马铃薯全生育期内根际微生物组变化规律

[目的]陆生植物根际环境与土壤中的微生物菌群关系密切,其根际微生物群落动态极可能直接影响着植物健康及养分高效利用。虽然根际益生菌已被证实可用于提高作物生产力,但由于缺乏对这些菌群组成动态变化规律的认识了解,它们的开发受到限制。研究马铃薯全生育期根际菌群的动态变化规律,探讨根际菌群变化与马铃薯发育时期的相关性,为针对马铃薯不同生长时期开发专用生物益生菌肥奠定理论基础。[方法]本研究着眼于马铃薯田间全生命周期微生物组动态变化,通过Illumina MiSeq高通量测序技术对不同时间点马铃薯根际细菌16S rRNA基因V3-V4区和真菌ITS区测序并对操作分类单位(OTU)进行聚类,分析样品间微生物群落的多样性特征,并通过机器学习的方法建立模型,将根际菌群与田间马铃薯发育时间相关联。[结果]根际菌群在马铃薯各个发育阶段随时间变化明显,营养生长阶段的微生物群落结构发生了显著变化,随着结薯期的开始逐渐稳定,直到块茎成熟后期根际菌群再次出现较大变化,且在不同施肥处理间呈现较大差异。进一步基于模型挖掘了与马铃薯发育时间相关联的22个特征细菌类群和16个特征真菌类群,其中苗期和结薯末期的特征类群分别为梭菌(Clostridium)和放线菌(Actinobacteria)。[结论]马铃薯的生长发育时期是影响根际微生物群落组成的主要因素,益生菌肥的添加主要影响马铃薯结薯末期的细菌微生物菌群结构。     

根际微生物组组装与植物健康

土壤微生物拥有高度多样化的群落结构,其通过与植物发生复杂的相互作用影响植物健康,也被称为植物的第二基因组。最近研究表明植物能通过改变根际分泌物的组成影响根际微生物群落的组装,反之,根际微生物群落组成的改变能够通过影响植物营养吸收和抵御生物及非生物胁迫的能力影响植物健康。除此之外,农艺管理也是影响土壤微生物群落组装方式的重要因素。但到目前为止,根际微生物与宿主植物及土壤微生物之间互作机制的研究尚不清楚。本文将从农艺管理和宿主植物对微生物群落组装的影响及根际微生物组对植物健康的影响进行总结,为增加作物产量提供机会。     

Effects of plant and influent C:N:P ratio on microbial diversity in pilot-scale constructed wetlands

Microbial processes within the rhizosphere of constructed wetlands are crucial to wastewater treatment, but the relation between microbial community diversity in rhizosphere, plant growth and water quality are unclear at present. The effects of plant growth, water C:N:P ratio and their interaction on microbial diversity in the rhizosphere were studied in synthetic wastewater in planted and unplanted wetlands during three different seasons. The physiological profile of microbial community-level in each wetland was assessed using substrate utilization patterns gathered via BIOLOG? ECO plates. Plant had a significant effect on AWCD parameter, since the planted wetlands usually had a higher the total microbial activity than the unplanted over the study period. The Shannon, Simpson and McIntosh indices in the planted wetlands were apparently higher than those in the unplanted wetlands under any C:N:P ratio influent condition especially in summer. It was also shown that the unplanted wetlands have a greater shift of the interstitial microbial community than the planted at different seasons, since plant rhizospheres produce a more ecologically stable system in order to resist against shifts in microbial community composition in response to C:N:P ratio change in wastewater. Principal component analysis and clustering analysis indicated that influent C:N:P ratio would induce similar microbial species in the planted wetlands and detach them from the unplanted wetlands.     

Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops

Seasonal shifts in rhizosphere microbial populations were investigated to follow the influence of plant developmental stage. A field study of indigenous microbial rhizosphere communities was undertaken on pea (Pisum satvium var. quincy), wheat (Triticum aestivum var. pena wawa) and sugar beet (Beta vulgaris var. amythyst). Rhizosphere community diversity and substrate utilization patterns were followed throughout a growing season, by culturing, rRNA gene density gradient gel electrophoresis and BIOLOG. Culturable bacterial and fungal rhizosphere community densities were stable in pea and wheat rhizospheres, with dynamic shifts observed in the sugar beet rhizosphere. Successional shifts in bacterial and fungal diversity as plants mature demonstrated that different plants select and define their own functional rhizosphere communities. Assessment of metabolic activity and resource utilization by bacterial community-level physiological profiling demonstrated greater similarities between different plant species rhizosphere communities at the same than at different developmental stages. Marked temporal shifts in diversity and relative activity were observed in rhizosphere bacterial communities with developmental stage for all plant species studied. Shifts in the diversity of fungal and bacterial communities were more pronounced in maturing pea and sugar beet plants. This detailed study demonstrates that plant species select for specialized microbial communities that change in response to plant growth and plant inputs.     

