Deterministic processes dominate nematode community structure in the Fynbos Mediterranean heathland of South Africa

In many ecosystems, the factors that determine landscape-scale community structure of soil nematodes are poorly understood. We were interested in discovering whether deterministic or stochastic factors dominate nematode community variation. We used a novel metagenetic approach to investigate variation in nematode community structure in the Fynbos vegetation of South Africa. We compared 23 samples of soil nematode communities from five different Fynbos landscapes. Nematode DNA was 454-pyrosequenced for the 18S rRNA gene. We investigated the community structure, diversity, and the relative role of both deterministic (niche-based) and neutral processes may play in delimiting the nematode phylogenetic community structure in different Fynbos vegetation types. Nematode diversity showed no relationship to any measured soil parameter. The phylogenetic signal showed that more closely related types of nematodes in the Fynbos tended to co-occur more often than would be expected by chance, demonstrating that (a) closely related lineages occupy similar niches spatially and (b) community variation is influenced more by determinism than stochasticity. The standardised beta mean nearest taxon distance (ses.βMNTD) index showed no association with vegetation type. Both ses.NTI (nearest taxon index) and ses.βMNTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of nematode communities. Furthermore, at local scale, the ses.NTI was significantly higher than null expectations, indicating that co-occurrence of related nematode lineages is determined by the differences in environmental conditions across the sites. We conclude that in the Fynbos there is niche overlap between closely related types of nematodes, that nematode speciation tends to occur conservatively into closely related niches, and that the phylogenetic community structure reveals that deterministic (rather than stochastic) processes are more important in delimiting the community assembly.     

黄土高原半干旱区不同林龄柠条人工林土壤线虫群落特征

为了解柠条人工林对半干旱地区脆弱生态环境的改善作用,在黄土高原柠条种植的重点区域——宁夏南部山区,选取4个林龄(4、14、24和34年生)的柠条人工林作为对象,调查林中土壤线虫群落的组成、结构与多样性特征,并分析它们与土壤理化性质之间的关系,探明黄土高原半干旱区柠条林植被恢复过程中土壤线虫群落的演变特征及其环境影响因素...     

Overview of organic amendments for management of plant-parasitic nematodes, with case studies from Florida

Organic amendments have been widely used for management of plant-parasitic nematodes. Relatively rapid declines in nematode population levels may occur when decomposing materials release toxic compounds, while longer-term effects might include increases in nematode antagonists. Improved crop nutrition and plant growth following amendment use may lead to tolerance of plant-parasitic nematodes. Results depend on a great variety of factors such as material used, processing/composting of material, application rate, test arena, crop rotation and agronomic practices, soil type, climate, and other environmental factors. Reasons for variable performance and interpretation of results from amendment studies are discussed. Case studies of amendments for nematode management are reviewed from Florida, where composts and crop residues are the most frequently used amendments. Plant growth was often improved by amendment application, free-living nematodes (especially bacterivores) were often stimulated, but suppression of plant-parasitic nematodes was inconsistent. Amendments were generally not as effective as soil fumigation with methyl bromide for managing root-knot nematodes (Meloidogyne spp.), and often population levels or galling of root-knot nematodes in amended plots did not differ from those in non-amended control plots. While amendments may improve plant growth and stimulate soil food webs, additional study and testing are needed before they could be used reliably for management of plant-parasitic nematodes under Florida conditions.     

公路源重金属对青藏高原高寒草甸土壤线虫群落的影响

为了解重金属对青藏高原高寒草甸土壤线虫群落的影响,在邦杰塘草原利用公路源重金属含量差异,采用高通量测序技术,分析重金属对高寒草甸土壤线虫群落多样性及群落组成的影响。结果表明：在重金属含量较低样本中,土壤线虫群落Shannon指数、Ace指数、Chao指数比重金属含量较高样本均要小,且整体上Shannon指数、Ace指数、Chao指数与重金属含量较高样本差异显著（P<0.05）。重金属含量升高改变了高寒草甸土壤线虫纲水平和目水平的群落结构,使近自然状况下的色矛纲（Chromadorea）、小杆目（Rhabdtida）优势土壤线虫群落转变为一类未分类线虫纲（unclassified_p_Nematoda）、一类未分类线虫目（unclassified_p_Nematoda）的优势土壤线虫群落。重金属Cu、Pb、Zn、Cd与线虫门（Nematoda）和刺嘴纲（Enoplea）正相关,但与色矛纲（Chromadorea）负相关,且对土壤线虫Chao指数的变异解释比例依次减小。研究表明土壤重金属含量对青藏高原高寒草甸土壤线虫群落多样性及组成产生很大影响,但仍需对高寒草甸区域进行系统的土壤线虫调查,并丰富土壤线虫生物信息数据库。     

