• ISSN 1008-505X
  • CN 11-3996/S

水稻根际微生物及其驱动的土壤碳氮磷循环

尹丹, 朱忆雯, 胡敏, 徐乐, 于焕云

尹丹, 朱忆雯, 胡敏, 徐乐, 于焕云. 水稻根际微生物及其驱动的土壤碳氮磷循环[J]. 植物营养与肥料学报, 2024, 30(11): 2207-2220. DOI: 10.11674/zwyf.2024096
引用本文: 尹丹, 朱忆雯, 胡敏, 徐乐, 于焕云. 水稻根际微生物及其驱动的土壤碳氮磷循环[J]. 植物营养与肥料学报, 2024, 30(11): 2207-2220. DOI: 10.11674/zwyf.2024096
YIN Dan, ZHU Yi-wen, HU Min, XU Le, YU Huan-yun. Rice rhizosphere microbiomes and their driving cycling of soil carbon, nitrogen, and phosphorus[J]. Journal of Plant Nutrition and Fertilizers, 2024, 30(11): 2207-2220. DOI: 10.11674/zwyf.2024096
Citation: YIN Dan, ZHU Yi-wen, HU Min, XU Le, YU Huan-yun. Rice rhizosphere microbiomes and their driving cycling of soil carbon, nitrogen, and phosphorus[J]. Journal of Plant Nutrition and Fertilizers, 2024, 30(11): 2207-2220. DOI: 10.11674/zwyf.2024096

水稻根际微生物及其驱动的土壤碳氮磷循环

基金项目: 国家自然科学基金(42077113);广东省科学院建设国内一流研究机构行动专项资金(2020GDASYL-20200104017)。
详细信息
    作者简介:

    尹丹 E-mail: 1912114516@qq.com

    通讯作者:

    徐乐E-mail: 501140@yangtzeu.edu.cn

    于焕云 E-mail: hyyu@soil.gd.cn

Rice rhizosphere microbiomes and their driving cycling of soil carbon, nitrogen, and phosphorus

  • 摘要:

    水稻根际微生物是指水稻根系与土壤紧密接触区域内的微生物,其对水稻生长、养分利用及土壤碳、氮、磷等养分循环具有重要影响。探讨水稻根际微生物驱动的土壤碳、氮和磷循环的关键过程及主要影响因子,为创造有利于微生物活性的微环境,提高养分利用效率提供理论基础。水稻根际微生物驱动的碳循环过程主要涵盖微生物固碳、有机碳矿化、甲烷排放。这些过程主要受外源有机质输入,如秸秆还田、施用有机肥的影响,其次是受水分条件的影响;氮循环过程则主要包括微生物固氮、硝化作用、反硝化作用和厌氧氨氧化,这些过程主要受施肥管理和土壤理化性质如pH和有机碳含量的显著影响;而磷循环的主要过程则为有机磷矿化和无机磷溶解,这些过程主要受到土壤含磷水平及微生物可利用性碳的影响。为了更好地利用水稻根际功能微生物,在今后的研究中,需要定量评估水稻根际微生物驱动的碳、氮、磷循环关键过程的不同影响因子的相对贡献,并通过优化关键影响因子来实现对这些关键过程的定向调控;同时利用单细胞拉曼光谱技术结合合成微生物组的方法,在控制条件下设计和优化功能可靠的“有益碳、氮、磷循环功能微生物群落”,从而促进生物肥料的研发应用,并改善全球农业生产对化学物质的依赖,保障粮食安全。

    Abstract:

    Rice rhizosphere microbiomes refer to the microbial communities in the soil near the root system of rice. These microorganisms play a crucial role in rice growth, nutrient utilization, and the cycling of soil nutrients such as carbon (C), nitrogen (N), and phosphorus (P). Investigating the key processes and major influencing factors of soil C, N, and P cycling driven by rice rhizosphere microorganisms provides a theoretical foundation for creating microenvironments that enhance microbial activity and improve nutrient utilization efficiency. The rice rhizosphere microbial-driven carbon cycle primarily encompasses microbial carbon sequestration, organic carbon mineralization, and methane emission. These processes are significantly influenced by the addition of exogenous organic matter, such as straw incorporation and the application of organic fertilizers, along with varying water conditions. The nitrogen cycle processes mainly include microbial nitrogen fixation, nitrification, denitrification, and anaerobic ammonia oxidation. These processes are predominantly affected by fertilization practices and soil physicochemical properties, such as pH and organic carbon content. The primary processes of the phosphorus cycle involve the mineralization of organic phosphate and the dissolution of inorganic phosphorus, which are chiefly influenced by soil phosphorus content and the availability of microbial carbon. To maximize the utilization of functional microorganisms in the rice rhizosphere, it is necessary to quantitatively evaluate the relative contributions of different influencing factors in the key processes of carbon, nitrogen, and phosphorus cycling driven by rice rhizosphere microorganisms in future research. It is also essential to engineer a “beneficial carbon, nitrogen, and phosphorus cycling functional microbial community” with reliable function using single-cell Raman spectroscopy, combined with synthetic microbiota methods. Ultimately, the goal is to contribute to the development and application of biofertilizers, reducing the global agriculture's reliance on chemical substances, and ensuring food security.

