Characteristics of root-associated microbiomes and their responses to soil nitrogen levels in different wheat cultivars
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摘要: 植物根区微生物在植物养分吸收以及生长发育过程中发挥重要作用。为研究不同小麦品种根区微生物群落结构差异, 本研究选择‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’ 4个小麦品种, 于高氮[300 kg(N)·hm−2]和低氮[0 kg(N)·hm−2]条件下进行田间试验, 在分蘖期、拔节期和灌浆期采集根区样品。通过16S rRNA基因高通量测序技术比较分析不同小麦品种根际土壤和根内生细菌群落结构和多样性, 同时测定小麦植株的生理参数。结果表明, ‘科农9204’在3个生育期及不同氮素水平下相对其他3个品种均具有较高的地上部氮素吸收量(除分蘖期低氮条件)。小麦根际土壤和根内生细菌群落的优势菌门均为变形菌门(Proteobacteria)和放线菌门(Actinobacteria)。相比其他3个品种, ‘科农 9204’ 的根际土壤细菌群落在拔节期低氮水平下富集了根瘤菌目(Rhizobiales)和芽单胞菌属(Gemmatimonas), 在灌浆期高氮水平下富集了弗兰克氏菌目(Frankiales)。相关性分析表明, 根际土壤细菌群落中的节杆菌属(Arthrobacter)、链霉菌属(Streptomyces)、红色杆菌属(Rubrobacter)和类诺卡氏菌属(Nocardioides)与小麦地上部生物量和地上部氮素吸收量呈显著正相关, 马赛菌属(Massilia)、砂单胞菌属(Arenimonas)、假单胞菌属(Pseudomonas)和黄杆菌属(Flavobacterium)与小麦地上部全氮含量呈显著正相关。上述结果表明, 小麦可能通过调控根区微生物群落来影响养分吸收, 且这种影响具有品种特异性。本研究为明确小麦与微生物互作机制、发掘对小麦有益的微生物并应用到农业生产中提供了依据。Abstract: Plant root-associated microorganisms play important roles in nutrient uptake and plant growth. In order to illustrate the differences in the root-associated microbial community structure of different wheat cultivars, four wheat cultivars (i.e., ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’) were planted under 0 kg(N)·hm−2 (low nitrogen level) and 300 kg(N)·hm−2 (high nitrogen level), and the rhizosphere and root samples were collected at the tillering, jointing, and filling stages. The bacterial diversity and community structure in the rhizosphere and root endosphere of different wheat cultivars were analyzed using 16S rRNA high-throughput sequencing, and the physiological parameters of wheat were determined. Compared with the other three cultivars, ‘Ke-nong 9204’ had higher aboveground nitrogen accumulation at the three growth stages and under two nitrogen levels, except at the tillering stage with a low nitrogen level. Proteobacteria and Actinobacteria were the dominant bacteria in the wheat rhizosphere and root endosphere. Compared to the other three cultivars, ‘Kenong 9204’ enriched Rhizobiales and Gemmatimonas in the rhizosphere soil bacterial community under low nitrogen level at the jointing stage and enriched Frankiales under high nitrogen level at the filling stage. Correlation analysis showed that Arthrobacter, Streptomyces, Rubrobacter, and Nocardioides in the rhizosphere soil bacterial communities were significantly positively correlated with aboveground biomass and nitrogen accumulation; Massilia, Arenimonas, Pseudomonas, and Flavobacterium were significantly positively correlated with aboveground nitrogen content. Our results indicate that wheat may affect nutrient uptake by regulating the composition of the microbial community in the root zone and that this effect is cultivar-specific. This study provides useful information for understanding plant-microbe interactions in wheat and harnessing beneficial microbes for agricultural production.
