作物驯化对根际微生物组的选择

作物驯化是人类活动影响下的生物进化过程,不仅会引起作物生理生态以及微生物群落结构和多样性的改变,还对根际微生物的相互关系、功能特征以及作物调控等方面产生影响。同时,根际微生物生态变化也体现了作物在驯化过程中对环境的适应力。本文综述了作物驯化与根际微生物组间的研究进展,讨论了作物驯化可能对根际微生物组的选择及其驱动要素,为改善根际微生物的生态特征及功能,寻找潜在的特殊的微生物资源,提高作物的抗性及养分吸收及实现土壤可持续发展奠定理论基础。     

作物驯化对根际微生物组的选择效应

驯化是指经过人为干预技术对野生物种的某些可利用性状加以选择、修饰和利用的过程。驯化不仅会引起植物表型的变化,还会进一步导致植物根系形态结构以及相应根际次生代谢产物含量的变化,最终导致根际微生物群落结构和功能发生变化。本文综述了作物驯化过程对作物表型、根系形态及对根际微生物群落结构的影响,初步探讨了作物驯化对根际微生物影响机制,并着重阐述了共生微生物包括丛枝菌根真菌以及根瘤菌与作物驯化的关系,为更好地利用作物野生近缘种的根际有益微生物奠定理论基础。     

植物多样性对土壤微生物的影响

生物多样性强烈地影响生态系统的过程，生态系统过程的变化可导致生物多样性衰减并因素导致生态系统功能衰退，植物种丰度和植物功能多样性对土壤细菌群落的代谢活性和代谢多样性有成正比的影响。土壤细菌的代谢活性和代谢多样性随植物种数量的对数和植物功能组的数量而直线上升，其原因可能是由植被流入土壤的物质和能量的多样性和数量的增加，也可能是由土壤动物区系起作用的土壤微生境的多样性的增加造成的，由于植物多样性的丧失所引起的植物生物量的减少对分解者群落有强烈的影响，微生物生物量将可能减少，因为在大多数陆地生态系统中，有机碳源限制着土壤微生物的活性。     

植物修复对重金属镍污染土壤微生物群落的影响

采用室内盆栽试验方法,研究了外源镍污染土壤的植物修复对土壤微生物群落的影响。试验用水稻土中添加NiSO4.6H2O(100~1 600 mg kg-1)经过12周的驯化培养后,种植了2种超累积植物和1种耐性植物,经110 d的试验后进行了植物修复后土壤微生物活性的分析。结果表明,非根区土中添加镍的质量分数为100 mg kg-1时,对土壤中细菌、真菌和放线菌总数有一定的促进作用,土壤中微生物生物量最大;当添加镍的质量分数大于100 mg kg-1时,将对土壤微生物群落造成不利的影响。在植物修复过程中,通过植物的减毒(吸收重金属)作用和根系分泌物的作用,改善了土壤微生物的生存环境,提高了土壤微生物的数量和生物量。经过植物修复后,根区土壤微生物较非根区土壤的丰富,土壤微生物群落总DNA序列多样性指数相应增加,但不同植物对根区土壤微生物的贡献是不同的。     

土壤微生物多样性与地上植被类型关系的研究进展

土壤微生物是生态系统中重要的组成成分,土壤微生物多样性代表着微生物群落的稳定性,对植物的生长发育和群落结构的演替具有重要作用.同时地上植被也影响土壤微生物多样性,地上植被和地下微生物间具协同作用和正负反馈效应的互作机制.探讨植被和土壤微生物多样性之间的互作关系,为植物保护和生态系统的可持续发展研究提供参考.     

变性梯度凝胶电泳(DGGE)技术在土壤微生物多样性研究中的应用

应用变性梯度凝胶电泳(DGGE)谱图分析技术对土壤微生物多样性进行描述,可以克服传统微生物分离纯化培养方法和显微技术的局限性.本文介绍了变性梯度凝胶电泳指纹图谱分析方法及其在土壤微生物多样性中的应用,包括对土壤特殊微生物生理类群,自然环境条件下微生物多样性变化,污染土壤微生物的多样性,不同种植制度下的土壤微生物多样性,转基因植物、微生物介入的土壤微生物多样性等方面的研究.     

