Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter

Abstract

Particles in aquatic environments host distinct communities of microbes, yet the evolution of particle-specialized taxa and the extent to which specialized microbial metabolism is associated with particles is largely unexplored. Here, we investigate the hypothesis that a widely distributed and uncultivated microbial group—the marine group II euryarchaea (MGII)—interacts with living and detrital particulate organic matter (POM) in the euphotic zone of the central California Current System. Using fluorescent in situ hybridization, we verified the association of euryarchaea with POM. We further quantified the abundance and distribution of MGII 16 S ribosomal RNA genes in size-fractionated seawater samples and compared MGII functional capacity in metagenomes from the same fractions. The abundance of MGII in free-living and >3 μm fractions decreased with increasing distance from the coast, whereas MGII abundance in the 0.8–3 μm fraction remained constant. At several offshore sites, MGII abundance was highest in particle fractions, indicating that particle-attached MGII can outnumber free-living MGII under oligotrophic conditions. Compared with free-living MGII, the genome content of MGII in particle-associated fractions exhibits an increased capacity for surface adhesion, transcriptional regulation and catabolism of high molecular weight substrates. Moreover, MGII populations in POM fractions are phylogenetically distinct from and more diverse than free-living MGII. Eukaryotic phytoplankton additions stimulated MGII growth in bottle incubations, providing the first MGII net growth rate measurements. These ranged from 0.47 to 0.54 d−1. However, MGII were not recovered in whole-genome amplifications of flow-sorted picoeukaryotic phytoplankton and heterotrophic nanoflagellates, suggesting that MGII in particle fractions are not physically attached to living POM. Collectively, our results support a linkage between MGII ecophysiology and POM, implying that marine archaea have a role in elemental cycling through interactions with particles.

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

“…The site was selected because of the historic presence of a significant picoeukaryote population M. pusilla (Thomsen and Buck, 1998), and previous characterization of particleassociated taxa (Orsi et al, 2015). Water for the SIP incubation was acquired from 20 m depth.…”

“…At the end of the incubation 1-2 l of seawater was filtered sequentially through 3 μm (Pall Versapor-3000 T, Port Washington, NY, USA), 0.8 μm (Pall Supor-800, Port Washington, NY, USA) and 0.2 μm (Pall Supor-200, Port Washington, NY, USA) filters using a peristaltic pump, and DNA was extracted as previously described (Santoro et al, 2010). Catalyzed reporter depositionfluorescence in situ hybridization for Archaea and Euryarchaeota, DAPI staining and epifluorescence microscopy followed the protocol of Orsi et al (2015). This protocol utilized the Eury806 probe that is specific for Euryarchaeota (Tiera et al, 2004) and the Arch915 probe that targets the domain Archaea (Stahl and Amann, 1991), but also binds non-specifically to some pelagic marine bacteria (Pernthaler et al, 2002).…”

“…The uncultivated Marine Group II Euryarchaeaota (MGII) are also predicted to have a role in DON transformations, based on the recovery of protein degradation pathways in metagenomic data (Iverson et al, 2012;Orsi et al, 2015). MGII are thought to be heterotrophs, through their utilization of LMW-DON (Alderkamp et al, 2006) and available metagenomic data (Frigaard et al, 2006;Zhang et al, 2015).…”

“…However, direct evidence of their role in utilizing dissolved proteins has not been demonstrated, and interactions between archaea and HWM organic matter are largely unexplored. Several of the aforementioned groups, including the MGII, have been found in association with particulate organic matter (Delong et al, 1993), where they have an enhanced genomic capacity for HMW substrate utilization (Orsi et al, 2015).…”

“…We further hypothesized that MGII archaea are actively involved in protein turnover, and that this activity would be enhanced in association with particles (Orsi et al, 2015). To this end, we performed DNA stable-isotope probing (SIP) using isotopically labeled ( 13 C and 15 N) proteins from the picoeukaryotic phytoplankter Micromonas pusilla.…”