  • 根际是指位于植物根系周围、受根系影响的狭窄(几毫米宽)土体[1]。根际微生物是指紧密附着在根际土上的微生物,其数量众多、类型多样、功能各异,在生态系统功能和植物健康中起着重要作用[2]。水稻作为一种重要的农作物,与其它作物不同的是,其大部分生长期均为淹水条件。然而,水稻根系泌氧作用可使其根际形成一个狭窄的有氧区和微氧区,因而从水稻根表至土体土壤(非根际土壤)的氧化还原电位逐渐降低[3]。水稻根际的这一氧化还原梯度供不同生态位的各种微生物功能群栖息,从而驱动关键元素[特别是碳(C)、氮(N)、磷(P)]的生物地球化学循环[4]

    水稻生长过程中的甲烷排放与水稻根际的产甲烷菌群落组成密切相关[5]。水稻根际接种枯草芽孢杆菌(Bacillus subtilis)和沼泽红假单胞菌(Rhodopseudomonas palustris)可显著提高根际碳、氮、磷循环相关的功能基因丰度,加速土壤碳、氮、磷的周转,从而促进水稻的生长[6]。此外,水稻根际溶磷微生物可提高土壤磷的有效性从而帮助水稻从土壤中获取磷[7]。另一方面,水稻根际微生物群落的组成和功能受水稻基因型、生育期、土壤理化性质等多种因素影响[8]。例如,籼稻和粳稻招募不同的根际微生物,而且籼稻富集的细菌类群更多样化,并含有更多具有氮代谢功能的属,而粳稻富集的类群则较少[9]。参与氨氧化过程的氨氧化细菌主要存在于pH 6.5~7.5、溶解氧浓度大于3 mg/L条件下,而氨氧化古菌在酸性条件下具有氧化氨的能力[10]。水稻土中溶磷菌的丰度随土壤有机碳含量及不溶性磷、钾和镁含量的增加而增加[11]。总之,水稻根际微生物是驱动土壤碳、氮、磷循环的引擎,其组成和功能受到水稻自身及外界多种因素的影响。

    因此,研究水稻土中驱动碳、氮、磷循环的根际微生物的组成和功能及其影响因素,对于保障水稻生产力并促进水稻根际微生物固碳、固氮及温室气体减排均具有重要的指导意义[12]。本综述旨在概述水稻根际微生物多样性和功能基础上,重点阐述水稻根际微生物驱动的碳、氮、磷循环的关键过程,并解析影响这些关键过程的主要因子,以期通过调控这些主要的影响因子优化水稻根际微生物群落组成和功能,为根际调控提供理论依据。

    水稻根际定殖了许多微生物,主要包括细菌、真菌和古菌。其中,细菌的数量占比最大,包括根际促生菌(PGPR)、产甲烷菌、甲烷氧化菌、固氮菌、溶磷菌等[5, 1314]。Chen等[15]对水稻根际微生物群落的分析发现,在属水平上,根际土壤中主要有AnaeromyxobacterHaliangiumGemmatimonasAcidibacterTerrimonasMassilia。进一步研究发现,不同水稻品种、土壤类型以及不同生育期的水稻根际土壤微生物物种多样性和丰度均具有差异性[16]。Zhang等[9]通过16S rRNA基因高通量测序分析了不同类型土壤中栽培的籼稻和粳稻的根际微生物群落组成,研究发现籼稻和粳稻的根际微生物在门水平上主要有Deltaproteobacteria、Actinobacteria、Acidobacteria、Bacteroidetes、Spirochaetes、Chloroflexi、Nitrospirae 和Verrucomicrobia,且以上微生物在籼稻根际的丰度高于粳稻。

    已有的研究表明,水稻根际微生物的主要功能有[2, 13]:1)促进水稻的生长及营养吸收。例如,水稻根际促生菌可通过固氮、溶磷、分泌植物激素等方式调节水稻营养,提高水稻抗氧化能力和光合作用,改善水稻的生长状况[17];2)帮助水稻抵抗逆境胁迫并提高其耐受性。Lian等[18]研究发现,水稻SST基因(一种耐盐相关基因)的变化对水稻根际微生物群落结构有显著影响,且根际微生物有助于水稻抵抗盐胁迫。此外,水稻根际微生物还能够提高水稻对重金属的耐受性[19]。例如,从水稻根际分离的一株高效抗重金属的PGPR菌株—产气肠杆菌K6菌株对Cd2+、Pb2+和As3+都表现出很强的抗性,帮助水稻抵御重金属胁迫;3)根际微生物有助于水稻抵御病原体的入侵。水稻在生长过程中会受到多种病原体影响,包括破坏性病害,如白叶枯病、条斑病以及稻瘟病等,而根际微生物可以抑制病原体的生长。例如,从水稻根际分离的Pseudomonas mosselii (摩氏假单胞菌) 923菌株可以特异性地抑制植物细菌病原体Xanthomonas和真菌病原体Magnaporthe oryzae的生长[20];4)促进根际元素生物地球化学循环。水稻根际微生物可驱动碳、氮、磷等元素循环。例如,水稻根际的Rhizophlytis属和Cladochytrium属微生物是纤维素和碳水化合物的有效分解者[2021]。此外,水稻土中氨化、氮固定,硝化、反硝化、异化硝酸盐还原为铵,厌氧氨氧化等氮循环过程都是由相关的功能微生物驱动[2223]。水稻根际曲霉菌(子囊菌门)的真菌类微生物可以极大地促进土壤磷溶解,而丛枝菌根真菌可以促进磷运输和吸收[12, 24]

    水稻根际微生物的群落组成是动态变化的,特别是细菌群落结构[25],且这种动态变化可受外界环境因素变化的影响[26],如栽培管理方式、生育期、土壤类型、施肥等[2627]。同理,驱动碳、氮、磷等元素循环的水稻根际微生物群落的组成和功能也受到以上因素的影响,且不同元素循环过程的关键影响因子具有差异性。

