Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic.

Fungi are abundant and functionally important in the Arctic, yet comprehensive studies of their diversity in relation to geography and environment are not available. We sampled soils in paired plots along the North American Arctic Transect (NAAT), which spans all five bioclimatic subzones of the Arctic. Each pair of plots contrasted relatively bare, cryoturbated patterned-ground features (PGFs) and adjacent vegetated between patterned-ground features (bPGFs). Fungal communities were analysed via sequencing of 7834 ITS-LSU clones. We recorded 1834 OTUs - nearly half the fungal richness previously reported for the entire Arctic. These OTUs spanned eight phyla, 24 classes, 75 orders and 120 families, but were dominated by Ascomycota, with one-fifth belonging to lichens. Species richness did not decline with increasing latitude, although there was a decline in mycorrhizal taxa that was offset by an increase in lichen taxa. The dominant OTUs were widespread even beyond the Arctic, demonstrating no dispersal limitation. Yet fungal communities were distinct in each subzone and were correlated with soil pH, climate and vegetation. Communities in subzone E were distinct from the other subzones, but similar to those of the boreal forest. Fungal communities on disturbed PGFs differed significantly from those of paired stable areas in bPGFs. Indicator species for PGFs included lichens and saprotrophic fungi, while bPGFs were characterized by ectomycorrhizal and pathogenic fungi. Our results suggest that the Arctic does not host a unique mycoflora, while Arctic fungi are highly sensitive to climate and vegetation, with potential to migrate rapidly as global change unfolds.

Initial sequencing and analysis of the human genome.

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Radiation hybrid map of the mouse genome.

Radiation hybrid (RH) maps are a useful tool for genome analysis, providing a direct method for localizing genes and anchoring physical maps and genomic sequence along chromosomes. The construction of a comprehensive RH map for the human genome has resulted in gene maps reflecting the location of more than 30,000 human genes. Here we report the first comprehensive RH map of the mouse genome. The map contains 2,486 loci screened against an RH panel of 93 cell lines. Most loci (93%) are simple sequence length polymorphisms (SSLPs) taken from the mouse genetic map, thereby providing direct integration between these two key maps. We performed RH mapping by a new and efficient approach in which we replaced traditional gel- or hybridization-based assays by a homogeneous 5'-nuclease assays involving a single common probe for all genetic markers. The map provides essentially complete connectivity and coverage across the genome, and good resolution for ordering loci, with 1 centiRay (cR) corresponding to an average of approximately 100 kb. The RH map, together with an accompanying World-Wide Web server, makes it possible for any investigator to rapidly localize sequences in the mouse genome. Together with the previously constructed genetic map and a YAC-based physical map reported in a companion paper, the fundamental maps required for mouse genomics are now available.

A YAC-based physical map of the mouse genome.

A physical map of the mouse genome is an essential tool for both positional cloning and genomic sequencing in this key model system for biomedical research. Indeed, the construction of a mouse physical map with markers spaced at an average interval of 300 kb is one of the stated goals of the Human Genome Project. Here we report the results of a project at the Whitehead Institute/MIT Center for Genome Research to construct such a physical map of the mouse. We built the map by screening sequenced-tagged sites (STSs) against a large-insert yeast artificial chromosome (YAC) library and then integrating the STS-content information with a dense genetic map. The integrated map shows the location of 9,787 loci, providing landmarks with an average spacing of approximately 300 kb and affording YAC coverage of approximately 92% of the mouse genome. We also report the results of a project at the MRC UK Mouse Genome Centre targeted at chromosome X. The project produced a YAC-based map containing 619 loci (with 121 loci in common with the Whitehead map and 498 additional loci), providing especially dense coverage of this sex chromosome. The YAC-based physical map directly facilitates positional cloning of mouse mutations by providing ready access to most of the genome. More generally, use of this map in addition to a newly constructed radiation hybrid (RH) map provides a comprehensive framework for mouse genomic studies.

Dosage compensation proteins targeted to X chromosomes by a determinant of hermaphrodite fate.

In many organisms, master control genes coordinately regulate sex-specific aspects of development. SDC-2 was shown to induce hermaphrodite sexual differentiation and activate X chromosome dosage compensation in Caenorhabditis elegans. To control these distinct processes, SDC-2 acts as a strong gene-specific repressor and a weaker chromosome-wide repressor. To initiate hermaphrodite development, SDC-2 associates with the promoter of the male sex-determining gene her-1 to repress its transcription. To activate dosage compensation, SDC-2 triggers assembly of a specialized protein complex exclusively on hermaphrodite X chromosomes to reduce gene expression by half. SDC-2 can localize to X chromosomes without other components of the dosage compensation complex, suggesting that SDC-2 targets dosage compensation machinery to X chromosomes.

Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome.

Single-nucleotide polymorphisms (SNPs) are the most frequent type of variation in the human genome, and they provide powerful tools for a variety of medical genetic studies. In a large-scale survey for SNPs, 2.3 megabases of human genomic DNA was examined by a combination of gel-based sequencing and high-density variation-detection DNA chips. A total of 3241 candidate SNPs were identified. A genetic map was constructed showing the location of 2227 of these SNPs. Prototype genotyping chips were developed that allow simultaneous genotyping of 500 SNPs. The results provide a characterization of human diversity at the nucleotide level and demonstrate the feasibility of large-scale identification of human SNPs.

The Caenorhabditis elegans gene sdc-2 controls sex determination and dosage compensation in XX animals.

