Gene expression in the deep biosphere

Abstract

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). ...

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

“…Similarly, we show that at Station L4 both mycoplankton diversity and abundance are linked to changes in availability of particulate organic matter. Active fungal communities within deep sub-seafloor sediments also show similar positive links to changes in the availability of organic material (Orsi et al, 2013a), and the expression of metabolic pathways involved in the cycling of a variety of organic substrates (Orsi et al, 2013b). The utilisation of particulate organic matter by benthic and pelagic marine fungi is analogous to the well-established functional roles of fungi in freshwater ecosystems, such as lakes (Wurzbacher et al, 2010).…”

“…Metagenomic analysis of microbial communities associated with the coral Porites astreoides has shown a high prevalence of fungal genes involved in nitrogen metabolism, including ammonia assimilation and nitrite ammonification (Wegley et al, 2007). Nitrite reduction by fungi in deep sub-seafloor sediments has also been proposed (Orsi et al, 2013b). Changes in substrate availability and associated niche differentiation could be one mechanism through which saprotrophic mycoplankton diversity and abundance is controlled in pelagic ecosystems.…”

Microorganisms persist at record depths in the subseafloor of the Canterbury Basin

“…), as revealed by molecular, metagenomic and metatranscriptomic studies (Lipp et al, 2008;Roussel et al, 2008;Biddle et al, 2011;Pawlowski et al, 2011;Orsi et al, 2013a). It harbors representatives from the three domains of life, for example, numerous endemic and/or as yet uncultured Archaea and Bacteria (for example, Inagaki et al, 2006;Orcutt et al, 2011), in addition to bacterial endospores (Lomstein et al, 2012), protists and fungi belonging to Eukarya (Schippers and Neretin, 2006;Edgcomb et al, 2011;Orsi et al, 2013a,b).…”

Metagenomics of extreme environments

“…Recently reports of the first subsurface metatranscriptomes, representing over 1 billion cDNA sequence reads from anaerobic sediments 159 metres beneath the sea floor, demonstrated that anaerobic metabolism of amino acids, carbohydrates and lipids were the main drivers of metabolic processes [53]. The study also confirmed that dissimilatory sulphite reductase (dsr) catalysed sulphate reduction by subsurface microbial guilds may be a key source of energy [57,58].…”

“…Extremely high pressures, nutrient limitation, and osmotic stressors combine to produce an extreme environment dominated by microbial communities. It has been estimated that up to 25 x 10 29 bacterial cells may be present in the terrestrial subsurface [51] and it is therefore like that these populations play an important role in biogeochemical cycling [52,53]. However, despite this numerical abundance of cells, crucial questions regarding deep subterranean habitats remain largely unaddressed.…”