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微生物与植物间存在密切且复杂的相互作用, 对植物生长具有重要意义[1-2]。植物根区微生物种类繁多, 它们与植物共同进化, 其多样性和功能是影响植物生长和健康的重要因素[3-4]。植物根区微生物的组成和功能受多种因素影响, 如土壤环境、农田管理措施、植物基因型以及生长阶段等[5-6]。
植物基因型是影响根区微生物组成的重要因素。不同基因型植物可以通过根系分泌物选择特定微生物从而影响自身生长发育, 如玉米(Zea mays)分泌黄酮类化合物驱动根际富集了草酸杆菌(Oxalobacteraceae), 进而促进玉米氮素吸收[7]。Kwak等[8]选择了对青枯菌(Ralstonia solanacearum)具有抗性的番茄(Solanum lycopersicum)品种以及易受青枯菌侵染的番茄品种, 通过16S rRNA基因测序发现两个番茄品种的根际土壤微生物存在差异, 宏基因组学数据表明抗性品种根际土壤中存在更加丰富的黄杆菌(Flavobacteriaceae)基因组。有研究发现抗尖孢镰刀(Fusarium oxysporum)品种的菜豆(Phaseolus vulgaris)根际土壤细菌中假单胞菌科(Pseudomonadaceae)、芽孢杆菌科(Bacillaceae)和噬纤维菌科(Cytophagaceae)等微生物的丰度高于易感品种, 网络分析表明, 抗尖孢镰刀菌菜豆品种的根际土壤细菌网络比易感品种更复杂、联系更紧密[9]。不同氮素耐受性的苹果(Malus domestica)砧木根际土壤细菌群落结构差异显著, 其中假黄单胞菌属(Pseudoxanthomonas)、芽孢杆菌属(Bacillus)和不动杆菌属(Acinetobacter)的相对丰度与苹果砧木氮含量呈正相关, 并且在低氮耐受性的苹果砧木根际土壤中相对丰度较高[10]。Mahoney等[11]对9个冬小麦(Triticum aestivum)品种的根际土壤微生物组进行研究, 结果表明有24个操作分类单元(Operational Taxonomic Unit, OTU)在小麦品种间存在显著差异, 并且与品种相关的OTUs可能对宿主植物具有有益作用。Kavamura等[12]研究发现高杆小麦品种根际土壤细菌群落的放线菌门、拟杆菌门(Bacteroidota)和变形菌门的相对丰度较高, 而半矮秆小麦品种的疣微菌门(Verrucomicrobia)、浮霉菌门(Planctomycetes)和酸杆菌门(Acidobacteria)的相对丰度较高。因此, 植物基因型对根区微生物组成有显著影响, 深入研究作物与根区微生物之间复杂的相互作用, 为促进作物生产提供了新途径。
氮素是作物生长发育过程中所需的关键营养元素[13], 对作物的生命活动以及产量具有重要意义。化肥的使用对促进粮食生产至关重要, 但在农业生产过程中为了追求作物产量, 过量的氮输入也给生态环境带来了负面影响, 如土壤酸化以及温室气体排放等[14-15]。同时, 土壤氮素水平通常会驱动土壤微生物多样性、结构和功能的变化[16-17]。研究表明, 过量施氮显著降低了玉米根际土壤和非根际土壤中固氮细菌群落的香农指数, 此外, 还降低了伯克氏菌属(Burkholderia)的相对丰度, 提高了鞘脂菌属(Sphingobium)的相对丰度[18]。缺氮胁迫使得小麦根际土壤微生物群落的Alpha多样性增加, 糖酵解、过氧化物代谢和磷酸肌醇代谢等过程增强[19]。然而, 关于不同氮素水平下作物品种影响根区微生物群落的相关研究较少。因此, 研究不同作物品种微生物组在不同氮素水平下的差异对于实现农业的绿色发展至关重要。
小麦是我国重要的粮食作物, 其生产对于保障国家粮食安全具有重要意义。‘科农9204’是高产氮高效小麦品种, 童依平等[20]分析了包括‘科农9204’和‘京411’在内的12个冬小麦品种的氮素利用效率, 结果发现, ‘科农9204’在高氮和低氮条件下均具有较高的以生物量为基础和以籽粒产量为基础的氮素利用效率。Shi等[21]从基因组水平和转录组水平阐述了‘科农9204’氮素高效吸收和利用的分子机制, 该研究发现‘科农9204’相比‘京411’在生殖发育阶段具有较高的氮素利用效率和发达的根系, 并且营养吸收相关基因持续高表达, 表明‘科农9204’氮高效的机理是受多方面调控的结果。此外, 小麦品种氮素利用效率受施氮水平影响较大[22], 因此应在不同氮素水平对小麦氮素吸收利用能力进行综合评估。
宿主品种和土壤氮素水平会影响根区微生物群落的组成, 但小麦在不同生长阶段下根区微生物组的品种特异性差异以及对土壤氮素水平的响应机制仍不明确。本研究选择‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’ 4个小麦品种, 分别在2个氮素水平进行种植, 于分蘖期、拔节期和灌浆期采集根际土和根样品。采用16S rRNA基因高通量测序技术, 分析不同小麦品种间根区微生物群落组成和多样性, 同时分析小麦生理指标与根际土壤微生物的关系, 以期获得不同品种小麦根区微生物的差异, 为筛选对小麦生长有益的微生物提供依据。
1. 材料和方法
1.1 试验设计
本研究田间试验在中国科学院栾城农业生态系统试验站(37°53ʹN, 114°41ʹE, 海拔50 m)进行。田间试验设置2个氮素水平, 高氮水平尿素施用量为300 kg(N)·hm−2, 低氮水平不施肥。分别在分蘖期、拔节期和灌浆期进行灌溉, 每次灌溉水量约90 mm。氮肥条件为主区, 品种为副区, 播种方式为机械条播, 每小区6行, 行长8 m, 高氮和低氮间过渡区为2 m, 两个施氮区各3次重复, 共计24个小区。供试小麦品种分别为: ‘科农9204’ (KN9204, 分蘖力强、株型紧凑、氮吸收利用效率较高)、‘科农2011’ (KN2011, 抗倒伏、耐旱)、‘京411’ (J411, 抗寒性强、适应性广)和‘百农207’ (B207, 根系活力强、抗寒性好)。播种时间为2021年10月中旬, 取样时间分别为2021年11月底(分蘖期)、2022年4月初(拔节期)和2022年5月中旬(灌浆期)。
1.2 地上部指标测定