濒危植物大别山五针松根际细菌群落特征与功能分析

植物根际微生物群落对植物健康生长有重要影响, 每种植物根际都有其特定的微生物群落。大别山五针松(Pinus dabeshanensis)被国际自然保护联盟列为濒危物种, 具有重要研究价值。该研究采用16S rRNA高通量测序技术与生物信息学方法, 对濒危植物大别山五针松根际细菌群落特征与功能进行分析。结果表明, 大别山五针松根际微生物的主要种类为变形菌门、放线菌门、酸杆菌门和疣微菌门。网络分析表明, 大别山五针松根际细菌类群存在显著相关性, 其中Bryobacter属、Bradyrhizobium属和未定义的TK10属是互作网络中的重要节点。PICRUSt1功能预测表明其微生物组功能主要为氨基酸运输和代谢、细胞壁/膜/膜生物发生以及能量产生和转换。FAPROTAX功能预测表明, 大别山五针松根际富含的优势菌群具有丰富的化学异养、纤维素水解、需氧化学异养和固氮功能, 其对植物生长发育具有重要作用。研究结果可为培育健康的大别山五针松根际微生物菌群及微生物资源的开发利用提供重要依据。     

Feedbacks of plant identity and diversity on the diversity and community composition of rhizosphere microbiomes from a long‐term biodiversity experiment

Soil microbes are known to be key drivers of several essential ecosystem processes such as nutrient cycling, plant productivity and the maintenance of plant species diversity. However, how plant species diversity and identity affect soil microbial diversity and community composition in the rhizosphere is largely unknown. We tested whether, over the course of 11 years, distinct soil bacterial communities developed under plant monocultures and mixtures, and if over this time frame plants with a monoculture or mixture history changed in the bacterial communities they associated with. For eight species, we grew offspring of plants that had been grown for 11 years in the same field monocultures or mixtures (plant history in monoculture vs. mixture) in pots inoculated with microbes extracted from the field monoculture and mixture soils attached to the roots of the host plants (soil legacy). After 5 months of growth in the glasshouse, we collected rhizosphere soil from each plant and used 16S rRNA gene sequencing to determine the community composition and diversity of the bacterial communities. Bacterial community structure in the plant rhizosphere was primarily determined by soil legacy and by plant species identity, but not by plant history. In seven of the eight plant species the number of individual operational taxonomic units with increased abundance was larger when inoculated with microbes from mixture soil. We conclude that plant species richness can affect below‐ground community composition and diversity, feeding back to the assemblage of rhizosphere bacterial communities in newly establishing plants via the legacy in soil.     

植物根际微生物群落构建的研究进展

植物根际是指植物根系与土壤的交界面,是根系自身生命活动和代谢对土壤影响最直接、最强烈的区域,其物理、化学和生物性质不同于土体土壤。在这个区域里,与植物发生相互作用的大量微生物,被称为根际微生物。根际微生物在植物的生长发育和植物病虫害的生物防治等方面都具有十分重要的意义。本文总结了根际微生物群落构建的研究现状,介绍了根际微生物的经典和最新的研究方法,包括根箱法、同位素技术以及高通量测序、菌群定量分析、高通量分离培养等方法在根际微生物研究中的应用,讨论了植物根系分泌物(碳水化物、氨基酸、黄酮类、酚类、激素及其信号物质)和土壤物理化学性质对根际微生物群落的影响,概述了根际微生物-植物的互作机制,以及根际微生物群落对植物的促生作用、提高植物抗逆性和抑制作用,并对根际微生物群落研究中存在的问题和未来发展方向进行了展望。     

Differences in vegetation composition and plant species identity lead to only minor changes in soil-borne microbial communities in a former arable field

To examine the relationship between plant species composition and microbial community diversity and structure, we carried out a molecular analysis of microbial community structure and diversity in two field experiments. In the first experiment, we examined bacterial community structure in bulk and rhizosphere soils in fields exposed to different plant diversity treatments, via a 16S rRNA gene clone library approach. Clear differences were observed between bacterial communities of the bulk soil and the rhizosphere, with the latter containing lower bacterial diversity. The second experiment focused on the influence of 12 different native grassland plant species on bacterial community size and structure in the rhizosphere, as well as the structure of Acidobacteria and Verrucomicrobia community structures. In general, bacterial and phylum-specific quantitative PCR and PCR-denaturing gradient gel electrophoresis revealed only weak influences of plant species on rhizosphere communities. Thus, although plants did exert an influence on microbial species composition and diversity, these interactions were not specific and selective enough to lead to major impacts of vegetation composition and plant species on below-ground microbial communities.     

The rhizosphere microbiome and plant health

The diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant-microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production.     

Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields

Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.     

