景观生态学与退化生态系统恢复

退化生态系统的恢复是一项艰巨任务,它需要考虑到所要恢复的退化生态系统的结构,多样性和其动态的整体性和长期性。现在对于退化生态系统恢复研究已经要使生态学家们关注受损生态系统的理论和实际问题。退化生态系统恢复所面临的挑战是理解和利用生态演替理论来完成并加速恢复进程。恢复的主要目标是建立一个自维持的,由不同的群落或生态系统组成的能够满足不同需要如生物保护和粮食生产需要的景观。景观生态学关注于大的空间尺度的生态学问题。景观生态学研究方法可以为退化生态系统恢复实践提供指导。在解决退化生态系统的恢复问题时,景观生态学的方法在理论和实践上是有效的。景观生态学中的核心概念和其一般原理斑块形状、生态系统间相互作用、镶嵌系列等都同退化生态系统的恢复有着密切的关系。如恢复地点的选择和适当的恢复要素的空间配置。在评价退化生态系统的恢复是否取得成功,利用景观生态学也具有重要的意义。景观生态学理论如景观格局与景观异质性理论,干扰理论和尺度理论都能够指导退化生态系统的恢复实践。同样地,退化生态系统的恢复可以为景观生态学的研究提供非常恰当的实验场。寓景观生态学思想于退化生态系统恢复过程是一种新的有效途径。     

Apps can help bridge restoration science and restoration practice

Scientists need to find innovative ways to communicate their findings with restoration practitioners in an era of global change. Apps are a promising bridge between restoration science and practice because they apply broad scientific concepts to specific situations. For example, habitat connectivity promotes ecological function, but practitioners lack ways to incorporate connectivity into decision‐making. We created an app where users calculate how habitat restoration or loss affects connectivity. By providing our app as an example and discussing the benefits and challenges in creating apps for practitioners, we encourage other restoration ecologists to similarly create apps that bridge science with practice.     

Barriers to ecosystem restoration presented by soil legacy effects of invasive alien N2‐fixing woody species: implications for ecological restoration

Impacts of invasive alien N₂‐fixing woody species and how they can persist as soil legacy effects after invasive species control are well appreciated, but how soil legacy effects can present barriers to restoration is poorly understood. Finding better ways to deal with these barriers to restoration is essential to improving restoration outcomes. In this study, we review 440 studies to identify barriers to restoration and potential management actions for the barriers to restoration, and provide practical application examples of the management actions. Our findings suggest that altered soil microbial communities, depleted native soil seed banks, elevated N status, secondary invasion and weedy native species dominance, and reinvasion are potential barriers to restoration. Furthermore, carbon addition, litter removal, soil microbial treatments, establishing species adapted to low N levels, prescribed burning, classical biological control, grazing, mowing, herbicide or graminicide application, manual weeding, soil N management, soil solarization, weed mats, native species reintroduction, and nurse plants are potential management actions for these barriers to restoration. However, there is little evidence suggesting that several of these barriers to restoration hinder improved restoration outcomes and this could be due to little research on them. More research is needed to assess their relative importance in hindering improved restoration outcomes. Management actions are rarely applied in combination, despite that they often address distinct barriers to restoration. Management actions should be combined into an integrated management effort to improve restoration outcomes.     

Making environmental DNA count

The arc of reception for a new technology or method – like the reception of new information itself – can pass through predictable stages, with audiences’ responses evolving from ‘I don't believe it’, through ‘well, maybe’ to ‘yes, everyone knows that’ to, finally, ‘old news’. The idea that one can sample a volume of water, sequence DNA out of it, and report what species are living nearby has experienced roughly this series of responses among biologists, beginning with the microbial biologists who developed genetic techniques to reveal the unseen microbiome. ‘Macrobial’ biologists and ecologists – those accustomed to dealing with species they can see and count – have been slower to adopt such molecular survey techniques, in part because of the uncertain relationship between the number of recovered DNA sequences and the abundance of whole organisms in the sampled environment. In this issue of Molecular Ecology Resources, Evans et al. ( 2015 ) quantify this relationship for a suite of nine vertebrate species consisting of eight fish and one amphibian. Having detected all of the species present with a molecular toolbox of six primer sets, they consistently find DNA abundances are associated with species’ biomasses. The strength and slope of this association vary for each species and each primer set – further evidence that there is no universal parameter linking recovered DNA to species abundance – but Evans and colleagues take a significant step towards being able to answer the next question audiences tend to ask: ‘Yes, but how many are there?’     

