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The Cladorhizidae is a unique family of carnivorous marine sponges characterised by either the absence or reduction of the aquiferous system and by the presence of specialised structures to trap and digest mesoplanktonic prey. Previous studies have postulated a key role of host-associated bacteria in enabling carnivory in this family of sponges. In this study, we employed high-throughput Illumina-based sequencing to identify the bacterial community associated with four individuals of the deep-sea sponge Chondrocladia grandis sampled in the Gulf of Maine. By characterising the V6 through V8 region of the 16S rRNA gene, we compared the bacterial community composition and diversity in three distinct anatomical regions with predicted involvement in prey capture (sphere), support (axis) and benthic substrate attachment (root). A high abundance of Tenacibaculum, a known siderophore producing bacterial genus, was present in all anatomical regions and specimens. The abundance of Colwellia and Roseobacter was greater in sphere and axis samples, and bacteria from the hydrocarbon-degrading Robiginitomaculum genus were most abundant in the root. This first description of the bacterial community associated with C. grandis provides novel insights into the contribution of bacteria to the carnivorous lifestyle while laying foundations for future cladorhizid symbiosis studies., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

A set of tests for generic detection and identification of tospoviruses has been developed. Based on a multiple sequence alignment of the nucleocapsid gene and its 5' upstream untranslated region sequence from 28 different species, primers were designed for RT-PCR detection of tospoviruses from all recognized clades, i.e. the American, Asian and Eurasian clades, and from the small group of distinct and floating species. Pilot experiments on isolates from twenty different species showed that the designed primer sets successfully detected all species by RT-PCR, as confirmed by nucleotide sequence analysis of the amplicons. In a final optimized design, the primers were applied in a setting of five RT-PCR tests. Seven different tospoviruses were successfully identified from diagnostic samples and in addition a non-described tospovirus species from alstroemeria plants. The results demonstrate that the newly developed generic RT-PCR tests provide a relevant tool for broad detection and identification of tospoviruses in plant quarantine and diagnostic laboratories., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Despite the scientific method's central tenets of reproducibility (the ability to obtain similar results when repeated) and repeatability (the ability to replicate an experiment based on methods described), published ecological research continues to fail to provide sufficient methodological detail to allow either repeatability of verification. Recent systematic reviews highlight the problem, with one example demonstrating that an average of 13% of studies per year (±8.0 [SD]) failed to report sample sizes. The problem affects the ability to verify the accuracy of any analysis, to repeat methods used, and to assimilate the study findings into powerful and useful meta-analyses. The problem is common in a variety of ecological topics examined to date, and despite previous calls for improved reporting and metadata archiving, which could indirectly alleviate the problem, there is no indication of an improvement in reporting standards over time. Here, we call on authors, editors, and peer reviewers to consider repeatability as a top priority when evaluating research manuscripts, bearing in mind that legacy and integration into the evidence base can drastically improve the impact of individual research reports.

A future higher risk of severe flooding of streams and rivers has been projected to change riparian plant community composition and species richness, but the extent and direction of the expected change remain uncertain. We conducted a meta-analysis to synthesize globally available experimental evidence and assess the effects of increased flooding on (1) riparian adult plant and seedling survival, (2) riparian plant biomass and (3) riparian plant species composition and richness. We evaluated which plant traits are of key importance for the response of riparian plant species to flooding. We identified and analysed 53 papers from ISI Web of Knowledge which presented quantitative experimental results on flooding treatments and corresponding control situations. Our meta-analysis demonstrated how longer duration of flooding, greater depth of flooding and, particularly, their combination reduce seedling survival of most riparian species. Plant height above water level, ability to elongate shoots and plasticity in root porosity were decisive for adult plant survival and growth during longer periods of flooding. Both 'quiescence' and 'escape' proved to be successful strategies promoting riparian plant survival, which was reflected in the wide variation in survival (full range between 0 and 100%) under fully submerged conditions, while plants that protrude above the water level (>20 cm) almost all survive. Our survey confirmed that the projected increase in the duration and depth of flooding periods is sufficient to result in species shifts. These shifts may lead to increased or decreased riparian species richness depending on the nutrient, climatic and hydrological status of the catchment. Species richness was generally reduced at flooded sites in nutrient-rich catchments and sites that previously experienced relatively stable hydrographs (e.g. rain-fed lowland streams). Species richness usually increased at sites in desert and semi-arid climate regions (e.g. intermittent streams)., (© 2015 John The Authors. Global Change Biology Published by John Wiley & Sons Ltd.)

