Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings

Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here, we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following ¹³CO₂-pulse-labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate-consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root-associated microbiomes.     

Influence of the zinc hyperaccumulator Thlaspi caerulescens J. & C. Presl. and the nonmetal accumulator Trifolium pratense L. on soil microbial populations

Metal hyperaccumulator plants like Thlaspi caerulescens J. & C. Presl. are used for phytoremediation of contaminated soils. Since little is known about the rhizosphere of hyperaccumulators, the influence of T. caerulescens was compared with the effects of Trifolium pratense L. on soil microbes. High- and low-metal soils were collected near a zinc smelter in Palmerton, Penn. Soil pH was adjusted to 5.8 and 6.8 by the addition of Ca(OH)2. Liming increased bacterial populations and decreased metal toxicity to levels allowing growth of both plants. The effects of the plants on total (culturable) bacteria, total fungi, as well as cadmium- and zinc-resistant populations were assessed in nonrhizosphere and rhizosphere soil. Both plants increased microbial populations in rhizosphere soil compared with nonrhizosphere soil. Microbial populations were higher in soils planted with T. pratense, but higher ratios of metal-resistant bacteria were found in the presence of T. caerulescens. We hypothesize that T. caerutescens acidifies its rhizosphere. Soil acidification in the rhizosphere of T. caerulescens would affect metal uptake by increasing available metals around the roots and consequently, increase the selection for metal-resistant bacteria. Soil acidification may be part of the hyperaccumulation process enhancing metal uptake from soil.     

基于高通量测序的杨树人工林根际土壤真菌群落结构

研究不同根序细根根际土壤微生物群落组成结构对深入了解根系-微生物互作关系具有重要意义.本研究采用Illumina MiSeq测序平台,对杨树人工林非根际土壤和不同根序细根根际土壤的真菌群落结构进行分析.物种注释结果显示: 杨树1～2级根(R1)、3级根(R2)和4～5级(R3)根际及非根际土壤(NR)中分别包含128、124、130和101个真菌属,表明杨树根际存在对真菌群落构建的选择性机制.不同根序根际土壤中相对丰度>1%的真菌属有7个,木霉属在1～2级根根际土壤中丰度较高,毛孢子菌属和曲霉属分别是3级根和4～5级根根际土壤中丰度最高的真菌属.α多样性指数表明: 根际土壤真菌的多样性在不同根序间存在显著差异,低级根显著高于高级根(P<0.05).β多样性指数表明: 真菌群落随着序级的升高差异性不断上升,相似性不断降低.不同根序细根根际真菌群落的趋异化组成和结构与细根功能具有密切关系.     

健康与凋萎病杨梅树体及根围菌群的差异

凋萎病是制约杨梅产业发展的严重病害。为了有效防控凋萎病,本研究分析了杨梅健康和感染凋萎病树体各部位及根表土和根围土中细菌和真菌群落的丰富度与多样性的差异。结果表明: 与健康树相比,病树根围土、根表土、根、枝干、枝皮和叶片的细菌和真菌丰富度均发生了显著变化,其中,根表土细菌和枝皮内真菌的丰富度和多样性均显著降低,而枝皮内细菌和根表土的真菌丰富度和多样性均显著升高。病树各部位及根表、根围土细菌和真菌的优势菌相对丰度在门、纲和属水平上发生了明显的变化,在病树枝干、根和根表土中的假单胞菌属及根表土、根围土中的镰刀菌属的相对丰度明显降低,病树根表土及根围土中青霉菌属的相对丰度明显增加。与凋萎病菌同属的拟盘多毛孢菌在病树根内显著减少,而在其他位置均大量增殖,其相对丰度与多数相对丰度较高的真菌呈正相关。本研究结果将为开发杨梅凋萎病的生态改良、培育健康树体和生物防治技术提供有效的理论依据。     