在每个取样期, 每个品种选择3株小麦进行地上部指标测定。剪下小麦地上部分装入信封, 置于烘箱在105 ℃下杀青30 min, 然后于65 ℃条件下将小麦植株样品烘干至恒重, 称重记录, 计算地上部生物量(ADW)。将小麦干物质样品粉碎, 采用硫酸-双氧水消解-凯氏定氮法测定全氮含量(ANC)。地上部氮素吸收量(ANA)为地上部生物量和全氮含量的乘积[23]。
1.3 样品采集
在每个取样期, 每个小区选择5处进行样品采集, 每处选择5株小麦将根系挖出, 混合为该小区的代表样本, 3次重复。紧附在小麦根部的土壤作为根际土, 首先抖落小麦根部附着的松散土壤, 将小麦根部放入装有20 mL无菌PBS缓冲液(8.1 mmol·L−1 Na2HPO4, 1.9 mmol·L−1 NaH2PO4, 145 mmol·L−1 NaCl, pH 7.2~7.4)的50 mL离心管中, 再于摇床中180 r·min−1震荡30 min。用无菌镊子取出根, 静置后的沉淀为根际土壤样品, 收集于2 mL离心管内。将小麦根部用灭菌水冲洗3次, 置于含PBS缓冲液的离心管中, 超声震荡5次, 每次30 s, 两次间歇30 s, 无菌水清洗后于2%次氯酸钠中浸泡5 min, 无菌水清洗3次, 再用70%的乙醇浸泡1 min。最后用无菌水清洗3次, 使用无菌滤纸吸干根表面水分, 将根样品在无菌研钵中用液氮研磨后, 用作根内生菌样品DNA的提取。
1.4 DNA提取和高通量测序
所有土壤和根系样品的DNA均使用FastDNA Spin Kit for Soil试剂盒(MP Biomedicals, USA)提取, 具体方法参照说明书。DNA的浓度和纯度用NanoDrop One (ThermoFisher Scientific, USA)超微量分光光度计测定。将提取的DNA送至上海派森诺生物科技有限公司进行16S rRNA基因高通量测序, PCR扩增引物为799F (AACMGGATTAGATACCCKG)和1193R (ACGTCATCCCCACCTTCC)[24], 对16S rRNA基因的V5-V7区进行扩增, 采用测序平台Illumina NovaSeq-PE250测序。测序数据通过QIIME2 (Quantitative Insights Into Microbial Ecology)进行分析[25], 对原始数据进行双端序列拼接、去除引物、去噪并生成特征表, 用 Silva138数据库进行微生物物种注释[26], 在各分类水平上进行分类学分析、细菌群落Alpha多样性分析、Beta多样性分析、差异物种分析以及相关性分析。
1.5 统计分析
采用R语言4.1.2的Duncan test方法分析不同小麦品种间地上部指标以及细菌群落Alpha多样性差异的显著性。采用R语言中的vegan包和ggplot2包基于Bray-Curtis距离完成主坐标分析(PCoA)。采用R语言中的vegan包的Adonis功能分析不同小麦品种对细菌群落结构的影响。采用线性判别分析(LEfSe)筛选不同品种小麦根际土壤微生物的差异物种, 其中分蘖期低氮水平下的筛选标准为LDA≥4且P<0.05, 其他条件下的筛选标准均为LDA≥2且P<0.05。采用R语言中stats包的Spearman相关性分析方法分析微生物和小麦地上部指标的相关性。
2. 结果与分析
2.1 不同小麦品种地上部性状分析
图1为不同品种小麦的地上部生物量、地上部全氮含量和地上部氮素吸收量。分蘖期高氮水平下, ‘科农9204’地上部生物量为46 g∙m−2, 比‘科农2011’和‘京411’分别高44%和60% (P<0.05)。灌浆期高氮水平下, ‘科农9204’的地上部生物量为4954 g∙m−2, 比‘百农207’高108% (P<0.05)。灌浆期低氮水平下, ‘科农9204’的地上部生物量为1633 g∙m−2, 比‘科农2011’和‘京411’分别高53%和68% (P<0.05)。
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图 1 不同小麦品种地上部性状对比分析不同小写字母代表不同小麦品种间差异显著(P<0.05)。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。Different lowercase letters represent significant differences among different wheat cultivars (P<0.05). KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively.Figure 1. Comparative analysis of aboveground part traits of different wheat cultivars在分蘖期、拔节期和灌浆期, 高氮水平下4个小麦品种的地上部全氮含量无显著差异。在分蘖期, 低氮水平下‘科农2011’的地上部全氮含量分别比‘科农9204’ ‘京411’和‘百农207’高18%、8%和8% (P<0.05)。
分蘖期高氮水平下, ‘科农9204’的地上部氮素吸收量为1.62 g∙m−2, 比‘科农2011’和‘京411’分别高32%和51% (P<0.05)。拔节期高氮水平下, ‘科农9204’的地上部氮素吸收量为14 g∙m−2, 比‘百农207’高40% (P<0.05)。灌浆期高氮水平下, ‘科农9204’的地上部氮素吸收量为77 g∙m−2, 比‘百农207’高119% (P<0.05)。灌浆期低氮水平下, ‘科农9204’的地上部氮素吸收量为21 g∙m−2, 比‘科农2011’ ‘京411’和‘百农207’分别高132%、90%和88% (P<0.05)。
2.2 不同小麦品种根区细菌群落分析
2.2.1 多样性分析
在分蘖期, 高氮水平下‘京411’根际土壤细菌群落的Alpha多样性显著低于其他3个品种(P<0.05), 低氮水平下显著低于‘科农9204’和‘科农2011’ (P<0.05)。在拔节期, 低氮水平下‘科农9204’根际土壤细菌群落的Alpha多样性显著高于‘科农2011’和‘百农207’ (P<0.05)。在分蘖期, 低氮水平下‘科农9204’根内生细菌群落的Alpha多样性显著高于‘京411’和 ‘百农207’ (P<0.05) (表1)。