In symptomless plants of portulaca a potential new pospiviroid was characterized. Analysis by both double and return PAGE showed the presence of a circular RNA. RT-PCR and sequencing revealed a genome of 351 nt with properties characteristic of members of the genus Pospiviroid and with highest sequence identity (circa 80%) with iresine viroid 1 (IrVd-1). The circular RNA from portulaca was shown to replicate independently in its original host, thus showing that it is indeed a viroid. Based on its molecular characteristics, it should be considered a new species. However, since no biological differences have yet been found with its closest relative IrVd-1, the viroid from portulaca does not fulfil all criteria for species demarcation of the ICTV., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Nutrient enrichment of mangroves, a common phenomenon along densely populated coastlines, may negatively affect mangrove ecosystems by modifying internal carbon and nutrient cycling. The decomposition of litter exerts a strong influence on these processes and is potentially modified by eutrophication. This study describes effects of N and P enrichment on litter decomposition rate and mineralisation/immobilisation patterns. By making use of reciprocal litter transplantation experiments among fertiliser treatments, it was tested if nutrient addition primarily acts on the primary producers (i.e. changes in litter quantity and quality) or on the microbial decomposers (i.e. changes in nutrient limitation for decomposition). Measurements were done in two mangrove forests where primary production was either limited by N or by P, which had been subject to at least 5 years of experimental N and P fertilisation. Results of this study indicated that decomposers were always N-limited regardless of the limitation of the primary producers. This leads to a differential nutrient limitation between decomposers and primary producers in sites where mangrove production was P-limited. In these sites, fertilisation with P caused litter quality to change, resulting in a higher decomposition rate. This study shows that direct effects of fertilisation on decomposition through an effect on decomposer nutrient availability might be non-significant, while the indirect effects through modifying litter quality might be quite substantial in mangroves. Our results show no indication that eutrophication increases decomposition without stimulating primary production. Therefore we do not expect a decline in carbon sequestration as a result of eutrophication of mangrove ecosystems., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Dutch peatlands have been subsiding due to peat decomposition, shrinkage and compression, since their reclamation in the 11th century. Currently, subsidence amounts to 1-2 cm/year. Water management in these areas is complex and costly, greenhouse gases are being emitted, and surface water quality is relatively poor. Regional and local authorities and landowners responsible for peatland management have recognized these problems. In addition, the Netherlands Royal Meteorological Institute predicts higher temperatures and drier summers, which both are expected to enhance peat decomposition. Stakeholder workshops have been organized in three case study areas in the province of Friesland to exchange knowledge on subsidence and explore future subsidence rates and the effects of land use and management changes on subsidence rates. Subsidence rates were up to 3 cm/year in deeply drained parcels and increased when we included climate change in the modeling exercises. This means that the relatively thin peat layers in this province (ca 1 m) would shrink or even disappear by the end of the century when current practices continue. Adaptation measures were explored, such as extensive dairy farming and the production of new crops in wetter conditions, but little experience has been gained on best practices. The workshops have resulted in useful exchange of ideas on possible measures and their consequences for land use and water management in the three case study areas. The province and the regional water board will use the results to develop land use and water management policies for the next decades.

The complete genome sequence of chrysanthemum stem necrosis virus (CSNV) was determined using Roche 454 next-generation sequencing. CSNV is a tentative member of the genus Tospovirus within the family Bunyaviridae, whose members are arthropod-borne. This is the first report of the entire RNA genome sequence of a CSNV isolate. The large RNA of CSNV is 8955 nucleotides (nt) in size and contains a single open reading frame of 8625 nt in the antisense arrangement, coding for the putative RNA-dependent RNA polymerase (L protein) of 2874 aa with a predicted Mr of 331 kDa. Two untranslated regions of 397 and 33 nt are present at the 5' and 3' termini, respectively. The medium (M) and small (S) RNAs are 4830 and 2947 nt in size, respectively, and show 99 % identity to the corresponding genomic segments of previously partially characterized CSNV genomes. Protein sequences for the precursor of the Gn/Gc proteins, N and NSs, are identical in length in all of the analysed CSNV isolates.

Viroids are the smallest autonomous infectious nucleic acids known so far. With a small circular RNA genome of about 250-400 nt, which apparently does not code for any protein, viroids replicate and move systemically in host plants. Since the discovery of the first viroid almost forty-five years ago, many different viroids have been isolated, characterized and, frequently, identified as the causal agents of plant diseases. The first viroid classification scheme was proposed in the early 1990s and adopted by the International Committee on Taxonomy of Viruses (ICTV) a few years later. Here, the current viroid taxonomy scheme and the criteria for viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group. The impact of correct taxonomic annotation of viroid sequence variants is also addressed, taking into consideration the increasing application of next-generation sequencing and bioinformatics for known and previously unrecognized viroids.