植物病害防治相关微生物组研究进展与展望

微生物是人类活动过程中重要的生物资源。植物及其根围土壤中生存着大量多种多样的微生物,这些微生物与植物健康之间存在着密不可分的关系。近年来,基因测序技术的快速发展为植物微生物组结构和功能的研究提供了极大的便利,多种植物相关的微生物组得到了解析。同时更多研究者聚焦于植物病害相关的微生物组研究,通过差异分析,发现了一些特定的有益于植物健康的微生物菌群。此外,植物根围或根内微生物塑造的内在原理也得到了进一步的揭示。一系列植物微生物组研究为植物病害防治和新的微生物资源的挖掘提供了更多思路。     

Rhizosphere microbial community and its response to plant species and soil history

The plant rhizosphere is a dynamic environment in which many parameters may influence the population structure, diversity and activity of the microbial community. Two important factors determining the structure of microbial community present in the vicinity of plant roots are plant species and soil type. In the present study we assessed the structure of microbial communities in response to four plant species (i.e. maize (Zea mays L.), oat (Avena sativa L.), barley (Hordeum vulgare L.) and commercial grass mix) planted in soil with different land use history (i.e. arable land under crop rotation, maize monoculture and permanent grassland). Both factors, plant species and land use history, showed clear effects on microbial community and diversity as determined by PCR-DGGE fingerprinting with universal and group-specific bacterial primers. Moreover, we explored the rhizosphere effect of these plant species on the abundance of bacterial antagonists of the potato pathogen Rhizoctonia solani AG3. The data showed that the abundance and taxonomic composition of antagonists differed clearly between the different plants. The highest percentages of antagonists were found in maize and grass rhizosphere. When antagonistic Pseudomonas populations were compared, the highest, abundance and diversity of antagonists were detected in barley and oat rhizospheres, as compared to maize and grass rhizosphere. The results obtained in our study demonstrate clearly that plant species and soil type are two important factors affecting the structure of total bacterial, Pseudomonas and Bacillus community.     

Vertical vs. horizontal transmission of the microbiome in a key disease vector,Ixodes pacificus

Vector‐borne pathogens are increasingly found to interact with the vector's microbiome, influencing disease transmission dynamics. However, the processes that regulate the formation and development of the microbiome are largely unexplored for most tick species, an emerging group of disease vectors. It is not known how much of the tick microbiome is acquired through vertical transmission vs. horizontally from the environment or interactions with bloodmeal sources. Using 16S rRNA sequencing, we examined the microbiome of Ixodes pacificus, the vector of Lyme disease in the western USA, across life stages and infection status. We also characterized microbiome diversity in field and laboratory‐collected nymphal ticks to determine how the surrounding environment affects microbiome diversity. We found a decrease in both species richness and evenness as the tick matures from larva to adult. When the dominant Rickettsial endosymbiont was computationally removed from the tick microbial community, we found that infected nymphs had lower species evenness than uninfected ticks, suggesting that lower microbiome diversity is associated with pathogen transmission in wild‐type ticks. Furthermore, laboratory‐reared nymph microbiome diversity was found to be compositionally distinct and significantly depauperate relative to field‐collected nymphs. These results highlight unique patterns in the microbial community of I. pacificus that is distinct from other tick species. We provide strong evidence that ticks acquire a significant portion of their microbiome through exposure to their environment despite a loss of overall diversity through life stages. We provide evidence that loss of microbial diversity is at least in part due to elimination of microbial diversity with bloodmeal feeding but other factors may also play a role.     

Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations

Even in homogeneous conditions, plants facing a soilborne pathogen tend to show a binary outcome with individuals either remaining fully healthy or developing severe to lethal disease symptoms. As the rhizosphere microbiome is a major determinant of plant health, we postulated that such a binary outcome may result from an early divergence in the rhizosphere microbiome assembly that may further cascade into varying disease suppression abilities. We tested this hypothesis by setting up a longitudinal study of tomato plants growing in a natural but homogenized soil infested with the soilborne bacterial pathogen Ralstonia solanacearum. Starting from an originally identical species pool, individual rhizosphere microbiome compositions rapidly diverged into multiple configurations during the plant vegetative growth. This variation in community composition was strongly associated with later disease development during the later fruiting state. Most interestingly, these patterns also significantly predicted disease outcomes 2 weeks before any difference in pathogen density became apparent between the healthy and diseased groups. In this system, a total of 135 bacterial OTUs were associated with persistent healthy plants. Five of these enriched OTUs (Lysinibacillus, Pseudarthrobacter, Bordetella, Bacillus, and Chryseobacterium) were isolated and shown to reduce disease severity by 30.4–100% when co-introduced with the pathogen. Overall, our results demonstrated that an initially homogenized soil can rapidly diverge into rhizosphere microbiomes varying in their ability to promote plant protection. This suggests that early life interventions may have significant effects on later microbiome states, and highlights an exciting opportunity for microbiome diagnostics and plant disease prevention.Subject terms: Microbial ecology, Microbial ecology     