表 1 不同品种小麦根际土壤和根内生细菌群落的Alpha多样性Table 1. Alpha diversity of rhizosphere soil and endosphere bacterial community in different wheat cultivars取样部位
Compartment施氮水平
Nitrogen level时期
Growth stage科农9204
Kenong 9204京411
Jing 411科农2011
Kenong 2011百农207
Bainong 207根际土壤
Rhizosphere soil高氮
High nitrogen分蘖期 Tillering 8.72±0.41a 7.49±0.79b 8.92±0.60a 9.18±0.46a 拔节期 Jointing 8.89±0.29a 8.97±0.03a 9.00±0.30a 9.18±0.10a 灌浆期 Filling 9.34±0.21a 9.47±0.06a 9.29±0.07a 9.25±0.14a 低氮
Low nitrogen分蘖期 Tillering 9.29±0.21a 8.56±0.55b 9.58±0.10a 7.85±0.17c 拔节期 Jointing 9.23±0.06a 9.06±0.09ab 8.93±0.06b 8.97±0.17b 灌浆期 Filling 9.29±0.1ab 9.36±0.05a 9.24±0.10ab 9.16±0.12b 根内
Root endosphere高氮
High nitrogen分蘖期 Tillering 5.56±0.18a 5.43±0.33a 5.48±0.22a 5.32±0.61a 拔节期 Jointing 6.79±0.20a 6.42±0.47a 6.84±0.14a 6.64±0.18a 灌浆期 Filling 6.55±0.38b 6.51±0.12b 6.96±0.55ab 7.36±0.39a 低氮
Low nitrogen分蘖期 Tillering 5.54±0.33a 4.58±0.6bc 5.19±0.08ab 4.09±0.68c 拔节期 Jointing 6.17±0.16a 6.53±0.56a 6.68±0.35a 6.81±0.35a 灌浆期 Filling 6.50±0.60a 6.89±0.06a 6.87±0.20a 7.10±0.06a 不同小写字母代表不同小麦品种间差异显著(P<0.05)。Different lowercase letters represent significant differences among different wheat cultivars (P<0.05). 为探究小麦品种对根区细菌群落Beta多样性的影响, 基于Bray-Curtis距离在ASV (amplicon sequence variants)水平对不同小麦品种根区细菌群落进行主坐标分析和Adonis分析。结果发现, 拔节期高氮水平下, 小麦品种对根际土壤群落组成无显著影响, 在其他条件下, 小麦品种间根际土壤细菌群落组成差异显著(P<0.05) (图2)。 拔节期低氮水平下, 小麦品种对根内生细菌群落组成无显著影响, 在其他条件下, 小麦品种间根内生细菌群落组成差异显著(P<0.05)(图3)。
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图 2 不同施氮水平下不同小麦品种根际土壤细菌群落的主坐标分析(PCoA)a: 分蘖期-高氮; b: 拔节期-高氮; c: 灌浆期-高氮; d: 分蘖期-低氮; e: 拔节期-低氮; f: 灌浆期-低氮。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。PCoA1和PCoA2是两个主坐标成分。a: tillering stage at high nitrogen level; b: jointing stage at high nitrogen level; c: filling stage at high nitrogen level; d: tillering stage at low nitrogen level; e: jointing stage at low nitrogen level; f: filling stage at low nitrogen level. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. PCoA1 and PCoA2 are the two principal coordinate components.Figure 2. Principal coordinate analysis (PCoA) of rhizosphere soil bacterial communities of different wheat cultivars at different nitrogen levels![]()
图 3 不同施氮水平下不同小麦品种根内生细菌群落的主坐标分析(PCoA)a: 分蘖期-高氮; b: 拔节期-高氮; c: 灌浆期-高氮; d: 分蘖期-低氮; e: 拔节期-低氮; f: 灌浆期-低氮。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。PCoA1和PCoA2是两个主坐标成分。a: tillering stage at high nitrogen level; b: jointing stage at high nitrogen level; c: filling stage at high nitrogen level; d: tillering stage at low nitrogen level; e: jointing stage at low nitrogen level; f: filling stage at low nitrogen level. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. PCoA1 and PCoA2 are the two principal coordinate components.Figure 3. Principal coordinate analysis (PCoA) of root endosphere bacterial communities of different wheat cultivars at different nitrogen levels2.2.2 物种组成分析