Peat soils comprise a large part of the western and northern Netherlands. Drainage for agriculture has caused increased soil aeration which has stimulated decomposition and, hence, soil subsidence, currently amounting to 1-2 cm/yr. River water is supplied to these peat areas in summer to prevent drying out of the peat soils. Saltwater intrusion and evaporation make this surface water slightly brackish during drought periods. In addition, brackish seepage can surface more easily during such dry periods. We performed an incubation experiment in which the effects of salinization on aerobic decomposition and mineralization of shallow peat samples and anaerobic decomposition and mineralization of deep peat samples were studied. We considered four different types of peat samples: peat sampled in agricultural peat meadows and in nature reserves, originally formed under either eutrophic or oligotrophic conditions. The aerobic decomposition was approximately reduced by 50% after salinization, whereas the anaerobic decomposition rates remained unchanged. Remarkably, the response to salinization did not differ between the peat types and land uses. Ammonium concentrations increased while nitrate concentrations decreased after salinization, probably as a result of reduced nitrification. Especially in the oligotrophic peat, ammonium concentrations increased substantially. Phosphate concentrations increased, possibly caused by changes in desorption and adsorption processes due to higher ion concentrations. DOC concentrations decreased in the brackish samples due to precipitation. Furthermore, the eutrophic peat samples showed increasing sulfate concentrations, both in oxic and anoxic incubations, which was attributed to pyrite oxidation. Independently of salinization, nitrification rates were higher in the agricultural, fertilized, peat soils. In conclusion, while salinization might reduce subsidence rates, it will have adverse effects on water quality., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Mangroves are important for coastal protection, carbon sequestration and habitat provision for plants and animals in the tropics and subtropics. Mangroves are threatened by habitat destruction and sea level rise, but management activities such as impounding for mosquito control can also have negative effects. We studied the effects of Rotational Impoundment Management (RIM) on nitrogen dynamics in impoundments dominated by three types of Black mangrove (Avicennia germinans) stands along the Indian River Lagoon (Florida). RIM, designed for noxious insect control, involves pumping estuarine water into impoundments in this area during spring and summer to raise water levels by 30 cm. We compared aspects of the nitrogen cycle before and after the start of the RIM and measured the same variables in an impoundment without RIM management. RIM led to the accumulation of ammonium in the substrate which coincided with a lowering of nitrification rates and decreased denitrification rates. Salt pan habitats dominated by dwarf mangroves became less saline following RIM initiation. Shoot growth of mangroves increased in response to higher nitrogen availability and lower pore water salinity. Mangrove responses were greatest in areas with dwarf and sparse mangrove cover. Overall, RIM resulted in lower nitrification and denitrification leading to lower nitrogen losses and increased Black mangrove growth, all benefits of RIM beyond those associated with noxious insect control., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Extreme summer droughts are expected to occur more often in the future in NW Europe due to climate change. These droughts might accelerate the rate of peat oxidation in drained peat areas, with impacts on soil subsidence, GHG emission and water quality. This study aimed at providing more insight in the oxidation of deep peat layers that had not previously been exposed to air, the so-called secondary decomposition. We incubated two types of peat (eutrophic and oligotrophic), sampled from permanently anoxic peat layers from nature reserves and agricultural peat meadows. Peat samples were incubated for thirteen weeks under anoxic conditions, but were exposed to air for one to eight weeks. The production of CO2 and CH4 was quantified as a proxy for decomposition; concentrations of soluble nutrients and phenolic compounds were also measured. The results showed that oxygenation led to a steep increase in the rate of decomposition, indicated by higher carbon loss rates during and after oxygenation compared to non-oxygenated samples. Carbon loss rates increased more for eutrophic peat (agricultural area: 352%, nature reserve: 182%) than for oligotrophic peat (83% and 159% respectively). Most peat samples investigated showed higher post-oxygenation CO2 and/or CH4 production compared to the anoxic pre-oxygenation period. This indicates that oxygenation stimulates decomposition, even after anoxic conditions have returned. Contrary to the enzymic latch theory, no effects of oxygenation on the concentrations of soluble or condensed phenolic compounds were detected. Soluble nutrient concentrations did not change due to oxygenation either. Noteworthy is the occurrence of pyrite mineralization and associated acidification in eutrophic peat. Thus, low summer water levels, for example due to climate change, should be avoided in order to limit exceptionally high decomposition rates and associated problems such as increasing subsidence rates, greenhouse gas emission, sulfate release and acidification., (Copyright © 2014 Elsevier B.V. All rights reserved.)

1. Frequency and duration of summer droughts are predicted to increase in the near future in many parts of the world, with considerable anticipated effects on riparian plant community composition and species richness. Riparian plant communities along lowland streams are characterised by high species richness due to their system-specific environmental gradients. As these streams and their hydrological gradients are mainly rain-fed, they are sensitive to precipitation changes. 2. We conducted a literature survey and meta-analysis to examine the effects of an increase in summer drought on: (i) riparian plant biomass; (ii) riparian seedling survival and (iii) riparian plant species composition and richness. We also aimed to determine whether hydrological thresholds related to drought tolerance can be distinguished for riparian plant species. 3. ISI Web of Knowledge was searched for relevant peer-reviewed studies, and 23 papers were found that met our criteria and contained quantitative study results. To detect overall responses of biomass and seedling survival, a random-effects model was applied using Comprehensive Meta-analysis™ software. Regression curves were then fitted to response ratio data relating the effects on drought-impacted groups to those on control groups. 4. Our results showed that a drought duration of approximately >30 days strongly reduces riparian plant biomass and that a duration of approximately >30-35 days and high drought intensities (starting from 3 to 4 cm water table decline per day) can be detrimental for riparian seedling survival. Especially Populus and Salix seedlings showed a reduced survival in response to drought, in contrast to Tamarix seedlings, which have the ability to rapidly and expansively elongate their roots. The data also revealed that an increase in drought conditions rapidly leads to a decline of riparian species richness and an increased presence of species adjusted to drier conditions. 5. Riparian groundwater level, surface water permanence and certain plant traits, especially plasticity in rooting depth, were mentioned most frequently as factors determining species responses. Very few studies mentioned hydrological thresholds, such as critical values for ground- and/or surface water levels, and so far these results have proved difficult to generalise. 6. Our meta-analysis has shown that the projected increase in the duration and intensity of drought periods, especially intense droughts lasting more than 30 days, can be expected to narrow the riparian wetland zone with typical hydric species and accelerate riparian wetland species losses in the near future. This may require extra efforts in terms of management and restoration of species-rich riparian areas.

A new virus was isolated from a lettuce plant grown in an open field in the Netherlands in 2011. This plant was showing conspicuous symptoms that consisted of necrosis and moderate leaf curling. The virus was mechanically transferred to indicator plants, and a total RNA extract of one of these indicator plants was used for next-generation sequencing. Analysis of the sequences that were obtained and further biological studies showed that the virus was related to, but clearly distinct from, viruses belonging to the genus Torradovirus. The name "lettuce necrotic leaf curl virus" (LNLCV) is proposed for this new torradovirus.

In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e., Cluster 1) and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA). Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests.

