Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and Discovery Deep brine pools

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e42872, doi:10.1371/journal.pone.0042872.The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools - water bodies characterized by a unique combination of extreme conditions. The ‘polyextremophiles’ that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied. We report a comparative taxonomic analysis of the prokaryotic communities of the sediments directly below the Red Sea brine pools, namely, Atlantis II, Discovery, Chain Deep, and an adjacent brine-influenced site. Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S- and N-rich sections. Relative abundance-based hierarchical clustering of the 16S rDNA pyrotags assigned to major taxonomic groups allowed us to categorize the archaeal and bacterial communities into three major and distinct groups; group I was unique to the S-rich Atlantis II section (ATII-1), group II was characteristic for the N-rich Discovery sample (DD-1), and group III reflected the composition of the remaining sediments. Many of the groups detected in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program

Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

DNA Microarray-Based Genome Comparison of a Pathogenic and a Nonpathogenic Strain of Xylella fastidiosa Delineates Genes Important for Bacterial Virulence

Xylella fastidiosa is a phytopathogenic bacterium that causes serious diseases in a wide range of economically important crops. Despite extensive comparative analyses of genome sequences of Xylella pathogenic strains from different plant hosts, nonpathogenic strains have not been studied. In this report, we show that X. fastidiosa strain J1a12, associated with citrus variegated chlorosis (CVC), is nonpathogenic when injected into citrus and tobacco plants. Furthermore, a DNA microarray-based comparison of J1a12 with 9a5c, a CVC strain that is highly pathogenic and had its genome completely sequenced, revealed that 14 coding sequences of strain 9a5c are absent or highly divergent in strain J1a12. Among them, we found an arginase and a fimbrial adhesin precursor of type III pilus, which were confirmed to be absent in the nonpathogenic strain by PCR and DNA sequencing. The absence of arginase can be correlated to the inability of J1a12 to multiply in host plants. This enzyme has been recently shown to act as a bacterial survival mechanism by down-regulating host nitric oxide production. The lack of the adhesin precursor gene is in accordance with the less aggregated phenotype observed for J1a12 cells growing in vitro. Thus, the absence of both genes can be associated with the failure of the J1a12 strain to establish and spread in citrus and tobacco plants. These results provide the first detailed comparison between a nonpathogenic strain and a pathogenic strain of X. fastidiosa, constituting an important step towards understanding the molecular basis of the disease

Cluster dendrogram illustrating the relationship of the (4a) archaeal and (4b) bacterial communities in the Red Sea to those in other oceanic systems.

<p>The dendrogram shows the complete linkage hierarchical clustering of the different sediment sections based on the relative abundance of the OTUs in each section. The height indicates the relative distances between the datasets. The data of other oceanic systems from the Guaymas Methane Seep (ICM GMS) project included <i>Estuarine bulk water, North Atlantic Ocean</i> (ICM GMS 1–2): oxic sediment from the White Oak River; <i>Cold Seep¹ Gulf of Mexico</i> (ICM GMS 3–4): microbial mat; <i>Cold Seep^2,3 Gulf of Mexico</i> (ICM GMS 5–8): sediments from anoxic deep-sea hydrocarbon seeps in the Gulf of Mexico; <i>Continental shelf, Norwegian Sea</i> (ICM GMS 13–14): an oxic microbial mat from the continental shelf at the Storegga seep enrichment in the Norwegian Sea; <i>Carbonate reef Black Sea</i> (ICM GMS 15–16): an anoxic microbial mat from the Black Sea; <i>Marine hydrothermal vent^1–2, Gulf of California</i> (ICM GMS 17–20): microbial mat from the Gulf of California, oxic hydrothermal vent from Guaymas Basin.</p

Taxonomic assignment of OTUs to major archaeal and bacterial groups.

<p>Water Col.¹: Average OTU in the water column</p><p>Water Col.²: Highest OTU in the water column</p

Taxonomic assignment and abundance of archaeal communities in ATII, DD, CD and BI sediment samples.

<p>Maximum-likelihood phylogenetic tree showing the taxonomic diversity and relative abundance of archaeal OTUs in all sediment samples. Bootstrap support values greater than 50% are indicated by the size of the circle on each branch. The taxonomically assigned OTUs are represented in ST-1.</p

Chemical profiling of the sediments.

<p>Chemical profiling of the sediments.</p

Pyrotag 16S rDNA data sets.

<p>Pyrotag 16S rDNA data sets.</p

Sediment samples.

<p>(<b>1a</b>) <b><i>Map of the sampling and water depth in the Atlantis II Deep area.</i></b> The Atlantis II Deep area (between latitudes 21° 13′N and 21° 30′N and longitudes 37° 58′E and 38° 9′E) is in the central rift zone of the Red Sea, between Saudi Arabia and Sudan. The four sample sites are represented. (<b>1b</b>)<b>: </b><b><i>Schematic representation of the Atlantis II (ATII), Discovery (DD), Chain Deep (CD) and Brine-Influenced (BI) sediment cores.</i></b> The sediment cores are represented individually. Each subsection in each core is presented to scale, and sections are numbered from bottom to top. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042872#pone-0042872-t001" target="_blank">Table 1</a> for sampling and sample details. ATII (Atlantis II; with a total of six distinctive sediment sections), DD (Discovery Deep; with seven sections), CD (Chain Deep; one section), and adjacent brine sections (BI; two sections).</p