不同小麦品种根际土壤细菌群落门水平的组成如图4a。变形菌门和放线菌门是小麦根际土壤细菌群落的优势菌门。分蘖期时, 小麦根际土壤中的变形菌门相对丰度显著高于拔节期和灌浆期(P<0.05)。在分蘖期, 低氮水平下‘科农9204’和‘科农2011’根际土壤变形菌门的相对丰度显著低于‘京411’和‘百农207’ (P<0.05)。放线菌门和变形菌门是小麦根内生细菌群落的优势菌门(图4b)。高氮水平下, 拔节期时小麦根内拟杆菌门相对丰度显著高于分蘖期和灌浆期(P<0.05), 拔节期和灌浆期时小麦根内绿弯菌门(Chloroflexi)的相对丰度显著高于分蘖期(P<0.05)。在分蘖期, 高氮水平下‘科农2011’根内放线菌门的相对丰度显著低于‘科农9204’ ‘京411’和‘百农207’ (P<0.05), 低氮水平下‘京411’和‘百农207’根内变形菌门的相对丰度显著低于‘科农9204’和‘科农2011’ (P<0.05)。
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图 4 不同施氮水平下不同小麦品种根际土壤细菌(a)和根内生细菌(b)群落门水平相对丰度KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively.Figure 4. Relative abundance of rhizosphere soil (a) and root endosphere (b) bacterial community at the phylum level of different wheat cultivars at different nitrogen levels2.2.3 根际土壤微生物差异分析
通过LEfSe分析筛选不同小麦品种根际土壤微生物群落中的差异物种。在分蘖期高氮水下, 相比其他3个品种, ‘科农9204’的根际土壤细菌群落中显著富集的菌群包括寡养单胞菌属(Stenotrophomonas)、生丝微菌科(Hyphomicrobiaceae)、福格斯氏菌属(Vogesella)、色杆菌科(Chromobacteriaceae)、代尔夫特菌属(Delftia)和Ferrovibrio (图5a)。在分蘖期, 低氮水平下(因差异物种较多, 图中仅展示LDA≥4的微生物), ‘科农9204’ 的根际土壤细菌群落中显著富集的菌群为Alpha变形菌纲(Alphaproteobacteria)(图5b)。
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图 5 不同施氮水平下分蘖期不同小麦品种根际土壤微生物差异分析纵坐标中的字母p、c、o、f和g为分类水平, 分别代表门、纲、目、科和属。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。LDA SCORE表示差异显著物种的影响力。 p, c, o, f and g in the labels for vertical axis represent classification level, representing phylum, class, order, family and genus, respectively. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. LDA SCORE refers to the effect size of significantly different species.Figure 5. Analysis on the difference in rhizosphere soil microorganisms among different wheat cultivars at tillering stage at different nitrogen levels在拔节期高氮水平下, 微杆菌科(Microbacteriaceae)对4个品种根际土壤细菌群落组间差异影响最大, 并且在‘科农9204’ 根际土壤细菌群落中显著富集。此外, ‘科农9204’ 的根际土壤细菌群落还显著富集四折叠球菌属(Quadrisphaera)、 动孢菌目(Kineosporiales)、动孢囊菌科(Kineosporiaceae)和Rubellimicrobium (图6a)。在拔节期低氮水平下, 对4个品种根际土壤细菌群落组间影响最大的差异物种为Alpha变形菌纲, 并且在‘科农9204’ 的根际土壤细菌群落中显著富集。此外, 根瘤菌目、根瘤菌科(Rhizobiaceae)、黄色杆菌科(Xanthobacteraceae)和芽单胞菌属也在‘科农9204’中显著富集(图6b)。
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图 6 不同施氮水平下拔节期不同品种小麦根际土壤微生物差异分析纵坐标中的字母p、c、o、f和g为分类水平, 分别代表门、纲、目、科和属。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。LDA SCORE表示差异显著物种的影响力。p, c, o, f and g in the labels for vertical axis represent classification level, representing phylum, class, order, family and genus, respectively. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. LDA SCORE refers to the effect size of significantly different species.Figure 6. Analysis on the difference in rhizosphere soil microorganisms among different wheat cultivars at jointing stage at different nitrogen levels在灌浆期高氮水平下, ‘科农9204’ 根际土壤细菌群落中的弗兰克氏菌目和全噬菌纲(Holophagae)显著高于其他3个品种(图7a)。在灌浆期低氮水平下, ‘科农9204’ 的根际土壤细菌群落中显著富集的菌群包括黄色杆菌科和链孢囊菌属(Streptosporangium) (图7b)。
