Oomycetes along a 120,000 year temperate rainforest ecosystem development chronosequence

The occurrence of plant-associated oomycetes in natural ecosystems and particularly during long-term ecosystem development is largely unknown. Using DNA sequencing, we investigated the frequency and host relationships of plant-root-associated oomycete communities along a 120 000 y glacial chronosequence, comprising site ages with rapid compositional change (“early succession”; 5–70 y old soil); relatively stable higher-diversity sites (“mature”, 280–12000 y); and ancient, nutrient-limited soils with declining plant biomass and stature (“retrogression”, 60 000, 120 000 y). Plant-associated oomycetes were frequent in early successional sites, occurring in 38–65% of plant roots, but rare (mean 3%) in all older ecosystems. Oomycete OTUs occurred non-randomly with plant host species, and were more frequent on those plant species that declined most strongly in abundance between ecosystem ages. While oomycetes were common in early succession, their absence in older sites suggests a limited role in later stages of ecosystem development.     

Agronomic Practices for Improving Gentle Remediation of Trace Element-Contaminated Soils

The last few decades have seen the rise of Gentle soil Remediation Options (GRO), which notably include in situ contaminant stabilization (“inactivation”) and plant-based (generally termed “phytoremediation”) options. For trace element (TE)-contaminated sites, GRO aim to either decrease their labile pool and/or total content in the soil, thereby reducing related pollutant linkages. Much research has been dedicated to the screening and selection of TE-tolerant plant species and genotypes for application in GRO. However, the number of field trials demonstrating successful GRO remains well below the number of studies carried out at a greenhouse level. The move from greenhouse to field conditions requires incorporating agronomical knowledge into the remediation process and the ecological restoration of ecosystem services. This review summarizes agronomic practices against their demonstrated or potential positive effect on GRO performance, including plant selection, soil management practices, crop rotation, short rotation coppice, intercropping/row cropping, planting methods and plant densities, harvest and fertilization management, pest and weed control and irrigation management. Potentially negative effects of GRO, e.g., the introduction of potentially invasive species, are also discussed. Lessons learnt from long-term European field case sites are given for aiding the choice of appropriate management practices and plant species.     

Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health

Background

To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known.

Methodology/Principal Findings

We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH.

Conclusions/Significance

After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.     

Effects of long-term management practices on grassland plant assemblages in Mediterranean cork oak silvo-pastoral systems

The assessment of the effects of long-term management practices is relevant in understanding the current patterns of plant assemblages in semi-natural ecosystems. We hypothesized that the variety of management practices across different farming systems under the same ecological conditions directly and indirectly shapes these patterns via the long-term changes induced in soil features. The aims of this paper were to evaluate the influence of two sets of variables describing long-term management practices and soil features on plant assemblages and their importance in the context of Mediterranean silvo-pastoral systems. The analysis of variance revealed that richness and grazing value were not affected at all by grazing livestock species and soil tillage frequency and that they both showed relatively high absolute values for the specific context under study. Trifolium subterraneum was a key species in contributing to grassland grazing value and habitat biodiversity. The Canonical Correspondence Analysis highlighted the influence of management practices and soil features on plant assemblage composition, which was significantly affected by grazing livestock species and stocking rate and by soil pH and K content. The Redundancy Analysis showed that soil pH and related features were in turn affected by stocking rate, supporting our hypothesis that management practices influenced plant assemblage composition directly and indirectly via their long-term effects on soil features. The results also highlighted that a systemic analytical perspective applied at a grazing system scale can be effective in addressing sustainable grassland management issues in Mediterranean silvo-pastoral systems.     

