Nico Koedam

Bio: Nico Koedam is an academic researcher from Vrije Universiteit Brussel. The author has contributed to research in topics: Mangrove & Rhizophora mucronata. The author has an hindex of 37, co-authored 121 publications receiving 3862 citations.

Urban plant species patterns are highly driven by density and function of built-up areas

Abstract: This paper aims to assess the relative importance of the type of built-up area in structuring plant species composition and richness in urbanised environments. The study was carried out in the city of Brussels where all vascular plant species were recorded in 189 grid cells of 1 km2 each. The effect of urban land use type on species composition was investigated using first Canonical Correspondence Analysis. Densely built-up area was the most powerful predictor for species composition, followed by industrial built-up areas, half open or open built-up areas with plantations, and open built-up areas with much natural vegetation in the surroundings. Indicator species were found for each type of built-up area and a response curve to the amount of built land was produced using Generalised Additive Modelling. Various types of built-up areas had different effects on environmental conditions as inferred by Ellenberg’s indicator values, as well as on the species richness, species rarity, number of exotic species and proportion of extinction-prone species. It is concluded that future ecological studies should not treat urban areas as homogeneous areas by combining all anthropogenic factors into one aggregated variable. Instead, the urban matrix should be categorised in subsystems as it is multidimensional and highly variable across space.

Resource utilization patterns of epifauna from mangrove forests with contrasting inputs of local versus imported organic matter

Abstract: Mangrove epifaunal communities have access to various carbon and nitrogen sources and we hypothesized that the degree of material exchange with the aquatic environment might influence the overall use of different substrates by intertidal communities. Therefore, we analyzed C and N stable isotope ratios in primary producers, sediments and 245 samples of epifauna hand-collected from 5 sites in India, Sri Lanka and Kenya (representing estuarine, lagoonal and basin-type mangrove forests). Several patterns emerged from this data set. First, epifaunal communities used a range of available food substrates at all sites studied, including mangrove-derived organic matter, local microphytobenthos and micro-epiflora, as well as imported C and N from the aquatic environment (i.e. phytoplankton- and/or seagrass-derived organic matter). Secondly, our data indicate that at sites with significant inputs of aquatic sources, use of mangrove carbon is rather limited on a community basis, whereas in systems with less material exchange with adjacent waters, the relative importance of mangroves is higher. Thus, despite the unquestionable impact some epifaunal species may have on leaf litter dynamics, the dependency of the invertebrate community as a whole on mangrove litter is not ubiquitously large and varies according to the availability of local versus tidally imported sources. Precise quantification of the relative importance of different substrates with δ 13 C and δ 15 N is, however, not always straightforward due to the multitude of available sources and the overlap in source stable isotope signatures. Micro-epiflora on mangroves trees were remarkably depleted in 15 N in all systems (δ 15 N between -8.2 and -2.4‰) and thus form an example where δ 15 N is a useful source indicator, as low δ 15 N values of several gastropod species indicated substantial feeding on such epiflora.

conservation of the woodland flora in an urban context

Abstract: Aim To test whether, in an urban area, small forest fragments are more important than large ones, the present study aimed at firstly exploring the relationship between plant functional groups or individual species and urban woodlot characteristics such as patch area and isolation, and secondly investigating whether equal-sized combinations of islands tend to differ in species richness. Location The city of Brussels. Methods We considered the relationship between size, species richness and plant functional groups among one very large (1666 ha) and 11 rather small (2-123 ha) woodlots. Results The largest woodlot harboured species missing in the smaller ones. The species-area relationship plotted for these wooded patches fitted the semilog model very well. Twenty-three species had a significantly higher frequency in the main forest. Only six species had a significantly higher frequency in smaller woodlots. The occurrence of species groups with high conservation value (e.g. ancient forest species, rare species) was higher in large patches. However, a SLOSS analysis showed that habitat subdivision appeared to be associated with increased species counts. A marginally nonsignificant effect of distance to the main forest became significant when matrix species were removed from the patch samples. Conclusions Although overall the data showed a higher conservation value for large woods, some plant functional groups (e.g. woodland species vs. ancient forest species) responded differently to fragmentation. This illustrates that, for conservation strategies, studies considering the biotic characteristics of remnants should focus on the species number of particular plant functional groups, especially those with high conservation value. Furthermore, matrix species should be removed from the analysis in order not to mask underlying patch size and distance effects.

How important are large vs. small forest remnants for the conservation of the woodland flora in an urban context

Abstract: Aim To test whether, in an urban area, small forest fragments are more important than large ones, the present study aimed at firstly exploring the relationship between plant functional groups or individual species and urban woodlot characteristics such as patch area and isolation, and secondly investigating whether equal-sized combinations of islands tend to differ in species richness. Location The city of Brussels. Methods We considered the relationship between size, species richness and plant functional groups among one very large (1666 ha) and 11 rather small (2‐123 ha) woodlots. Results The largest woodlot harboured species missing in the smaller ones. The species-area relationship plotted for these wooded patches fitted the semilog model very well. Twenty-three species had a significantly higher frequency in the main forest. Only six species had a significantly higher frequency in smaller woodlots. The occurrence of species groups with high conservation value (e.g. ancient forest species, rare species) was higher in large patches. However, a SLOSS analysis showed that habitat subdivision appeared to be associated with increased species counts. A marginally nonsignificant effect of distance to the main forest became significant when matrix species were removed from the patch samples. Conclusions Although overall the data showed a higher conservation value for large woods, some plant functional groups (e.g. woodland species vs. ancient forest species) responded differently to fragmentation. This illustrates that, for conservation strategies, studies considering the biotic characteristics of remnants should focus on the species number of particular plant functional groups, especially those with high conservation value. Furthermore, matrix species should be removed from the analysis in order not to mask underlying patch size and distance effects.