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图 7 不同施氮水平下灌浆期不同品种小麦根际土壤微生物差异分析纵坐标中的字母p、c、o、f和g为分类水平, 分别代表门、纲、目、科和属。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。LDA SCORE表示差异显著物种的影响力。p, c, o, f and g in the lables for vertical axisrepresent classification level, representing phylum, class, order, family and genus, respectively. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. LDA SCORE refers to the effect size of significantly different species.Figure 7. Analysis on the difference in rhizosphere soil microorganisms among different wheat cultivars at filling stage at different nitrogen levels2.3 小麦地上部性状和根际土壤微生物相关性分析
通过对小麦根际土壤细菌群落中相对丰度前20的菌属和地上部相关指标进行相关性分析。结果表明, 根际土壤细菌群落与地上部性状存在显著相关性。节杆菌属、德沃斯氏菌属(Devosia)、土壤红杆菌属(Solirubrobacter)、红色杆菌属、链霉菌属、原小单孢菌属(Promicromonospora)、壤霉菌属(Agromyces)、叶杆菌属(Phyllobacterium)、Gaiella、类诺卡氏菌属和鞘氨醇单胞菌属(Sphingomonas)的相对丰度与小麦地上部氮素吸收量和地上部生物量呈显著正相关(P<0.05), 而马赛菌属、砂单胞菌属、假单胞菌属和黄杆菌属与全氮含量呈显著正相关(P<0.05)(图8)。
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图 8 小麦根际土壤微生物与地上部性状的相关性分析**和*分别表示在P<0.01和P<0.05水平显著相关。ANC、ADW和ANA分别为地上部全氮含量、地上部生物量和地上部氮素吸收量。** and * represent significant differences at P<0.01 and P<0.05 levels, respectively. ANC, ADW and ANA are nitrogen content, aboveground biomass and nitrogen accumulation of wheat, respectively.Figure 8. Correlation analysis between rhizosphere soil microorganisms and traits of wheat aboveground part3. 讨论与结论
植物微生物组主要包括根际、叶际和内生微生物, 对于植物的养分吸收、生长发育以及抵御生物和非生物胁迫至关重要[3,8,27-29]。影响植物微生物组成的因素包括人为干扰因素(如耕作)[30]、土壤因素(如理化性质)[31]以及宿主基因型[32]等。Zhang等[33]研究发现水稻(Oryza sativa)亚种间根系微生物群落的Alpha多样性存在显著差异, 其中氮利用效率较高的籼稻品种多样性要显著高于粳稻, 说明籼稻的根系相比粳稻招募了更多种类的微生物, 并且含有更多氮代谢相关的菌属。在本研究中, 灌浆期低氮水平下, ‘科农9204’的地上部氮素吸收量显著高于其他3个品种。不同小麦品种影响了根区微生物群落多样性。低氮水平下, ‘科农9204’的根际土壤细菌多样性在分蘖期显著高于‘京411’, 在拔节期显著高于‘科农2011’, 在分蘖期和拔节期均显著高于‘百农207’。此外, ‘科农9204’的根内细菌群落多样性在分蘖期低氮水平下显著高于‘京411’和‘百农207’。较高的微生物多样性可能意味着生态过程的多样性, 这对于土壤健康以及植物生产力至关重要[34]。研究发现, 根区微生物群落的组成会受植物基因型影响[35], 这与本研究结果一致。小麦品种影响了根际土壤细菌群落组成, 这可能是因为不同品种小麦根系分泌物的组成和数量不同, 而植物可以通过改变根系分泌物驱动根际过程以适应环境[36-37]。
本研究对小麦根际土壤微生物群落的物种组成分析表明, 变形菌门和放线菌门为优势菌门。付博阳等[38]研究发现, 小麦根际土壤细菌群落的优势菌门包括放线菌门和变形菌门等。本研究中小麦根内生细菌群落的优势菌门为放线菌门和变形菌门; 而Chen等[16]研究发现在小麦根内细菌群落中, 变形菌门、放线菌门和拟杆菌门为优势菌门。绿弯菌门具有代谢和生态作用多样性[39], 在氮循环中参与硝化作用的NO2−氧化过程[40], 经富集培养后的热泉微生物群落中得到了较多属于绿弯菌门的细菌, 其中Ca.Nitrocaldera等携带编码亚硝酸盐氧化还原酶的基因, 具有亚硝酸盐氧化的潜力[41]。本研究中, 高氮水平下, 在拔节期和灌浆期时小麦根内生菌群落的绿弯菌门相对丰度均显著高于分蘖期, 可能有利于小麦在后两个时期吸收硝态氮。
