Weeds influence soil bacterial and fungal communities

Background and aims

Vineyards harbour a variety of weeds, which are usually controlled since they compete with grapevines for water and nutrients. However, weed plants may host groups of fungi and bacteria exerting important functions.

Methods

We grew three different common vineyard weeds (Taraxacum officinalis, Trifolium repens and Poa trivialis) in four different soils to investigate the effects of weeds and soil type on bacterial and fungal communities colonising bulk soil, rhizosphere and root compartments. Measurements were made using the cultivation-independent technique Automated Ribosomal Intergenic Spacer Analysis (ARISA).

Results

Weeds have a substantial effect on roots but less impact on the rhizosphere and bulk soil, while soil type affects all three compartments, in particular the bulk soil community. The fungal, but not the bacterial, bulk soil community structure was affected by the plants at the late experimental stage. Root communities contained a smaller number of Operational Taxonomic Units (OTUs) and different bacterial and fungal structures compared with rhizosphere and bulk soil communities.

Conclusions

Weed effect is localised to the rhizosphere and does not extend to bulk soil in the case of bacteria, although the structure of fungal communities in the bulk soil may be influenced by some weed plants.     

典型农田退耕后土壤真菌与细菌群落的演替

土壤真菌和细菌作为地下生态系统的重要组成部分,其群落的恢复状况是评价农田退耕还林生态效益的重要指标。以云南省维西县典型退耕还林农田为对象,利用高通量测序等方法比较了不同退耕年限的农田土壤中真菌和细菌群落随植被演替的变化特征。结果发现,农田撂荒后土壤细菌多样性先显著降低后缓慢上升,真菌多样性变化不明显;地上部植被由草本经灌丛再向林地演替的过程中,土壤真菌的群落组成随植被变化呈现明显的改变,主要体现在粪壳菌纲(Sordariomycetes)所占比例的减少(由30%减至10%左右)和伞菌纲(Agaricomycetes)所占比例的增加(由5%以下增至20%以上);而细菌的群落组成无明显变化。聚类分析的结果显示,真菌的群落组成变化与植物群落的演替规律更为同步。不同演替阶段的退耕农田土壤真菌和细菌群落均明显区别于未经扰动的天然林,表明人为扰动对土壤微生物群落的影响可能在较长时间内持续存在。研究揭示了云南典型农田退耕后地下土壤真菌和细菌群落随植被演替的变化特征,为全面评价该地区退耕还林的生态效益提供了数据支撑。     

Azoxystrobin and soil interactions: degradation and impact on soil bacterial and fungal communities

Aims: To provide an independent assessment of azoxystrobin effects on nontarget soil bacteria and fungi and generate some baseline information on azoxystrobin’s persistence in soil. Methods and Results: Plate based assay showed that azoxystrobin exhibited differential toxicity upon cultured fungi at different application rates. While ¹⁴C labelled isotopes experiments showed that less than 1% of azoxystrobin was mineralized, degradation studies revealed over 60% azoxystrobin breakdown over 21 days. PCR DGGE analysis of 16S and 18S rRNA genes from different soil microcosms showed that azoxystrobin had some effects on fungal community after 21 days (up to 84 days) of incubation in either light or dark soil microcosms. Light incubations increased fungal diversity while dark incubations reduced fungal diversity. Bacterial diversity was unaffected. Conclusions: Significant biotic breakdown of parent azoxystrobin occurred within 21 days even in the absence of light. Azoxystrobin under certain conditions can reduce fungal soil diversity. Significance and Impact of the Study: One of the few independent assessments of azoxystrobin (a widely used strobilurins fungicide) effects on soil fungi when used at the recommended rate. Azoxystrobin and metabolites may persist after 21 days and affect soil fungi.     