    碳循环是生态系统中最重要的物质循环之一,而稻田是地球上最大的人工湿地,同时也是地球上重要的碳库,因此研究稻田土壤碳循环对全球碳循环具有重要意义[2829]。微生物是稻田土壤碳循环的重要参与者,它驱动着多个碳循环过程[3031],包括碳固定、有机碳矿化、甲烷代谢等(图1)。

    图  1  水稻根际微生物驱动碳、氮、磷元素循环模式[3234]
    Figure  1.  Microbial driven carbon, nitrogen, and phosphorus cycling patterns in rice rhizosphere

    稻田是温室气体排放的主要来源之一,同时也是一个重要的碳汇,具有很强的碳固存能力,温室气体减排是其重要的生态功能[35]。气候变化是全人类面临的重大挑战之一,因此充分发挥稻田碳汇功能,提高其土壤固碳能力至关重要[36]

    自养微生物在稻田土壤中广泛存在,根据其能量来源可分为光能自养型和化能自养型[37]。化能自养微生物可通过氧化各种还原性底物(如铵、亚硝酸盐和硫化物)获得代谢能,固定大气、海洋、湿地、土壤和极端环境中的CO2,这一过程称为化能自养固碳过程[38]。化能自养微生物的主要固碳途径包括卡尔文−本森循环(Clavin-Benson-Bassham cycle,CBB循环)、还原性(逆向)三羧酸循环(reductive tricarboxylic acid cycle,rTCA循环)、还原性乙酰辅酶A途径(reductive acetyl-CoA pathway,WL途径)及3-羟基丙酸/4-羟基丁酸循环(3-HP/4-HB循环)[38]。在自然界中,化能自养微生物进行固碳的首要途径是通过CBB循环,该过程普遍存在于好氧环境下的化能自养型α-、β-以及γ-proteobacteria纲的微生物中[38]。Rubisco酶是CBB循环的关键限速酶。cbbLcbbM基因,分别编码核糖体辅助蛋白质(Rubisco) I型和II型的大亚基,是关键的功能性基因,已被普遍应用于环境样本中自养微生物(包括化能自养细菌)多样性的分析[39]。rTCA循环是另一种重要的化能自养固碳途径。编码柠檬酸裂解酶的aclAaclB基因可作为rTCA循环的生物标记基因。关于这一固碳途径的研究主要集中在厌氧或微需氧环境中的化能自养微生物[38]。WL途径被认为是严格厌氧细菌和古菌最古老的固碳途径[40]acsAacsB是编码该途径关键酶一氧化碳脱氢酶(CODH)和乙酰辅酶A合酶(ACS)的功能基因。通过WL途径实现自养碳固定的化能自养微生物是一些能够利用氢作为电子供体的严格厌氧菌株,主要包括产乙酸菌、硫酸盐还原菌和产甲烷菌等[38]。3-HP/4-HB循环是贫营养环境中化能自养微生物的主要固碳途径,乙酰辅酶A羧化酶是该循环途径的关键酶之一,accA基因是编码这种酶的功能基因。

    根据以上分析,我们推测水稻根际化能自养固碳微生物的固碳途径以CBB循环、rTCA循环及WL途径为主,但目前对水稻根际环境中研究比较多的化能自养微生物主要为参与CBB循环的微生物[41]。Zhu等[42]采用DNA-SIP技术研究了稻田土壤中自养微生物的组成,发现大约28.9%的OTUs属于氨氧化细菌(AOB)和亚硝酸盐氧化细菌(NOB)。在所有土壤中,Nitrosospira类群占据主导地位,并且在升温条件下,80.4%的固碳细菌被归类为Nitrosomonasnitrosa。Tang等[38]采用cbbL基因高通量测序技术结合qPCR分析,研究了水稻根际携带cbbL基因的化能自养微生物的组成,发现水稻根际携带cbbL基因的化能自养微生物主要属于变形菌门和放线菌门。其中,丰度水平最高的前5 (TOP 5)物种为Variovorax paradoxus、uncultured proteobacterium、Ralstonia pickettiiThermononospora curvataAzoarcus sp.KH33C。水稻根际携带cbbL基因的化能自养微生物组成受土壤有机碳、微生物生物量碳、溶解有机碳含量和土壤容重显著影响[41]

    研究发现,秸秆还田和施用有机肥可提高土壤有机碳、微生物生物量碳、溶解性有机碳及总氮含量,从而显著提高根际土壤固碳基因cbbL的相对丰度及土壤微生物固碳关键酶RubisCO的活性,促进自养微生物固碳[41]。柏菁等[43]采用qRCR技术研究了磷素添加对水稻根际土壤中3条重要CO2固定途径关键基因(cbbLcbbMaccAaclB)丰度的影响,发现磷素添加改变了根际土壤自养固碳微生物的丰度,随水稻生长,磷素添加对自养固碳微生物数量的影响减弱;但与添加磷素相比,水分条件对微生物固碳过程的影响更大。持续淹水由于可提高土壤中微生物可利用碳的含量,从而有利于微生物固碳[40]。Zhang等[44]探讨了有机污染物2,3,4,5-四氯联苯(CB 61),4'-羟基-2,3,4,5-四氯联苯(4'-OH-CB 61),2,2',4,4'-四溴二苯醚(BDE 47),三环唑(TRI)和芘对水稻根际固碳途径的影响,发现4'-OH-CB 61、TRI及BDE 47导致Calvin循环中限速酶核酮糖-1,5-二磷酸羧化/氧化酶(Rubisco)活性降低(6.96%~33.44%),以及编码Rubisco小亚基的基因OsRBCS2-5下调(−6.80<log2 FC<−2.13),这与水稻产量的降低相吻合。以上研究结果揭示了有机污染导致水稻减产的分子机制,有助于提高人们对全球有机污染土壤作物生长和碳固存能力的认识。