植物根系分泌物与根际微生物交互作用机制研究进展

根际是受植物根系影响最为强烈的微域环境,是植物和土壤交流的桥梁。根系能通过调控根系分泌物的种类和数量影响根际微生物的种群结构和多样性,根际微生物通过改变根际土壤特性影响根系的分泌作用,进而影响植物的生长发育过程。因此,很有必要对这些研究进展进行梳理,提出未来该领域的研究重点。本文以1999 ~ 2022年中国知网（CNKI）和Web of Science核心数据库为文献来源,对根系分泌物与根际微生物互作相关的64篇论文进行分析。总结了近年来根系分泌物和根际微生物互作的最新研究成果,重点介绍了根系分泌物对根际微生物种类、数量和分布的影响,环境胁迫对根系分泌物和根际微生物的影响,以及根际微生物对植物生长的影响。基于此,我们对该领域未来的研究方向进行了展望。深入理解根系分泌物和根际微生物之间复杂的互作关系及其机理,对揭示根际微生态调控过程、土壤微生物组功能、促进农作物增产等方面具有重要的意义。     

根际微生物对植物与土壤交互调控的研究进展

土壤中拥有非常丰富的微生物群落,这些微生物对植物与土壤之间的交互作用起到了非常重要的调节作用,尤其是根际微生物,其中一些重要的功能微生物作为主要的共生功能体参与到植物根系养分转化中。对根际与根际土壤微生物的形成及其与土壤环境、植物根系之间互作关系的最新研究进展进行了综述,这些研究成果均肯定了根际微生物群落和多样性是积极促进植物个体和维持生态系统功能的活跃因子,并展望了今后土壤微生物在多组学、植物功能性状和全球变化方面的研究前景。     

Factors Affccting Change of Microbial Community During Plant Residue Decomposition: A Review

植物残体是土壤有机质的重要来源,研究分解植物残体的微生物群落结构及其演替规律日益受到重视.本文综述了影响植物残体分解过程中微生物群落结构和功能变化的3个主要因素;植物残体的性质、土壤和气候环境因素、农艺措施,这些因素通过影响微生物本身的活性和植物残体分解过程中化学组成的变化从而导致微生物群落的变化,同时植物残体腐解过程中微生物群落存在明显的演替现象.以上因素的影响并不是孤立的,而是相互联系和制约的.未来针对野外田问条件下植物残体的分解过程,仍需深入研究关键微生物群落的演替规律以及不同影响因素的交互作用机制.     

复垦年限及植被模式对煤矿复垦土壤微生物多样性的影响

了解露天煤矿区复垦状况及其对土壤微生物的影响机制,对于估算受损生态系统的恢复程度至关重要。该文以采用多种模式复垦的安太堡露天煤矿为研究区域,通过野外调查与采样分析,借助于Biolog EcoPlatesTM方法对复垦区和原地貌(对照)表层土壤中的微生物功能多样性状况进行了探索,评价了复垦年限和复垦植被模式对土壤微生物特征的恢复效应;并从土壤物理化学性质(土壤容重、pH值、土壤有机碳、总氮、速效氮、速效磷和速效钾)和生物性质(土壤微生物量碳和微生物量氮)中筛选可反映土壤微生物功能多样性变化的代表性指示物质。结果表明:1)露天煤矿复垦年限和复垦植被模式均对土壤微生物的功能多样性有明显影响。复垦年限越长的样地中土壤微生物有较高的活性和均匀度,但丰富度较低;若样地的复垦年限较长,复垦植物种植模式对土壤微生物多样性的作用强于复垦时长对其的影响。2)从土壤微生物多样性恢复层面分析,单一植物复垦配置的优化次序为杏树、榆树和柠条,混交林配置较优的选择为柠条×刺槐。3)土壤微生物生物量碳的含量与土壤微生物功能多样性指标Shannon-Wiener指数(ρ=–0.69,P0.01)和McIntosh指数(ρ=–0.69,P0.05)显著负相关,在一定程度上可作为复垦区生物多样性指示物质。研究成果将为露天煤矿及其所在区域的生态恢复、治理和监测提供参考。     

Potential of plant growth-promoting rhizobacteria-plant interactions in mitigating salt stress for sustainable agriculture: A review