Effects of physico-chemical parameters on the bacterial and fungal communities during agricultural waste composting

The goal of this study was to identify and prioritize some of the physico-chemical parameters that contributed to bacterial and fungal community compositions during agricultural waste composting. Relationships between those parameters and microbial community compositions determined by PCR-DGGE were simultaneously evaluated by redundancy analysis (RDA). The results showed that the temporal variation of bacterial community composition was significantly related to water soluble carbon (WSC), ammonium and nitrate (P<0.05), while the most variation in distribution of fungal community composition was statistically explained by pile temperature, WSC, and moisture content (P<0.05). Significant amounts of the variation (54.9% and 56.0% for bacterial and fungal species data, respectively) were explained by those parameters, suggesting that those parameters were the most likely ones to influence, or be influenced by the bacterial and fungal species. Variation partitioning analyses indicated that WSC and pile temperature showed predominant effect on the bacterial and fungal community composition, respectively.     

不同环境条件下土壤微生物对模拟大气氮沉降的响应

研究了林内及林缘两个生境中,在有苔藓覆盖和无苔藓覆盖条件下,人工加氮对土壤理化性质及土壤微生物群落的影响。结果显示加氮使土壤pH下降,有效态氮和有效态磷的含量上升,但不同生境及有无苔藓植物覆盖在一定程度上影响土壤理化性质及其对加氮的反应。苔藓植物覆盖可以缓解加氮引起的土壤酸化及有效氮含量上升压力,促进有效态磷含量上升。不同生境中,土壤微生物对氮沉降的响应亦不同。低氮使林缘生境土壤微生物的胁迫程度减小,中高氮使其胁迫程度上升,而任何加氮均增加林内生境中土壤微生物的胁迫程度。两个生境中,苔藓植物覆盖均可以缓解过量氮沉降对土壤微生物造成的压力,降低过量氮沉降对土壤微生物的伤害,提高土壤微生物的代谢活性。     

基于Illumina MiSeq测序平台分析长期不同施肥处理对黑土真菌群落的影响

【目的】不合理施肥所引发的土壤环境问题逐渐成为制约我国农业可持续发展的重要因素之一,土壤真菌作为一类重要的土壤微生物,研究长期施肥对土壤真菌多样性及群落分布格局,探讨其理化因子对真菌群落结构的影响具有一定意义。【方法】本研究以东北黑土玉米田长期定位施肥试验(1984–2017)为基础,通过常规分析和Illumina Mi Seq高通量测序技术,分析长期施肥对黑土玉米田土壤养分含量和真菌群落结构变化的影响。【结果】长期施用氮肥明显降低土壤p H,却增加了玉米产量,秸秆与化肥配施可以增加土壤有机质和全氮的含量。稀释曲线结果表明长期施肥降低了土壤真菌序列的丰度和均匀度,并且在秸秆与化肥配施中序列数最低;在优势菌群中,共检测出5个已知真菌门,分别是子囊菌门(Ascomycota)、担子菌门(Basidiomycota)、接合菌门(Zygomycota)、球囊菌门(Glomeromycota)和壶菌门(Chytridiomycota),子囊菌门占总序列平均值的57.0%,并且在氮磷钾配施高量秸秆有机肥(NPK+S0.5)的土壤中,子囊菌门丰度高达70.35%。在土壤真菌属水平的物种丰度分析中,共检测出109个已知真菌属,Humicola、Fusarium、Verticillium、Mortierella这4个菌属为优势菌属;Chaetomium、Trichocladium、Podospora、Preussia 4个菌属在秸秆与化肥配施处理中丰度较高,并同属一个分支聚类。从多样性指数分析得出,秸秆与化肥配施可以增加物种丰度和群落多样性;从热图分析可知,施用氮肥和不施用氮肥处理间真菌群落组成存在明显差异。RDA分析中,土壤理化性质影响着土壤真菌群落结构,尤其是土壤的p H、全量氮磷钾(T-N、T-P、T-K)、有效磷钾(A-P、A-K)和铵态氮(NH4+-N)浓度是重要环境因素。【结论】因此,施用氮肥虽然增加了产量,但也造成土壤酸化,真菌数量增加,其丰富度和多样性明显降低。而秸秆与化肥配施可以维持土壤健康生态环境和真菌群落多样性。     