稀土尾矿土壤细菌群落结构对植被修复的响应

选用赣州-安远稀土弃废尾矿及其不同植被修复的堆浸田为研究对象,调查废弃尾矿及6种不同植被修复方案下土壤理化性质的变化,并利用变性凝胶梯度电泳(DGGE)技术,分析土壤微生物群落结构对植被修复的响应。结果表明:与未修复尾矿土壤相比,经不同植被修复后的土壤理化性质均得到明显改良,其中土壤含水量、有机质含量均比未修复尾矿土壤增加2—3倍。微生物群落结构分析表明,植被修复后土壤微生物群落与废弃尾矿土壤微生物群落亲缘度仅为0.21,表明植被修复后,土壤微生物群落结构发生了明显变化,且微生物多样性、均匀度、丰富度与未修复尾矿土壤相比均有了明显的提高。而在不同植被修复方案中,以湿地松和山胡椒为优势群落的两种植被修复方案对土壤改良效果最为明显,这两种修复方案不仅能显著改善土壤的固水性、有机质含量,并且对微生物群落的改善作用也最为显著。典范对应分析表明,废弃尾矿土壤微生物群落结构受土壤p H影响最为显著,而植被修复后土壤微生物群落的环境影响因子则转变为含水量、有机质、有机碳及总磷含量。进一步揭示了微生物在植被修复过程中所起到的重要作用,并为矿山生态重建过程中的土壤改良工作提供了丰富的理论依据。     

A review of the world's active seabird restoration projects

Within the past several decades, seabird populations have been actively restored in locales where they were reduced or extirpated. Chick translocation, acoustic vocalization playbacks, and decoys are now used widely to lure breeding seabirds to restoration sites. In this first worldwide review of seabird restoration projects we evaluate the factors affecting project success or failure and recommend future directions for management. We identified 128 active restoration projects that were implemented to protect 47 seabird species in 100 locales spanning 14 countries since active restoration methods were pioneered in 1973. Active seabird restoration can achieve conservation goals for threatened and endangered species, and for species affected by anthropogenic impacts (e.g., oil spills, invasive species, fisheries). It also can be used to relocate populations from undesired breeding locales to more favorable locations, and to establish multiple breeding locations to reduce risks posed by catastrophic events. Active restoration can help to restore ecological processes, as large seabird colonies function to cycle marine nutrients to terrestrial ecosystems and create habitats for commensal species. Active restoration is especially appropriate where the original causes of decline are no longer working to suppress colony establishment and growth. Successful restoration efforts require careful planning and long-term commitments. We introduce the different forms of active seabird restoration techniques, review their utility for different seabird species, and use case studies to suggest how to optimize this technique to restore seabird species globally. Wildlife managers can use this review to guide their seabird restoration projects in the planning, implementation, and monitoring stages; tailor their restoration to seabird-specific life histories; and identify areas for further research to improve restoration utility in the future. © 2011 The Wildlife Society.     

DNA amplification in the field: move over PCR,here comes LAMP

It would not be an exaggeration to say that among molecular technologies, it is PCR (polymerase chain reaction) that underpins the discipline of molecular ecology as we know it today. With PCR, it has been possible to target the amplification of particular fragments of DNA, which can then be analysed in a multitude of ways. The capability of PCR to amplify DNA from a mere handful of copies further means that conservationists and ecologists are able to sample DNA unobtrusively and with minimal disturbance to the environment and the organisms of interest. However, a key disadvantage of PCR‐based methods has been the necessity for a generally non‐portable, laboratory setting to undertake the time‐consuming thermocycling protocols. LAMP (loop‐mediated isothermal amplification) offers a logistically simpler protocol: a relatively rapid DNA amplification reaction occurs at one temperature, and the products are visualized with a colour change within the reaction tubes. In the first field application of LAMP for an ecological study, Centeno‐Cuadros et al. ( 2016 ) demonstrates how LAMP can be used to determine the sex of three raptor species. By enabling DNA amplification in situ and in ‘real‐time’, LAMP promises to revolutionize how molecular ecology is practised in the field.     