    有机碳矿化是指土壤中的有机碳在微生物作用下分解为CO2的过程,同时也是土壤碳循环中一个重要的过程[36, 45]。植物根际激发效应对土壤有机碳矿化有重要影响,可能会导致原土壤有机质矿化抵消部分土壤固碳作用。因此,研究植物根际激发效应及其主要影响因子,对于理解土壤有机碳矿化与平衡具有重要意义[46]。根际激发效应是根−微生物−土壤有机质共同作用的结果,其通过增加微生物的生物量和活性实现,并受生物和非生物因子的调控[4748]。植物可通过根际激发效应调节有机质的分解,包括提高或抑制土壤有机碳的分解,被称为正、负激发效应[49]。Zhu等[50]采用13C稳定性同位素标记技术研究了水稻根际激发效应,发现水稻生长过程中根际分泌物输入的量与速率影响CO2的释放,水稻生长前期(40天前)表现为负激发效应,在水稻生长后期(52天后)表现为正激发效应;而对CH4的释放整个水稻生育期均表现为正激发效应,并随水稻生长逐渐增加。此外,施加氮肥可减少水稻根系和微生物之间的氮竞争,提供额外的电子受体,降低胞外酶活性,从而降低水稻根际激发效应[50]。水分管理条件显著影响水稻根际激发效应[46]。持续淹水条件下,CO2的根际激发效应为正激发效应,而落干条件下为负激发效应;持续淹水条件下,CH4的根际激发效应为较强的正激发效应,而落干条件可降低CH4的根际激发效应。

    水稻土有机碳的矿化过程还受到温度、微塑料、施肥制度、Fe(III)含量等多种因素的影响。研究发现,升温没有显著改变微生物生物量,但提高了寡营养细菌的相对丰度,而底层土壤(15—30 cm)中寡营养细菌占优势,因此寡营养细菌驱动的稳定性有机质的分解对增温更敏感,全球变暖更易引起底层土壤的碳损失[51]。此外,微塑料添加增强了土壤水解酶活性,并提高了有机质分解相关微生物Ruminiclostridium_1MobilitaleaXylanophilumAnaerobacteriuPapillibacterSyntrophomonadaceaeRuminococcaceae_UCG_013的相对丰度,从而促进了有机碳矿化[52]。张雅蓉等[53]研究了5种施肥模式(不施肥、平衡施用化肥、25% 和50%有机肥氮替代化肥氮和单施有机肥)下,黄壤性水稻土有机碳的矿化特征,发现长期有机肥与化肥配施显著提高水稻根际和非根际土壤的总有机碳及活性碳组分含量,增加有机碳矿化量。此外,含氧淹水条件下,添加Fe(III)显著降低土壤有机碳矿化,而淹水厌氧条件下,添加Fe(III)显著降低有机质分解,但提高CO2排放并抑制CH4排放[54]

    甲烷是一种强效的温室气体,对全球变暖有重要影响[55]。水稻土甲烷排放是甲烷产生,氧化并通过水稻通气系统从土壤释放到大气中的最终结果。甲烷排放与产甲烷菌和甲烷氧化菌的活动密切相关[2, 56]

    乙酸营养型和氢营养型是稻田土壤中产甲烷菌最主要的微生物类群[57]。通常认为产甲烷菌主要存在于缺氧的非根际土中,而有些研究发现相比非根际土,水稻根际支持更高的甲烷产量和更多产甲烷古菌的存在,这可能与根际的根系分泌物可提供更多的能量及有机底物有关[2, 26]。据报道,氢营养型的Methanocellales及乙酸营养型的Methanosaetaceae在稻田根际甲烷生成中发挥了关键的作用,而MethanomicrobiaceaeMethanosarcinaceae也是活跃的根际产甲烷菌[2]

    稻田土壤中,CH4可以通过好氧或者厌氧途径代谢,但由于CH4的厌氧氧化速率极低,所以CH4被认为主要由好氧甲烷氧化菌氧化,这些好氧细菌隶属于变形菌门(如I型和II型)和疣微菌门[2]。与产甲烷菌类似,根际土壤中好氧甲烷氧化菌的丰度高于非根际土壤,但非根际土壤仍然是稻田生态系统中甲烷氧化菌的最大储库[5859]。已从稻田生态系统分离鉴定的甲烷氧化菌大部分都属于γ变形菌纲的I型甲烷氧化细菌,而分离的α变形菌纲II型甲烷氧化细菌在物种水平上仍未被完全鉴定,这可能是由Methylocystis属和Methylosinus属II型成员中16S rRNA和pmoA基因序列的高度相似性造成的[60]。水稻根际土中甲烷氧化菌主要分属于两个科:变形菌纲γ亚类的甲基球菌科和α亚类的甲基孢囊菌科。甲基球菌科主要的属为MethylobacterMethylomonasMethylomicrobiumMethylococcusMethylocaldumMethylosphaera;甲基孢囊菌科主要包含MethylosinusMethylocystis[5859]