不同施肥模式对雷竹林土壤真菌群落特征的影响

为探明施肥处理对雷竹林土壤真菌群落特征的影响,采用末端限制性片段长度多态性(T-RFLP)和荧光定量PCR技术,分析有机肥(M)、化肥(CF)、化肥配施有机肥(CFM)、化肥配施有机肥加覆盖(CFMM)及不施肥(CK)处理土壤真菌群落结构和数量特征.结果表明:施肥显著影响真菌群落结构与多样性,表层(0～20 cm)土壤中M、CFMM处理与CK,亚表层(20～40 cm)土壤中CF、CFMM处理与CK之间真菌群落结构均存在明显差异;且表层土壤中CF、CFMM处理真菌Shannon指数和均匀度指数显著低于CK.M、CFM处理表层土壤真菌数量显著高于CK.土壤有机质、全氮、铵态氮和速效钾含量显著影响了真菌群落结构的变异;全氮、铵态氮、硝态氮含量与真菌数量均呈显著正相关.表明雷竹林表层和亚表层土壤中真菌群落对施肥处理的响应存在明显差异,表层土壤真菌群落明显受有机质添加的影响,而亚表层则对化肥投入较为敏感;施肥对真菌群落多样性的影响主要集中在表层土壤.     

Effect of winter cover crops on soil nitrogen availability,corn yield,and nitrate leaching

Biculture of nonlegumes and legumes could serve as cover crops for increasing main crop yield, while reducing NO3 leaching. This study, conducted from 1994 to 1999, determined the effect of monocultured cereal rye (Secale cereale L.), annual ryegrass (Lolium multiflorum), and hairy vetch (Vicia villosa), and bicultured rye/vetch and ryegrass/vetch on N availability in soil, corn (Zea mays L.) yield, and NO3-N leaching in a silt loam soil. The field had been in corn and cover crop rotation since 1987. In addition to the cover crop treatments, there were four N fertilizer rates (0, 67, 134, and 201 kg N ha(-1), referred to as N0, N1, N2, and N3, respectively) applied to corn. The experiment was a randomized split-block design with three replications for each treatment. Lysimeters were installed in 1987 at 0.75 m below the soil surface for leachate collection for the N 0, N 2, and N 3 treatments. The result showed that vetch monoculture had the most influence on soil N availability and corn yield, followed by the bicultures. Rye or ryegrass monoculture had either no effect or an adverse effect on corn yield and soil N availability. Leachate NO3-N concentration was highest where vetch cover crop was planted regardless of N rates, which suggests that N mineralization of vetch N continued well into the fall and winter. Leachate NO3-N concentration increased with increasing N fertilizer rates and exceeded the U.S. Environmental Protection Agency's drinking water standard of 10 mg N l(-1) even at recommended N rate for corn in this region (coastal Pacific Northwest). In comparisons of the average NO3-N concentration during the period of high N leaching, monocultured rye and ryegrass or bicultured rye/vetch and ryegrass/vetch very effectively decreased N leaching in 1998 with dry fall weather. The amount of N available for leaching (determined based on the presidedress nitrate test, the amount of N fertilizer applied, and N uptake) correlated well with average NO3-N during the high N leaching period for vetch cover crop treatment and for the control without the cover crops. The correlation, however, failed for other cover crops largely because of variable effectiveness of the cover crops in reducing NO3 leaching during the 5 years of this study. Further research is needed to determine if relay cover crops planted into standing summer crops is a more appropriate approach than fall seeding in this region to gain sufficient growth of the cover crop by fall. Testing with other main crops that have earlier harvest dates than corn is also needed to further validate the effectiveness of the bicultures to increase soil N availability while protecting the water quality.     