Discovery of new viruses has been boosted by novel deep sequencing technologies. Currently, many viruses can be identified by sequencing without knowledge of the pathogenicity of the virus. However, attributing the presence of a virus in patient material to a disease in the patient can be a challenge. One approach to meet this challenge is identification of viral sequences based on enrichment by autologous patient antibody capture. This method facilitates identification of viruses that have provoked an immune response within the patient and may increase the sensitivity of the current virus discovery techniques. To demonstrate the utility of this method, virus discovery deep sequencing (VIDISCA-454) was performed on clinical samples from 19 patients: 13 with a known respiratory viral infection and 6 with a known gastrointestinal viral infection. Patient sera was collected from one to several months after the acute infection phase. Input and antibody capture material was sequenced and enrichment was assessed. In 18 of the 19 patients, viral reads from immunogenic viruses were enriched by antibody capture (ranging between 1.5x to 343x in respiratory material, and 1.4x to 53x in stool). Enriched reads were also determined in an identity independent manner by using a novel algorithm Xcompare. In 16 of the 19 patients, 21% to 100% of the enriched reads were derived from infecting viruses. In conclusion, the technique provides a novel approach to specifically identify immunogenic viral sequences among the bulk of sequences which are usually encountered during virus discovery metagenomics.

Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified and characterized the full genome of a novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) in cerebrospinal fluid (CSF) specimens of two Vietnamese patients with CNS infections of unknown etiology. CyCV-VN was subsequently detected in 4% of 642 CSF specimens from Vietnamese patients with suspected CNS infections and none of 122 CSFs from patients with noninfectious neurological disorders. Detection rates were similar in patients with CNS infections of unknown etiology and those in whom other pathogens were detected. A similar detection rate in feces from healthy children suggested food-borne or orofecal transmission routes, while high detection rates in feces from pigs and poultry (average, 58%) suggested the existence of animal reservoirs for such transmission. Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus.

In many countries phytosanitary regulations apply to Potato spindle tuber viroid, because it can cause serious diseases in potato and tomato crops. Other pospiviroids, some of which are distributed widely in ornamental crops, can cause similar diseases. Consequently, there is a need for a reliable and cost-effective generic testing method. An assay was developed that detects all known species of the genus Pospiviroid, using real-time RT-PCR based on TaqMan technology. This GenPospi assay consists of two reactions running in parallel, the first targeting all pospiviroids, except Columnea latent viroid, the second specifically targeting the latter viroid (already published). To monitor the RNA extraction a nad5 internal control was included. Method validation on tomato leaves showed that the GenPospi assay detects all pospiviroids up to a relative infection rate of 0.13% (equals 770 times dilution). The assay was specific because no cross reactivity was observed with other viroids, viruses or nucleic acid from plant hosts. Repeatability and reproducibility were 100% and the assay appeared robust in an inter-laboratory comparison. The GenPospi assay has been shown to be a suitable tool for large-scale screening for all known pospiviroids. Although it has been validated for tomato leaves it can potentially be used for any crop., (Copyright © 2012 Elsevier B.V. All rights reserved.)

In this study, we test whether the δ(13)C and δ(15)N in a peat profile are, respectively, linked to the recent dilution of atmospheric δ(13)CO(2) caused by increased fossil fuel combustion and changes in atmospheric δ(15)N deposition. We analysed bulk peat and Sphagnum fuscum branch C and N concentrations and bulk peat, S. fuscum branch and Andromeda polifolia leaf δ(13)C and δ(15)N from a 30-cm hummock-like peat profile from an Aapa mire in northern Finland. Statistically significant correlations were found between the dilution of atmospheric δ(13)CO(2) and bulk peat δ(13)C, as well as between historically increasing wet N deposition and bulk peat δ(15)N. However, these correlations may be affected by early stage kinetic fractionation during decomposition and possibly other processes. We conclude that bulk peat stable carbon and nitrogen isotope ratios may reflect the dilution of atmospheric δ(13)CO(2) and the changes in δ(15)N deposition, but probably also reflect the effects of early stage kinetic fractionation during diagenesis. This needs to be taken into account when interpreting palaeodata. There is a need for further studies of δ(15)N profiles in sufficiently old dated cores from sites with different rates of decomposition: These would facilitate more reliable separation of depositional δ(15)N from patterns caused by other processes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11270-011-1001-8) contains supplementary material, which is available to authorized users.

The distribution of species of aerobic chemolitho-autotrophic microorganisms such as ammonia-oxidizing bacteria are governed by pH, salinity, and temperature as well as the availability of oxygen, ammonium, carbon dioxide, and other inorganic elements required for growth. Impounded mangrove forests in the Indian River Lagoon, a coastal estuary on the east coast of Florida, are dominated by mangroves, especially stands of Black mangrove (Avicennia germinans) that differ in the size and density of individual plants. In March 2009, the management of one impoundment was changed to a regime of pumping estuarine water into the impoundment at critical times of the year to eliminate breeding sites for noxious insects. We collected soil samples in three different Black mangrove habitats before and after the change in management to determine the impacts of the altered hydrologic regimes on the distribution of 16s rRNA genes belonging to ammonia-oxidizing betaproteobacteria (β-AOB). We also sampled soils in an adjacent impoundment in which there had not been any hydrologic alteration. At the level of 97% mutual similarity in the 16s rRNA gene, 13 different operational taxonomic units were identified; the majority related to the lineages of Nitrosomonas marina (45% of the total clones), Nitrosomonas sp. Nm143 (23%), and Nitrosospira cluster 1 (19%). Long-term summer flooding of the impoundment in 2009, after initiation of the pumping regime, reduced the percentage of N. marina by half between 2008 and 2010 in favor of the two other major lineages and the potential ammonia-oxidizing activity decreased by an average of 73%. Higher interstitial salinities, probably due to a prolonged winter drought, had a significant effect on the composition of the β-AOB in March 2009 compared to March 2008: Nitrosomonas sp. Nm143 was replaced by Nitrosospira cluster 1 as the second most important lineage. There were small, but significant differences in the bacterial communities between the flooded and non-flooded impoundments. There were also differences in the community composition of the bacteria in the three Black mangrove habitats. N. marina was most dominant in all three habitats, but was partly replaced by Nitrosospira cluster 1 in sites dominated by sparsely distributed trees and by Nitrosomonas sp. Nm143 in sites characterized by taller, more densely distributed Black mangrove trees.