内蒙草原不同植物功能群及物种对土壤微生物组成的影响

为了分析不同植物群落组成对内蒙古典型草原土壤微生物群落组成的影响,本研究利用植物功能群剔除处理实验平台,采用荧光定量PCR(real-timePCR)和自动核糖体间隔区基因分析(automated ribosomal intergenic spacer analysis,ARISA)技术,对不同植物功能群组成的非根际土壤和常见物种的根际土壤中细菌和真菌的数量及群落结构进行了分析。结果表明,在非根际土壤中,不同植物功能群组成对细菌数量有显著影响,而对真菌数量及细菌和真菌的群落结构影响不明显;在根际土壤中,不同植物物种对细菌、真菌的数量都有显著影响。此外,聚类分析表明,不同物种的根际土中细菌和真菌的群落结构也有所不同,尤其以细菌的群落结构变化较为明显。研究结果表明不同植物物种可以通过根系影响土壤微生物群落组成。     

Rhizosphere disturbance influences fungal colonization and community development on dead fine roots

Little is known about the community dynamics of fungi on decomposing fine roots, despite the importance of fine roots as a source of carbon to detrital systems in forests. We examined fungal communities on dead roots in a sugar-maple dominated northern hardwood forest to test the hypothesis that community development is sensitive to rhizosphere disruption. We generated cohorts of dead fine roots in root windows and disturbed the rhizosphere microbial community in half of the windows by moving roots into sieved bulk soil. We sampled root fragments repeatedly over time and cultured fungi from these fragments to explore temporal patterns of fungal species composition. Disturbing the root rhizosphere prior to initiating decomposition changed the dominant fungal taxa, the distribution of dominant species within the community, and the temporal development in the culturable fungal community. Dominance in control roots shifted from Neonectria in early decay to Umbelopsis in later decay. Disturbance roots were more evenly dominated over time by Trichoderma, Neonectria, another species of Umbelopsis, and Pochonia. Our results suggest that species interactions are important in the ecology of fine root decay fungi, with the rhizosphere community of the living root influencing development of the decay community.     

Vertical patterns of fine root biomass, morphology and nitrogen concentration in a subalpine fir-wave forest

To clarify the nutrient acquisition strategies for below-ground resources in a subalpine Abies forest with shallow soils, we examined the vertical patterns of fine root biomass, morphology, nitrogen concentration of fine root tissue and soil chemical characteristics in nine quadrats of sapling, young and mature stands in a subalpine fir-wave forest, central Japan. The community characteristics changed with stand development, but stand development did not influence the vertical pattern of fine root characteristics. Fine root biomass decreased with soil depth. Specific root length did not differ among soil depths, and neither average diameter nor tissue density of fine roots changed vertically. The nitrogen concentration of fine roots differed significantly among soil depths, and was higher in surface soils than in deeper soils. Moreover, soil pH, soil electrical conductivity and soil nitrogen concentration were higher in surface layers than deeper layers. Therefore, we suggest that the subalpine Abies community has a nutrient acquisition strategy that allows uptake of more nutrients near the surface in shallow soils due to the larger investment in biomass and more active metabolism, but not due to phenotypic plasticity in fine root morphology. In addition, we observed that fine root biomass changed with stand development, where specific root length was greater in sapling stands than in older stands.     

Enhancement of Population Densities of Pseudomonas putida PpG7 in Agricultural Ecosystems by Selective Feeding with the Carbon Source Salicylate