Adaptive Long-Term Monitoring of Soil Health in Metal Phytostabilization: Ecological Attributes and Ecosystem Services Based on Soil Microbial Parametersxs

Phytostabilization is a promising option for the remediation of metal contaminated soils which requires the implementation of long-term monitoring programs. We here propose to incorporate the paradigm of “adaptive monitoring”, which enables monitoring programs to evolve iteratively as new information emerges and research questions change, to metal phytostabilization. Posing good questions that cover the chemical, toxicological and ecological concerns associated to metal contaminated soils is critical for an efficient long-term phytostabilization monitoring program. Regarding the ecological concerns, soil microbial parameters are most valuable indicators of the effectiveness of metal phytostabilization processes in terms of recovery of soil health. We suggest to group soil microbial parameters in higher-level categories such as “ecological attributes” (vigor, organization, stability) or “ecosystem services” in order to facilitate interpretation and, most importantly, to provide long-term phytostabilization monitoring programs with the required stability through time against changes in techniques, methods, interests, etc. that will inevitably occur during the monitoring program. Finally, a Phytostabilization Monitoring Card, based on both ecological attributes and ecosystem services, for soil microbial properties is provided.     

Fish as proxies of ecological and environmental change

Anthropogenic impacts have shifted aquatic ecosystems far from prehistoric baseline states; yet, understanding these impacts is impeded by a lack of available long-term data that realistically reflects the organisms and their habitats prior to human disturbance. Fish are excellent, and largely underused, proxies for elucidating the degree, direction and scale of shifts in aquatic ecosystems. This paper highlights potential sources of qualitative and quantitative data derived from contemporary, archived and ancient fish samples, and then, using key examples, discusses the types of long-term temporal information that can be obtained. This paper identifies future research needs with a focus on the Southern Hemisphere, as baseline shifts are poorly described relative to the Northern Hemisphere. Temporal data sourced from fish can improve our understanding of how aquatic ecosystems have changed, particularly when multiple sources of data are used, enhancing our ability to interpret the current state of aquatic ecosystems and establish effective measures to safeguard against further adverse shifts. The range of biological, ecological and environmental data obtained from fish can be integrated to better define ecosystem baseline states on which to establish policy goals for future conservation and exploitation practices.     

Woodland restoration on agricultural land: long‐term impacts on soil quality

Woodland restoration is underway globally to counter the negative soil quality and ecological impacts of agricultural expansion and woodland fragmentation, and restore or enhance biodiversity, ecosystem functions and services. However, we lack information about the long‐term effects of woodland restoration on agricultural soils, particularly at temporal scales meaningful to woodland and soil development. This study utilized soil and earthworm sampling across a chronosequence of sites transitioning from “agricultural land” to “secondary woodland” (50–110 years) and “ancient woodland” (>400 years), with the goal of quantifying the effects of woodland restoration on agricultural land, on key soil quality parameters (soil bulk density, pH, carbon and nitrogen stocks, and earthworm abundance, biomass, species richness and diversity). Broad‐leaved woodland restoration led to significantly greater soil organic carbon (SOC) stocks compared to arable land, and young (50–60 years) secondary woodland increased earthworm species and functional diversity compared to both arable and pasture agricultural land. SOC stocks in secondary broad‐leaved woodlands (50–110 years) were comparable to those found in long‐term ancient woodlands (>400 years). Our findings show that broad‐leaved woodland restoration of agricultural land can lead to meaningful soil ecological improvement and gains in SOC within 50–110 years, and provide intel on how restoration activities may be best targeted to maximize soil quality and functions.     

