Links between Geographic Location, Environmental Factors, and Microbial Community Composition in Sediments of the Eastern Mediterranean Sea

The bacterial community composition of marine surface sediments originating from various regions of the Eastern Mediterranean Sea (12 sampling sites) was compared by parallel use of three fingerprinting methods: analysis of 16S rRNA gene fragment heterogeneity by denaturing gradient electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and analysis of phospholipid-linked fatty acid composition (PLFA). Sampling sites were located at variable depths (30–2860 m; water column depth above the sediments) and the sediments differed greatly also in their degree of petroleum contamination (0.4–18 μg g⁻¹), organic carbon (0.38–1.5%), and chlorophyll a content (0.01–7.7 μg g⁻¹). Despite a high degree of correlation between the three different community fingerprint methods, some major differences were observed. DGGE banding patterns showed a significant separation of sediment communities from the northern, more productive waters of the Thermaikos Gulf and the oligotrophic waters of the Cretan, S. Ionian, and Levantine Sea. T-RFLP analysis clearly separated the communities of deep sediments (>1494 m depth) from their shallow (<617 m) counterparts. PLFA analysis grouped a shallow station from the productive waters of the north with the deep oligotrophic sediments from the Ionian and Levantine Sea, with low concentrations of PLFAs, and hence low microbial biomass, as the common denominator. The degree of petroleum contamination was not significantly correlated to the apparent composition of the microbial communities for any of the three methods, whereas organic carbon content and sediment chlorophyll a were important in this regard.     

Vertical distribution of picoeukaryotic diversity in the Sargasso Sea

Eukaryotic molecular diversity within the picoplanktonic size-fraction has primarily been studied in marine surface waters. Here, the vertical distribution of picoeukaryotic diversity was investigated in the Sargasso Sea from euphotic to abyssal waters, using size-fractionated samples (< 2 microm). 18S rRNA gene clone libraries were used to generate sequences from euphotic zone samples (deep chlorophyll maximum to the surface); the permanent thermocline (500 m); and the pelagic deep-sea (3000 m). Euphotic zone and deep-sea data contrasted strongly, the former displaying greater diversity at the first-rank taxon level, based on 232 nearly full-length sequences. Deep-sea sequences belonged almost exclusively to the Alveolata and Radiolaria, while surface samples also contained known and putative photosynthetic groups, such as unique Chlorarachniophyta and Chrysophyceae sequences. Phylogenetic analyses placed most Alveolata and Stramenopile sequences within previously reported 'environmental' clades, i.e. clades within the Novel Alveolate groups I and II (NAI and NAII), or the novel Marine Stramenopiles (MAST). However, some deep-sea NAII formed distinct, bootstrap supported clades. Stramenopiles were recovered from the euphotic zone only, although many MAST are reportedly heterotrophic, making the observed distribution a point for further investigation. An unexpectedly high proportion of radiolarian sequences were recovered. From these, five environmental radiolarian clades, RAD-I to RAD-V, were identified. RAD-IV and RAD-V were composed of Taxopodida-like sequences, with the former solely containing Sargasso Sea sequences, although from all depth zones sampled. Our findings highlight the vast diversity of these protists, most of which remain uncultured and of unknown ecological function.     

Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis.

PCR was used to amplify DNA-dependent RNA polymerase gene sequences specifically from the cyanobacterial population in a seawater sample from the Sargasso Sea. Sequencing and analysis of the cloned fragments suggest that the population in the sample consisted of two distinct clusters of Prochlorococcus-like cyanobacteria and four clusters of Synechococcus-like cyanobacteria. The diversity within these clusters was significantly different, however. Clones within each Synechococcus-like cluster were 99 to 100% identical, while each Prochlorococcus-like cluster was only 91% identical at the nucleotide level. One Prochlorococcus-like cluster was significantly more closely related to a Mediterranean Sea (surface) Prochlorococcus isolate than to the other cluster, showing the highly divergent nature of this group even in one sample. The approach described here can be used as a general method for examining cyanobacterial diversity, while an oligotrophic ocean ecosystem such as the Sargasso Sea may be an ideal model for examining diversity in relation to environmental parameters.     

Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea

Genetic variation was surveyed at nine microsatellite loci and the mitochondrial control region (868 bp) to test for the presence of genetic stock structure in young-of-the-year Atlantic bluefin tuna (Thunnus thynnus thynnus) from the Mediterranean Sea. Bluefin tuna were sampled over a period of 5 years from the Balearic and Tyrrhenian seas in the western basin of the Mediterranean Sea, and from the southern Ionian Sea in the eastern basin of the Mediterranean Sea. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences revealed no significant heterogeneity among collections taken from the same location in different years; however, significant spatial genetic heterogeneity was observed across all samples for both microsatellite markers and mitochondrial control region sequences (FST=0.0023, P=0.038 and PhiST=0.0233, P=0.000, respectively). Significant genetic differentiation between the Tyrrhenian and Ionian collections was found for both microsatellite and mitochondrial markers (FST=0.0087, P=0.015 and PhiST=0.0367, P=0.030, respectively). These results suggest the possibility of a genetically discrete population in the eastern basin of the Mediterranean Sea.     

Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria

Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2 m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this cluster was only detected on aggregates up to a few meters above the sediment surface, but never in the fraction of free-living bacteria. A quantitative real-time PCR approach revealed that the MMC constituted up to 13% of total bacterial 16S rRNA genes in surface sediments of the North Sea. In a global survey, including sediments from the Mediterranean Sea, the Atlantic, Pacific and Indian Ocean and various climatic regions, the MMC was detected in most samples and to a water depth of 4300 m. Two fosmids of a library from sediment of the southern North Sea containing 16S rRNA genes affiliated with the MMC were sequenced. Both fosmids have a single unlinked 16S rRNA gene and no complete rRNA operon as found in most bacteria. No synteny to other myxobacterial genomes was found. The highest numbers of orthologues for both fosmids were assigned to Sorangium cellulosum and Haliangium ochraceum. Our results show that the MMC is an important and widely distributed but largely unknown component of marine sediment-associated bacterial communities.     

Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea

Little is known about the biodiversity of microbial eukaryotes in the South China Sea, especially in waters at bathyal depths. Here, we employed SSU rDNA gene sequencing to reveal the diversity and community structure across depth and distance gradients in the South China Sea. Vertically, the highest alpha diversity was found at 75‐m depth. The communities of microbial eukaryotes were clustered into shallow‐, middle‐, and deep‐water groups according to the depth from which they were collected, indicating a depth‐related diversity and distribution pattern. Rhizaria sequences dominated the microeukaryote community and occurred in all samples except those from less than 50‐m deep, being most abundant near the sea floor where they contributed ca. 64–97% and 40–74% of the total sequences and OTUs recovered, respectively. A large portion of rhizarian OTUs has neither a nearest named neighbor nor a nearest neighbor in the GenBank database which indicated the presence of new phylotypes in the South China Sea. Given their overwhelming abundance and richness, further phylogenetic analysis of rhizarians were performed and three new genetic clusters were revealed containing sequences retrieved from the deep waters of the South China Sea. Our results shed light on the diversity and community structure of microbial eukaryotes in this not yet fully explored area.     

