Jaap van Rijn

Bio: Jaap van Rijn is an academic researcher from Hebrew University of Jerusalem. The author has contributed to research in topics: Nitrate & Denitrification. The author has an hindex of 29, co-authored 51 publications receiving 2967 citations.

Steps in the construction of underwater coral nursery, an essential component in reef restoration acts

Abstract: Many coral reefs worldwide are rapidly declin- ing, but efficient restoration techniques are not yet available. Here, we evaluate methodologies for reef res- toration based on the ''gardening concept''. A floating mid-water prototype nursery was placed at 6 m depth (14 m above sea-bottom) within the nutrient-enriched environment of a fish farm (Eilat, Red Sea). Ten colonies from five branching coral species provided 6,813 frag- ments (0.5-3 cm height). The fragments, each attached to a plastic pin, were inserted into plastic nets that were tied to a rope-net floating nursery. After 144 nursery days, only 13.1% of the fragments died and 21.2% were de- tached by mechanical forces. Small colonies ready for transplantation developed within 144-200 days. Ramets' ecological volumes increased 13-46 folds and their heights by a factor of 3.5. After 306 days, the ecological volumes of the colonies increased 147-163 fold as com- pared to original volumes (revealing a daily growth rate constant of 1.67% during the first 5-10 months) and height values by a factor of six. Building and maintenance costs of the nursery were low. This nursery prototype demonstrates the feasibility of the coral ''gardening concept'' by fulfilling several important needs, namely, mass production of coral colonies at low costs, high survivorship, fast growth, short nursery phase and im- proved methodologies for handling farmed colonies.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

Abstract: The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Complete nitrification by Nitrospira bacteria

Abstract: Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.

Harmful algal blooms: Their ecophysiology and general relevance to phytoplankton blooms in the sea

Abstract: From 60 to 80 species of phytoplankton have been reported to be harmful; of these, 90% are flagellates, notably dinoflagellates. The effects of turbulence on harmful algal bloom (HAB) taxa, their photoadaptive strategies, growth rate, and nutrient uptake affinity (Ks) are considered. Flagellates, including HAB taxa, collectively have a lower nutrient uptake affinity than diatoms. Four major adaptations are suggested to have been evolved to offset the ecological disadvantages of their low nutrient affinity: nutrient retrieval migrations; mixotrophic tendencies; alle-lelochemically enhanced interspecific competition; and allelopathic, antipredation defense mechanisms. Motility-based behavioral features of flagellates contributing to their blooms include: phototaxis, vertical migration, pattern swimming, and aggregation, which facilitate nutrient retrieval, trace metal detoxification, antipredation, depth-keeping, and turbulence avoidance. Neither a general physiological syndrome nor distinctive physiological profile distinguishes harmful flagellate species from nonharmful taxa. However, HAB flagellates exhibit significant ecophysiological differences when compared to diatoms, including greater biophysical vulnerability to turbulence, greater bloom dependence on water-mass stratification, greater nutritional diversity involving mixotrophic tendencies, greater potential use of allelochemical mechanisms in interspecific competition and antipredation defenses, and unique behaviorial consequences of their motility. Flagellates use a “swim” strategy; diatoms a “sink” strategy.