Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.nitrification | marine metagenomics | genome streamlining | archaea

1, 4,, 6, 9, 10 that exhibits peaks of cell abundance, and profiles of sulfate and methane 43 suggestive of microbial activity 1 (Figure 1). 44Picogram quantities of total RNA were extracted from 25 grams of Peru Margin sediment 45 from six depths (5, 30, 50, 70, 91, 159 mbsf), consistent with basal levels of microbial activity 46 predicted for this environment 3, 4 . Illumina ® sequencing of total cDNA produced over 1 billion 47 reads, with 50% to 85% of reads mapping to open reading frames that were assigned a functional 48 annotation (Table S1). 49The dominance of transcripts from Firmicutes, Actinobacteria, Alphaproteobacteria, and 50 Gammaproteobacteria (Fig. S1) is consistent with previous cultivation-based, metagenomic, and 51 phylogenetic surveys from Peru Margin subsurface sediment 1, 5, 13, 14 , and suggests these to be 52 some of the most active microbial groups. The abundance of gammaproteobacterial transcripts 53 ( Fig. S1) suggests that they are likely the most active microbial group in the deeper, anoxic, 54 subseafloor sediment at this site. Fungal transcripts were also present in every sample ranging in 55representation from 3% at 70 mbsf to 20% at 5 mbsf. Archaea and Chloroflexi are present in 56 noticeably low abundance, despite their previous detection at this site 6, 13, 15 , suggesting that our 57 approach might miss organisms with lower mRNA expression levels. As such, interpretations of 58 relative abundances should be treated cautiously 16 . Changes in pressure and temperature may 59 have altered gene expression during sampling. However, low representation of heat shock 60 proteins (a proxy for physiological stress response 17 ) in protein coding reads (< 10 -5 %) suggests 61 the physiological state of most microbes was not significantly altered during sample retrieval and 62 storage. 63Dissimilatory sulfate reduction may represent a major form of microbial metabolism and 64 energy production in the sub-seafloor 1, 2, 18 and is indicated by porewater sulfate concentrations at 65Site 1229 1 (Fig. 1). Representation of Dsr transcripts was highest in sediment with sulfate 66 profiles suggestive of biogenic sulfate reduction (Fig. 1) and supports biogeochemical evidence 67 for sulfate reduction at this site 1, 4 . Surprisingly, transcripts coding for dissimilatory nitrate 68 reductases (Nar) were represented throughout the sediment column, despite no measureable 69 nitrate. The origin of nitrate as a substrate in this sediment is unknown, but could potentially be 70 produced as a by-product of anaerobic ammonium oxidation. Once produced, nitrate would 71likely not accumulate to measurable concentrations given the higher free energy yield of nitrate 72 as electron acceptor compared to the dominant electron acceptors in this environment, sulfate 73 and iron. Nitrate reduction appears to be performed predominantly by Alphaproteobacteria and 74Betatproteobacteria at most depths (Fig. 1) and the resulting nitrite is likely reduced by Fungi, 75Gammaproteobacteria, and Firmicutes (Fig. S3). ...

The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.

Microbial diversity and distribution are topics of intensive research. In two companion papers in this issue, we describe the results of the Cariaco Microbial Observatory (Caribbean Sea, Venezuela). The Basin contains the largest body of marine anoxic water, and presents an opportunity to study protistan communities across biogeochemical gradients. In the first paper, we survey 18S ribosomal RNA (rRNA) gene sequence diversity using both Sanger-and pyrosequencing-based approaches, employing multiple PCR primers, and state-of-the-art statistical analyses to estimate microbial richness missed by the survey. Sampling the Basin at three stations, in two seasons, and at four depths with distinct biogeochemical regimes, we obtained the largest, and arguably the least biased collection of over 6000 nearly full-length protistan rRNA gene sequences from a given oceanographic regime to date, and over 80 000 pyrosequencing tags. These represent all major and many minor protistan taxa, at frequencies globally similar between the two sequence collections. This large data set provided, via the recently developed parametric modeling, the first statistically sound prediction of the total size of protistan richness in a large and varied environment, such as the Cariaco Basin: over 36 000 species, defined as almost full-length 18S rRNA gene sequence clusters sharing over 99% sequence homology. This richness is a small fraction of the grand total of known protists (over 100 000-500 000 species), suggesting a degree of protistan endemism.