Marco Pautasso

Wood-decaying fungi in the forest: conservation needs and management options

Wood-decaying fungi are essential for the functioning of forest ecosystems. They provide habitat for many other organisms and enable the regeneration of forests throughout the world. Since wood decomposition is a decisive process in nutrient recycling, soil formation and the carbon budget of forest ecosystems, it is receiving increasing attention from forest ecologists, pathologists and managers. Research has focussed on the factors driving the species-richness of wood-decomposing organisms and is moving on to analyse the effects of this species-richness on ecosystem functioning. Coarse woody debris (CWD) and its associated wood-decaying organisms have been drastically reduced in abundance and diversity by forestry and so these features often have potential as conservation indicators. Protective measures at a landscape level are needed for threatened wood-inhabiting fungi. These include restricting salvage operations in windthrow stands, actively encouraging the accumulation of deadwood in forests, and facilitating decay in standing trees by inoculating them with fungi. Here, we aim to collect and summarize recently produced work on deadwood ecology, pointing out research gaps and perspectives.

Plant health and global change – some implications for landscape management

Global change (climate change together with other worldwide anthropogenic processes such as increasing trade, air pollution and urbanization) will affect plant health at the genetic, individual, population and landscape level. Direct effects include ecosystem stress due to natural resources shortage or imbalance. Indirect effects include (i) an increased frequency of natural detrimental phenomena, (ii) an increased pressure due to already present pests and diseases, (iii) the introduction of new invasive species either as a result of an improved suitability of the climatic conditions or as a result of increased trade, and (iv) the human response to global change. In this review, we provide an overview of recent studies on terrestrial plant health in the presence of global change factors. We summarize the links between climate change and some key issues in plant health, including tree mortality, changes in wildfire regimes, biological invasions and the role of genetic diversity for ecosystem resilience. Prediction and management of global change effects are complicated by interactions between globalization, climate and invasive plants and/or pathogens. We summarize practical guidelines for landscape management and draw general conclusions from an expanding body of literature.

Evolution of the international regulation of plant pests and challenges for future plant health

Plant pathogens and invertebrates harmful to plants, collectively referred to as plant pests, continue to threaten food security. International cooperation and regulatory systems to inhibit the spread of plant pests began formally in 1878. Initially seven countries worked together and agreed phytosanitary measures against grape phylloxera, Phylloxera vastatrix (=Daktulosphaira vitifoliae). There are now 172 countries that are contracting parties to the International Plant Protection Convention, a treaty that aims to prevent the introduction and spread of pests of plants and plant products, and to promote appropriate measures for their control. Apparently contradictory interests between international trade, which has facilitated the spread of plant pests, and the protection of plants are mutually recognised in global trade and phytosanitary agreements. The principle that risk management measures should provide an appropriate level of protection without undue interference in trade was established within the plant protection agreements at the beginning of the 20th Century and is still fundamental to risk management policy today. Globally ten Regional Plant Protection Organizations facilitate more local cooperation and recommend the regulation of over 1,000 named quarantine plant pests. Member States of the European Union work together and regulate imported plant material on the grounds of plant health with each Member State taking into account the plant health concerns of every other Member State. However, decision making can be slow and border inspections poorly targeted. Close relationships between regulatory scientists and policy makers, focussed on agricultural and horticultural production, are changing to take a broader stakeholder community into consideration as decisions regarding the environment seek to draw upon a wider knowledge base. Challenges that impede the success of limiting international pest movement include increased international trade and climate change. International guidelines designed to prevent pest spread present challenges of their own if they remain difficult to implement.

Networks in plant epidemiology: from genes to landscapes, countries, and continents

There is increasing use of networks in ecology and epidemiology, but still relatively little application in phytopathology. Networks are sets of elements (nodes) connected in various ways by links (edges). Network analysis aims to understand system dynamics and outcomes in relation to network characteristics. Many existing natural, social, and technological networks have been shown to have small-world (local connectivity with short-cuts) and scale-free (presence of super-connected nodes) properties. In this review, we discuss how network concepts can be applied in plant pathology from the molecular to the landscape and global level. Wherever disease spread occurs not just because of passive/natural dispersion but also due to artificial movements, it makes sense to superimpose realistic models of the trade in plants on spatially explicit models of epidemic development. We provide an example of an emerging pathosystem (Phytophthora ramorum) where a theoretical network approach has proven particularly fruitful in analyzing the spread of disease in the UK plant trade. These studies can help in assessing the future threat posed by similar emerging pathogens. Networks have much potential in plant epidemiology and should become part of the standard curriculum.

Worsening file-drawer problem in the abstracts of natural, medical and social science databases

The file-drawer problem is the tendency of journals to preferentially publish studies with statistically significant results. The problem is an old one and has been documented in various fields, but to my best knowledge there has not been attention to how the issue is developing in a quantitative way through time. In the abstracts of various major scholarly databases (Science and Social Science Citation Index (1991–2008), CAB Abstracts and Medline (1970s–2008), the file drawer problem is gradually getting worse, in spite of an increase in (1) the total number of publications and (2) the proportion of publications reporting both the presence and the absence of significant differences. The trend is confirmed for particular natural science topics such as biology, energy and environment but not for papers retrieved with the keywords biodiversity, chemistry, computer, engineering, genetics, psychology and quantum (physics). A worsening file-drawer problem can be detected in various medical fields (infection, immunology, malaria, obesity, oncology and pharmacology), but not for papers indexed with strings such as AIDS/HIV, epidemiology, health and neurology. An increase in the selective publication of some results against some others is worrying because it can lead to enhanced bias in meta-analysis and hence to a distorted picture of the evidence for or against a certain hypothesis. Long-term monitoring of the file-drawer problem is needed to ensure a sustainable and reliable production of (peer-reviewed) scientific knowledge.