A full-scale remediation facility including a detention basin and a wetland was tested for retention of heavy metals and Poly-Aromatic Hydrocarbons (PAHs) from water drained from a motorway in The Netherlands. The facility consisted of a detention basin, a vertical-flow reed bed and a final groundwater infiltration bed. Water samples were taken of road water, detention basin influent and wetland effluent. By using automated sampling, we were able to obtain reliable concentration averages per 4-week period during 18 months. The system retained the PAHs very well, with retention efficiencies of 90-95%. While environmental standards for these substances were surpassed in the road water, this was never the case after passage through the system. For the metals the situation was more complicated. All metals studied (Cu, Zn, Pb, Cd and Ni) had concentrations frequently surpassing environmental standards in the road water. After passage through the system, most metal concentrations were lower than the standards, except for Cu and Zn. There was a dramatic effect of de-icing salts on the concentrations of Cu, Zn, Cd and Ni, in the effluent leaving the system. For Cu, the concentrations even became higher than they had ever been in the road water. It is advised to let the road water bypass the facility during de-icing periods., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Tomato planta macho viroid (TPMVd) and Mexican papita viroid (MPVd) are two closely related (>90% sequence identity) members of the genus Pospiviroid. Their current status as members of separate species is based upon the reported ability of TPMVd to replicate in Gomphrena globosa and the inability of this viroid to evoke flower break in N. glutinosa. Characterization of a viroid recently isolated from diseased tomato plants grown in Mexico (identical to GenBank accession GQ131573) casts doubt on this earlier report and indicates that these viroids should be classified as members of a single species. Giving priority to the older name, we propose including both of these viroids in the current species Tomato planta macho viroid.

A tospovirus causing necrotic streaks on leaves was isolated from Alstroemeria sp. in Colombia. Infected samples reacted positively with tomato spotted wilt virus (TSWV) antiserum during preliminary serological tests. Further analysis revealed a close serological relationship to tomato chlorotic spot virus (TCSV) and groundnut ringspot virus (GRSV). A major part of the S-RNA segment, encompassing the nucleocapsid (N) protein gene, the 5' untranslated region and a part of the intergenic region 3' of the N gene, was cloned and sequenced. The deduced N protein sequence showed highest amino acid identity (82%) to that of TCSV, indicating that the virus represents a new tospovirus species, for which the name Alstroemeria necrotic streak virus (ANSV) is coined. Phylogenetic analysis based on the N protein sequence revealed that this Alstroemeria-infecting tospovirus clustered with tospoviruses from the American continent. Frankliniella occidentalis was identified as potential vector species for ANSV.

Eleven pospiviroid isolates from ornamental plants and one from pepper were successfully transmitted to potato and tomato by mechanical inoculation. All isolates with characteristic predominant genotypes were inoculated to a series of potato and tomato plants and propagated for up to four passages. In total, 385 nucleotide sequences were determined, in which 17 new predominant genotypes were identified with minimal differences to the original predominant genotype. In addition, in the original ornamental hosts, only one of eleven predominant pospiviroid genotypes had changed during the experiments over a period of 2 years. These results confirm the high stability of predominant pospiviroid genotypes.

Background: Wetlands are species-rich habitats performing valuable ecosystem services such as flood protection, water quality enhancement, food chain support and carbon sequestration. Worldwide, wetlands have been drained to convert them into agricultural land or industrial and urban areas. A realistic estimate is that 50 % of the world's wetlands have been lost., Scope: This paper reviews the relationship between wetlands and agriculture with the aim to identify the successes and failures of agricultural use in different types of wetlands, with reference to short-term and long-term benefits and issues of sustainability. It also addresses a number of recent developments which will lead to pressure to reclaim and destroy natural wetlands, i.e. the continuous need for higher production to feed an increasing world population and the increasing cultivation of energy crops. Finally, attention is paid to the development of more flood-tolerant crop cultivars., Conclusions: Agriculture has been carried out in several types of (former) wetlands for millennia, with crop fields on river floodplain soils and rice fields as major examples. However, intensive agricultural use of drained/reclaimed peatlands has been shown to lead to major problems because of the oxidation and subsidence of the peat soil. This does not only lead to severe carbon dioxide emissions, but also results in low-lying land which needs to be protected against flooding. Developments in South-East Asia, where vast areas of tropical peatlands are being converted into oil palm plantations, are of great concern in this respect. Although more flood-tolerant cultivars of commercial crop species are being developed, these are certainly not suitable for cultivation in wetlands with prolonged flooding periods, but rather will survive relatively short periods of waterlogging in normally improved agricultural soils. From a sustainability perspective, reclamation of peatlands for agriculture should be strongly discouraged. The opportunities for agriculture in naturally functioning floodplains should be further investigated. The development and use of crop cultivars with an even stronger flood tolerance could form part of the sustainable use of such floodplain systems. Extensive use of wetlands without drastic reclamation measures and without fertilizer and pesticides might result in combinations of food production with other wetland services, with biodiversity remaining more or less intact. There is a need for research by agronomists and environmental scientists to optimize such solutions.