Restoration of Biodiversity and Ecosystem Services on Agricultural Land

Cultivation and cropping are major causes of destruction and degradation of natural ecosystems throughout the world. We face the challenge of maintaining provisioning services while conserving or enhancing other ecosystem services and biodiversity in agricultural landscapes. There is a range of possibilities within two types of intervention, namely “land sharing” and “land separation”; the former advocates the enhancement of the farmed environment, but the latter a separation between land designated for farming versus conservation. Land sharing may involve biodiversity-based agricultural practices, learning from traditional farming, changing from conventional to organic agriculture and from “simple” crops and pastures to agro-forestry systems, and restoring or creating specific elements to benefit wildlife and particular services without decreasing agricultural production. Land separation in the farmland context involves restoring or creating non-farmland habitat at the expense of field-level agricultural production—for example, woodland on arable land. Restoration by land sharing has the potential to enhance agricultural production, other ecosystem services and biodiversity at both the field and landscape scale; however, restoration by land separation would provide these benefits only at the landscape scale. Although recent debate has contrasted these approaches, we suggest they should be used in combination to maximize benefits. Furthermore, we suggest “woodland islets”, an intermediate approach between land abandonment and farmland afforestation, for ecological restoration in extensive agricultural landscapes. This approach allows reconciliation of farmland production, conservation of values linked to cultural landscapes, enhancement of biodiversity, and provision of a range of ecosystem services. Beyond academic research, restoration projects within agricultural landscapes are essential if we want to halt environmental degradation and biodiversity loss.     

Mycorrhizas and mycorrhizal fungal communities throughout ecosystem development

Background and scope

Plant communities and underlying soils undergo substantial, coordinated shifts throughout ecosystem development. However, shifts in the composition and function of mycorrhizal fungi remain poorly understood, despite their role as a major interface between plants and soil. We synthesise evidence for shifts among mycorrhizal types (i.e., ectomycorrhizas, arbuscular and ericoid mycorrhizas) and in fungal communities within mycorrhizal types along long-term chronosequences that include retrogressive stages. These systems represent strong, predictable patterns of increasing, then declining soil fertility during ecosystem development, and are associated with coordinated changes in plant and fungal functional traits and ecological processes.

Conclusions

Mycorrhizal types do not demonstrate consistent shifts through ecosystem development. Rather, most mycorrhizal types can dominate at any stage of ecosystem development, driven by biogeography (i.e., availability of mycorrhizal host species), plant community assembly, climate and other factors. In contrast to coordinated shifts in soil fertility, plant traits and ecological processes throughout ecosystem development, shifts in fungal communities within and among mycorrhizal types are weak or idiosyncratic. The consequences of these changes in mycorrhizal communities and their function for plant–soil feedbacks or control over long-term nutrient depletion remain poorly understood, but could be resolved through empirical analyses of long-term soil chronosequences.     

短花针茅荒漠草原土壤微生物群落组成及结构

为详细了解内蒙古短花针茅荒漠草原生态系统中土壤微生物群落组成与结构。对其土壤中微生物的总DNA提取后,采用高通量测序技术对土壤中细菌的16Sr DNA和真菌的ITS基因进行了序列测定,分析了短花针茅荒漠草原土壤中微生物群落结构特征。结果表明,共获得细菌OTUs13711个,真菌OTUs 5929个。物种分类显示,细菌种类隶属于29门57纲111目191科485属,其中优势类群为Gammaproteobacteria和Thermoleophilia,它们的相对丰度分别为32.68%和26.83%。真菌隶属于4门16纲45目78科105属,优势类群为Ascomycota和Basidiomycota,它们的相对丰度分别为35.76%和25.90%。土壤中细菌群落的多样性和丰富度均高于真菌。     

Comparing the recovery of richness,structure, and biomass in naturally regrowing and planted reforestation

The clearing of natural vegetation for agriculture has reduced the capacity of natural systems to provide ecosystem functions. Ecological restoration can restore desirable ecosystem functions, such as creating habitat for animal conservation and carbon sequestration as woody biomass. In order to maintain these beneficial ecosystem functions, restoration projects need to mature into self‐perpetuating communities. Here we compared the ecological attributes of two types of restoration, “active” tree plantings with “passive” natural forest regeneration (“natural regrowth”) to existing remnant vegetation in a cleared agricultural landscape. Specifically, we measured differences between forest categories in factors that may predict future restoration failure or ecosystem collapse: aboveground plant biomass and biomass accrual over time (for regrowing stands), plant density and size class distributions, and diversity of functional groups based on seed dispersal and growth strategy traits. We found that natural regrowth and planted forests were similar in many ecological characteristics, including biomass accrual. Despite this, planted stands contained fewer tree recruit and shrub individuals, which may be due to limited recruitment in plantings. If this continues, these forests may be at risk of collapsing into nonforest states after mature trees senesce. Lower shrub density and richness of mid‐story trees may lead to lower structural complexity in planting plots, and alongside lower richness of fleshy‐fruited plant species may reduce animal resources and animal use of the restored stand. In our study region, natural regrowth may result in restored woodland communities with greater conservation and carbon mitigation value.     