Research collaborations can improve the use of organic amendments for plant-parasitic nematode management

The concept of utilizing organic amendments to manage plant-parasitic nematodes is not new, but the widespread implementation of this management practice has still not been realized. The use of organic amendments for plant-parasitic nematode management is a complex process requiring an understanding of the transformation and generation of active compounds. As a result, research endeavors to understand and maximize the use of this management practice require a multidisciplinary approach which draws upon the expertise of nematologists, microbiologists, natural product chemists and soil scientists. Factors that require analysis and clarification include lethal concentration levels of organic amendments necessary to kill nematodes; chemical composition of incorporation material; fate and exposure potential to nematodes of compounds released into the soil; and the influence of environmental factors (i.e., temperature, microbial community, soil type) on the activity of organic amendments. Examples of research conducted in a collaborative manner with rye (Secale cereale) and a biosolid amendment demonstrate the power of multidisciplinary research. Only through collaborative research can consistent and reliable nematode suppression with organic amendments be achieved.     

Higher taxa vs. functional guilds vs. trophic groups as indicators of soil nematode diversity and community structure

Biodiversity surrogates are often used in ecology to save money and time. One such widely used surrogacy method is the higher taxon approach, also known in the literature as taxonomic sufficiency. This approach has rarely been applied to microscopic organisms like soil microfauna, although there is a lack of detailed taxonomic knowledge regarding the latter. We tested taxonomic sufficiency for genus alpha and beta diversity, as well as for community structure of soil nematodes. We also tested whether the functional classifications of nematodes into functional guilds and trophic groups can serve as efficient indicators of nematode diversity and community structure. We used data from soil nematode communities from five different microhabitats (soil, soil moss, rock moss, low tree trunk moss and high tree trunk moss) in forested and non forested areas at five different stations (differing in elevation and aspect). Our results showed that both the higher taxon approach and the functional surrogacy approach could serve as reliable indicators of alpha and beta diversity. Furthermore, our community analysis of both taxonomic and functional composition identified that the variability at the finer scales, and namely the habitat structure, played the leading role in shaping nematode communities.     

Assessing Cross-disciplinary Efficiency of Soil Amendments for Agro-biologically, Economically, and Ecologically Integrated Soil Health Management

Preventive and/or manipulative practices will be needed to maintain soil's biological, physiochemical, nutritional, and structural health in natural, managed, and disturbed ecosystems as a foundation for food security and global ecosystem sustainability. While there is a substantial body of interdisciplinary science on understanding function and structure of soil ecosystems, key gaps must be bridged in assessing integrated agro-biological, ecological, economical, and environmental efficiency of soil manipulation practices in time and space across ecosystems. This presentation discusses the application of a fertilizer use efficiency (FUE) model for assessing agronomic, economic, ecological, environmental, and nematode (pest) management efficiency of soil amendments. FUE is defined as increase in host productivity and/or decrease in plant-parasitic nematode population density in response to a given fertilizer treatment. Using the effects of nutrient amendment on Heterodera glycines population density and normalized difference vegetative index (indicator of physiological activities) of a soybean cultivar 'CX 252', how the FUE model recognizes variable responses and separates nutrient deficiency and toxicity from nematode parasitism as well as suitability of treatments designed to achieve desired biological and physiochemical soil health conditions is demonstrated. As part of bridging gaps between agricultural and ecological approaches to integrated understanding and management of soil health, modifications of the FUE model for analyzing the relationships amongst nematode community structure, soil parameters (eg. pH, nutrients, %OM), and plant response to soil amendment is discussed.     