Disease spread in small-size directed networks: epidemic threshold, correlation between links to and from nodes, and clustering.

Network epidemiology has mainly focused on large-scale complex networks. It is unclear whether findings of these investigations also apply to networks of small size. This knowledge gap is of relevance for many biological applications, including meta-communities, plant-pollinator interactions and the spread of the oomycete pathogen Phytophthora ramorum in networks of plant nurseries. Moreover, many small-size biological networks are inherently asymmetrical and thus cannot be realistically modelled with undirected networks. We modelled disease spread and establishment in directed networks of 100 and 500 nodes at four levels of connectance in six network structures (local, small-world, random, one-way, uncorrelated, and two-way scale-free networks). The model was based on the probability of infection persistence in a node and of infection transmission between connected nodes. Regardless of the size of the network, the epidemic threshold did not depend on the starting node of infection but was negatively related to the correlation coefficient between in- and out-degree for all structures, unless networks were sparsely connected. In this case clustering played a significant role. For small-size scale-free directed networks to have a lower epidemic threshold than other network structures, there needs to be a positive correlation between number of links to and from nodes. When this correlation is negative (one-way scale-free networks), the epidemic threshold for small-size networks can be higher than in non-scale-free networks. Clustering does not necessarily have an influence on the epidemic threshold if connectance is kept constant. Analyses of the influence of the clustering on the epidemic threshold in directed networks can also be spurious if they do not consider simultaneously the effect of the correlation coefficient between in- and out-degree.

Integrating natural and social science perspectives on plant disease risk, management and policy formulation

Plant diseases threaten both food security and the botanical diversity of natural ecosystems. Substantial research effort is focused on pathogen detection and control, with detailed risk management available for many plant diseases. Risk can be assessed using analytical techniques that account for disease pressure both spatially and temporally. We suggest that such technical assessments of disease risk may not provide an adequate guide to the strategies undertaken by growers and government to manage plant disease. Instead, risk-management strategies need to account more fully for intuitive and normative responses that act to balance conflicting interests between stakeholder organizations concerned with plant diseases within the managed and natural environments. Modes of effective engagement between policy makers and stakeholders are explored in the paper, together with an assessment of such engagement in two case studies of contemporary non-indigenous diseases in one food and in one non-food sector. Finally, a model is proposed for greater integration of stakeholders in policy decisions.

Urbanization and the more-individuals hypothesis.

1. Urbanization is a landscape process affecting biodiversity world-wide. Despite many urban-rural studies of bird assemblages, it is still unclear whether more species-rich communities have more individuals, regardless of the level of urbanization. The more-individuals hypothesis assumes that species-rich communities have larger populations, thus reducing the chance of local extinctions. 2. Using newly collated avian distribution data for 1 km(2) grid cells across Florence, Italy, we show a significantly positive relationship between species richness and assemblage abundance for the whole urban area. This richness-abundance relationship persists for the 1 km(2) grid cells with less than 50% of urbanized territory, as well as for the remaining grid cells, with no significant difference in the slope of the relationship. These results support the more-individuals hypothesis as an explanation of patterns in species richness, also in human modified and fragmented habitats. 3. However, the intercept of the species richness-abundance relationship is significantly lower for highly urbanized grid cells. Our study confirms that urban communities have lower species richness but counters the common notion that assemblages in densely urbanized ecosystems have more individuals. In Florence, highly inhabited areas show fewer species and lower assemblage abundance. 4. Urbanized ecosystems are an ongoing large-scale natural experiment which can be used to test ecological theories empirically.

Are the living collections of the world's botanical gardens following species-richness patterns observed in natural ecosystems?

Pautasso M. and Parmentier I. 2007. Are the living collections of the world’s botanical gardens following species-richness patterns observed in natural ecosystems? Bot. Helv. 117: 15 – 28.Botanical gardens aim to promote the awareness, study and conservation of plant species diversity, but little is known about the species diversity of botanical gardens themselves. We therefore investigated whether the species richness of the world’s botanical gardens is related to their size, age and geographical location by compiling data from gardens in 124 different countries. The data show that even in these highly managed ecosystems, species richness can be described in terms of a relatively small number of large-scale patterns. As with most natural ecosystems, there were positive species-area and species-age relationships. There was also a positive latitudinal gradient in species richness, which contrasts with the trend observed in natural ecosystems. This discrepancy may be due to the use of heated greenhouses at high latitudes, the rarity of old botanical gardens in the tropics, and the problem of poverty in developing countries, where most hotspots of plant biodiversity are located. There is thus a need to allocate more funds to botanical gardens in species-rich regions. This study also calls for an increase in the coordination of data management between botanical gardens.

Peer review delay and selectivity in ecology journals

Peer review is fundamental to science as we know it, but is also a source of delay in getting discoveries communicated to the world. Researchers have investigated the effectiveness and bias of various forms of peer review, but little attention has been paid to the relationships among journal reputation, rejection rate, number of submissions received and time from submission to acceptance. In 22 ecology/interdisciplinary journals for which data could be retrieved, higher impact factor is positively associated with the number of submissions. However, higher impact factor journals tend to be significantly quicker in moving from submission to acceptance so that journals which receive more submissions are not those which take longer to get them through the peer review and revision processes. Rejection rates are remarkably high throughout the journals analyzed, but tend to increase with increasing impact factor and with number of submissions. Plausible causes and consequences of these relationships for journals, authors and peer reviewers are discussed.