In autumn 2006, a new disease was observed in a glasshouse-grown crop of sweet pepper (Capsicum annuum L.) in the Netherlands. Fruit size of the infected plants was reduced up to 50%, and plant growth was also slightly reduced. Here we show that the disease is caused by a previously non-described viroid. The pepper viroid is transmitted by both mechanical inoculation and pepper seeds and, when inoculated experimentally, it infects several solanaceous plant species inducing vein necrosis and reduced fruit and tuber size in tomato and potato, respectively. The viroid RNA genome consists of 348 nucleotides and, with minor modifications, it has the central conserved and the terminal conserved regions characteristic of members of the genus Pospiviroid. Classification of the pepper viroid within the genus Pospiviroid is further supported by the presence and structure of hairpins I and II, the presence of internal and external RY motifs, and phylogenetic analyses. The primary structure of the pepper viroid only showed a maximum of 66% nucleotide sequence identity with other viroids, which is far below the main species demarcation limit of 90%. According to its biological and molecular properties, we propose to assign the pepper viroid to a new species within the genus Pospiviroid, and to name this new species Pepper chat fruit viroid.

Both eutrophication and SO4 pollution can lead to higher availability of nutrients and potentially toxic compounds in wetlands. To unravel the interaction between the level of eutrophication and toxicity at species and community level, effects of SO4 were tested in nutrient-poor and nutrient-rich fen mesocosms. Biomass production of aquatic and semi-aquatic macrophytes and colonization of the water layer increased after fertilization, leading to dominance of highly competitive species. SO4 addition increased alkalinity and sulphide concentrations, leading to decomposition and additional eutrophication. SO4 pollution and concomitant sulphide production considerably reduced biomass production and colonization, but macrophytes were less vulnerable in fertilized conditions. The experiment shows that competition between species, vegetation succession and terrestrialization are not only influenced by nutrient availability, but also by toxicity, which strongly interacts with the level of eutrophication. This implies that previously neutralized toxicity effects in eutrophied fens may appear after nutrient reduction measures have been taken.

Chronically nitrate-loaded riparian buffer zones show high N(2)O emissions. Often, a large part of the N(2)O is emitted from small surface areas, resulting in high spatial variability in these buffer zones. These small surface areas with high N(2)O emissions (hotspots) need to be investigated to generate knowledge on the factors governing N(2)O emissions. In this study the N(2)O emission variability was investigated at different spatial scales. Therefore N(2)O emissions from three 32 m(2) grids were determined in summer and winter. Spatial variation and total emission were determined on three different scales (0.3 m(2), 0.018 m(2) and 0.0013 m(2)) at plots with different levels of N(2)O emissions. Spatial variation was high at all scales determined and highest at the smallest scale. To test possible factors inducing small scale hotspots, soil samples were collected for slurry incubation to determine responses to increased electron donor/acceptor availability. Acetate addition did increase N(2)O production, but nitrate addition failed to increase total denitrification or net N(2)O production. N(2)O production was similar in all soil slurries, independent of their origin from high or low emission soils, indicating that environmental conditions (including physical factors like gas diffusion) rather than microbial community composition governed N(2)O emission rates.

Many lakes have experienced a transition from a clear into a turbid state without macrophyte growth due to eutrophication. There are several measures by which nitrogen (N) and phosphorus (P) concentrations in the surface water can be reduced. We used the shallow lake model PCLake to evaluate the effects of three measures (reducing external nutrient loading, increasing relative marsh area, and increasing exchange rate between open water and marsh) on water quality improvement. Furthermore, the contribution of different retention processes was calculated. Settling and burial contributed more to nutrient retention than denitrification. The model runs for a typical shallow lake in The Netherlands showed that after increasing relative marsh area to 50%, total phosphorous (TP) concentration in the surface water was lower than the Maximum Admissible Risk (MAR, a Dutch government water quality standard) level, in contrast to total nitrogen (TN) concentration. The MAR levels could also be achieved by reducing N and P load. However, reduction of nutrient concentrations to MAR levels did not result in a clear lake state with submerged vegetation. Only a combination of a more drastic reduction of the present nutrient loading, in combination with a relatively large marsh cover (approximately 50%) would lead to such a clear state. We therefore concluded that littoral marsh areas can make a small but significant contribution to lake recovery.

Dutch water policy aims for more frequent, controlled flooding of river valley floodplains to avoid unwanted flooding elsewhere; in anticipation of increased flooding risks resulting from climate changes. Controlled flooding usually takes place in winter in parts of the valleys which had not been subject to flooding in the last decades. It may thus affect existing nature with its conservation values. The goal of this study was to clarify the geochemical and hydrological factors determining plant species composition of winter-flooded river valley grasslands. A correlative study was carried out in 43 sites in 13 Dutch river valley floodplains, with measurements of flooding regime, vegetation composition, soil nutrients and soil pH status. With the use of canonical correspondence analysis (CCA) the plant species composition was investigated in relation to the geochemical variables and the winter winter-flooding regime. We found that the distributions of target species and non-target species were clearly correlated with geochemical characteristics and flooding regime. Clustering of sites within the CCA plots has led us to distinguish between four types of winter flooding in our areas: floodplains with (a) accumulating rain water, (b) low groundwater levels flooded with river water, (c) discharging groundwater and (d) high groundwater levels flooded with river water. Our major conclusions are (1) the winter groundwater level of winter-flooded grasslands was important for evaluating the effects of winter flooding on the geochemistry and plant species composition, and (2) winter winter-flooding effects were largely determined by the nature of the flooding. A high frequency of flooding particularly favoured a small set of common plant species. In areas with groundwater seepage, winter flooding may provide geochemical conditions suitable for diverse vegetation types with rare species. Rainwater flooded sites appeared less suitable for most target species.