Abundant proteorhodopsin genes in the North Atlantic Ocean

Proteorhodopsin (PR) is a light-driven proton pump that has been found in a variety of marine bacteria, including Pelagibacter ubique , a member of the ubiquitous SAR11 clade. The goals of this study were to explore the diversity of PR genes and to estimate their abundance in the North Atlantic Ocean using quantitative polymerase chain reaction (QPCR). We found that PR genes in the western portion of the Sargasso Sea could be grouped into 27 clusters, but five clades had the most sequences. Sets of specific QPCR primers were designed to examine the abundance of PR genes in the following four of the five clades: SAR11 ( P. ubique and other SAR11 Alphaproteobacteria ), BACRED17H8 ( Alphaproteobacteria ), HOT2C01 ( Alphaproteobacteria ) and an uncultured subgroup of the Flavobacteria . Two groups (SAR11 and HOT2C01) dominated PR gene abundance in oligotrophic waters, but were significantly less abundant in nutrient- and chlorophyll-rich waters. The other two groups (BACRED17H8 and Flavobacteria subgroup NASB) were less abundant in all waters. Together, these four PR gene types were found in 50% of all bacteria in the Sargasso Sea. We found a significant negative correlation between total PR gene abundance and nutrients and chlorophyll but no significant correlation with light intensity for three of the four PR types in the depth profiles north of the Sargasso Sea. Our data suggest that PR is common in the North Atlantic Ocean, especially in SAR11 bacteria and another marine alphaproteobacterial group (HOT2C01), and that these PR-bearing bacteria are most abundant in oligotrophic waters.     

A novel haloarchaeal-related lineage is widely distributed in deep oceanic regions

During our study of the 16S rRNA gene sequence-based archaeal diversity of a deep-sea site located at a 3000 m depth at the Antarctic Polar Front, we detected several phylotypes ascribed to already known Group II and III Euryarchaeota, and a cluster of distinct sequences that branched off at the base of haloarchaea. The position of this lineage (marine Group IV) was very robust using distance (neighbour-joining) and maximum-likelihood methods. Subsequently, we designed specific primers for the detection of this archaeal group in other marine environments using polymerase chain reaction amplification and sequence comparison. Group IV archaea were found in the Antarctic area (across a gradient from the Southern ocean to the South Atlantic), and also in North Atlantic and Mediterranean waters. In all oceanic locations, Group IV archaea were never detected in surface waters, but were vertically distributed in the deepest part of the water column.     

Community Structure of Archaea from Deep-Sea Sediments of the South China Sea

Using the archaeal 16S rRNA gene, we determined the community structures of archaea of subseafloor sediments (～9-11 m below seafloor) from two geographically distant cores (MD05-2896, south, water depth 1,657 m; MD05-2902, north, water depth 3,697 m) in the South China Sea. Euryarchaeota accounted for 61.4% of total archaeal clone libraries at MD05-2896 and 56.2% at MD05-2902. At both locations, the Euryarchaeota-related sequences were dominated by Marine Benthic Group D, Terrestrial Miscellaneous Eryarchaeotal Group, and South African GoldMine Euryarchaeotal Group; the Crenarchaeota-related sequences were dominated by Marine Benthic Group B, Marine Group I, pSL12, and C3. The community structure showed no significant difference with depth at each location, suggesting the lack of stratification of archaeal populations in the deep-sea marine sediments in the South China Sea. On the other hand, the community structure is significantly different between the two sites, which may be related to geographical difference in the South China Sea.     

Preliminary study of summer phytoplankton in coastal waters of the Gulf of Taranto (Ionian Sea)

Abstract

Phytoplankton abundances and species composition of coastal waters of the Gulf of Taranto (Ionian Sea) were investigated in July 1995. Abundances were lower than those of other Mediterranean coastal areas. Higher densities values were found in the central part of the studied area. In surface waters, small phytoflagellates (<10μm) and dinoflagellates, such as Heterocapsa niei and Oxytoxum variabile, were the dominant species. Diatoms, mainly belonging to the genus Chaetoceros, were also present.     