    稻田土壤甲烷排放受水稻品种、气候、有机质添加、施氮、水分管理等多种因素影响[61]。研究发现,高产水稻品种增加了分配给籽粒的光合产物的量,减少了根际沉积碳,因而降低了产甲烷菌的底物可利用率,从而可减少甲烷排放[62]。此外,高生物量的水稻品种通常具有发达的根系系统,可释放更多的氧气,从而促进甲烷氧化菌氧化甲烷[63]。升温和提高CO2浓度均可增加甲烷排放。据报道,每升温1℃,稻田甲烷排放量增加12.6%[64];在CO2浓度平均增加180 mg/L条件下,甲烷排放量可增加20%~40%[65]。与去除秸秆比,秸秆还田可以增加甲烷排放[66]。在有机碳含量高的稻田土壤中可以通过去除秸秆并减少粪肥施用量来降低甲烷排放并保持水稻产量。施用生物炭可使稻田甲烷排放量平均减少13%,这可能是由于土壤容重降低和土壤pH值增加,从而增加了甲烷氧化菌丰度和甲烷氧化速率[6364]。施氮对甲烷排放的影响表现为:低氮水平可促进甲烷排放,但随施氮量的增加,甲烷排放逐渐降低[6769]。与持续淹水比,非连续淹水条件可降低甲烷排放。甲烷排放量与非淹水的总天数密切相关,单次和多次排干水可分别将CH4排放量平均减少33%和64%[70]。总之,甲烷排放受产甲烷菌和甲烷氧化菌共同影响,调控这些微生物促进甲烷氧化并抑制甲烷产生,是减缓CH4排放的潜在可行方法[2, 71]

    氮是植物生长不可或缺的营养元素,施氮肥是提高水稻产量的重要途经之一[15]。但由于氮肥的利用效率通常较低[72],氮肥的过度使用和滥用已成为农业生产中一个很严峻的问题,因此提高作物氮肥利用效率一直备受关注。微生物驱动土壤氮循环,而植物可以通过根系分泌物重塑根际微生物群落,进而影响根际土壤氮循环及植物的氮利用效率[73]。所以根际微生物驱动的土壤氮素循环是研究的一大热点。土壤氮循环主要包括生物固氮、有机氮矿化、硝化、反硝化、硝酸盐异化还原为铵、厌氧氨氧化等[74](图1)。

    微生物固氮是指微生物将气态氮转化为氨的过程。大气中的氮气是自由可获得氮的最大储库,但只有携带固氮酶的微生物才能利用它,将氮气固定为氨[74]。目前已知的有铁铁(FeFe)、钒铁(VFe)及钼铁(MoFe) 3种不同类型的固氮酶。固氮酶复合物主要由nifH编码的固氮还原酶(铁蛋白)和nifDK编码的固氮酶(钼铁蛋白)两部分组成[7172]anfH、vnfHnifH编码含铁电子转移蛋白,又称铁蛋白或固氮酶还原酶,nifH被认为是研究固氮微生物的分子标记[7576]。固氮微生物是植物根际生态系统中调节氮营养的重要功能微生物[77]。据报道,地杆菌属(Geobacter)、赭黄嗜盐囊菌属(Haliangium)、厌氧粘细菌属(Anaeromyxobacter)、念珠菌固体杆菌属(Candidatus Solibacter)、厌氧绳菌属(Anaerolinea)、芽单胞菌属(Gemmatimonas)、酸杆菌属(Acidibacter)、(Terrimonas)、(Flavisolibacter)、马赛菌属(Massilia)、蔷薇色丝状菌属(Rhodomicrobium)和δ-变形菌纲(Deltaproteobactera)是水稻根际富集的固氮微生物[72]

    影响微生物固氮过程的因素较多,如土壤理化性质[78]、有机肥和无机肥的施用[79]、可利用的营养元素(氮、磷、钼、铁、钾)[80]等。Yang等[80]采用田间15N2标记实验测定了生物固氮量,并基于nifH基因高通量测序分析了土壤固氮微生物群落,研究发现RubrivivaxFrankiaAzospirillum 3个固氮关键属对生物固氮量具有显著影响,且土壤粉粒含量和pH与生物固氮量呈正相关。Tang等[81]研究了施肥管理对固氮微生物群落的影响,发现磷和钾的缺乏可导致nifH基因的表达显著降低,且磷的缺乏抑制效应更大;长期施用秸秆可显著增加固氮菌的数量,但显著降低nifH基因的表达和固氮活性。Liu等[82]研究了增加CO2和氮肥对水稻分蘖期和抽穗期根际固氮细菌群落的影响。研究发现,在增加CO2或常压CO2条件下,增施氮肥均显著降低水稻抽穗期根际土nifH基因的丰度;同时增加CO2和氮肥显著增加水稻抽穗期根际土nifH基因的丰度,而增加CO2不施氮肥对水稻抽穗期根际土nifH基因的丰度无显著影响。在增加CO2条件下,施氮显著增加了Methylosinus的相对丰度,而在常压CO2条件下,施氮显著降低了Rhizobium的相对丰度。外源施加水铁矿或Fe2O3可增强水稻土中AnaeromyxobacterGeobacter属微生物的固氮活性,这可能与AnaeromyxobacterGeobacter属同时具有铁还原功能,外源加入水铁矿或Fe2O3可提高二者的丰度有关[83]。此外,研究发现稻田土壤固氮菌群落在暖温带、热带、亚热带和中温带4个气候区中存在显著差异,这主要归因于气候和土壤pH的差异,且土壤碳/磷值、pH和固氮菌群落结构是影响稻田土壤潜在固氮酶活性的主要因素[84]

    硝化作用是土壤氮循环中的关键过程,其将还原性最强的氮化合物转化为氧化性最强的化合物[85]。硝化作用主要由携带硝化相关功能基因的微生物驱动,如编码氨单加氧酶基因(amoA)。研究发现,硝化作用易发生在距离根表2 mm处,且由于根系分泌物的存在,根际是硝化菌的热点区域[8283]