Multifunctionality debt in global drylands linked to past biome and climate

Past vegetation and climatic conditions are known to influence current biodiversity patterns. However, whether their legacy effects affect the provision of multiple ecosystem functions, that is, multifunctionality, remains largely unknown. Here we analyzed soil nutrient stocks and their transformation rates in 236 drylands from six continents to evaluate the associations between current levels of multifunctionality and legacy effects of the Last Glacial Maximum (LGM) desert biome distribution and climate. We found that past desert distribution and temperature legacy, defined as increasing temperature from LGM, were negatively correlated with contemporary multifunctionality even after accounting for predictors such as current climate, soil texture, plant species richness, and site topography. Ecosystems that have been deserts since the LGM had up to 30% lower contemporary multifunctionality compared with those that were nondeserts during the LGM. In addition, ecosystems that experienced higher warming rates since the LGM had lower contemporary multifunctionality than those suffering lower warming rates, with a ~9% reduction per extra degree Celsius. Past desert distribution and temperature legacies had direct negative effects, while temperature legacy also had indirect (via soil sand content) negative effects on multifunctionality. Our results indicate that past biome and climatic conditions have left a strong “functionality debt” in global drylands. They also suggest that ongoing warming and expansion of desert areas may leave a strong fingerprint in the future functioning of dryland ecosystems worldwide that needs to be considered when establishing management actions aiming to combat land degradation and desertification.     

黑河中游荒漠绿洲区土地利用的土壤养分效应

土地利用影响地表覆被状况和生态过程,关系到土壤肥力与土壤碳库功能"源-汇"关系的改变。黑河中游甘州区和临泽县是我国西北干旱区典型的荒漠绿洲区,以土壤表层(0-20 cm)养分变化为对象,利用2011-2012年甘州区和临泽县的土壤野外调查数据和该区全国第二次土壤普查数据,对两时期土壤表层养分(土壤有机质、全氮、全磷、全钾及pH值)的变化特征进行比较研究。结果表明:研究区土壤有机质、全磷含量分别降低了3.54%和12.5%;而全氮、全钾和pH值分别增加了74.4%、98.2%和4.9%。全国第二次土壤普查时期,荒漠、耕地与草地三者在各土壤养分上没有显著差异,但林地在土壤有机质、全氮、全钾上显著高于前三者。2011-2012年,耕地土壤的全磷、全氮与其它土地利用存在显著差异。土地利用的保持和改变对土壤养分变化有着重要影响,耕地的长期耕作使得土壤有机质含量降低4.94%,全氮增加86.93%,全磷减少5.02%,土壤碱性增强;荒漠植被的自然演替使土壤有机质含量增加66.21%,全氮增加71.70%,全磷含量减少37.33%,土壤碱性变弱。所以,耕地扩张及其长期耕作活动将导致地力退化并有盐碱化风险,而荒漠等自然生态系统保护有利于土壤肥力的改善和土壤固碳功能的发挥。     

运用Century模型模拟管理对鼎湖山森林生产力的影响

马毛松林是我国华南地区最主要的森林植被类型。为了寻求科学合理的马尾松林利用方式,我们运用Ｃｅｎｔｕｒｙ模型对马尾松林在不同管理措施下包括在严格保护措施下的演替各阶段的土壤有机质、Ｎ含量以及生产力进行了模拟预测。结果表明,除去地被物和林下层植物会使土壤肥力降低,导致生产力下降。除去的生物量越多,生产力降低的幅度越大。因此,此种利用方式不符合持续发展的要求,建议予以改变。应用Ｃｅｎｔｕｒｙ模型对鼎湖山     