Spatial distribution and life‐history aspects of blackspot seabream Pagellus bogaraveo (Osteichthyes: Sparidae)

Spatial distribution and life history aspects of Pagellus bogaraveo in the eastern Ionian Sea were investigated using the data from 13 different studies carried out in the area from 1983 to 2010. The spatial patterns of the abundance, biomass and mean size showed that the species inhabits the shallow waters of the shelf (<170 m depth) as juveniles up to a certain size (<180 mm total length, L_T), moving to deeper waters of the slope (mainly 400–500 m depth) as adults. The spatial pattern of abundance indicated a continuous distribution of the species in deep waters, with hot‐spot areas of high values, whereas in shallow waters distribution was more discontinuous, with higher concentrations of juveniles in estuaries and brackish waters. The study of biological aspects of the species revealed (1) a difference in the increase in mass between males and females, (2) protandrous hermaphroditism, accompanied by the presence of primary females and males that do not change sex, (3) a sex ratio in favour of females >250 mm L_T, (4) the presence of hermaphrodites between 200 and 370 mm, (5) a long reproduction period from June to March, (6) a size at first maturity around 300 mm and (7) a diet composition of adults based mainly on fishes, and also on opportunistic behaviour in the food scarce environment of deep waters. The results suggest that the species' distribution and feeding strategies are the most appropriate for the oligotrophic eastern Ionian waters and that these conditions result in smaller sizes of the species in the east Mediterranean Sea compared to the west basin and the east Atlantic Ocean, with implications for the growth and reproductive biology of the species.     

Different SAR86 subgroups harbour divergent proteorhodopsins

Proteorhodopsins (PRs), bacterial photoactive proton pumps, were originally detected in the uncultured marine gamma-proteobacterial SAR86 group. PRs are now known to occur in both the gamma and alpha marine proteobacterial lineages. Recent environmental shotgun sequence analysis in the Sargasso Sea has added yet more diversity, and a potentially broader taxonomic distribution, to the PR family. Much remains to be learned, however, about within-taxon PR variability and the broader organismal distribution of different PR types. We report here genomic analyses of large genome fragments from different subgroups of the SAR86 lineage, recovered from naturally occurring bacterioplankton populations in coastal Red Sea and open ocean Pacific waters. Sequence comparisons were performed on large bacterial artificial chromosomes (BACs) bearing both rRNA and PR genes, derived from different SAR86 subgroups. Our analyses indicated the presence of different PR sequence types within the same SAR86 rRNA subgroup. The data suggested that the distribution of particular PR types does not necessarily parallel the phylogenetic relationship inferred from highly conserved genes such as rRNA. Further analyses of the genomic regions flanking PR also revealed a potential pathway for the biosynthesis of retinal, the PR chromophore that is required to generate the functionally active photoprotein. Finally, comparison of our results with recently reported Sargasso Sea environmental shotgun sequence assemblies demonstrated the utility of BAC clones for interpreting environmental shotgun sequence data, much of which is represented in short contigs that have an overall low depth of coverage.     

Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea

The genetic diversity of 19 strains belonging to Alteromonas macleodii isolated from different geographic areas (Pacific and Indian Ocean, and different parts of the Mediterranean Sea) and at different depths (from the surface down to 3500 m) has been studied. Fragments of the 16S rRNA gene, the internal transcribed spacer (ITS) between 16S and 23S rDNA genes, the gyrB and the rpoB genes, have been sequenced for each strain. Amplified fragment length polymorphisms were used to characterize similarity at the level of the whole genome. Most of the diversity reflected the existence of a cluster of strains isolated from deep Mediterranean waters and two isolates from the Black Sea. Particularly the isolates from the deep sites were consistently different from all the others indicating the existence of a specific ecotype adapted to these conditions. Amplification of gyrB gene and ITS directly from DNA retrieved from deep Mediterreanean waters and one Atlantic sample showed that presence of this deep-sea ecotype is widespread and is not a product of culture bias. On the other hand, strains isolated from surface tropical waters showed a remarkable level of resemblance to the first isolate of this species obtained from Hawaii in 1972. The results indicate the existence of both lineages of global distribution and ecotypes adapted to specific conditions such as deep or more diluted (the Black Sea) waters.     