土壤微生物网络复杂性预测黄土高原造林恢复生态系统多功能性

人类活动导致黄土高原土地退化和生物多样性丧失,进而降低了生态系统功能。人工造林是该区域退化土地恢复的重要措施。现有的生态修复研究通常侧重于微生物群落物种多样性的恢复对单一生态系统功能的影响,而忽略了微生物间存在的相互作用与生态系统多功能性(Ecosystem multifunctionality, EMF)的关系。为探究造林恢复过程中土壤微生物多样性和网络复杂性与EMF的关系,本研究采用时空代换法(space-time substitution method),沿50年造林恢复时间序列,分析了黄土高原地区造林恢复对土壤微生物群落多样性、土壤微生物网络复杂性以及与土壤养分循环相关的10个生态系统功能指标的影响,明确了土壤微生物群落特征与EMF的关系。结果表明,随造林恢复时间序列的增加,土壤微生物群落的综合多样性、网络复杂性和EMF均呈现出显著增加后下降的趋势(P<0.05),其中土壤微生物综合多样性和网络复杂性在第8年达到最高值,EMF在第20年达到最大值。在未控制土壤环境因素时,细菌和古菌多样性与EMF无显著相关性,真菌多样性与EMF呈显著正相关(P<0.001);土壤微生...     

The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant

It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host–microbial associations.     

Reconnecting plants and pollinators: challenges in the restoration of pollination mutualisms

Ecological restoration of plant-pollinator interactions has received surprisingly little attention, despite animal-mediated pollination underpinning reproduction of the majority of higher plants. Here, we offer a conceptual and practical framework for the ecological restoration of pollination mutualisms. Through the use of targeted restoration plantings to attract and sustain pollinators and increased knowledge of the ecological requirements of pollinators, we propose that pollination could be successfully restored in degraded ecosystems. The challenge for pollination biologists is to integrate their findings with those of plant restoration ecologists to ensure sustainable pollination in restored ecosystems.     

Gut microbiota of a long‐distance migrant demonstrates resistance against environmental microbe incursions

Migratory animals encounter suites of novel microbes as they move between disparate sites during their migrations, and are frequently implicated in the global spread of pathogens. Although wild animals have been shown to source a proportion of their gut microbiota from their environment, the susceptibility of migrants to enteric infections may be dependent upon the capacity of their gut microbiota to resist incorporating encountered microbes. To evaluate migrants’ susceptibility to microbial invasion, we determined the extent of microbial sourcing from the foraging environment and examined how this influenced gut microbiota dynamics over time and space in a migratory shorebird, the Red‐necked stint Calidris ruficollis. Contrary to previous studies on wild, nonmigratory hosts, we found that stint on their nonbreeding grounds obtained very little of their microbiota from their environment, with most individuals sourcing only 0.1% of gut microbes from foraging sediment. This microbial resistance was reflected at the population level by only weak compositional differences between stint flocks occupying ecologically distinct sites, and by our finding that stint that had recently migrated 10,000 km did not differ in diversity or taxonomy from those that had inhabited the same site for a full year. However, recent migrants had much greater abundances of the genus Corynebacterium, suggesting a potential microbial response to either migration or exposure to a novel environment. We conclude that the gut microbiota of stint is largely resistant to invasion from ingested microbes and that this may have implications for their susceptibility to enteric infections during migration.     

A comparison of nonlethal sampling methods for amphibian gut microbiome analyses

Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.     

A new era in forest restoration monitoring

Monitoring ecological restoration has been historically dependent on traditional inventory methods based on detailed information obtained from field plots. New paradigms are now needed to successfully achieve restoration as a large‐scale, long‐lasting transformative process. Fortunately, advances in technology now allow for unprecedented shifts in the way restoration has been planned, implemented, and monitored. Here, we describe our vision on how the use of new technologies by a new generation of restoration ecologists may revolutionize restoration monitoring in the coming years. The success of the many ambitious restoration programs planned for the coming decade will rely on effective monitoring, which is an essential component of adaptive management and accountability. The development of new remote sensing approaches and their application to a restoration context open new avenues for expanding our capacity to assess restoration performance over unprecedented spatial and temporal scales. A new generation of scientists, which have a background in remote sensing but are getting more and more involved with restoration, will certainly play a key role for making large‐scale restoration monitoring a viable human endeavor in the coming decade—the United Nations' decade on ecosystem restoration.     