Involvement of phenazines and anthranilate in the antagonism of Pseudomonas aeruginosa PNA1 and Tn5 derivatives toward Fusarium spp. and Pythium spp.

Abstract: Pseudomonas aeruginosa PNA1, isolated from the rhizosphere of chickpea in India, suppressed Fusarium wilt of chickpea, caused by Fusarium oxysporum f. sp. ciceris, and Pythium damping-off of bean, caused by Pythium splendens. When grown in culture, PNA1 produced the phenazine antibiotics phenazine-1-carboxylic acid and oxychloraphine, and inhibited mycelial growth of F. oxysporum f. sp. ciceris, P. splendens, and certain other phytopathogenic fungi. Two mutants (FM29 and FM13) deficient in phenazine production were obtained following transposon mutagenesis of PNA1. The transposon in the genome of FM29 was localized to phnA, which is thought to encode a subunit of anthranilate synthase II involved in the phenazine biosynthesis. The FM13 mutation was complemented by trpC, which encodes indole glycerol phosphate synthase in the tryptophan biosynthesis pathway; consequently, FM13 could not grow on a minimal medium in the absence of tryptophan. Neither FM29 nor FM13 suppressed Fusarium wilt of chickpea to the ...

The Theory of Island Biogeography

Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The value of estuarine and coastal ecosystem services

Abstract: The global decline in estuarine and coastal ecosystems (ECEs) is affecting a number of critical benefits, or ecosystem services. We review the main ecological services across a variety of ECEs, including marshes, mangroves, nearshore coral reefs, seagrass beds, and sand beaches and dunes. Where possible, we indicate estimates of the key economic values arising from these services, and discuss how the natural variability of ECEs impacts their benefits, the synergistic relationships of ECEs across seascapes, and management implications. Although reliable valuation estimates are beginning to emerge for the key services of some ECEs, such as coral reefs, salt marshes, and mangroves, many of the important benefits of seagrass beds and sand dunes and beaches have not been assessed properly. Even for coral reefs, marshes, and mangroves, important ecological services have yet to be valued reliably, such as cross-ecosystem nutrient transfer (coral reefs), erosion control (marshes), and pollution control (mangroves). An important issue for valuing certain ECE services, such as coastal protection and habitat-fishery linkages, is that the ecological functions underlying these services vary spatially and temporally. Allowing for the connectivity between ECE habitats also may have important implications for assessing the ecological functions underlying key ecosystems services, such coastal protection, control of erosion, and habitat-fishery linkages. Finally, we conclude by suggesting an action plan for protecting and/or enhancing the immediate and longer-term values of ECE services. Because the connectivity of ECEs across land-sea gradients also influences the provision of certain ecosystem services, management of the entire seascape will be necessary to preserve such synergistic effects. Other key elements of an action plan include further ecological and economic collaborative research on valuing ECE services, improving institutional and legal frameworks for management, controlling and regulating destructive economic activities, and developing ecological restoration options.

Cell biology and molecular basis of denitrification.

Abstract: Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

Effects of urbanization on species richness: A review of plants and animals

Abstract: Many studies have described the effects of urbanization on species richness. These studies indicate that urbanization can increase or decrease species richness, depending on several variables. Some of these variables include: taxonomic group, spatial scale of analysis, and intensity of urbanization. Recent reviews of birds (the most-studied group) indicate that species richness decreases with increasing urbanization in most cases but produces no change or even increases richness in some studies. Here I expand beyond the bird studies by reviewing 105 studies on the effects of urbanization on the species richness of non-avian species: mammals, reptiles, amphibians, invertebrates and plants. For all groups, species richness tends to be reduced in areas with extreme urbanization (i.e., central urban core areas). However, the effects of moderate levels of urbanization (i.e., suburban areas) vary significantly among groups. Most of the plant studies (about 65%) indicate increasing species richness with moderate urbanization whereas only a minority of invertebrate studies (about 30%) and a very small minority of non-avian vertebrate studies (about 12%) show increasing species richness. Possible explanations for these results are discussed, including the importance of nonnative species importation, spatial heterogeneity, intermediate disturbance and scale as major factors influencing species richness.

Microbial interactions and biocontrol in the rhizosphere

Abstract: The loss of organic material from the roots provides the energy for the development of active microbial populations in the rhizosphere around the root. Generally, saproptrophs or biotrophs such as mycorrhizal fungi grow in the rhizosphere in response to this carbon loss, but plant pathogens may also develop and infect a susceptible host, resulting in disease. This review examines the microbial interactions that can take place in the rhizosphere and that are involved in biological disease control. The interactions of bacteria used as biocontrol agents of bacterial and fungal plant pathogens, and fungi used as biocontrol agents of protozoan, bacterial and fungal plant pathogens are considered. Whenever possible, modes of action involved in each type of interaction are assessed with particular emphasis on antibiosis, competition, parasitism, and induced resistance. The significance of plant growth promotion and rhizosphere competence in biocontrol is also considered. Multiple microbial interactions involving bacteria and fungi in the rhizosphere are shown to provide enhanced biocontrol in many cases in comparison with biocontrol agents used singly. The extreme complexity of interactions that can occur in the rhizosphere is highlighted and some potential areas for future research in this area are discussed briefly.