间作牧草对茶园螨类群落多样性的影响

螨类是茶园生态系统中重要且复杂的类群之一.为了了解不同植物问作后对茶园螨类群落的组成结构和多样性的影响,2006年3月至2008年4月,在武夷山市星村镇大坪洲茶园通过间作百喜草(Paspalum notatum)或圆叶决明(Cassia rotundifolia)、留养杂草和除杂草4种不同处理,对茶园茶冠层(采用盆拍法及剪枝条法)和凋落层(采用捡取凋落物法)的螨类进行系统采样、标本鉴定和统计分析.结果表明:与留养杂草对照相比,间作百喜草或圆叶决明均显著增加了茶冠层和凋落层捕食螨的物种丰富度(S)、有效多样性指数(eH')、个体数(M和绝对丰度(-/n).与留养杂草和除杂草这两种对照相比,间作百喜草或圆叶决明均显著增加了茶冠层和凋落层优势种圆果大赤螨(Anystis baccarum)的个体数(N).荼冠层植食螨和腐食螨及凋落层腐食螨的所有群落指标在不同处理茶园间均无显著差异.茶冠层和凋落层螨类群落物种丰富度(S)和个体数(N)季节性变化明显,物种组成相似性高.间作茶园和留养杂草茶园茶冠层的螨类总个体数与其对应的凋落层螨类总个体数呈显著正相关.多样化茶园有利于保护和利用捕食螨,从而对茶园有害生物进行生态控制,促进有机茶叶可持续生产.     

The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling

Many studies have shown that changes in nitrogen (N) availability affect primary productivity in a variety of terrestrial systems, but less is known about the effects of the changing N cycle on soil organic matter (SOM) decomposition. We used a variety of techniques to examine the effects of chronic N amendments on SOM chemistry and microbial community structure and function in an alpine tundra soil. We collected surface soil (0-5 cm) samples from five control and five long-term N-amended plots established and maintained at the Niwot Ridge Long-term Ecological Research (LTER) site. Samples were bulked by treatment and all analyses were conducted on composite samples. The fungal community shifted in response to N amendments, with a decrease in the relative abundance of basidiomycetes. Bacterial community composition also shifted in the fertilized soil, with increases in the relative abundance of sequences related to the Bacteroidetes and Gemmatimonadetes, and decreases in the relative abundance of the Verrucomicrobia. We did not uncover any bacterial sequences that were closely related to known nitrifiers in either soil, but sequences related to archaeal nitrifiers were found in control soils. The ratio of fungi to bacteria did not change in the N-amended soils, but the ratio of archaea to bacteria dropped from 20% to less than 1% in the N-amended plots. Comparisons of aliphatic and aromatic carbon compounds, two broad categories of soil carbon compounds, revealed no between treatment differences. However, G-lignins were found in higher relative abundance in the fertilized soils, while proteins were detected in lower relative abundance. Finally, the activities of two soil enzymes involved in N cycling changed in response to chronic N amendments. These results suggest that chronic N fertilization induces significant shifts in soil carbon dynamics that correspond to shifts in microbial community structure and function.     

Dissimilar responses of fungal and bacterial communities to soil transplantation simulating abrupt climate changes

Both fungi and bacteria play essential roles in regulating soil carbon cycling. To predict future carbon stability, it is imperative to understand their responses to environmental changes, which is subject to large uncertainty. As current global warming is causing range shifts toward higher latitudes, we conducted three reciprocal soil transplantation experiments over large transects in 2005 to simulate abrupt climate changes. Six years after soil transplantation, fungal biomass of transplanted soils showed a general pattern of changes from donor sites to destination, which were more obvious in bare fallow soils than in maize cropped soils. Strikingly, fungal community compositions were clustered by sites, demonstrating that fungi of transplanted soils acclimatized to the destination environment. Several fungal taxa displayed sharp changes in relative abundance, including Podospora, Chaetomium, Mortierella and Phialemonium. In contrast, bacterial communities remained largely unchanged. Consistent with the important role of fungi in affecting soil carbon cycling, 8.1%–10.0% of fungal genes encoding carbon‐decomposing enzymes were significantly (p < 0.01) increased as compared with those from bacteria (5.7%–8.4%). To explain these observations, we found that fungal occupancy across samples was mainly determined by annual average air temperature and rainfall, whereas bacterial occupancy was more closely related to soil conditions, which remained stable 6 years after soil transplantation. Together, these results demonstrate dissimilar response patterns and resource partitioning between fungi and bacteria, which may have considerable consequences for ecosystem‐scale carbon cycling.     

