The phylogenetic diversity of oligotrophic bacterioplankton communities was compared with 16s ribosomal RNA genes cloned from natural populations. The data reported here extend a previous analysis of a bacterioplankton 16s rRNA clone library with 15 additional nucleic acid clone sequences, to provide information on 60 16s rDNA clones from hydrostation S in the Sargasso Sea. The data were compared to partial sequences of 37 Bacterial 16s rDNA clones reported from a surface picoplankton population collected at the Aloha station in the North Pacific gyre, and partial sequences of 29 Bacterial 16s rRNA clones obtained from sites near Bermuda and the western California Current. The results support reports of diverse groups of previously unknown a-proteobacteria, y-proteobacteria, and cyanobacteria in oceanic surface samples.

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. While roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. However, the critical need to resolve this debate for ESA listings lead us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of Distinct Population Segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the Phylogenetic Species Concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

The majority of the Earth's shallow crust is composed of basalt that erupted on the seafloor and was subsequently altered by chemical exchange with seawater. One aspect of this alteration is the replacement of glass by secondary minerals, including clays. Petrographic thin sections from ODP Holes 504B and 896A revealed characteristic patterns of pitting (channels) at the interface of fresh basalt glass and secondary clay. Fluorescent dyes that bind specifically to nucleic acids (Hoechst 33342, PO-PRO-3, and Sytol 1) were used to examine thin sections for evidence of cellular life. Independent experiments with the three dyes indicated the presence of paniculate nucleic acids at the interface of altered and unaltered glass, particularly at the distal tips of channels. Organic material was extracted from crushed basalts from Holes 504B and 896A and examined for the presence of microbial DNA by a polymerase chain reaction (PCR) assay. This technique detects specific ribosomal RNA genes that are present in all cellular life-forms. The PCR assays demonstrated the presence of prokaryotic genomic DNA in the rock extracts. Among the geochemical reactions that could provide energy for biological processes are the oxidation of iron, manganese, and sulfur. Electron microprobe analyses of areas of glass that appear to be affected by microbial action have low iron relative to the fresh glass. Also, elements that are consistent with the presence of cellular life, phosphate and potassium, were elevated in the channels (P is 0.02 wt% in glass and up to 1.4 wt% in channels and K is 0.01 wt% in glass and up to 2.0 wt% in channels). These data raise the possibility that chemical transformations of basalt on the seafloor are mediated by microorganisms.

We examined the genetic structure of snowy plovers (Charadrius alexandrinus) in North America, the Caribbean, and the west coast of South America to quantify variation within and among breeding areas and to test the validity of three previously recognized subspecies. Sequences (676 bp) from domains I and II of the mitochondrial control region were analyzed for 166 snowy plovers from 20 breeding areas. Variation was also examined at 10 microsatellite loci for 144 snowy plovers from 14 breeding areas. The mtDNA and microsatellite data provided strong evidence that the Puerto Rican breeding group is genetically divergent from sites in the continental U.S. (net sequence divergence = 0.38%; F ST for microsatellites = 0.190). Our data also revealed high levels of differentiation between sites from South America and North America (net sequence divergence = 0.81%; F ST for microsatellites = 0.253). In contrast, there was little genetic structure among breeding sites within the continental U.S. Our results suggest that snowy plovers in Florida should be considered part of C. a. nivosus (rather than part of C. a. tenuirostris, where they are currently placed), whereas snowy plovers from Puerto Rico should be considered part of C. a. tenuirostris. Snowy plovers in South America should remain a separate subspecies (C. a. occidentalis). Although U.S. Pacific and Gulf Coast breeding areas were not genetically distinct from other continental U.S. sites, demographic isolation, unique coastal habitats, and recent population declines suggest they warrant special concern.

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).