We have identified a new X-linked gene, sdc-2, that controls the hermaphrodite (XX) modes of both sex determination and X chromosome dosage compensation in Caenorhabditis elegans. Mutations in sdc-2 cause phenotypes that appear to result from a shift of both the sex determination and dosage compensation processes in XX animals to the XO modes of expression. Twenty-eight independent sdc-2 mutations have no apparent effect in XO animals, but cause two distinct phenotypes in XX animals: masculinization, reflecting a defect in sex determination, and lethality or dumpiness, reflecting a disruption in dosage compensation. The dosage compensation defect can be demonstrated directly by showing that sdc-2 mutations cause elevated levels of several X-linked transcripts in XX but not XO animals. While the masculinization is blocked by mutations in sex determining genes required for male development (her-1 and fem-3), the lethality, dumpiness and overexpression of X-linked genes are not, indicating that the effect of sdc-2 mutations on sex determination and dosage compensation are ultimately implemented by two independent pathways. We propose a model in which sdc-2 is involved in the coordinate control of both sex determination and dosage compensation in XX animals and acts in the regulatory hierarchy at a step prior to the divergence of the two pathways.

Two semi-automatic elutriators for extracting nematodes and certain fungi from soil.

Two efficient, semi-automatic elutriators for assaying soil samples for nematodes are described. The first apparatus is a four-unit elutriator which combines conventional extraction methods with the following major features: automatic mixing of 500- to 1,500-cm(3) soil samples with water (+/- air); "turbinate" sample splitters from which fractions of 1/15 or greater are passed onto 26- or 38-microm sieves for collection of larvae and adult nematodes; the capacity for collecting roots, intact egg masses, and cysts on 250-425-microm sieves; and a variable speed motorized sieve-shaker. Nematodes, after being collected on 38-microm sieves, are separated from debris by centrifugation or by Baermann trays. Secondary features include: air cylinders, solenoid valves, and time clock for automatic dumping residual soil and water; relay-controlled coarse spray nozzles activated for 5 sec every 30 sec for washing nematodes through 250-425-mum sieves; adjustable rates of water amt air flow, and tinting. The second type of elutriator operates on similar principles but costs less to construct. It requires somewhat more operator participation; sieve spraying is carried out by the operator, anti elutriators are dumped manually. Both elutriators also show promise for monitoring populations of certain other soil microorganisms.

A Method for Estimating Numbers of Eggs of Meloidogyne spp. in Soil.

A procedure for extracting eggs of Meloidogyne spp. from soil was developed by modifying and combining certain existing techniques. Egg masses were elutriated from the soft, gelatinous matrices of the egg masses were dissolved, and the dispersed eggs were stained to facilitate counting. Data on egg population densities thus obtained facilitate the study of population dynamics of Meloidogyne spp. and the analysis of root-knot epidemics.

Interactions between Meloidogyne incognita, M. hapla, and Pratylenchus brachyurus in Tobacco.

In a greenhouse pot experiment on the pathogenicity and interactions of Meloidogyne incognita, M. hapla and Pratylenchus brachyurus on four cultivars o f tobacco the cultivars 'Hicks' and 'NC 2326' were susceptible to each nematode and "NC 95' and 'NC 2512' resistant only to M. incognita.Mean heights of susceptible plants were depressed but fresh weight of tops did not differ significantly. Meloidogyne spp. increased fresh weight of susceptible (but not the resistant) roots.Reproduction of M. incognita was decreased in the presence of P. brachyurus in one case. M. hapla reproduction was less with either of the other nematodes in five out of eight cases. In 12 combinations involving P. brachyurus, reproduction of this species was depressed in seven, not affected in four and increased in one.Mechanisms involved in associative interactions were not identified but appeared to be indirect and to involve individual host-nematode responses.

Seasonal Population Dynamics of Selected Plant-parasitic Nematodes as Measured by Three Extraction Procedures.

Seasonal fluctuations in field populations of Meloidogyne spp. (M. incognita and M. hapla), Pratylenchus zeae, Criconemoides ornatum, Tylenchorhynchus claytoni, Belonolaimus longicaudatus, and Helicotylenchus dihystera were determined monthly for 1 year by three extraction procedures. Baermann funnel method (BF) gave highest recoveries of Meloidogyne spp. and P. zeae during summer and fall, but centrifugal-flotation (CF) and sugar-flotation-sieving (SFS) usually yielded higher numbers of these nematodes during winter and spring. CF was t h e only effective method for recovery of C. ornatum with maximum numbers occurring in September. Recoveries of T. claytoni were similar with all methods in summer and fall. However, BF gave low numbers in winter and spring, whereas population peaks with the flotation methods occurred in January and February. All methods gave similar recoveries of B. longicaudatus with highest numbers occurring in November and December. This species declined drastically in late winter and spring. Yields of H. dihystera were similar for all three methods with CF consistently higher and the major peaks occurring in August.

Effects of Storage Temperature and Extraction Procedure on Recovery of Plant-parasitic Nematodes from Field Soils.

Storage of nematodes in soil at -15 C for 1 to 16 weeks greatly increased nematode recovery by a sugar-flotation-sieving procedure. One week of exposure to -15 C killed all nematodes except Pratylenchus zeae and Tylenchorhynchus claytoni which were recoverable in decreasing numbers up to 10 weeks by the Baermann funnel method. Optimum storage temperature for survival of most nematode species was 13 C. The numbers of Meloidogyne incognita, T. claytoni, Belonolaimus Iongicaudatus, and P. zeae recoverable by either extraction method remained constant or increased when stored at 13-24 C for 16 weeks. This was also true for Helicotylenchtts dihystera and Xiphinema americanum extracted by the Baermann funnel technique, whereas the numbers retrieved by the sugar-flotation-sieving method decreased slightly. All species except T. claytoni decreased appreciably in soil stored at 36 C.