Soil salinization affecting different crops is one of the serious threats to global food security.Soil salinity affects 20%and 33%of the total cultivated and irrigated agricultural lands,respectively,and has been reported to caused a global crop production loss of 27.3 billion USD.The conventional approaches,such as using salt-tolerant varieties,saline soil scrapping,flushing,leaching,and adding supplements (e.g.,gypsum and lime),often fail to alleviate stress.In this context,developing diverse arrays of microbes enhancing crop productivity under saline soil conditions without harming soil health is necessary.Various advanced omics approaches have enabled gaining new insights into the structure and metabolic functions of plant-associated beneficial microbes.Various genera of salt-tolerating rhizobacteria ameliorating biotic and abiotic stresses have been isolated from different legumes,cereals,vegetables,and oil seeds under extreme alkaline and saline soil conditions.Rapid progress in rhizosphere microbiome research has revived the belief that plants may be more benefited from their association with interacting diverse microbial communities as compared with individual members in a community.In the last decade,several salt-tolerating plant growth-promoting rhizobacteria (PGPR) that improve crop production under salt stress have been exploited for the reclamation of saline agrosystems.This review highlights that the interaction of salt-tolerating microbes with plants improves crop productivity under salinity stress along with potential salt tolerance mechanisms involved and will open new avenues for capitalizing on cultivable diverse microbial communities to strengthen plant salt tolerance and,thus,to refine agricultural practices and production under saline conditions.     

Two-year field study shows little evidence that PPO-transgenic rice affects the structure of soil microbial communities

There is global concern about the environmental consequences associated with transgenic crops. Their effects on the soil ecosystem are of special interest when assessing ecological safety and integrity. Although many efforts have been made to develop crops genetically modified to have resistance to protoporphyrin oxidase (PPO)-inhibiting herbicides, little is known about their influence on soil microbial communities. We conducted a 2-year field study and an analysis via terminal restriction fragment length polymorphism (T-RFLP) to assess the impacts of PPO-transgenic rice on bacterial and fungal communities. In the first year we sampled the rhizosphere and surrounding bulk soil, while in the second year we sampled rhizosphere soil only. No differences were observed in the diversity indices and community composition of microbial communities between transgenic rice and its parental non-transgenic counterpart (cultivar Dongjin). Instead, community variation was strongly dependent on growth stage and year. Therefore, we observed no adverse effects by these crops of modified rice on the microbial community composition in paddy soils.     

Integrated analysis reveals an association between the rhizosphere microbiome and root rot of arecanut palm

The rhizosphere microbial community is crucial to plant health. Many studies have explored the association between the rhizosphere microbiome and plant disease. However, few studies have focused on root rot in arecanut palm, a disease causing devastating effects and thus resulting in economic losses that considerably affect the development of the arecanut industry. Here, rhizosphere samples were collected from both healthy arecanut palm plants and root-rotted arecanut palm plants, and the microbial communities were analyzed using high-throughput sequencing. The root-rotted samples exhibited distinct microbial community richness, diversity, and composition compared with the healthy samples, which was associated with pH according to the Mantel test. Identified potential plant pathogens, including Proteobacteria, Bacteroidetes, Chytridiomycota, and Mortierellomycota, were significantly enriched in the root-rotted samples. In contrast, potentially beneficial plant microbes, such as Acidobacteria and Gemmatimonadetes, were significantly depleted in the root-rotted samples. Co-occurrence networks were constructed to further identify microbial relationships in the root-rotted samples. These findings revealed ecological imbalance among beneficial bacteria in the root-rotted samples. The present study therefore provides an integrated view of the association between the microbial community and root rot in arecanut palm.     

植物根际沉积与土壤微生物关系研究进展

【目的】活跃的根际微生物被喻为植物的第二套基因组,在植物的生长发育过程中发挥着关键作用。植物通过根际碳沉积影响根际土壤微生物群落的结构和功能;作为根际微生态系统中的物质流、能量流和信息流,根际碳沉积是连接大气、植物和土壤系统物质循环的重要纽带;因此,理解根际碳沉积在根际微生态中的作用对于提高植物抗逆性,增加作物产量,调控根际养分循环等方面具有重大的理论意义。【主要进展】本文就近年来关于根际微生物领域的研究成果,重点综述了根际微生物多样性和组学研究;根际碳沉积的组成和产生机理;根际微生物群落结构的形成机制;根际微生物在促进作物养分吸收、提高作物抗逆性等方面的生态功能;以及气候变化和长期施肥对植物-微生物互作关系的影响。在此基础上我们提出了未来可能的研究重点和发展方向:1)植物根际沉积物原位收集方法和检测技术的改进和发展;2)稳定同位素探针与分子生态学技术的结合,将植物、土壤和微生物三者有机地联系起来,综合分析根际界面中微生物的活性与功能;3)高通量测序、组学技术和生物信息学等新技术的引入势必使根际微生物学研究发生革命性的变化;4)随着全球气候变化和土壤肥力改变,例如全球变暖、CO2浓度升高和长期施用化肥,根际沉积物在植物-土壤-微生物中的分配与调节机制,以及这种环境选择压力下植物如何诱导根际促生菌发挥更大作用。希望通过平衡作物与微生物之间的相互关系来实现作物的高产高效,促进农田的可持续利用。     