生态恢复中生态系统服务的演变:趋势、过程与评估

经过10余年的发展,生态系统服务已经成为生态恢复研究关注的前沿和热点。生态恢复改变了生态系统格局与过程,对生态系统服务的产生和提供具有重要影响。但是目前对于生态系统服务在生态恢复过程中的演化仍缺少系统性研究。对国内外相关研究的最新成果进行综述,总结了生态系统服务评估中框架的构建和方法的选择(参数转移法、系统模型法和定量指标法),介绍了生态恢复对生态系统服务的促进作用、生态系统服务的演变过程以及不同生态系统服务间的协同与权衡关系,分析了社会经济因素对生态恢复和生态系统服务维持的影响。最后结合我国生态恢复实践,提出未来生态恢复和生态系统服务研究可以从深化作用机制研究、推动服务评估创新、增强研究成果应用3方面深化和拓展。     

Disturbances by desert rodents are more strongly associated with spatial changes in soil texture than woody encroachment

Background and Aims

Soil texture is an important determinant of ecosystem structure and productivity in drylands, and may influence animal foraging and, indirectly, plant community composition.

Methods

We measured the density and composition of surface disturbances (foraging pits) of small, soil-foraging desert vertebrates in shrubland and grasslands, both with coarse- and fine-textured soils. We predicted that the density and functional significance of disturbances would be related more to differences in texture than shrub encroachment.

Results

Soil texture had a stronger influence on animal foraging sites than shrub encroachment. There were more disturbances, greater richness and abundance of trapped seed, and greater richness of germinating plants on coarse- than fine-textured soils. Pits in coarse soils trapped 50 % more litter than those in finer soils. Apart from slightly more soil removal and greater litter capture in shrubland pits, there were no effects of encroachment.

Conclusions

Although the process of woody encroachment has been shown to have marked effects on some ecosystem properties, it is likely to have a more subordinate effect on surface disturbances and therefore their effects on desert plant communities than soil texture. Our results highlight the importance of animal activity in shaping desert plant communities, and potentially, in maintaining or reinforcing shrub dominant processes.     

西北干旱荒漠区生态系统可持续管理理念与模式

结合对西北干旱区水资源短缺、资源开发中的生态与经济矛盾突出、气候变暖可能加剧干旱区荒漠化以及生态水权与长效保障机制缺失等问题的分析诊断,探讨了荒漠区生态系统可持续管理面临的问题与难点,分析提出了荒漠生态系统植被保育的生态水位与生态阈值,阐述了荒漠-绿洲过渡带生态融合以及绿洲生态系统安全的生态防护梯度等干旱区生态系统管理理念;结合干旱区极端环境自然条件,在多年现场试验基础上,研发集成了退化群落改造与生态多样性构建技术、植物群落结构优化配置、组装与生态融合技术、生态系统恢复水分利用与生态自维持技术以及胡杨萌蘖更新技术等多种适宜荒漠植被恢复与重建的技术模式,并进行了成功实践和试验示范,为干旱荒漠区生态系统可持续管理提供了重要科技支撑。     