Impact of postfire logging on soil bacterial and fungal communities and soil biogeochemistry in a mixed-conifer forest in central Oregon

Plant and Soil - Postfire logging recoups the economic value of timber killed by wildfire, but whether such forest management activity supports or impedes forest recovery in stands differing in...     

Impacts of nursery-based propagation and out-planting on coral-associated bacterial communities

Coral Reefs - Efforts to manage coral reef declines are increasingly turning towards in situ propagation of corals to aid reef recovery. Understanding the factors that influence...     

Effect of continuous olive mill wastewater applications, in the presence and absence of nitrogen fertilization, on the structure of rhizosphere–soil fungal communities

Olive mill wastewater (OMW) is rich in potentially toxic organics precluding its disposal into water receptors. However, land application of diluted OMW may result in safe disposal and fertilization. In order to investigate the effects of OMW on the structure of soil fungal groups, OMW was applied daily to pepper plants growing in a loamy sand and a sandy loam at two doses for a period of 3 months (total OMW equivalents 900 and 1800 m³ ha⁻¹). Nitrogen (N) fertilization alleviated N scarcity and considerably enhanced plant biomass production; however, when applied in combination with the high OMW dose, it induced plant stress. OMW applications resulted in marked changes in the denaturing gradient gel electrophoresis patterns of soil basidiomycete communities, while concurrent N fertilization reduced these effects. In contrast, the ascomycete communities required N fertilization to respond to OMW addition. Cloning libraries for the basidiomycete communities showed that Cryptococcus yeasts and Ceratobasidium spp. dominated in the samples treated with OMW. In contrast, certain plant pathogenic basidiomycetes such as Thanatephorus cucumeris and Athelia rolfsii were suppressed. The observed changes may be reasonably explained by the capacity of OMW to enrich soils in organic substrates, to induce N immobilization and to directly introduce OMW-derived basidiomycetous yeasts.     

施肥方式对紫色土土壤异养呼吸的影响

采用静态暗箱-气相色谱法于2010年12月至2011年10月对不同施肥方式下的紫色土土壤呼吸进行了研究,以揭示施肥方式对紫色土异养呼吸的影响。结果表明:施肥可对土壤异养呼吸产生激发效应。施肥后第5天出现峰值,猪厩肥处理的异养呼吸峰值为2356.8 mg CO2m-2h-1,显著高于秸秆配施氮磷钾(970.1 mgCO2m-2h-1)和常规氮磷钾处理(406.8 mgCO2m-2h-1)(P0.01);小麦季常规氮磷钾、猪厩肥和秸秆配施氮磷钾处理的平均土壤异养呼吸速率为212.9、285.8和305.8mgCO2m-2h-1,CO2排放量为255.1、342.3和369.5 gC/m2,玉米季为408.2、642.8和446.4 mgCO2m-2h-1,CO2排放量为344.7、542.8和376.9 gC/m2,玉米季土壤异养呼吸平均速率及CO2排放量均高于小麦季。全年平均土壤异养呼吸速率分别为310.6、446.3和377.4 mg CO2m-2h-1,CO2排放总量分别为599.8、885.1和746.4 gC/m2。猪厩肥对土壤异养呼吸速率和CO2排放量的影响最大,秸秆配施氮磷钾肥次之,氮磷钾肥最小,说明有机物料的投入是紫色土土壤异养呼吸速率的主要调控措施,低碳氮比的有机物料能促进土壤异养呼吸和CO2的排放。猪厩肥和秸秆配施氮磷钾肥处理相应地表和地下5 cm温度的Q10值分别为2.64、1.88和2.77、1.99,表明低碳氮比的有机物料还能增加土壤异养呼吸Q10值,使土壤异养呼吸速率对温度的敏感性加强。     

Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape

Background

The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.

