Ecological restoration of rich fens in Europe and North America: from trial and error to an evidence‐based approach

Fens represent a large array of ecosystem services, including the highest biodiversity found among wetlands, hydrological services, water purification and carbon sequestration. Land‐use change and drainage has severely damaged or annihilated these services in many parts of North America and Europe; restoration plans are urgently needed at the landscape level. We review the major constraints on the restoration of rich fens and fen water bodies in agricultural areas in Europe and disturbed landscapes in North America: (i) habitat quality problems: drought, eutrophication, acidification, and toxicity, and (ii) recolonization problems: species pools, ecosystem fragmentation and connectivity, genetic variability, and invasive species; and here provide possible solutions. We discuss both positive and negative consequences of restoration measures, and their causes. The restoration of wetland ecosystem functioning and services has, for a long time, been based on a trial‐and‐error approach. By presenting research and practice on the restoration of rich fen ecosystems within agricultural areas, we demonstrate the importance of biogeochemical and ecological knowledge at different spatial scales for the management and restoration of biodiversity, water quality, carbon sequestration and other ecosystem services, especially in a changing climate. We define target processes that enable scientists, nature managers, water managers and policy makers to choose between different measures and to predict restoration prospects for different types of deteriorated fens and their starting conditions.     

The HOX-5 and surfeit gene clusters are linked in the proximal portion of mouse chromosome 2

Using an interspecies backcross, we have mapped the HOX-5 and surfeit (surf) gene clusters within the proximal portion of mouse chromosome 2. While the HOX-5 cluster of homeobox-containing genes has been localized to chromosome 2, bands C3-E1, by in situ hybridization, its more precise position relative to the genes and cloned markers of chromosome 2 was not known. Surfeit, a tight cluster of at least six highly conserved “housekeeping” genes, has not been previously mapped in mouse, but has been localized to human chromosome 9q, a region of the human genome with strong homology to proximal mouse chromosome 2. The data presented here place HOX-5 in the vicinity of the closely linked set of developmental mutations rachiterata, lethargic, and fidget and place surf close to the proto-oncogene Abl, near the centromere of chromosome 2.     

Enrichment and characterization of marine anammox bacteria associated with global nitrogen gas production

Microbiological investigation of anaerobic ammonium oxidizing (anammox) bacteria has until now been restricted to wastewater species. The present study describes the enrichment and characterization of two marine Scalindua species, the anammox genus that dominates almost all natural habitats investigated so far. The species were enriched from a marine sediment in the Gullmar Fjord (Sweden) using a medium based on Red Sea salt. Anammox cells comprised about 90% of the enrichment culture after 10 months. The enriched Scalindua bacteria displayed all typical features known for anammox bacteria, including turnover of hydrazine, the presence of ladderane lipids, and a compartmentalized cellular ultrastructure. The Scalindua species also showed a nitrate-dependent use of formate, acetate and propionate, and performed a formate-dependent reduction of nitrate, Fe(III) and Mn(IV). This versatile metabolism may be the basis for the global distribution and substantial contribution of the marine Scalindua anammox bacteria to the nitrogen loss from oxygen-limited marine ecosystems.     

In situ quantification of aberrant p53 in colorectal neoplasia

Aberrant p53 protein accumulation was measured immunohistologically in 342 colorectal paraffin-embedded tissue sections from 115 patients (24 with adenocarcinoma, 59 with adenoma and 32 'hospital controls'). Subjective scoring was compared with quantitative cell imaging, including dichotomous (p53⁺/p53^-) status, ng p53^mut mg^-1 enterocyte protein, and tumour burden and patient body 'burden' of aberrant p53. A total of 62.5% cancer patients, 23.7% adenoma patients and 3.1% hospital controls were accorded p53⁺ status on the basis of p53 quantification. Quantitative p53⁺/p53^- assignment had a stronger inverse association with survival (χ²=6.17, p=0.013, Kaplan-Meier test) than subjective 'visual estimation' (χ²=0.57, p=0.449). There was a strong inverse relationship between the p53 'body burden' and the months of post-diagnosis survival (hazard ratio=1.42, p=0.0004, Cox proportional hazards). Absolute quantification for inactivated p53 permits objective and reproducible scoring, adjusts for intra-laboratory immunostaining 'batch effects', corrects for fixation artefacts, and standardizes for inter-laboratory differences in fixation, antibody selection and staining method. Clinically, in situ quantification of p53 will permit more accurate survival prognoses and will inform therapy selection and dose. Ultimately, accurate quantitative tissue/blood p53 correlations may provide a minimally invasive and systemic surrogate measure for these same clinical purposes.     