Sodium salicylate (1,000 μg/ml) was delivered through a drip irrigation system to agricultural field soils planted to tomato and infested with Pseudomonas putida PpG7, the host of the salicylate catabolic plasmid NAH7. In nonfumigated soils infested with approximately 10³ CFU of PpG7 per g in the top 30 cm, population densities were increased up to 112-fold within 14 days of the initial application of salicylate compared with the densities in the respective nonamended soils. Mean season-long population densities of PpG7 in the top 30 cm of soil were significantly increased (P < 0.01) from 216 CFU/g in nonamended soils to 1,370 CFU/g in salicylate-amended soils. In the respective rhizosphere soils, mean population densities of PpG7 were significantly increased (P < 0.01) from 92 to 2,066 CFU/cm of root. Soil fumigation interacted (P < 0.01) with salicylate amendment and further increased the mean population densities of PpG7 in nonrhizosphere soil by an additional 5,689 CFU/g of soil. This fumigation effect was not detected in rhizosphere soils. The effect of salicylate in increasing population densities of PpG7 in soil also was affected by inoculum level, field site, and soil depth. Proportionate differences were greater in soils infested with approximately 10³ CFU of PpG7 per g than in comparable soils infested with 10⁵ CFU/g. In low-inoculum soils, increases from salicylate amendments were 26- and 29-fold in rhizosphere and nonrhizosphere soils, respectively, and in high-inoculum soils, the respective increases were 5.6- and 5-fold. No increases of fungi able to utilize salicylate were detected in soils amended with salicylate. However, soil fumigation with metham-sodium significantly reduced (P < 0.01) population densities of fungal salicylate utilizers in rhizosphere and nonrhizosphere soils.     

Effect of Root Agglutinin on Microbial Activities in the Rhizosphere

A total of 220 bacterial isolates were obtained from pea rhizosphere and nonrhizosphere samples. Of these samples, 100 isolates were chosen randomly to test for their agglutinative reaction against pea root exudate. The percentage of positive agglutination of bacteria isolated from the nonrhizosphere sample was significantly lower than that of bacteria isolated from the rhizosphere sample. Moreover, this agglutinative reaction could not be blocked either by treating the bacterial cells or root exudate with different carbohydrates before they were mixed or by boiling the root exudate first. Bacteria that could be agglutinated by pea root exudate followed the downward growth of the pea root through the soil profile. The greater abilities of such bacteria to colonize the pea rhizosphere were indicated by their higher rhizosphere-colonizing (rhizosphere/nonrhizosphere) ratios, whether the bacteria were added alone or together with nonagglutinating bacteria. However, bacteria did show different agglutinative reactions toward root exudates obtained from different plants.     

High turnover of fungal hyphae in incubation experiments

Soil biological studies are often conducted on sieved soils without the presence of plants. However, soil fungi build delicate mycelial networks, often symbiotically associated with plant roots (mycorrhizal fungi). We hypothesized that as a result of sieving and incubating without plants, the total fungal biomass decreases. To test this, we conducted three incubation experiments. We expected total and arbuscular mycorrhizal (AM) fungal biomass to be higher in less fertilized soils than in fertilized soils, and thus to decrease more during incubation. Indeed, we found that fungal biomass decreased rapidly in the less fertilized soils. A shift towards thicker hyphae occurred, and the fraction of septate hyphae increased. However, analyses of phospholipid fatty acids (PLFAs) and neutral lipid fatty acids could not clarify which fungal groups were decreasing. We propose that in our soils, there was a fraction of fungal biomass that was sensitive to fertilization and disturbance (sieving, followed by incubation without plants) with a very high turnover (possibly composed of fine hyphae of AM and saprotrophic fungi), and a fraction that was much less vulnerable with a low turnover (composed of saprotrophic fungi and runner hyphae of AMF). Furthermore, PLFAs might not be as sensitive in detecting changes in fungal biomass as previously thought.     

Survival ofPseudomonas syringae pv.lachrymans with cucumber roots

Summary Survival ofPseudomonas syringae pv.lachrymans with seedling cucumber roots, root washings, rhizosphere soil, and nonrhizosphere soil was determined 7–8 days after the soil surface was watered with a cell suspension of the bacterium. Plants were in pots in the green-house and soil was not sterilized. Survival was best with roots and root washings, next best in rhizosphere soil, and poor in nonrhizosphere soil.     