Rhizosphere shapes the associations between protistan predators and bacteria within microbiomes through the deterministic selection on bacterial communities

The assembly of bacterial communities in the rhizosphere is well-documented and plays a crucial role in supporting plant performance. However, we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rhizosphere selection. To address this, we examined bacterial and protistan taxa from 443 agricultural soil samples including bulk and rhizosphere soils. Our results presented distinct patterns of bacteria and protistan predators in rhizosphere microbiome assembly. Community assembly of protistan predators was determined by a stochastic process in the rhizosphere and the diversity of protistan predators was reduced in the rhizosphere compared to bulk soils, these may be attributed to the indirect impacts from the altered bacterial communities that showed deterministic process assembly in the rhizosphere. Interestingly, we observed that the plant rhizosphere facilitates more close interrelationships between protistan predators and bacterial communities, which might promote a healthy rhizosphere microbial community for plant growth. Overall, our findings indicate that the potential predator–prey relationships within the microbiome, mediated by plant rhizosphere, might contribute to plant performance in agricultural ecosystems.     

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere. This revised version was published online in August 2006 with corrections to the Cover Date.     

Impacts of Saltwater Incursion on Plant Communities,Anaerobic Microbial Metabolism,and Resulting Relationships in a Restored Freshwater Wetland

Saltwater incursion carries high concentrations of sea salts, including sulfate, which can alter anaerobic microbial processes and plant community composition of coastal freshwater marshes. We studied these phenomena in a recently restored wetland on the coastal plain of North Carolina. We measured water inundation patterns, porewater chemistry, microbial process rates, plant tissue chemistry and iron plaque on plant roots, and quantified plant community composition across a hydrologic and salinity gradient to understand the potential interactions between saltwater incursion and changes in microbial processes and plant communities. Plant communities showed no obvious response to incursion, but were structured by inundation patterns and plant growth form (for example, graminoid versus forb). Saltwater incursion increased chloride and sulfate concentrations in surface and porewater, and drove resulting spatial patterns in anaerobic microbial metabolism rates. Plots experiencing saltwater incursion had higher sulfate reduction rates and were dominated by graminoid plant species (for example, sedges, rushes, and grasses). Graminoid plant species’ roots had greater iron plaque formation than forb and submerged species, indicative that graminoid plant species are supplying more oxygen to the rhizosphere, potentially influencing microbial metabolism. Future studies should focus on how plant and microbial communities may respond to saltwater incursion at different time scales, and on parsing out the influence that plants and microbes have on each other as freshwater wetlands experience sea level rise.     

小麦/蚕豆，玉米/蚕豆和小麦/玉米间作对根际细菌群落结构的影响

利用PCR-DGGE技术研究了小麦/蚕豆、玉米/蚕豆和小麦/玉米间作对作物根际细菌群落结构的影响.结果表明：间作能够提高作物根际细菌群落多样性、改变根际细菌群落结构组成.其中,小麦/蚕豆间作对根际细菌群落结构的影响最为突出,作物花期时小麦/蚕豆间作显著提高和改变两种作物根际细菌多样性和群落结构组成.玉米/蚕豆间作主要表现出对苗期玉米根际细菌多样性的显著提高和群落结构组成的改变.小麦/玉米间作对作物根际细菌群落结构的影响程度较弱.同时,3种间作体系都具有不同程度的产量优势.结果证明了间作体系中地上部植物多样性与地下部微生物多样性存在紧密联系.     

Local soil characteristics determine the microbial communities under forest understorey plants along a latitudinal gradient

The soil microbial community is essential for maintaining ecosystem functioning and is intimately linked with the plant community. Yet, little is known on how soil microbial communities in the root zone vary at continental scales within plant species. Here we assess the effects of soil chemistry, large-scale environmental conditions (i.e. temperature, precipitation and nitrogen deposition) and forest land-use history on the soil microbial communities (measured by phospholipid fatty acids) in the root zone of four plant species (Geum urbanum, Milium effusum, Poa nemoralis and Stachys sylvatica) in forests along a 1700 km latitudinal gradient in Europe.Soil microbial communities differed significantly among plant species, and soil chemistry was the main determinant of the microbial community composition within each plant species. Influential soil chemical variables for microbial communities were plant species-specific; soil acidity, however, was often an important factor. Large-scale environmental conditions, together with soil chemistry, only explained the microbial community composition in M. effusum and P. nemoralis. Forest land-use history did not affect the soil microbial community composition.Our results underpin the dominant role of soil chemistry in shaping microbial community composition variation within plant species at the continental scale, and provide insights into the composition and functionality of soil microbial communities in forest ecosystems.