Water quality in many stream catchments and river basins is severely impacted by nutrient enrichment as a result of agriculture. Water-resource managers worldwide are considering the potential role of riparian zones and floodplain wetlands in improving stream-water quality, as there is evidence at the site scale that such wetlands are efficient at removing nutrients from through-flowing water. However, recent studies have highlighted disadvantages of such use of wetlands, including emissions of greenhouse gases and losses of biodiversity that result from prolonged nutrient loading. Here, we discuss the water purification function of wetlands at the site and catchment scale and suggest ways in which these disadvantages could be overcome.

The efficacy and feasibility of annual harvesting of Phragmites australis and Typha latifolia shoots in autumn for nutrient removal was evaluated in a wetland system used for polishing sewage treatment plant (STP) effluent. Aboveground biomass and nutrient dynamics nutrient removal through harvest were studied in parallel ditches with stands of Phragmites or Typha that were mown in October during two successive years. The inflow rate of STP effluent to the ditches was experimentally varied, resulting in pairs of ditches with mean hydraulic retention times (HRT) of 0.3, 0.8, 2.3, and 9.3 days, corresponding to N and P mass loading rates of 122-4190 g N m(-2) yr(-1) and 28.3-994 g P m(-2) yr(-1). Nitrogen and P removal efficiency by harvest of Phragmites and Typha shoots in October increased with increasing HRT, despite the opposite HRT effect on N and P standing stocks. This removal through harvest appeared to be useful in treatment wetlands with N and P mass loading rates lower than approximately 120 g N m(-2) yr(-1) and 30 g P m(-2) yr(-1), corresponding to a HRT of roughly 9 days in the ditches of this wetland system. At the HRT of 9.3 days, the annual mass input to the ditches was reduced through the harvest by 7.0-11% and 4.5 -9.2% for N and P, respectively. At the higher nutrient mass loading rates, the nutrient removal through harvest was insignificant compared to the mass inputs. The vitality of Phragmites and Typha, measured as maximum aboveground biomass, was not affected by the annual cutting of the shoots in autumn over two years. The Typha stands yielded higher N and P removal efficiencies through shoot harvest than the Phragmites stands, which was largely the result of lower decreases in N and P standing stocks between August and October. This difference in nutrient standing stocks between the two species was caused by a combined effect of greater decreases in nutrient concentrations largely due to higher nutrient retranslocation efficiencies of Phragmites plants and greater reductions in shoot Phragmites biomass because of leaf fall and mass resorption. Nutrient removal by harvesting Phragmites shoots can probably be doubled without a reduction in vitality of the stands by advancing the harvest date to mid-September, which would at least approach the nutrient removal by harvesting Typha shoots in October. Phragmites also may be more profitable in very low-loaded wetland systems because the vigor of Typha stands seemed to be more sensitive to a lower nutrient availability at N and P mass input rates lower than the range indicated.

The usefulness of various suggested species demarcation criteria was compared in attempts to determine the taxonomic status of ten new tombusvirus isolates. Five of them (Lim 1, 2, 3, 5 and 6) were obtained from different sources of commercially grown statice (Limonium sinuatum), two (Gyp 1 and 2) from different sources of commercially grown Gypsophila paniculata and three from water samples, i.e. from a small river (Schunter) in Northern Germany, from a brook (near Dossenheim) in Southern Germany and from the groundwater in a Limonium production glasshouse in the Netherlands (Lim 4). The immunoelectron microscopical decoration test allowed a quick preliminary assignment of various isolates to several known tombusviruses. A more precise analysis of the relationships was achieved by comparing the deduced amino acid sequences of the coat proteins. Sequence as well as serological data suggested that eight of the isolates should be classified as strains or variants of either Carnation Italian ringspot virus, Grapevine Algerian latent virus, Petunia asteroid mosaic virus or Sikte waterborne virus, respectively, whereas the 9th isolate (Lim 2) appears to represent a distinct new tombusvirus species. The case of the 10th isolate (Lim 5) illustrates the classification problems experienced when the properties of a virus place it close to the more or less arbitrary man-made borderline between virus species and virus strains. The coat protein gene sequences were also determined for some viruses for which these data had not yet been available, i.e. Neckar river virus, Sikte waterborne virus and Eggplant mottled crinkle virus. The sequences of the coat protein gene and also of ORF 1 of the latter virus proved to be almost identical to the corresponding genome regions of the recently described Pear latent virus, which for priority reasons should be renamed. Criteria which have been suggested in addition to serology and sequence comparisons for tombusvirus species demarcation, i.e. differences in natural and in experimental host ranges, in cytopathological features and in coat protein size, appear to be of little value for the classification of new tombusviruses.

A comprehensive metabolomic profiling of Catharanthus roseus L. G. Don infected by 10 types of phytoplasmas was carried out using one-dimensional and two-dimensional NMR spectroscopy followed by principal component analysis (PCA), an unsupervised clustering method requiring no knowledge of the data set and used to reduce the dimensionality of multivariate data while preserving most of the variance within it. With a combination of these techniques, we were able to identify those metabolites that were present in different levels in phytoplasma-infected C. roseus leaves than in healthy ones. The infection by phytoplasma in C. roseus leaves causes an increase of metabolites related to the biosynthetic pathways of phenylpropanoids or terpenoid indole alkaloids: chlorogenic acid, loganic acid, secologanin, and vindoline. Furthermore, higher abundance of Glc, Glu, polyphenols, succinic acid, and Suc were detected in the phytoplasma-infected leaves. The PCA of the (1)H-NMR signals of healthy and phytoplasma-infected C. roseus leaves shows that these metabolites are major discriminating factors to characterize the phytoplasma-infected C. roseus leaves from healthy ones. Based on the NMR and PCA analysis, it might be suggested that the biosynthetic pathway of terpenoid indole alkaloids, together with that of phenylpropanoids, is stimulated by the infection of phytoplasma.