Soil amendment with dried weed leaves as non-chemical approach for the management of Meloidogyne incognita infecting tomato

In pot trial, dried ground weed leaves of Cynodon dactylon, Datura stramonium, Eichhomia crassipes, Emex spinosus, Ricinus communis and Sisymbrium irio were mixed with soil at the rate of 1, 3, 5 and 10 g/kg soil and compared their nematicidal potential with carbofuran as a standard against the root-knot nematode, M. incognita infecting tomato. In addition, their effects on growth rate of tomato plants were also investigated. The results showed that M. incognita populations in the soil and root galling were significantly suppressed when the dried leaves of the tested weeds at all rates were allowed to decompose in the soil. All amendments exhibited varying degree of reduction compared to control. The highest reduction was noticeable with the plants grown in Sisymbrium irio amended soil followed by Datura stramonium and Emex spinosus. In addition, employing high rate of the tested weeds gave higher activity in suppressing the nematode both in the soil and in tomato roots than using low rate. The data also indicated that all amendments at low rates significantly increased growth indices of tomato over control treatment, except Cynodon dactylon and Emex spinosus which decreased it, particularly in the shoot system. On the other hand, their high rates showed phytotoxic effects. These weed species may offer considerable promise as soil amendments for control of root-knot nematode, M. incognita.     

Preliminary study of the soil nematode community at Machu Picchu Station, King George Island, Antarctica

We studied the distribution and abundance of nematodes in one of the most extreme terrestrial environments in the world, at Machu Picchu, King George Island, off the coast of Admiralty Bay, Antarctica. We can report that the nematode community structure under the two most common plant covers was composed of three to four species. These species were found to belong functionally to microbial and omnivore/predator feeding types. Abundances of each of the nematode species were found to be negatively correlated to soil water content, generally decreasing their abundance with increasing soil water content. The results of this study demonstrate the importance of moisture availability to the nematode community and its species composition in this Antarctic soil ecosystem.     

典型黑土区农田土壤线虫群落的纬度分布格局及其驱动机制

东北黑土区是保障我国粮食安全的重要土壤资源, 了解该区域内农田土壤线虫的群落组成及其对环境驱动因子的响应机制, 对于研究黑土区农田土壤生态系统的生物多样性分布格局具有重要意义。2018年9月, 我们在42°50°‒49°08° N的典型黑土区采集了93个农田土壤样品, 利用形态学鉴定技术分析了土壤线虫群落的组成与结构。共鉴定出47个线虫属(相对丰度 > 1%), 其中食细菌线虫中的拟丽突属(Acrobeloides)是典型黑土区农田土壤中的优势属(相对丰度 > 5%)。土壤线虫总丰富度和总多度均随纬度增加而显著增加, 然而类似的变化趋势只出现在食细菌和杂食/捕食线虫中。土壤有机碳是影响土壤线虫丰富度和多度最为重要的环境因子, 其次是月平均温度。典型黑土区农田土壤线虫群落结构以47° N为分界线分为南部和北部两类, 主要归因于线虫群落中植物寄生和杂食/捕食线虫的相对多度在南、北特征属中存在差异。土壤pH值和容重分别是影响南部与北部黑土区线虫群落最重要的环境因子。本研究明确了典型黑土区农田土壤线虫群落的纬度分布格局及其与环境因素的关系, 可为揭示农业活动干扰下土壤生物对环境因子的响应机制提供基础数据和理论参考。     

Characteristics of soil nematode community along an age sequence of sandy desert soil cultivation in a marginal oasis of middle reaches of Heihe River

This paper studied the characteristics of soil nematode community following the conversion of native sandy desert soil to irrigated farmland in a marginal oasis of the middle reaches of Heihe River basin, aimed to approach the bioindicating function of soil nematodes in soil evolution process. A total of 27921 soil nematode individuals were captured, belonging to 25 families and 34 genera. The total number of nematodes increased gradually with increasing age of cultivation. At all sampling sites, bacterivores and plant parasites were the dominant trophic groups, and made up the main parts of nematode community in oasis farmland. Through the analysis of the evenness index (J) and dominance index (lambda) of nematode community, the ecosystems were found to be fragile for the farmlands having cultivated for 0, 10, and > 50 years. The maturity index MI2-5 and MMI decreased with increasing cultivation age, suggesting that the practice of agricultural use enhanced the disturbance on farmland. The soil properties changed significantly after 10 years of cultivation, which was at a significant change stage for the structure stability of soil ecosystems. The characteristics of soil nematode community could be used as the bioindicator of soil evolution following the conversion of native desert soil to irrigated farmland.     