    硝化作用主要有两步反应,氨氧化(NH4+→NO2)和亚硝化(NO2→NO3)[86]。氨氧化作为硝化作用的限速反应,一直被认为是由氨氧化细菌(AOB)驱动;后来的研究证明,大量的氨氧化古菌(AOA)也参与了氨氧化[8789]。2015年年底,科学家发现了全程氨氧化细菌,能够直接完成从NH4+到NO3的氧化[90]。最近的研究表明,全程氨氧化细菌普遍存在于稻田土壤中[91]。根据16S rRNA基因序列的系统发育关系,AOB可分为3个属,即亚硝化单胞菌属(β-变形菌门)、亚硝化螺菌属(β-变形菌门)及亚硝化球菌属(γ-变形菌门)[92]。水稻根际的AOA主要属于奇古菌门(Thaumarchaeota)[2]。硝化作用的第二步是将亚硝酸盐氧化为硝酸盐,它由亚硝酸盐氧化细菌(NOB)驱动。与其它氮循环微生物相比,NOB研究相对较少[23, 93]。NOB是一种化学自养型微生物,生理功能有限,只能进行亚硝酸盐到硝酸盐的氧化。根据细胞形态和16S rRNA基因序列的系统发育关系,NOB可分为4个属:硝化杆菌属(α-变形菌门)、硝化刺菌属(δ-变形菌门)、硝化球菌属(γ-变形菌门)和硝化螺菌属(硝化螺菌纲和硝化螺菌门)[8889]

    水稻根际环境中,AOB群落对于水稻基因型和环境变化(如土壤深度、水稻生长阶段和氮肥施用)具有高度的响应性,而AOA群落则相对稳定[2]。在稻田土壤中,AOB及AOA在水稻根际和非根际土的群落组成均具有明显差异性[9495]。AOB及AOA在根际土中的丰度均高于非根际土,而且相对于AOB,AOA在水稻根际占主导,这可能是由于AOA受到根系渗出物(氧气、二氧化碳)以及根际效应的影响大于AOB[9697]。但在氮受限条件下,AOB及AOA在非根际土的丰度会高于根际土[98]。水分条件也显著影响水稻根际AOA和AOB的丰度[99]。AOA在半干旱条件下丰度最高,而AOB在间歇灌溉条件下丰度最高。Wang等[100]研究了4种不同类型的水稻土中AOA、AOB以及NOB对硝化作用的贡献。研究发现,在微碱性水稻土中AOA占主导,而中性水稻土中以AOB为主,亚硝盐氧化主要由Nitrospira属微生物驱动。Zhao等[101]研究了两种不同类型土壤(分别采自五常和常熟)的氮肥利用效率,发现在同种气候和管理措施下,相较于常熟地区采集的土壤,从五常地区采集的土壤表现出更高的氮肥利用效率,其氮肥损失率较低。微生物群落分析发现,氨氧化古菌(Nitrososphaeraceae)和亚硝酸盐氧化细菌(Nitrospira-like)的差异可能是两种类型水稻土氮肥利用效率不同的主要原因。此外,长期秸秆还田可降低油菜−水稻轮作土壤中亚硝酸盐氧化菌(Nitrospira-like)群落的多样性并影响其群落结构,这主要与秸秆还田后土壤铵态氮、硝态氮、速效磷和速效钾等理化性质的变化有关[102]

    反硝化作用是微生物将氮氧化物(NO3和NO2)逐步还原为气体形式(NO,N2O及N2)的微生物呼吸过程[23, 92, 103104]。反硝化是陆地生态系统中氮损失的重要途径[9596]。稻田特有的生境为反硝化作用的发生提供了必要条件,而根际是土壤氮循环的独特区域,在土壤反硝化中扮演重要角色[105106]。反硝化过程由4个独立的步骤组成,分别由硝酸还原酶、亚硝酸还原酶、一氧化氮还原酶和氧化亚氮还原酶催化,对应的编码基因分别为narnirnornos[107]。反硝化第二步NO2还原为NO是反硝化过程的限速步骤,该步骤的关键基因为nirKnirS[107]。反硝化最后一步N2O还原为N2可直接影响水稻根际N2O排放,该步骤的关键基因为nosZ[107, 98]。水稻根际土中nirKnirS基因的丰度显著高于非根际土,而根际土中nosZ基因的丰度显著低于非根际土,这进一步证实了根际土壤N2O释放高于非根际土壤的观测结果[98]。在门水平上,反硝化微生物主要属于变形菌门,携带功能基因nirKnosZ I和nosZ II的变形菌门微生物主要为α-变形菌和γ-变形菌,而携带功能基因nirS的变形菌门微生物主要为γ-变形菌[108]。在科或属水平上,水稻根际发现的反硝化细菌主要有Rhodospirillaceae、AlcaligenesSorangiumFlavobacteriumHydrogenophagaFerritrophicum、rhodococcus、AcinetobacterAzospirillum[109]

    反硝化过程为微生物驱动,影响微生物活性的因素都可影响反硝化过程[110]。影响反硝化过程的因素较多,如水分管理、pH、秸秆还田等[106]。Chen等[110]研究了3种不同的水分管理即连续灌溉(C)、干湿交替(J)、控水模式(G)对水稻整个生育期根际土壤反硝化强度的影响,发现水稻根际土壤硝酸盐还原酶及亚硝酸盐还原酶活性随水分管理的不同而不同,表现为C>J>G,且随着水稻生长,3种水分管理模式下土壤硝酸盐还原酶亚硝酸盐还原酶活性均呈下降趋势,成熟期活性最低。不同类型的秸秆还田也可影响水稻根际反硝化的潜力。谢婉玉等[111]研究了施用水稻、小麦及玉米3种不同类型的秸秆对水稻生育期内N2O排放的影响,发现在水稻生育期内,水稻秸秆处理显著增加了nosZnirS的基因丰度,从而增加了水稻生长期N2O排放量,而小麦秸秆和玉米秸秆处理对反硝化功能基因及N2O排放量无显著影响。