Methodology/Principal Findings

Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.

Conclusions/Significance

Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.     

Rhizosphere soil bacterial communities and nitrogen cycling affected by deciduous and evergreen tree species

Deciduous and evergreen trees differ in their responses to drought and nitrogen (N) demand. Whether or not these functional types affect the role of the bacterial community in the N cycle during drought remains uncertain. Two deciduous tree species (Alnus cremastogyne, an N₂‐fixing species, and Liquidambar formosana) and two evergreen trees (Cunninghamia lanceolata and Pinus massoniana) were used to assess factors in controlling rhizosphere soil bacterial community and N cycling functions. Photosynthetic rates and biomass production of plants, 16S rRNA sequencing and N‐cycling‐related genes of rhizosphere soil were measured. The relative abundance of the phyla Actinobacteria and Firmicutes was higher, and that of Proteobacteria, Acidobacteria, and Gemmatimondaetes was lower in rhizosphere soil of deciduous trees than that of evergreen. Beta‐diversity of bacterial community also significantly differed between the two types of trees. Deciduous trees showed significantly higher net photosynthetic rates and biomass production than evergreen species both at well water condition and short‐term drought. Root biomass was the most important factor in driving soil bacterial community and N‐cycling functions than total biomass and aboveground biomass. Furthermore, 44 bacteria genera with a decreasing response and 46 taxa showed an increased response along the root biomass gradient. Regarding N‐cycle‐related functional genes, copy numbers of ammonia‐oxidizing bacteria (AOB) and autotrophic ammonia‐oxidizing archaea (AOA), N₂ fixation gene (nifH), and denitrification genes (nirK, nirS) were significantly higher in the soil of deciduous trees than in that of the evergreen. Structural equation models explained 50.2%, 47.6%, 48.6%, 49.4%, and 37.3% of the variability in copy numbers of nifH, AOB, AOA, nirK, and nirS, respectively, and revealed that root biomass had significant positive effects on copy numbers of all N‐cycle functional genes. In conclusion, root biomass played key roles in affecting bacterial community structure and soil N cycling. Our findings have important implications for our understanding of plants control over bacterial community and N‐cycling function in artificial forest ecosystems.     

葡萄连作对土壤细菌和真菌种群的影响

分别采集种植葡萄30年的连作园和3年的新植园根围土、非根围土及葡萄园周边的空地土壤,采用PCR DGGE技术,研究葡萄连作对土壤细菌和真菌种群结构及多样性的影响,并对分离出的优势种扩增条带进行测序.结果表明：葡萄连作后土壤细菌和真菌的多样性增加,且根围土壤的微生物多样性高于非根围土壤.聚类分析显示：葡萄长期连作后根围与非根围土壤细菌和真菌的种群结构趋于一致,两者不同于空地土壤;而短期种植葡萄的根围土壤细菌和真菌的种群结构不同于非根围土壤和空地土壤.与新植园相比,连作园根围土壤中微生物种群结构发生较大变化,细菌中Flavobacterium sp.（DQ339585）和Bacillus sp.（AY039821）种群数量减少,Pedobacter sp.（AJ871084）种群数量增多;真菌中Omphalina farinolens（EF413029）出现,Pestalotiopsis sp.(DQ657877,DQ657875,DQ657871）、Phacidium lacerum（DQ470976）和Lecythophora decumbens（AF353597）种群数量减少,Pilidium acerinum voucher（AY48709）种群数量增多.其中Bacillus sp.、Flavobacterium sp.和Pestalotiopsis sp.对病原菌具有颉颃作用,连作园根围土中上述微生物种群数量的减少,不利于葡萄对病原菌的颉颃;Pilidium acerinum voucher数量的增加可能与葡萄连作后病害加重有关.