土壤碳库积累与分配对热带森林恢复的响应

为探明土壤有机碳沉积对热带森林恢复的响应过程与机理,选取西双版纳处于不同恢复阶段的热带森林类型(前期的白背桐群落、中期的崖豆藤群落、后期的高檐蒲桃群落)为研究对象,探讨土壤有机碳库各组分积累与分配(微生物量碳储量/总有机碳储量、易氧化有机碳储量/总有机碳储量、惰性有机碳储量/总有机碳储量)的时空变化规律,分析乔木与林下物种的丰富度和多样性、土壤温湿度、容重、pH及氮库(全氮、水解氮、铵氮、硝氮)对土壤有机碳库组分积累与分配的影响。结果表明:(1)热带森林恢复显著促进土壤碳库各组分的蓄积(P<0.05),相较于恢复前期,恢复中后期土壤总有机碳、微生物量碳、易氧化有机碳、惰性有机碳储量增幅达9.25%-50.84%;恢复促进了土壤微生物量碳和易氧化有机碳的分配(8.98%-25.36%)(P<0.05),但对惰性有机碳分配无显著影响;(2)不同恢复阶段热带森林土壤碳组分积累与分配的时空变化存在一定的差异。其中上述4种碳组分积累最大值均出现在6月、垂直变化均沿土层递减;土壤易氧化有机碳和微生物量碳分配最大值出现在6月、惰性有机碳分配则在12月最大,易氧化有机碳和微生物量碳分配沿土层递减、惰性有机碳分配无显著垂直变化;(3)土壤微生物量碳、易氧化有机碳、惰性有机碳的储量在土壤碳库储量的分配占比分别维持在2.40%-5.00%、18.22%-39.34%、18.50%-26.55%,土壤有机碳组分对总有机碳储量变化的解释率表现为:微生物量碳(83.71%)>惰性有机碳(82.17%)>易氧化有机碳(78.54%);(4)相较于恢复初期,恢复后期乔木与林下物种丰富度和Shannon多样性提升了42.78%-490.82%,氮库(全氮、水解氮、铵氮、硝氮)含量仅提升了12.73%-25.51%;(5)冗余分析表明,林下物种丰富度、温湿度、水解氮是影响土壤有机碳组分积累的主要驱动因子,而乔木香农多样性、湿度、容重则是影响土壤有机碳库组分分配的主控因子。因此,西双版纳热带森林恢复进程显著促进了土壤有机碳库组分积累与分配,影响程度取决于样地林下物种丰富度、乔木香农多样性、土壤温湿度、容重与水解氮的状况。     

Local habitat restoration in streams: Constraints on the effectiveness of restoration for stream biota

Summary   The restoration of physical habitat has emerged as a key activity for managers charged with reversing the damage done by humans to streams and rivers, and there has been a great expenditure of time, money and other resources on habitat restoration projects. Most restoration projects appear to assume that the creation of habitat is the key to restoring the biota ('the field of dreams hypothesis'). However, in many streams where new habitat is clearly required if populations and communities are to be restored, there may be numerous other factors that cause the expected link between habitat and biotic restoration to break down. We discuss five issues that are likely to have a direct bearing on the success, or perceived success of local habitat restoration projects in streams: (i) barriers to colonization, (ii) temporal shifts in habitat use, (iii) introduced species, (iv) long-term and large-scale processes, and (v) inappropriate scales of restoration. The purpose of the study was primarily to alert ecologists and managers involved in stream habitat restoration to the potential impacts of these issues on restoration success. Furthermore, the study highlights the opportunities provided by habitat restoration for learning how the factors we discuss affect populations, communities and ecosystems.     