An assessment of macroinvertebrate functional feeding groups as water quality indicators in the Buffalo River, eastern Cape Province, South Africa

The aim of this paper was to investigate the potential for using functional feeding groups (FFGs) as indicators of water quality conditions in rivers, using the Buffalo River, South Africa, as a specific example. Multivariate classification and ordination techniques were used to investigate species and FFG distributions in relation to a number of physico-chemical variables at 16 sites from the headwaters to the estuary of the Buffalo River.Two-way indicator species analysis (TWINSPAN) of species composition ranked most of the sites sequentially down the river, irrespective of water quality conditions. Ordination of FFGs from a set of riffle samples collected in mid-late summer showed only weak relationships between FFG distribution and water quality changes, except where variables changed sequentially down the river (e.g. pH and temperature). Individual species responses to water quality gradients were examined for nine riffle-dwelling species representing diverse FFGs. Following correspondence analysis of a matrix of environmental variables and species frequencies, some species showed strong associations with defined ranges of some variables. In particular, Adenophlebia auriculata (Leptophlebiidae, Ephemeroptera) from the headwater sampling site, was associated with low pH and low temperature. Simulium damnosum occurred under conditions of high turbidity, while Afronurus harrisoni was found under high concentrations of potassium, ammonium and nitrite ions.We conclude that although there was a distinct headwaters fauna in the Buffalo River, and sequential downstream changes in species composition, most FFGs (apart from shredders) were represented down the whole length of the river. FFG classifications are therefore unlikely to provide useful indications of water quality conditions in the Buffalo River.Using a categorical approach to classifying water quality variables, and by applying correspondence analysis to the resulting matrix, we recognised nine species that could be used to define water quality. These indicator species can be used to define tolerance ranges of the fauna for water quality conditions in different parts of the Buffalo river.     

New pathways for ammonia conversion in soil and aquatic systems

Ammonia conversion processes are essential for most soil and aquatic systems. Under natural conditions, the many possible reactions are difficult to analyze. For example, nitrification and denitrification have long been regarded as separate phenomena performed by different groups of bacteria in segregated areas of soils, sediments or aquatic systems sequentially in time. It has now been established that strict segregation in place and time of the two processes is not necessary and that both denitrifiers and nitrifiers have versatile metabolisms. However, the rates described for aerobic denitrifiers are very low compared to the rates observed under anoxic conditions. Also the rates of nitrifier denitrification are quite low, indicating that these conversions may not play an important role under natural conditions. In addition, these processes often result in the emission of quite large amounts of undesirable products, NO and N₂O. Heterotrophic nitrification might be of relevance for systems, that contain a high carbon to nitrogen ratio. Recently, a novel process (Anammox) has been discovered in which ammonium serves as the electron donor for denitrification of nitrite into dinitrogen gas. ¹⁵N labeling studies showed that hydrazine and hydroxylamine were important intermediates in this process. Enrichment cultures on ammonium, nitrite and bicarbonate resulted in the dominance of one morphotypical microorganism. The growth rate of the cultures is extremely low (doubling time 11 days), but the affinity for ammonium and nitrite and the conversion rates (9.2 10^–4 mol kg^–1 s^–1) are quite high. Some of the reported high nitrogen losses in soil and aquatic systems might be attributed to anaerobic ammonium oxidation. In addition, this conversion offers new opportunities for nitrogen removal, when it is combined with recently developed processes for partial nitrification.     