Distribution of soil fractions and location of soil bacteria in a vertisol under cultivation and perennial grass

Effects of soil management on soil characteristics were investigated on the rhizosphere (RPP) and the nonrhizosphere (NRPP) soil of a re-grass vertisol underDigitaria decumbens and in the soil under continuous cultivation (CC). A low energy technique allowed to separate eight size and density fractions, including macro- and micro-aggregates while preserving soil bacteria. Organic C and N, microbial biomass C and the number of total bacteria (AODC) and ofAzospirillum brasilense and their distribution were determined in soil fractions isolated from the CC, NRPP and RPP soils. Soil macroaggregates (>2000 m) were similarly predominant in the NRPP and RPP soils when the dispersible clay size fraction (<2 m) respresented more than 25% of the CC soil mass. The main increase of C content in RPP originated from the macroaggregates (> 2000 m) and from the root fraction, not from the finer separates. The proportion of organic C as microbial biomass C revealed the low turnover of microbial C in the PP situations, especially in the clay size fraction of the NRPP soil. A common shift of AODC toward the finer separates from planted soils (CC and RPP) revealed the influence of living plants on the distribution of soil bacteria. The relative abundance ofA. brasilense showed the presence of the active roots ofDigitaria in the macroaggregates and their contact with the dispersible clay size fraction of the rhizosphere soil.     

玉米根际与非根际解磷细菌的分布特点

植物光合作用产物约有 12 %～ 5 0 %通过根系进入根际土壤中 ,不同的植物 ,同一植物不同的生长发育时期 ,不仅根际分泌物的数量有差异 ,而且分泌物的种类也不同[4 ] 。这些分泌物不仅是微生物很好的培养基 ,而且一些分泌物可能抑制或有利于甚至刺激某些微生物的繁殖 ,从而导致根际微生物种群结构的变化。根际微生物的数量、活性和群落结构及其变化 ,直接影响到植物吸收水分、养分 ,也影响植物对恶劣环境的抵抗能力 ,尤其是与病菌的侵入和感染关系非常密切[6] 。Ｐ是植物最重要的营养元素之一 ,大多数土壤都具有很强的固定Ｐ的能力 ,Ｐ肥的利…     

Fertilization effects on fineroot biomass, rhizosphere microbes and respiratory fluxes in hardwood forest soils

Fertilizer-induced reductions in CO(2) flux from soil ((F)CO(2)) in forests have previously been attributed to decreased carbon allocation to roots, and decreased decomposition as a result of nitrogen suppression of fungal activity. Here, we present evidence that decreased microbial respiration in the rhizosphere may also contribute to (F)CO(2) reductions in fertilized forest soils. Fertilization reduced (F)CO(2) by 16-19% in 65-yr-old plantations of northern red oak (Quercus rubra) and sugar maple (Acer saccharum), and in a natural 85-yr-old yellow birch (Betula allegheniensis) stand. In oak plots, fertilization had no effects on fine root biomass but reduced mycorrhizal colonization by 18% and microbial respiration by 43%. In maple plots, fertilization reduced root biomass, mycorrhizal colonization and microbial respiration by 22, 16 and 46%, respectively. In birch plots, fertilization reduced microbial respiration by 36%, but had variable effects on root biomass and mycorrhizal colonization. In plots of all three species, fertilization effects on microbial respiration were greater in rhizosphere than in bulk soil, possibly as a result of decreased rhizosphere carbon flux from these species in fertile soils. Because rhizosphere processes may influence nutrient availability and carbon storage in forest ecosystems, future research is needed to better quantify rhizo-microbial contributions to (F)CO(2).     

Response characteristics of Scirpus trioueter and its rhizosphere to pyrene contaminated soils at different growth stages

Scirpus triqueter (Triangular club-rush), a typical wetland species, is used to study the response characteristics to pyrene. A pot experiment was conducted to investigate the growth parameters (height, diameter, shoot number, total volume, underground biomass, above-ground biomass and total biomass), and enzymes (catalase and superoxide dismutase) of S. triqueter. The characteristics of soil enzymes (catalase and polyphenol oxidase) and microorganisms (bacteria and fungi) were also assessed after pyrene treatment. Elevated pyrene concentration (80 mgkg(-1)) in the soil reduced the shoot number and biomass significantly, especially at the early growth stage. In root tissue, the enzyme catalase was activated at 80 mgkg(-1) of pyrene. Compared to roots, shoots had higher enzyme activities. Catalase activities in the rhizosphere increased throughout the growth period of S. triqueter. Polyphenol oxidase activities in the rhizosphere were higher than those in the bulk soil and unplanted soil. The populations of bacteria (total bacteria, pyrene-tolerant bacteria, and actinomyces) and fungi decreased under the stress of high pyrene concentration, while that of pyrene-tolerant bacteria increased with the increasing pyrene concentration. The presence of pyrene did not benefit the growth of S. triqueter. S. triqueter and soil enzymes varied within the growth stages. The presence of S. triqueter could improve the activity of soil enzymes and facilitate the propagation of microorganisms which could help eliminate pyrene contamination.     