A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes

Agricultural intensification is a leading cause of global biodiversity loss, which can reduce the provisioning of ecosystem services in managed ecosystems. Organic farming and plant diversification are farm management schemes that may mitigate potential ecological harm by increasing species richness and boosting related ecosystem services to agroecosystems. What remains unclear is the extent to which farm management schemes affect biodiversity components other than species richness, and whether impacts differ across spatial scales and landscape contexts. Using a global metadataset, we quantified the effects of organic farming and plant diversification on abundance, local diversity (communities within fields), and regional diversity (communities across fields) of arthropod pollinators, predators, herbivores, and detritivores. Both organic farming and higher in‐field plant diversity enhanced arthropod abundance, particularly for rare taxa. This resulted in increased richness but decreased evenness. While these responses were stronger at local relative to regional scales, richness and abundance increased at both scales, and richness on farms embedded in complex relative to simple landscapes. Overall, both organic farming and in‐field plant diversification exerted the strongest effects on pollinators and predators, suggesting these management schemes can facilitate ecosystem service providers without augmenting herbivore (pest) populations. Our results suggest that organic farming and plant diversification promote diverse arthropod metacommunities that may provide temporal and spatial stability of ecosystem service provisioning. Conserving diverse plant and arthropod communities in farming systems therefore requires sustainable practices that operate both within fields and across landscapes.     

Quantifying ecological memory during forest succession: A case study from lower subtropical forest ecosystems in South China

The concept of ecological memory provides a new perspective for research on forest succession by including historical factors and the initial state of ecological processes. However, there are still significant gaps between the concept and its application. We selected nine proxy indicators (plant species, soil seed banks, soil microbes, soil animals, birds, soil age, soil pollen, soil mineral distribution, and light environment) and developed a method to quantify ecological memory and succession in a subtropical forest succession in South China. Taking the climax-monsoon evergreen broad-leaved forest as the reference ecosystem, we found that ecological memory increased nonlinearly and accumulated following a specific assembly rule during succession. Memory concerning major soil microbes and soil animals, which improve the soil substrate, mainly accumulated from the initial to the early successional stage. Memory concerning the number of bird species and the availability of light, which ensure a source of regenerative seeds and the survival of understory seedlings, mainly accumulated from the early to middle successional stages. Memory concerning vegetation and soil seed banks mainly accumulated late in succession, guaranteeing that the ecosystem would reach the regional climax stage. Prospective memory was greater than retrospective memory in every successional stage except the late stage, which indicated that all stages but the late stage were undergoing progressive succession. Our study demonstrates that the concept of ecological memory and the proposed evaluation framework are useful for guiding research on succession and restoration, and especially for assessing how “far” a restored ecosystem is from a reference ecosystem or how far a restored ecosystem has deviated from its natural succession trajectory.     

A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming

Background

Traditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, in the sight of “reverse desertification”. Nevertheless, the impact of desert farming practices on the diversity and abundance of the plant associated microbiome is poorly characterized, including its functional role in supporting plant development under drought stress.

Methodology/Principal Findings

We assessed the structure of the microbiome associated to the drought-sensitive pepper plant (Capsicum annuum L.) cultivated in a traditional Egyptian farm, focusing on microbe contribution to a crucial ecosystem service, i.e. plant growth under water deficit. The root system was dissected by sampling root/soil with a different degree of association to the plant: the endosphere, the rhizosphere and the root surrounding soil that were compared to the uncultivated soil. Bacterial community structure and diversity, determined by using Denaturing Gradient Gel Electrophoresis, differed according to the microhabitat, indicating a selective pressure determined by the plant activity. Similarly, culturable bacteria genera showed different distribution in the three root system fractions. Bacillus spp. (68% of the isolates) were mainly recovered from the endosphere, while rhizosphere and the root surrounding soil fractions were dominated by Klebsiella spp. (61% and 44% respectively). Most of the isolates (95%) presented in vitro multiple plant growth promoting (PGP) activities and stress resistance capabilities, but their distribution was different among the root system fractions analyzed, with enhanced abilities for Bacillus and the rhizobacteria strains. We show that the C. annuum rhizosphere under desert farming enriched populations of PGP bacteria capable of enhancing plant photosynthetic activity and biomass synthesis (up to 40%) under drought stress.

Conclusions/Significance

Crop cultivation provides critical ecosystem services in arid lands with the plant root system acting as a “resource island” able to attract and select microbial communities endowed with multiple PGP traits that sustain plant development under water limiting conditions.