Plant nitrogen uptake drives rhizosphere bacterial community assembly during plant growth

When plants establish in novel environments, they can modify soil microbial community structure and functional properties in ways that enhance their own success. Although soil microbial communities are influenced by abiotic environmental variability, rhizosphere microbial communities may also be affected by plant activities such as nutrient uptake during the growing season. We predicted that during the growing season, plant N uptake would explain much of the variation in rhizosphere microbial community assembly and functional traits. We grew the invasive C₃ grass Bromus tectorum and three commonly co-occurring native C₃ grasses in a controlled greenhouse environment, and examined rhizosphere bacterial community structural and functional characteristics at three different plant growth stages. We found that soil N availability and plant tissue N levels strongly correlated with shifts in rhizosphere bacterial community structure. It also appeared that the rapid drawdown of soil nutrients in the rhizosphere during the plant growing season triggered a selection event whereby only those microbes able to tolerate the changing nutrient conditions were able to persist. Plant N uptake rates inversely corresponded to microbial biomass N levels during periods of peak plant growth. Mechanisms which enable plants to influence rhizosphere bacterial community structure and function are likely to affect their competitive ability and fitness. Our study suggests that plants can alter their rhizosphere microbiomes through influencing nutrient availability. The ways in which plants establish their rhizosphere bacterial communities may now be viewed as a selection trait related to intrinsic plant species nutrient demands.     

Soil Characteristics Overwhelm Cultivar Effects on the Structure and Assembly of Root-Associated Microbiomes of Modern Maize

Modern breeding primarily targets crop yield traits and is likely to influence root-associated microbiomes, which play significant roles in plant growth and health. The relative importance of soil and cultivar factors in shaping root-associated microbiomes of modern maize (Zea mays L.) remains uncertain. We conducted a pot experiment in a controlled environment using three soils (Mollisol, Inceptisol, and Ultisol) and four contrasting cultivars, Denghai 605, Nonghua 816, Qiaoyu 8, and Zhengdan 958, which are widely planted in China. We used 16S rRNA gene amplicon sequencing to characterize the bacterial communities in the bulk soil, rhizosphere, and endosphere. Our results showed that the four cultivars had different shoot biomass and root exudate total organic carbon and organic acid contents. The microbiomes in the bulk soil, rhizosphere, and endosphere were different. We observed apparent community divergence between soils rather than cultivars, within which edaphic factors substantially contributed to microbiome variation. Moreover, permutational multivariate analysis of variance corroborated significant contributions of soil type but not cultivar on the root-associated microbiome structure. Differential abundance analysis confirmed that each soil presented a distinct root microbiome, while network analysis indicated different co-occurrence patterns of the root microbiome among the three soils. The core root microbiome members are implicated in plant growth promotion and nutrient acquisition in the roots. In conclusion, root-associated microbiomes of modern maize are much more controlled by soil characteristics than by cultivar root exudation. Our study is anticipated to help improve breeding strategies through integrative interactions of soils, cultivars, and their associated microbiomes.     

Manipulating the soil microbiome to increase soil health and plant fertility

A variety of soil factors are known to increase nutrient availability and plant productivity. The most influential might be the organisms comprising the soil microbial community of the rhizosphere, which is the soil surrounding the roots of plants where complex interactions occur between the roots, soil, and microorganisms. Root exudates act as substrates and signaling molecules for microbes creating a complex and interwoven relationship between plants and the microbiome. While individual microorganisms such as endophytes, symbionts, pathogens, and plant growth promoting rhizobacteria are increasingly featured in the literature, the larger community of soil microorganisms, or soil microbiome, may have more far-reaching effects. Each microorganism functions in coordination with the overall soil microbiome to influence plant health and crop productivity. Increasing evidence indicates that plants can shape the soil microbiome through the secretion of root exudates. The molecular communication fluctuates according to the plant development stage, proximity to neighboring species, management techniques, and many other factors. This review seeks to summarize the current knowledge on this topic.     

Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities

We studied the microbial communities in maize (Zea mays) rhizosphere to determine the extent to which their structure, biomass, activity and growth were influenced by plant genotype (su1 and sh2 genes) and the addition of standard and high doses of different types of fertilizer (inorganic, raw manure and vermicompost). For this purpose, we sampled the rhizosphere of maize plants at harvest, and analyzed the microbial community structure (PLFA analysis) and activity (basal respiration and bacterial and fungal growth rates). Discriminant analysis clearly differentiated rhizosphere microbial communities in relation to plant genotype. Although microorganisms clearly responded to dose of fertilization, the three fertilizers also contributed to differentiate rhizosphere microbial communities. Moreover, larger plants did not promoted higher biomass or microbial growth rates suggesting complex interactions between plants and fertilizers, probably as a result of the different performance of plant genotypes within fertilizer treatments, i.e. differences in the quality and/or composition of root exudates.     

In situ dynamics of soil fungal communities under different genotypes of potato, including a genetically modified cultivar

Fungi are key to the functioning of soil ecosystems, and exhibit a range of interactions with plants. Given their close associations with plants, and importance in ecosystem functioning, soil-borne fungi have been proposed as potential biological indicators of disturbance and useful agents in monitoring strategies, including those following the introduction of genetically modified (GM) crops. Here we report on the impact of potato crop varieties, including a cultivar that was genetically modified for its starch quality, on the community composition of the main phyla of fungi in soils, i.e. Ascomycota, Basidiomycota and Glomeromycota in rhizosphere and bulk soil. Samples were collected at two field sites before sowing, at three growth stages during crop development and after the harvest of the plants, and the effects of field site, plant growth stage and plant cultivar (genotype) on fungal community composition assessed using three phylum-specific T-RFLP profiling strategies and multivariate statistical analysis (NMDS ordinations with ANOSIM test). In addition, fungal biomass, arbuscular mycorrhizal colonization of roots and activities of extracellular fungal enzymes (laccases, Mn-peroxidases and cellulases) involved in degradation of lignocelluloses-rich organic matter were determined. Fungal community compositions, densities and activities were observed to differ significantly between the rhizosphere and bulk soil. The most important factors determining fungal community composition and functioning were plant growth stage for the rhizosphere communities and location and soil properties for the bulk soil communities. The basidiomycetes were the most numerous fungal group in the bulk soils and in the rhizosphere of young plants, with a shift toward greater ascomycete numbers in the rhizosphere at later growth stages. There were no detectable differences between the GM cultivar and its parental cultivar in terms of influence on fungal community structure of function. Fungal community structure and functioning of both GM- and parental cultivars fell within the range of other cultivars at most sampling moments.     

不同作物根际土壤微生物的群落结构特征分析

为探究根际微生物群在支持植物生长、发育和健康方面的重要作用,本研究在2017年7月采集同一农田中大豆[Glycine max (L.) Merr.]、玉米[Zea mays)、花生(Arachis hypogaea L.]、四季豆[Phaseolus vulgaris L.]、豇豆[Vigna unguiculata (L.) Walp]、番薯[Ipomoea batatas (L.) Lam.]和芋艿[Colocasia esculenta (L.) Schoot]7种不同作物,通过Illumina MiSeq测序技术和磷脂脂肪酸(PLFA)对这7种不同作物的根际微生物群落结构和组成进行了分析。结果显示,不同作物根际土壤微生物的PLFA种类和组成差异显著,但均以表征革兰氏阴性菌、革兰氏阳性菌和真菌的特征脂肪酸为主。花生根际土中微生物的PLFAs含量最高,花生根际土中的真菌细菌比(F/B)显著高于其他作物,且其革兰氏阳性菌与革兰氏阴性菌比(G⁺/G^-)最低。尽管在门水平,变形菌门、放线菌门、酸杆菌门和厚壁菌门是7种作物根际微生物的主要优势门,但是在纲水平和目水平不同作物根际微生物组成存在差异。Alpha多样性分析表明,大豆根际的OTU丰富度(Chao1,P<0.001)和细菌群落多样性(Shannon,P<0.001)在7种作物中最高。非度量多维尺度分析(NMDS)表明,根际微生物群落结构在OTU和PLFAs水平下均以不同作物形成聚类,不同聚类间的差异显著。根际敏感微生物的筛选和比较进一步说明不同作物对根际微生物的选择具有差异性,群落中某些特定菌群优势度存在区别,不同作物具有不同敏感微生物的选择倾向。本研究为构建健康的植物根际微生物群落以促进植物育种提供了基础。