异丙甲草胺对芹菜根际与非根际生物活性的影响

通过根际袋法土培试验,研究了异丙甲草胺对芹菜根际与非根际土壤酶活性、土壤微生物数量的影响以及异丙甲草胺在根际与非根际土壤中的降解特性.结果表明,异丙甲草胺对土壤过氧化氢酶活性有一定的抑制作用,对土壤脱氢酶活性有激活作用.一般情况下根际土壤酶活性均要大于非根际土壤.异丙甲草胺作用45 d后,芹菜根际土壤细菌、真菌数量大于非根际土壤,根际效应R/S在1.76～2.51之间;异丙甲草胺对土壤放线菌数量影响不大,根际效应不明显.异丙甲草胺在根际土壤与非根际土壤中的降解速率分别为0.0217和0.0176,相应的半衰期分别为31.9和39.4 d.在根际土壤中异丙甲草胺更易降解.     

Effects of Elevated Carbon Dioxide and Nitrogen Fertilization on Mycorrhizal Fine Roots and the Soil Microbial Community in Beech-Spruce Ecosystems on Siliceous and Calcareous Soil

To study the responses of forests to global change, model ecosystems consisting of beech and spruce trees were maintained in open top chambers for 4 years under four conditions, namely with normal and elevated CO2 and with low and high nitrogen input, each replicated four times. Each open top chamber (height 3 m, diameter 3 m, soil depth 1.5 m) contained two separate soil compartments containing nutrient-poor siliceous and nutrient-rich calcareous soil. Here, we focus on the fine roots and the soil microbial community in these model ecosystems. At the time of planting, the fine roots were cut back according to forestry practice, and the newly formed roots were colonized by the indigenous soil microflora. After 4 years, the total biomass of fine roots, when averaged over all treatments, was almost the same in each of the two soil types; it was highest in the top 100 mm of soil (60%) and decreased sharply in deeper soil layers. Fungal biomass associated with the fine roots, consisting mainly of ectomycorrhizal fungi, was estimated using the ergosterol content as a marker. It was much higher in fine roots in the siliceous than in the calcareous soil, indicating considerably enhanced ectomycorrhiza formation in the nutrient-poor siliceous soil. Elevated atmospheric CO2 stimulated fine root production by ca. 85% and 43% in the top 100 mm of calcareous and siliceous soils respectively. Increased nitrogen input caused a slightly reduced production of fine root biomass in the calcareous soil but increased it by 33% in the siliceous soil. Marker substances for microorganisms were analyzed in the root-free soil. The amounts of carbon released by fumigation/extraction (a general marker for microbial biomass) and chitin (a marker for fungal biomass) were significantly higher in the top layer of the siliceous than of the calcareous soil, but they did not respond significantly to the treatments with elevated CO2 or the nitrogen fertilizer. The total concentration of the phospholipid fatty acids (PLFAs) and the number of the PLFAs did not differ between the two soil types. However, four of the eight most abundant PLFAs differed significantly between the two soil types. Principal component analysis revealed clearly separated clusters for the two soil types. Although analysis did not reveal any significant changes in response to the treatments, the concentration of the PLFA typical for ectomycorrhizal fungi was significantly higher under conditions of elevated CO2 in the nutrient-rich calcareous soil.     