    稻田反硝化是N2O的重要排放源,其对全球气候变化具有重要影响[106]。另一方面,反硝化是稻田生态系统中重要的氮损失途径,降低了氮肥的利用效率,造成了严重的经济损失[112]。所以很多研究致力于探索如何减少稻田N2O排放及氮素的损失。目前认为,优化氮施用量、以铵态氮肥代替硝态氮肥、生物炭改良、施用硝化抑制剂并采用先进的灌溉技术可有效降低反硝化和N2排放[103]

    厌氧氨氧化(anammox)是在厌氧条件下,以氨为电子供体,亚硝酸根为电子受体,产生氮气和水的生物反应,通常被描述为NO2 + NH4+ → N2[70, 106107]。厌氧氨氧化过程是氮循环过程中一个重要的环节,同反硝化过程一样,厌氧氨氧化过程是稻田合成氮肥损失的重要途径[113116]。水稻根际被认为是厌氧氨氧化的热点区域[117118]。Nie等[119]采用CARD-FISH、同位素示踪技术、qPCR分析和16S rRNA基因克隆文库,研究了根际和非根际稻田土壤中anammox细菌的存在、活性、功能基因丰度及其对氮气产生的贡献,发现水稻根际土存在显著的厌氧氨氧化反应,其对氮气产生的贡献为31%~41%,速率为N2 0.33~0.64 nmol/(g·h, 土)。类似的,Xu等[120]利用15N稳定同位素技术测定了水稻根际及非根际土中厌氧氨氧化的原位活性,发现厌氧氨氧化在非根际土的活性高于根际土,其对铵消耗的贡献分别为13.3% (非根际)和5.3% (根际)。因此,根际为anammox细菌提供了一个有利的生境,这些细菌对氮循环过程具有重要影响。稻田土壤厌氧氨氧化细菌主要有如下5个属:Candidatus Brocadia、Candidatus Kuenenia、Candidatus Anammoxoglobus、Candidatus Jettenia、Candidatus Scalindua[115]。功能基因hzs由3个亚基组成,分别是hzsA、hzsBhzsC,是定量厌氧氨氧化细菌的特异性分子标记,而厌氧氨氧化细菌的多样性和功能基因的丰度通常可作为评价生物脱氮的微生物指标[121123]

    稻田中影响厌氧氨氧化过程的因素较多,如温度、pH、施肥方式、有机碳、底物及生育期的变化等,且不同深度和类型的稻田土壤中,厌氧氨氧化活性在水平和垂直方向有很大差异[118, 124126]。Shan等[117]研究发现,当温度从5℃增加到25℃时,厌氧氨氧化活性在N 0.4~1.7 nmol/(g·h)变化,但当温度从25℃增加到35℃时,厌氧氨氧化活性反而下降;类似的,在pH为7.3时,厌氧氨氧化活性最高,且在此基础上调高pH对厌氧氨氧化速率的抑制大于调低pH。此外,添加葡萄糖和乙酸盐显著降低厌氧氨氧化速率,这可能与厌氧氨氧化细菌属于化能自养微生物有关[110, 118119]。厌氧氨氧化的基因(hzsB)丰度随水稻生育期变化而不同,其中,分蘖期根际土壤hzsB基因丰度最高,且根系分泌物中琥珀酸的浓度与hzsB基因的丰度显著相关[118]。施肥管理也会影响厌氧氨氧化活性,Sun等[127]设置了化肥、化肥+秸秆、化肥+秸秆+绿肥及化肥+秸秆+绿肥+综合管理4种不同的管理模式,4年田间试验结果表明,绿肥配合化肥处理下厌氧氨氧化活性最高。

    磷在很多土壤中含量丰富,但可被植物利用的磷只占一小部分,因为大多数磷是以正磷酸盐形式与土壤颗粒紧密结合[128129]。磷在土壤中以有机和无机两种形式存在,无机磷溶解和有机磷矿化是最重要的土壤磷循环过程(图1)[122123]。微生物在土壤磷循环及调节磷有效性方面发挥着关键作用[130132]

    无机磷溶解的主要机制为微生物产生有机酸,降低土壤pH,而较低的土壤pH可促进有机磷在土壤中的溶解,这是因为酸性环境有利于有机磷的分解和解吸[132133]。参与无机磷溶解的典型基因gcd可直接控制葡萄糖的氧化途径和周质空间的酸化[134]。据研究报道,古菌、细菌和真菌是溶解磷和动员磷的主要微生物。据估计,土壤中能够溶解磷的细菌和真菌分别占细菌和真菌总数的1%~50%和0.1%~0.5%[135]。研究发现,水稻根际同时存在厌氧和好氧溶磷微生物,根际溶磷菌的丰度高于非根际,厌氧溶磷菌丰度高于好氧溶磷菌丰度[136]。已报道的水稻根际溶磷微生物包括BacillusPseudomonasRhizobiumEnterobacter等属[137]。Panhwar等[138]从好氧水稻土和植物样品中分离出43株溶磷细菌,分离的菌株主要隶属于芽孢杆菌属。