Response of soil nematode community structure and diversity to long-term land use in the black soil region in China

Soil nematodes are sensitive to environmental changes and are used widely as indicators of soil conditions. The community structure and diversity of soil nematodes were studied in different long-term land use regimes in the black soil area in Northeast China. The land use regimes were maintained for 22?years, and included crop land (CL), grass land (GL) and bare land (BL). Soil samples were taken throughout the growing season, and nematodes were extracted and identified. A total of 39 nematode genera with relative abundance over 0.1?% were identified. Heterodera was the dominant genus in CL; Boleodorus was the dominant genus in GL, and Boleodorus, Eucephalobus and Filenchus were the dominant genera in BL. Land use had a significant effect on abundance of all soil nematode tropic groups and ecological indices. Sampling time had an effect on soil nematode abundance, but only on three of the eight nematode ecological indices MI (maturity index of free-living nematode), CI (channel index) and EI (enrichment index). SR (species richness index) was highest in GL where plant species diversity was also high. The CI was the highest in BL among three land uses, which means the soil food web dominated, with fungal decomposition channels in BL. Soil nematode community structure and diversity was shown to be an effective and informative tool for analyzing ecological aspects of land use in black soil regions. The data are inconclusive as to whether the effect of land use on soil nematode parameters is direct, or indirect via inducing changes in soil physicochemical properties.     

Organic and Inorganic Nitrogen Amendments to Soil as Nematode Suppressants

Inorganic fertilizers containing ammoniacal nitrogen or formulations releasing this form of N in the soil are most effective for suppressing nematode populations. Anhydrous ammonia has been shown to reduce soil populations of Tylenchorhynchus claytoni, Helicotylenchus dihystera, and Heterodera glycines. The rates required to obtain significant suppression of nematode populations are generally in excess of 150 kg N/ha. Urea also suppresses several nematode species, including Meloidogyne spp., when applied at rates above 300 kg N/ha. Additional available carbon must be provided with urea to permit soil microorganisms to metabolize excess N and avoid phytotoxic effects. There is a direct relation between the amount of "protein" N in organic amendments and their effectiveness as nematode population suppressants. Most nematicidal amendments are oil cakes, or animal excrements containing 2-7% (w:w) N; these materials are effective at rates of 4-10 t/ha. Organic soil amendments containing mucopolysaccharides (e.g., mycelial wastes, chitinous matter) are also effective nematode suppressants.     

宁南山区不同植被恢复方式下土壤线虫群落特征:形态学鉴定与高通量测序法比较

线虫是土壤食物网的重要组分, 也是土壤健康与生态系统恢复的重要指示生物, 因此准确测定线虫群落特征是发挥其生态指示作用的基础。传统线虫学研究多采用形态学鉴定方法, 但高通量测序技术近年来也逐渐受到重视。然而, 关于这两种方法的对比研究目前仍比较缺乏。本研究同时采用形态学鉴定和高通量测序法, 在黄土高原宁夏南部山区, 对不同植被恢复方式下(农田、自然恢复草地、柠条(Caragana korshinskii)人工林地和苜蓿人工草地)土壤线虫的数量、群落格局和生态指数进行了测定和比较。结果表明: (1)高通量测序仅能提供线虫类群的相对多度, 而形态学鉴定法能够测定土壤线虫的绝对多度, 后者测定结果表明3种植被恢复样地, 特别是自然恢复草地和柠条人工林地, 较农田具有更高的土壤线虫多度; (2)高通量测序法检获的线虫类群数(3纲4目26科42属)高于形态学鉴定法的测定结果(2纲3目18科27属), 但两种方法仅检获15个共有线虫属, 前者检测到的植物寄生线虫属数(22属)较后者(7属)显著增加, 而食细菌线虫和杂食-捕食线虫则相反; (3)在两种方法下, 相比农田, 3种植被恢复样地尤其是自然恢复草地和柠条人工林地, 其食微线虫的相对多度均显著下降, 而植物寄生线虫和杂食-捕食线虫的相对多度大幅上升, 这也导致线虫成熟度指数(MI)和植物寄生线虫指数(PPI)的提高及瓦斯乐卡指数(WI)的显著下降; (4)相比形态学鉴定法, 高通量测序法能检测到更丰富多样的植物寄生线虫, 在该方法下土壤线虫群落的组成、结构和生态指数在植被恢复样地与农田之间的差异也更为显著。综上所述, 采用形态学鉴定和高通量测序法测定的不同植被恢复方式下的线虫群落特征具有显著差异。     