Development of a technology for commercial phytoextraction of nickel: economic and technical considerations

In recent R&D work, we have made progress in developing a commercial technology using hyperaccumulator plant species to phytoextract nickel (Ni) from contaminated and/or Ni-rich soils. An on-going program is being carried out to develop a genetically improved phytoextraction plant that combines favorable agronomic and Ni accumulation characteristics. Genetically diverse Ni hyperaccumulator species and ecotypes of Alyssum were collected and then evaluated in both greenhouse and field using serpentine and Ni-refinery contaminated soils. Large genetic variation was found in those studies. Mean shoot Ni concentrations in field-grown plants ranged from 4200 to 20400 mg kg^–1. We have been studying several soil management practices that may affect the efficiency of Ni phytoextraction. Soil pH is an important factor affecting absorption of metals by plants. An unexpected result of both greenhouse and field experiments was that Ni uptake by two Alyssum species was reduced at lower soil pH and increased at higher soil pH. At higher pH, plant yield was improved also. In soil fertility management studies, we found that N application significantly increased plant biomass, but did not affect plant shoot Ni concentration. These findings indicate that soil management will be important for commercial phytoextraction. A number of field trials have been carried out to study planting methods, population density, weed control practices, harvest schedule and methods, pollination control, and seed processing. Such crop management studies have improved phytoextraction efficiency and provide a tool for farmers to conduct commercial production. We have done some work to develop efficient and cost-effective methods of Ni recovery. Recovery of energy by biomass burning or pyrolysis could help make phytoextraction more cost-effective. The progress made in our recent studies will enable us to apply this technology commercially in the near future.     

Cell-surface markers for the isolation of pancreatic cell types derived from human embryonic stem cells

Using a flow cytometry-based screen of commercial antibodies, we have identified cell-surface markers for the separation of pancreatic cell types derived from human embryonic stem (hES) cells. We show enrichment of pancreatic endoderm cells using CD142 and of endocrine cells using CD200 and CD318. After transplantation into mice, enriched pancreatic endoderm cells give rise to all the pancreatic lineages, including functional insulin-producing cells, demonstrating that they are pancreatic progenitors. In contrast, implanted, enriched polyhormonal endocrine cells principally give rise to glucagon cells. These antibodies will aid investigations that use pancreatic cells generated from pluripotent stem cells to study diabetes and pancreas biology.     

Impacts of harmful algae on seafarming in the Asia-Pacific areas

Seafarming to produce human food has recently intensified, particularly in the Asia-Pacific region. Disastrous impacts of harmful phytoplankton blooms, however, have been experienced during the past 20 years. In extreme cases, these render shellfish and finfish toxic or cause massive fish and shrimp kills. Problems from marine algae in the region include paralytic shellfish poisoning, diarrhetic shellfish poisoning, ciguatera, tetrodotoxin poisoning, fish kills and tainting of fish and shellfish. An analysis of 72 incidents since 1934 showed that 57% were fish and shrimp kills; almost all the remainder were PSP events. By mid-1994 there had been 3164 recorded cases of human poisoning and 148 reported deaths from these events in Asia-Pacific. Economic losses may exceed one million US dollars per event, while monitoring costs may be up to $50000 annually for each affected area. Research needs, management strategies and international cooperation are discussed. National action plan considerations include shellfish sanitation programs, public awareness and education, coastal engineering and classification of waters to protect public health.     

Microbial structural diversity estimated by dilution-extinction of phenotypic traits and T-RFLP analysis along a land-use intensification gradient

The present work tested whether the relationship between functional traits and inoculum density reflected structural diversity in bacterial communities from a land-use intensification gradient applying a mathematical model. Terminal restriction fragment length polymorphism (T-RFLP) analysis was also performed to provide an independent assessment of species richness. Successive 10-fold dilutions of a soil suspension were inoculated onto Biolog GN(R) microplates. Soil bacterial density was determined by total cell and plate counts. The relationship between phenotypic traits and inoculum density fit the model, allowing the estimation of maximal phenotypic potential (Rmax) and inoculum density (KI) at which Rmax will be half-reduced. Though Rmax decreased with time elapsed since clearing of native vegetation, KI remained high in two of the disturbed sites. The genetic pool of bacterial community did not experience a significant reduction, but the active fraction responding in the Biolog assay was adversely affected, suggesting a reduction in the functional potential.