Herbaceous vegetation under temperate climatic conditions generally shows nitrogen- or phosphorus-limited plant growth, which creates conditions for a high botanical diversity. Is nitrogen (N) or phosphorus (P) the most important limiting factor, or are both generally in short supply? What are the consequences of Increased N and P inputs that result from anthropogenic disturbances? A new indicator of N or P limitation, that is, the vegetation N:P ratio, allows us to address these questions for a range of mires, dune slacks and moist grasslands.

The application of fractal analysis to parametric imaging of B-mode echograms and to differentiation of echographic speckle textures was investigated. Echograms were obtained from realistic simulations and from a clinical study on diffuse liver disease. The simulations comprised tissue models with randomly positioned scatterers in a 3-D volume in which the number density was varied over a range from 0.5 to 25 mm-3. The clinical echograms comprised both normals and patients with liver cirrhosis. Three methods of estimating the fractal dimension were investigated, two in the spatial image domain and one in the spatial frequency domain. The results of these methods are compared and the applicability and the limitations of texture differentiation using fractal analysis is discussed. The main conclusion is that fractal analysis offers no obvious advantage over statistical analysis of the texture of echographic images. Its use for parametric imaging is further limited by the need to use relatively large windows for local estimation of the fractal dimension.

Three different methods were investigated to determine their ability to detect and classify various categories of diffuse liver disease. A statistical method, i.e., discriminant analysis, a supervised neural network called backpropagation and a nonsupervised, self-organizing feature map were examined. The investigation was performed on the basis of a previously selected set of acoustic and image texture parameters. The limited number of patients was successfully extended by generating additional but independent data with identical statistical properties. The generated data were used for training and test sets. The final test was made with the original patient data as a validation set. It is concluded that neural networks are an attractive alternative to traditional statistical techniques when dealing with medical detection and classification tasks. Moreover, the use of generated data for training the networks and the discriminant classifier has been shown to be justified and profitable.

An objective measure (Lesion Signal-to-Noise Ratio) quantifying the detectability of lesions in echographic images was employed. This measure was used to determine the performance of digital speckle reduction filters, which were applied to computer simulated ultrasound B-mode images. One linear (mean filter) and two nonlinear filters (median and L2-mean filters) have been investigated. A comparison was made between fixed and adaptive versions of these filters. The influence of the size of the filter window on the Lesion Signal-to-Noise Ratio was systematically investigated. Also, the effect of the shape of the filter window is illustrated. The difference in performance of the linear and nonlinear filters was found to be small. Adaptive filters did not perform significantly better than fixed filters. The maximum improvement of lesion detectability was in the order of 40 percent. The choice of a correct window size was critical. For all types of filters, an optimum window size appeared to be present in the curves relating the Lesion Signal-to-Noise Ratio to this size.

Signal-to-noise-ratio (SNR) images were constructed by a sliding window technique. Theoretical derivations of the first order statistical properties of SNR images are given for the case of intensity coding of the original images for low number densities and for the limit case of fully developed speckle. The original images were obtained by realistic simulations of backscattering by homogeneous media, while using a range of number densities of the scatterers (isotropic scattering). The SNR imaging method is illustrated by results obtained from simulated scattering media containing a lesion that is contrasting in reflectivity level or in number density of the scatterers. A considerable improvement in lesion detection is obtained if the primary difference from the background speckle is due to a different number density of the scatterers within the lesion.

Release of inorganic N and P in the organic soils of three small quaking fens in The Netherlands was studied by means of in situ incubation of the peat soil in plastic bottles. One of the fens had higher biomass production and lower species richness than the other two. The former fen is located in an area with downward groundwater percolation, whereas the latter fens are situated in an area of upward seepage of groundwater rich in calcium and bicarbonate.Mineralization of N proved to be slow in the low-productive fens, and 6 times faster in the highly productive fen. In the latter fen the amount of N mineralized during a certain period exceeded by far the amount accumulated in that period in the above-ground parts of the vegetation.The release of inorganic P was extremely slow in the two low-productive fens and rapid in the highly productive fen. The release rates were not related to the total P content of the soils. The slow P release in the low-productive fens may be due to the continuous inflow of groundwater rich in Ca, Al and Fe compounds.It can be concluded that the soil is a potentially large source of inorganic N and P in quaking fens. The importance of the soil versus other N and P sources is greater in nutrient-rich fens.

In a typical Dutch polder landscape the effects of nutrient transport from cultivated grassland to mesotrophic fen communities were studied. In a comparative approach, biomass production and nutrient (N, P and K) uptake were determined monthly in four fens and a hayfield differeing in productivity and species composition. The interstitial ground water was sampled every two weeks for determinations of inorganic nutrient concentrations.The differences in productivity between the fens were clearly reflected in the amount of N, P and K taken up in the above-ground vegetation. N and P proved to be limiting plant growth in the fens, whereas K was the main limiting factor in the hayfield. The ground water welling up from the sandy bottom into the fens proved to be rich in ammonia (3-5 ppm). There are strong indications that this continual seepage leads to a considerable input of N into the fens but not to a higher productivity, as the ammonia is absorbed by the lowermost peat layers covering the sand.At this moment, the differences in productivity between the fens must be caused by differences in the rates of mineralization of the superficial peat layer. The degree of fixation of the floating vegetation mat, determining whether or not low water levels lead to an aerated soil top layer, is important in this respect. Within a period of decades, however, the continuous inflow of ammonia may eventually cause an increase in the productivity and a change in the species composition of the fens.