通过对4个小麦品种根际土壤微生物进行差异分析, 发现在‘科农9204’的根际土壤中显著富集了根瘤菌目、弗兰克氏菌目和芽单胞菌属等微生物物种。其中根瘤菌目中包含固氮细菌, 如根瘤菌属和慢生根瘤菌属[42]。弗兰克氏菌作为植物根际促生菌可与非豆科植物共生并实现生物固氮, 研究表明, 弗兰克氏菌提高了植株生物量、总氮含量和叶绿素含量, 显著促进植物生长, 并增强了植物对非生物胁迫的抵抗力[43-44]。芽单胞菌属是农业生态系统中的主要群体之一, 与土壤微生物群落的稳定性相关[45]。本研究发现‘科农9204’的根际土壤中显著富集的微生物包含Alpha变形菌纲, 该纲中的微生物具有重要生物学作用, 包括固氮、氨氧化和光合作用等[46]。根际土壤微生物伴随植物的整个生育周期, 和植物性状联系十分密切, 其多样性和功能在作物生长和养分吸收中发挥至关重要的作用[47]。相关性分析表明节杆菌属、红色杆菌属、链霉菌属和类诺卡氏菌属与氮素吸收量和地上部生物量呈显著正相关。其中节杆菌属是重要的植物根际促生菌[48], 链霉菌属、红色杆菌属和类诺卡氏菌属丰度的增加可能影响根际土壤的氮代谢过程[49]。
本研究揭示了不同品种小麦根区微生物群落组成差异以及与小麦氮素吸收量相关的微生物物种类群。这些结果为利用微生物区系组成调控作物生产和养分利用提供了依据。植物基因型会影响植物微生物群落的组成, 但宿主基因如何驱动特征微生物装配并发挥功能仍需要进一步探索, 后续研究可将宿主遗传学和微生物组联系起来, 如利用全基因组关联分析(GWAS)研究植物与微生物组的互作机制。此外, 后续可以进一步通过宏基因组学测序对不同品种小麦根区微生物群落的功能进行探究。
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图 1 不同小麦品种地上部性状对比分析
不同小写字母代表不同小麦品种间差异显著(P<0.05)。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。Different lowercase letters represent significant differences among different wheat cultivars (P<0.05). KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively.
Figure 1. Comparative analysis of aboveground part traits of different wheat cultivars
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图 2 不同施氮水平下不同小麦品种根际土壤细菌群落的主坐标分析(PCoA)
a: 分蘖期-高氮; b: 拔节期-高氮; c: 灌浆期-高氮; d: 分蘖期-低氮; e: 拔节期-低氮; f: 灌浆期-低氮。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。PCoA1和PCoA2是两个主坐标成分。a: tillering stage at high nitrogen level; b: jointing stage at high nitrogen level; c: filling stage at high nitrogen level; d: tillering stage at low nitrogen level; e: jointing stage at low nitrogen level; f: filling stage at low nitrogen level. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. PCoA1 and PCoA2 are the two principal coordinate components.
Figure 2. Principal coordinate analysis (PCoA) of rhizosphere soil bacterial communities of different wheat cultivars at different nitrogen levels
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图 3 不同施氮水平下不同小麦品种根内生细菌群落的主坐标分析(PCoA)
a: 分蘖期-高氮; b: 拔节期-高氮; c: 灌浆期-高氮; d: 分蘖期-低氮; e: 拔节期-低氮; f: 灌浆期-低氮。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。PCoA1和PCoA2是两个主坐标成分。a: tillering stage at high nitrogen level; b: jointing stage at high nitrogen level; c: filling stage at high nitrogen level; d: tillering stage at low nitrogen level; e: jointing stage at low nitrogen level; f: filling stage at low nitrogen level. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. PCoA1 and PCoA2 are the two principal coordinate components.
Figure 3. Principal coordinate analysis (PCoA) of root endosphere bacterial communities of different wheat cultivars at different nitrogen levels
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图 4 不同施氮水平下不同小麦品种根际土壤细菌(a)和根内生细菌(b)群落门水平相对丰度
KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively.