Genetic analyses of Dinophysis spp. support kleptoplastidy

The question of whether the toxin-producing and bloom-forming dinoflagellate genus Dinophysis contains plastids that are permanent or contains temporary so-called kleptoplastids is still unresolved. We sequenced plastid 16S rRNA gene, the complete trnA gene and the intergenic transcribed spacer region located between the trnA gene and the 23S rRNA gene, and performed diagnostic PCR on cells of the genus Dinophysis. Dinophysis spp. were collected from five different geographical regions: the Baltic Sea, the North Sea, the Greenland Sea and the Norwegian fjord Masfjorden. In most cases the sequence analysis showed that the sequences were identical to each other and to sequences from the cryptophyte Teleaulax amphioxeia SCCAP K0434, regardless of the place of sampling or the species analyzed. The exception was some cells of Dinophysis spp. from the Greenland Sea. These contained a 16S rRNA gene sequence that was more closely related to the cryptophyte Geminigera cryophila. The cells of Dinophysis contained either one of the 16S rRNA gene sequences or both in the same cell. Our results challenge the hypothesis that the plastids in Dinophysis are permanent and suggest that they are more likely to be kleptoplastids.     

Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing.

The phylogenetic diversity of an oligotrophic marine picoplankton community was examined by analyzing the sequences of cloned ribosomal genes. This strategy does not rely on cultivation of the resident microorganisms. Bulk genomic DNA was isolated from picoplankton collected in the north central Pacific Ocean by tangential flow filtration. The mixed-population DNA was fragmented, size fractionated, and cloned into bacteriophage lambda. Thirty-eight clones containing 16S rRNA genes were identified in a screen of 3.2 x 10(4) recombinant phage, and portions of the rRNA gene were amplified by polymerase chain reaction and sequenced. The resulting sequences were used to establish the identities of the picoplankton by comparison with an established data base of rRNA sequences. Fifteen unique eubacterial sequences were obtained, including four from cyanobacteria and eleven from proteobacteria. A single eucaryote related to dinoflagellates was identified; no archaebacterial sequences were detected. The cyanobacterial sequences are all closely related to sequences from cultivated marine Synechococcus strains and with cyanobacterial sequences obtained from the Atlantic Ocean (Sargasso Sea). Several sequences were related to common marine isolates of the gamma subdivision of proteobacteria. In addition to sequences closely related to those of described bacteria, sequences were obtained from two phylogenetic groups of organisms that are not closely related to any known rRNA sequences from cultivated organisms. Both of these novel phylogenetic clusters are proteobacteria, one group within the alpha subdivision and the other distinct from known proteobacterial subdivisions. The rRNA sequences of the alpha-related group are nearly identical to those of some Sargasso Sea picoplankton, suggesting a global distribution of these organisms.     

Sponge-specific Bacterial Associations of the Mediterranean Sponge <Emphasis Type="Italic">Chondrilla nucula</Emphasis> (Demospongiae,Tetractinomorpha)

A stable and specific bacterial community was shown to be associated with the Mediterranean sponge Chondrilla nucula. The associated bacterial communities were demonstrated to be highly similar for all studied specimens regardless of sampling time and geographical region. In addition, analysis of 16S rDNA clone libraries revealed three constantly C. nucula-associated bacterial phylotypes belonging to the Acidobacteria, the Gamma- and Deltaproteobacteria present in sponge specimens from two Mediterranean regions with distinct water masses (Ligurian Sea and Adriatic Sea). For the first time, candidate division TM7 bacteria were found in marine sponges. A major part (79%) of the C. nucula-derived 16S rDNA sequences were closely related to other sponge-associated bacteria. Phylogenetic analysis identified 14 16S rRNA gene sequence clusters, seven of which consisted of exclusively sponge-derived sequences, whereas the other seven clusters contained additional environmental sequences. This study adds to a growing database on the stability and variability of microbial consortia associated with marine sponges.     