青稞根腐病对根际土壤微生物及酶活性的影响

选取甘肃省卓尼县青稞种植区为研究地点,调查青稞根腐病的发病情况,并分别采集其健康植株和发病株根际的土壤,对比分析其土壤微生物生物量(碳、氮、磷)、微生物数量(细菌、真菌、放线菌)以及过氧化氢酶、蔗糖酶、脲酶、碱性磷酸酶、纤维素酶5种酶活性。结果发现,研究区10个采样点均有青稞根腐病的发生,发病率在5%—20%之间,不同地点发病率不同。根腐病的发生,会显著影响青稞根际微生物生物量,导致微生物生物量碳、氮、磷的含量发生变化,其中微生物生物量氮和磷含量整体降低,且不同采样点微生物量不同。土壤微生物数量总体呈现细菌放线菌真菌的趋势,但不同微生物对根腐病发病的响应不同,细菌和放线菌数量因根腐病的发生而减少,真菌的数量则增多;不同采样点土壤微生物数量不相同,细菌和真菌呈现区域性特征,放线菌的数量不呈现地域性。根腐病的发生还造成土壤酶活性的改变,其中蔗糖酶、脲酶、磷酸酶的含量因根腐病的发生而降低,而纤维素酶则升高,过氧化氢酶的变化没有规律。总而言之,根腐病的发生会使青稞根际土壤微生物组成发生改变,碳、氮、磷等物质代谢受到抑制,而能量代谢发生紊乱。因此,研究和防治青稞根腐病就必须重视土壤微生物及土壤酶的作用。     

黑老虎内生真菌及根际土壤真菌的群落结构与生态功能分析

为探讨黑老虎(Kadsura coccinea)根际土壤和组织内生真菌菌群的组成及其生态功能，该研究采用ITS高通量测序技术对成熟黑老虎(根、茎、叶)内生真菌及根际土壤真菌群落结构、多样性和生态功能进行了分析。结果表明：(1)从12个样品中共获得2 241个可操作分类单元(OTU),涉及10门、41纲、95目、212科、367属，内生真菌(根、茎、叶)和根际土壤真菌OTU数分别为386、536、258、1 435个，其中共有的OTU为18个。在门水平上，黑老虎内生真菌及根际土壤真菌优势群落均为子囊菌门和担子菌门，其中子囊菌门在叶和茎中占比分别高达96.99%和95.37%;在属水平上，黑老虎根际土壤真菌中腐生真菌被孢霉属占比较高(为13.5%),叶和茎等生长旺盛的组织中子囊菌门未分类属和痂囊腔菌属占比较高。(2)α多样性分析结果显示，黑老虎根际土壤真菌群落的丰度和多样性明显高于内生真菌，茎中内生真菌丰度显著高于根和叶，而根、茎和叶组织间内生真菌多样性差异不显著；PCoA分析结果显示，叶和茎的真菌群落结构相似性更高。(3)利用FUNGuild数据库进行的功能预测分析结果显示，黑老虎根际土...     

翅荚木人工林不同径阶间细根主要功能性状与根际土壤养分的关系

细根能敏感地感知土壤环境变化,对植物生长发育具有重要影响.以6年生翅荚木人工林为对象,对其不同径阶的细根主要功能性状与根际土壤养分特征及两者间关系进行分析.结果表明:细根生物量、根长密度与根体积密度均随径阶增加而增加,比根长与比根面积则随径阶增加呈先升高再下降后升高的趋势,根组织密度则与径阶大小不相关.不同径阶翅荚木根际土壤的pH值及含水率、全碳、全磷、铵态氮、硝态氮和总有效氮含量均存在显著差异,大径阶林木的根际土壤全碳、全氮、硝态氮、总有效氮含量相对较高,小径阶林木的根际土壤含水率、土壤全磷、铵态氮含量相对较高.土壤全氮、全碳、硝态氮和总有效氮含量与林木细根的生物量、根长密度、根体积密度呈显著正相关;土壤全磷与林木细根的根组织密度呈显著正相关,与比根长、比根面积呈显著负相关;土壤含水率与林木细根的生物量和根体积密度均呈显著正相关;根际土壤pH和林木细根的比根长、比根面积呈显著正相关,与根组织密度则呈显著负相关.研究结果可为翅荚木优良种质资源选育提供科学依据.