Figure 4. Relative abundance of rhizosphere soil (a) and root endosphere (b) bacterial community at the phylum level of different wheat cultivars at different nitrogen levels
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图 5 不同施氮水平下分蘖期不同小麦品种根际土壤微生物差异分析
纵坐标中的字母p、c、o、f和g为分类水平, 分别代表门、纲、目、科和属。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。LDA SCORE表示差异显著物种的影响力。 p, c, o, f and g in the labels for vertical axis represent classification level, representing phylum, class, order, family and genus, respectively. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. LDA SCORE refers to the effect size of significantly different species.
Figure 5. Analysis on the difference in rhizosphere soil microorganisms among different wheat cultivars at tillering stage at different nitrogen levels
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图 6 不同施氮水平下拔节期不同品种小麦根际土壤微生物差异分析
纵坐标中的字母p、c、o、f和g为分类水平, 分别代表门、纲、目、科和属。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。LDA SCORE表示差异显著物种的影响力。p, c, o, f and g in the labels for vertical axis represent classification level, representing phylum, class, order, family and genus, respectively. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. LDA SCORE refers to the effect size of significantly different species.
Figure 6. Analysis on the difference in rhizosphere soil microorganisms among different wheat cultivars at jointing stage at different nitrogen levels
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图 7 不同施氮水平下灌浆期不同品种小麦根际土壤微生物差异分析
纵坐标中的字母p、c、o、f和g为分类水平, 分别代表门、纲、目、科和属。KN9204、KN2011、J411和B207分别为小麦品种‘科农9204’ ‘科农2011’ ‘京411’和‘百农207’。LDA SCORE表示差异显著物种的影响力。p, c, o, f and g in the lables for vertical axisrepresent classification level, representing phylum, class, order, family and genus, respectively. KN9204, KN2011, J411 and B207 represent wheat cultivars of ‘Kenong 9204’ ‘Kenong 2011’ ‘Jing 411’ and ‘Bainong 207’, respectively. LDA SCORE refers to the effect size of significantly different species.
Figure 7. Analysis on the difference in rhizosphere soil microorganisms among different wheat cultivars at filling stage at different nitrogen levels
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图 8 小麦根际土壤微生物与地上部性状的相关性分析
**和*分别表示在P<0.01和P<0.05水平显著相关。ANC、ADW和ANA分别为地上部全氮含量、地上部生物量和地上部氮素吸收量。** and * represent significant differences at P<0.01 and P<0.05 levels, respectively. ANC, ADW and ANA are nitrogen content, aboveground biomass and nitrogen accumulation of wheat, respectively.
Figure 8. Correlation analysis between rhizosphere soil microorganisms and traits of wheat aboveground part
表 1 不同品种小麦根际土壤和根内生细菌群落的Alpha多样性
Table 1 Alpha diversity of rhizosphere soil and endosphere bacterial community in different wheat cultivars
取样部位
Compartment施氮水平
Nitrogen level时期
Growth stage科农9204
Kenong 9204京411
Jing 411科农2011
Kenong 2011百农207
Bainong 207根际土壤
Rhizosphere soil高氮
High nitrogen分蘖期 Tillering 8.72±0.41a 7.49±0.79b 8.92±0.60a 9.18±0.46a 拔节期 Jointing 8.89±0.29a 8.97±0.03a 9.00±0.30a 9.18±0.10a 灌浆期 Filling 9.34±0.21a 9.47±0.06a 9.29±0.07a 9.25±0.14a 低氮
Low nitrogen分蘖期 Tillering 9.29±0.21a 8.56±0.55b 9.58±0.10a 7.85±0.17c 拔节期 Jointing 9.23±0.06a 9.06±0.09ab 8.93±0.06b 8.97±0.17b 灌浆期 Filling 9.29±0.1ab 9.36±0.05a 9.24±0.10ab 9.16±0.12b 根内
Root endosphere高氮
High nitrogen分蘖期 Tillering 5.56±0.18a 5.43±0.33a 5.48±0.22a 5.32±0.61a 拔节期 Jointing 6.79±0.20a 6.42±0.47a 6.84±0.14a 6.64±0.18a 灌浆期 Filling 6.55±0.38b 6.51±0.12b 6.96±0.55ab 7.36±0.39a 低氮
Low nitrogen分蘖期 Tillering 5.54±0.33a 4.58±0.6bc 5.19±0.08ab 4.09±0.68c 拔节期 Jointing 6.17±0.16a 6.53±0.56a 6.68±0.35a 6.81±0.35a 灌浆期 Filling 6.50±0.60a 6.89±0.06a 6.87±0.20a 7.10±0.06a 不同小写字母代表不同小麦品种间差异显著(P<0.05)。Different lowercase letters represent significant differences among different wheat cultivars (P<0.05). 
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