Polyphasic classification of 0.2 microm filterable bacteria from the western Mediterranean Sea

The 0.2 microm filtration of sea water samples from the Mediterranean Sea (Bay of Calvi, Corsica), collected from 10 m and 35 m depth led to the isolation of several gram-negative bacterial strains able to grow on full-strength media as well as on diluted media. The analysis of the 16S rRNA gene sequences and estimation of the phylogenetic relationships of these facultative oligotrophic bacteria indicated that they grouped into two phylogenetic branches. The strains RE10F/2, RE10F/5 (10 m depth samples) and RE35/F12 (35 m depth samples) were assigned to the gamma-subclass, while RE35F/1 (35m depth sample) was assigned to the alpha-4-subclass of the Proteobacteria. The strains RE10/F2 and RE10/F5 were most closely related to species and strains of the Pseudoalteromonas group, whereas the strain RE35F/12 placed adjacent to the family Vibrionaceae. The phylogenetic analysis of strain RE35F/1 revealed that this bacterium clusters with marine strains and species of the aerobic anoxygenic phototrophic bacteria Erythrobacter as well as Erythromicrobium and more distantly to Sphingomonas spp. Supplementary to those genotypic classifications the chemotaxonomic signatures including the major respiratory lipoquinone systems, the cellular fatty acid compositions as well as the polyamine contents of the bacteria were investigated. The isolated organisms displayed differences in their physiological and biochemical properties to already described strains belonging to the same genera or families, as revealed by the comparative 16S rRNA analysis. Despite the fact that these bacteria were isolated from a 0.2 microm filtrate, the cultured organisms which were all rod-shaped, displayed width dimensions ranging from 0.4 up to 0.7 microm, indicating that these bacteria were starvation forms at the time of isolation and not ultramicrobacteria as defined by Torella and Morita (1981) or by Schut et al. (1993). Because our isolated strains represent potentially new taxa, this first investigation on 0.2 pm filterable bacteria from the Western Mediterranean Sea supports the hypothesis that this bacterial fraction contributes to the diversity of marine bacteria.     

Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea

Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24°C throughout the year, and a remarkable uniform temperature (∼22°C) and salinity (∼41 psu) from the mixed layer (∼200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea’s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.     

Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

Although copious qualitative information describes the members of the diverse microbial communities on Earth, statistical approaches for quantifying and comparing the numbers and compositions of lineages in communities are lacking. We present a method that addresses the challenge of assigning sequences to operational taxonomic units (OTUs) based on the genetic distances between sequences. We developed a computer program, DOTUR, which assigns sequences to OTUs by using either the furthest, average, or nearest neighbor algorithm for each distance level. DOTUR uses the frequency at which each OTU is observed to construct rarefaction and collector's curves for various measures of richness and diversity. We analyzed 16S rRNA gene libraries derived from Scottish and Amazonian soils and the Sargasso Sea with DOTUR, which assigned sequences to OTUs rapidly and reliably based on the genetic distances between sequences and identified previous inconsistencies and errors in assigning sequences to OTUs. An analysis of the two 16S rRNA gene libraries from soil demonstrated that they do not contain enough sequences to support a claim that they contain different numbers of bacterial lineages with statistical confidence (P > 0.05), nor do they contain enough sequences to provide a robust estimate of species richness when an OTU is defined as containing sequences that are no more than 3% different from each other. In contrast, the richness of OTUs at the 3% level in the Sargasso Sea collection began to plateau after the sampling of 690 sequences. We anticipate that an equivalent extent of sampling for soil would require sampling more than 10,000 sequences, almost 100 times the size of typical sequence collections obtained from soil.     

An analysis of the Sargasso Sea resource and the consequences for database composition

Background  

The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information. Unlike the protein sequences held in the current searchable databases, the Sargasso Sea sequences originate from a single marine environment and have been sequenced from species that are not easily obtainable by laboratory cultivation. The resource also contains very many fragments of whole protein sequences, a side effect of the shotgun sequencing method.