原生动物——研究方法及其在土传病害防控中的作用
Nitrogen transformations in soil as affected by bacterial-microfaunal interactions
DOI:10.1016/0038-0717(82)90050-5 URL [本文引用: 1]
Reduction of microbial diversity in grassland soil is driven by long- term climate warming
DOI:10.1038/s41564-022-01147-3 URL [本文引用: 1]
Rhizosphere protists are key determinants of plant health
DOI:10.1186/s40168-020-00799-9
PMID:32127034
[本文引用: 2]
Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators-protists-are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions.We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success.We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance. Video Abstract.
Effects of agricultural chemicals on DNA sequence diversity of soil microbial community: A study with RAPD marker
The DNA sequence diversities for microbial communities in four soils affected by agricultural chemicals (mainly triadimefon and ammonium bicarbonate and their intermediates) were evaluated by Random Amplified Polymorphic DNA (RAPD) analysis. Fourteen random primers were used to amplify RAPDs from four soil microbial community DNAs. The products of 12 primers were separated in gel and generated 155 reliable fragments, of which 134 were polymorphic. The richness, modified richness, Shannon-Weaver index, and a similarity coefficient of DNA were calculated to quantify the diversity to access DNA sequence diversities for four soil microbial communities. The results showed that agricultural chemicals affected soil microbial community diversity at the DNA level. The four soil microbial communities were distinguishable in terms of DNA sequence richness, modified richness, Shannon-Weaver index, and coefficient of DNA similarity. Analysis also showed that the amounts of organic C and microbial biomass C were low in the soil polluted by pesticide (mainly triadimefon and its intermediates), but high in the soil polluted by chemical fertilizer (mainly ammonium bicarbonate and its intermediates). The above results combined may indicate that pesticide pollution caused a decrease in the soil microbial biomass but kept high diversity at DNA level, compared with the control without chemical pollution. In contrast, chemical fertilizer pollution caused an increase in the soil biomass but decrease in the DNA diversity. The RAPD marker technique combined with analysis of soil microbial biomass appears to be an effective approach for studying the diversity of soil microbial communities, although the effects of PCR bias on community composition, such as dominating and rare populations in soils, on the diversity needed to be addressed further. </hea
Monitoring of heavy metal pollution by moss-dwelling protozoa communities in a Hg-Tl mineralized area
藓类附生原生动物群落对汞铊矿重金属污染的监测
Soil algae composition under different agro-ecosystems in North-Eastern Italy
DOI:10.1016/j.agee.2005.06.018 URL [本文引用: 2]
Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: A review
DOI:10.1007/s003740050533 URL [本文引用: 1]
Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
DOI:10.1186/s40168-019-0647-0 URL [本文引用: 1]
Soil protozoa as monitors of the environment
土壤原生动物在环境监测中的应用
Linking the soil microbiome to soil health
土壤微生物组与土壤健康