Organic amendments increase phylogenetic diversity of arbuscular mycorrhizal fungi in acid soil contaminated by trace elements

In 1998, a toxic mine spill polluted a 55-km² area in a basin southward to Doñana National Park (Spain). Subsequent attempts to restore those trace element-contaminated soils have involved physical, chemical, or biological methodologies. In this study, the restoration approach included application of different types and doses of organic amendments: biosolid compost (BC) and leonardite (LEO). Twelve years after the last addition, molecular analyses of arbuscular mycorrhizal (AM) fungal communities associated with target plants (Lamarckia aurea and Chrysanthemum coronarium) as well as analyses of trace element concentrations both in soil and in plants were performed. The results showed an improved soil quality reflected by an increase in soil pH and a decrease in trace element availability as a result of the amendments and dosages. Additionally, the phylogenetic diversity of the AM fungal community increased, reaching the maximum diversity at the highest dose of BC. Trace element concentration was considered the predominant soil factor determining the AM fungal community composition. Thereby, the studied AM fungal community reflects a community adapted to different levels of contamination as a result of the amendments. The study highlights the long-term effect of the amendments in stabilizing the soil system.     

黄土高原半干旱区不同种植年限紫花苜蓿人工草地土壤微生物和线虫群落特征

建植紫花苜蓿人工草地是黄土高原植被恢复的重要措施之一。土壤微生物和线虫群落特征是评价和调控植被恢复的生态环境效应的重要依据。本研究在宁夏南部山区选取不同种植年限(1、2、6和12年)的紫花苜蓿人工草地为研究样地,以农田和天然草地作为对照,探索黄土高原人工草地植被恢复过程中土壤微生物和线虫群落的演变规律及其影响因素。结果表明: 1)种植苜蓿显著提高了土壤细菌群落的Chao1、ACE和Shannon多样性指数,并在种植苜蓿后第6年达到最高,但在种植6年和12年后真菌群落多样性降低;随着苜蓿种植年限的增加,真菌群落组成从农田逐渐向天然草地方向演变;2)土壤线虫数量与细菌群落多样性的变化趋势相同,在种植苜蓿后第6年出现峰值,该时期线虫群落结构组成与农田较相似,苜蓿12年样地则更接近天然草地;随着苜蓿种植年限的增加,食细菌线虫、植食性线虫比例总体呈上升趋势,食真菌线虫、杂食/捕食线虫比例呈下降趋势,土壤成熟度指数(MI)逐渐减小,植物寄生线虫指数(PPI)和线虫通路指数(NCR)则不断增大;3)在苜蓿人工草地植被恢复过程中,土壤有机碳、全氮和速效磷对土壤微生物群落结构影响较大,并进一步影响线虫群落结构;细菌和真菌群落优势类群和多样性与线虫的不同营养类群及生态指数之间存在密切联系,表明微生物群落结构与多样性对线虫群落具有显著影响;在不同种植年限苜蓿草地中,植物的生物量与多样性的变化可能通过影响土壤微生物与线虫食物资源状况从而引起其群落特征的改变。     

Organic amendments and land management affect bacterial community composition, diversity and biomass in avocado crop soils

Background and aims

The avocado-producing area of southern Spain includes conventional orchards and organic orchards that use different organic amendments. To gain insight into the effects of these amendments, physicochemical properties and microbial communities of the soil were analysed in a representative set of commercial and experimental orchards.