    研究发现,低磷水平更能激活水稻根际土壤溶磷微生物,且根瘤菌(Rhizobiales)和放线菌(Actinomycetales)在水稻土磷溶解过程中起主导作用[139]。此外,溶磷微生物能够影响植物的生长发育、营养吸收以及抗病抗逆等重要的生理过程。Aslam等[140]研究了转基因水稻TP-LaPAP12在干旱、正常施磷和干旱、不施磷条件下接种芽孢杆菌菌株(一种溶磷微生物)对水稻根系发育和磷吸收的影响,发现接种芽孢杆菌菌株显著促进了TP-LaPAP12水稻根的生长及其对磷的吸收,特别在干旱、不施磷条件下。单细胞拉曼光谱技术是一种不依赖培养的技术,能够从细胞中采集其分子振动谱。该技术能迅速、非侵入性地在原位获取单一细胞的生理与生化信息[141]。此外,单细胞拉曼光谱技术可与拉曼激活细胞分选技术结合使用,通过基于生物标记拉曼带,实现在复杂环境样本中对目标微生物的识别与分选[142]。Liu等[143]从生长于田间酸性土壤的水稻(南粳46)根际中分离获得了421株细菌并将其作为SynCom的候选菌株,然后采用拉曼-D2O光谱技术对筛选的12株代表性菌株进行耐铝水平评估,基于C-D比值发现Pseudomonas aeruginosaRhodococcus erythropolis 为耐铝菌株,并将R. erythropolisP. aeruginosa共培养作为耐铝SynCom,进一步研究发现该合成菌群在缓解水稻酸铝胁迫的同时,可增加根际溶磷菌的丰度,促进有机磷和残留态磷向可利用磷的转化,从而提高磷的利用率。

    有机磷矿化是微生物分解胞外磷酸酶将有机磷转化为植物可利用的无机磷的过程[144]。有机磷占土壤总磷库的30%~80%,其经过磷酸酶矿化后可被植物所利用[4]。参与土壤中有机磷矿化的基因有碱性磷酸酶(phoDphoA)、植酸酶(appA)和C-P裂合酶(phn),它们都具有很强的矿化能力[130]。作为编码微生物碱性磷酸单酯酶的同源基因,phoD的表达受土壤磷有效性的严格控制,从而在缺磷条件下促进土壤有机磷的矿化。同时,phoD基因也被认为是编码碱性磷酸酶的关键基因,通常被用作评估含碱性磷酸酶的微生物群落丰度和组成的标记基因[4, 145]。水稻根际携带phoD基因的微生物在纲水平上主要为Alphaproteobacteria、Betaproteobacteria、Gammaproteobacteria、Cyanobacteria及Actinobacteria;在属水平上主要为MethylobacteriumMethylomonasBradyrhizobium[4]

    Wei等[4]研究了施磷肥和不施磷肥如何影响水稻土中携带phoD基因微生物的丰度和组成。研究发现,phoD基因丰度与土壤磷有效性显著负相关,且不施磷处理下根际土和非根际土中phoD丰度均显著高于施磷处理,这表明在贫磷条件下携带phoD基因的微生物促进了有机磷矿化。除土壤磷有效性外,有机磷矿化还受微生物对碳的可利用性影响。外源添加碳源可提高微生物的活性,促进有机磷的矿化[146147]。Liu等[148]研究了施用生物炭及铁改性生物炭对盐碱水稻土中有机磷矿化的影响,发现携带phoD基因的溶磷细菌的多样性与有机磷矿化呈正相关;生物炭和铁改性生物炭处理均提高了携带phoD基因的溶磷菌相对丰度,在门水平上变形菌门和放线菌门是优势菌门,特别是施铁改性生物炭后,ProteobacteriaGemmatimonadetesVerrucomicrobiaFirmicutesAcidobacteria的相对丰度呈上升趋势,且phoD基因丰度均高于其他处理。因此生物炭特别是铁改性生物炭与无机肥混施,有利于促进盐碱性水稻土中有机磷矿化[148]

    水稻根际微生物驱动的碳、氮、磷循环发挥着双重积极作用。一方面,促进土壤碳、氮、磷元素的周转,提高水稻对养分的吸收利用,改善水稻生长并提高其产量;另一方面,水稻根际碳、氮循环功能微生物在土壤固碳、固氮、温室气体减排中也扮演着重要角色。

    水稻根际碳、氮、磷循环功能微生物相关研究展望如下:

    1) 目前针对新污染物对水稻根际碳、氮、磷循环的影响研究还较少,需加强新污染物(微塑料、抗生素等)对水稻根际碳、氮、磷循环关键过程的影响机理探讨。

    2) 影响水稻根际微生物驱动的土壤碳、氮、磷循环关键过程的因素较多,如何定量评估不同影响因子的相对贡献,以及如何通过优化关键影响因子来实现水稻根际微生物驱动的碳、氮、磷循环关键过程的定向调控仍有待进一步研究。

    3) 利用单细胞拉曼光谱技术结合合成微生物组的方法,在控制条件下设计和优化功能可靠的“有益碳、氮、磷循环功能微生物群落”,有利于在农业生产中更好地利用水稻根际功能微生物组。

    4) 针对当前关于碳、氮、磷循环功能微生物及功能基因的研究,更多集中在DNA水平上,建议未来加强基于RNA水平及与代谢组相结合的研究工作。

  • 图  1   水稻根际微生物驱动碳、氮、磷元素循环模式[3234]

    Figure  1.   Microbial driven carbon, nitrogen, and phosphorus cycling patterns in rice rhizosphere

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  • 收稿日期:  2024-03-07
  • 录用日期:  2024-06-01
  • 网络出版日期:  2024-09-24
  • 刊出日期:  2024-11-24

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