Towards more effective integration of tropical forest restoration and conservation

Conservation and restoration interventions can be mutually reinforcing and are converging through an increased focus on social dimensions. This paper examines how to more effectively integrate the complementary goals of conservation and restoration of tropical forests. Forest conservation and restoration interventions are integral components of a broad approach to forest ecosystem and landscape management that aims to maintain and restore key ecological processes and enhance human well‐being, while minimizing biodiversity loss. The forest transition model provides a useful framework for understanding the relative importance of forest conservation and restoration interventions in different regions. Harmonizing conservation and restoration presents serious challenges for forest policy in tropical countries, particularly regarding the use and management of secondary forests, fallow vegetation, and forests degraded by logging and fire. Research to implement restoration more effectively in tropical regions can be stimulated by transforming questions that initially focused on conservation issues. Examination of papers published in Biotropica from 2000–2018 shows that most studies relevant to tropical forest conservation do not address forest restoration issues. Forest restoration studies, on the other hand, show a consistent association with conservation issues. There is much scope for further integration of conservation and restoration in research, practice, and policy. Securing a sustainable future for tropical forests requires developing and applying integrated approaches to landscape management that effectively combine knowledge and tools from multiple disciplines with practical experience and engagement of local stakeholders. Abstract in Portuguese is available with online material.     

Deploying microbes as drivers and indicators in ecological restoration

Ecosystem degradation is a major environmental threat. Beyond conservation, restoration of degraded ecosystems is a prerequisite to reinstate their ability to provide essential services and benefits. Most of the restoration efforts focus on aboveground restoration, that is, plants, under the assumption that establishment of plant species will reestablish the faunal and microbial species. While this may be true for some cases, it is not a general rule. Reestablishment of microbial communities by dedicated efforts is also necessary for successful restoration, as cycling of essential nutrients for plant growth and decomposition of organic matter is dependent on them. The role of microbial fertilizers and efficient organisms used in agriculture needs to be explored in restoration. Testing of symbiotic interactions between potential plant growth-promoting Rhizobacteria and plants native to a degraded ecosystem can be conducted and utilized for successful establishment of plant species. However, utmost care must be taken while introducing new microbial species or non-native plant species to an area, as they can adversely affect the resident microbial community. Techniques like phospholipid fatty-acid analysis can be used for taxonomic identification of large microbial groups in non-degraded reference ecosystems before introducing microbial species into a degraded ecosystem. For use of microbes in restoration, more studies on microbe-plant interactions need to be conducted. For use of Soil Microbial Community (SMC) as indicators of restoration, their role and function in the ecology of the area need to be elucidated by employing all the available techniques.     

Exploring the Sources of Bacterial Spoilers in Beefsteaks by Culture-Independent High-Throughput Sequencing

Microbial growth on meat to unacceptable levels contributes significantly to change meat structure, color and flavor and to cause meat spoilage. The types of microorganisms initially present in meat depend on several factors and multiple sources of contamination can be identified. The aims of this study were to evaluate the microbial diversity in beefsteaks before and after aerobic storage at 4°C and to investigate the sources of microbial contamination by examining the microbiota of carcasses wherefrom the steaks originated and of the processing environment where the beef was handled. Carcass, environmental (processing plant) and meat samples were analyzed by culture-independent high-throughput sequencing of 16S rRNA gene amplicons. The microbiota of carcass swabs was very complex, including more than 600 operational taxonomic units (OTUs) belonging to 15 different phyla. A significant association was found between beef microbiota and specific beef cuts (P<0.01) indicating that different cuts of the same carcass can influence the microbial contamination of beef. Despite the initially high complexity of the carcass microbiota, the steaks after aerobic storage at 4°C showed a dramatic decrease in microbial complexity. Pseudomonas sp. and Brochothrix thermosphacta were the main contaminants, and Acinetobacter, Psychrobacter and Enterobacteriaceae were also found. Comparing the relative abundance of OTUs in the different samples it was shown that abundant OTUs in beefsteaks after storage occurred in the corresponding carcass. However, the abundance of these same OTUs clearly increased in environmental samples taken in the processing plant suggesting that spoilage-associated microbial species originate from carcasses, they are carried to the processing environment where the meat is handled and there they become a resident microbiota. Such microbiota is then further spread on meat when it is handled and it represents the starting microbial association wherefrom the most efficiently growing microbial species take over during storage and can cause spoilage.