Methods

The population size of several groups of culturable microorganisms was determined by plating on different selective media. Bacterial community structure was studied by denaturing gradient gel electrophoresis (DGGE)

Results

Commercial composts showed the largest effects, especially the animal compost, enhancing the population sizes of some microbial groups and affecting bacterial community structure in superficial and deep soil layers. Moreover, animal and vegetal compost, manure and blood meal addition are related to high bacterial diversity in the superficial soil layer.

Conclusions

All of the organic amendments used in this study affect soil properties in one or more of the characteristics that were analysed. Culturable microbial population data revealed the most evident effects of some of the organic treatments. However, molecular analysis of soil bacterial communities by DGGE allowed the detection of the influence of all of the analysed amendments on bacterial community composition. This effect was stronger in the superficial layer of the avocado soil.     

不同植被类型的滩涂湿地土壤线虫群落特征

对江苏盐城湿地保护区内不同植被带土壤线虫的群落结构特征进行了研究.结果表明：调查共鉴定出20科39属,优势属和常见属的数量占总个体数的90%以上;不同植被类型的滩涂湿地土壤线虫总数存在明显差异性,线虫数量范围为每100 g干土79～449条,小麦地显著高于其他植被带,光滩地数量最少.线虫群落生态指数对植被带有不同的响应,土壤线虫群落多样性指数H、均匀度指数J在不同植被带的分布依次为：苇草带＞盐蒿带＞小麦地＞米草带＞光滩带,而优势度指数λ的分布为：光滩带＞米草带＞小麦地＞盐蒿带＞苇草带,表明光滩带的线虫群落多样性和稳定性小于其他植被带,土壤线虫群落趋于单一化;成熟度指数MI表现为保护区内未开垦植被带高于已开垦的小麦地,说明农田受外界干扰明显.不同植被带间的线虫群落结构存在显著差异,各植被带的最大贡献物种各不相同.土壤理化性状与线虫数量、营养类群、生态指数存在明显的相关关系.表明线虫群落的变化能很好地反映植被带生境的多样性,土壤线虫可作为湿地生态系统中一个重要的生物指示因子.     

基于高通量测序分析西藏北部高寒草甸不同深度土壤线虫群落分布特征

为了研究藏北高寒草甸土壤线虫多样性,于2017年8月,采用Illumina MiSeq测序技术,研究了西藏北部高寒草甸0—25 cm范围内不同深度土层的土壤线虫群落组成与结构特征。结果表明:5个不同深度共获得OTU 990个,隶属于3个纲,7个目,25个科,30个属,刺嘴纲Enoplea为共有优势土壤线虫群落;对样品进行Alpha多样性评价,计算Chao 1指数、Shannon指数和Ace指数,发现5—10 cm的土壤样品群落有较高的丰富度;属水平Heatmap图分析可知20—25、15—20、0—5、5—10、10—15 cm土壤线虫群落的组成相似性有一个递增的趋势。与不同深度藏北高山嵩草(盛长期)线虫群落结构相关性较大的土壤化学指标是K~+、含水率、有机质和Zn~(2+)。研究发现不同深度土壤线虫种类及丰度存在一定的差异,可为研究藏北高寒草地土壤线虫群落特点提供依据。     

Nematode Assemblages in Bauxite Residue with Different Restoration Histories

Bauxite residue disposal areas may be amended and re‐vegetated to facilitate the ecosystem restoration process. However, the development of the belowground system during restoration is frequently overlooked. In turn, although vegetation establishment on bauxite residue is well studied, virtually nothing is known about concurrent changes in the soil biota. In order to understand how different amendments and re‐vegetation influence the belowground community, we compared nematode assemblages from bauxite residues that differed in their treatment history (compost addition, gypsum addition, and time since re‐vegetation), and examined whether any differences were related to changes in soil properties. No nematodes were present in the unamended treatment, thus indicating a need for amelioration of substrate properties. However, there were differences in the nematode assemblage between the other amended treatments. The quantity of gypsum reduced nematode density, but had no effect on taxa richness or the Maturity Index in treatments amended in the same year. Nematode taxa richness and the Maturity Index were greatest in the treatment re‐vegetated earliest. Moreover, the Maturity Index was negatively correlated to soil pH and percentage Na. These findings indicate that sufficient amendment and re‐vegetation are crucial to address inhibitory characteristics of the residue and aid restoration of the belowground system in bauxite residues.