• Research Brief
  • Integrated Microbial Biodiversity

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

by CIFAR Jun 20 / 17

This study seeks to better understand the organisms responsible for transforming high molecular weight (HMW) dissolved organic nitrogen in the upper ocean.

In particular, it explores whether microbial taxa previously implicated in HMW dissolved organic matter turnover could be specifically involved in HMW dissolved organic nitrogen (protein) cycling.


Dissolved organic nitrogen (DON) is the second most abundant form of fixed nitrogen in the ocean. The total DON pool consists of many low and high molecular weight compounds and compound classes of varying concentration and bioavailability. Microbial heterotrophy can control the flux and composition of DON, yet the specific organisms responsible for DON transformations and their biochemical mechanisms are poorly understood.

Various forms of phytoplankton cell death are a major source of DON. The liberated dissolved proteins and oligopeptides become refractory because of processes such as abiotic complexation with existing dissolved organic matter (DOM). Dissolved proteins are recycled faster relative to the bulk HMW-DON pool.

Protein in dissolved and particulate fractions can be readily degraded in seawater by microbial activity. LMWDON, such as dissolved free amino acids released by protein hydrolysis, is assimilated by bacteria in aquatic systems and can support up to around 50% of bacterial production in the oceans. Studies linking some microbial groups to LMW-DON uptake have demonstrated great seasonal and spatial variation in DON utilization. However, due to the need to select target groups beforehand, these studies have not revealed the full diversity of bacteria and archaea involved in DON cycling.

A large number of bacterial groups in the ocean, however, have been implicated in HMW-DOM turnover, and some specifically in the cycling of HMW-DON and proteins including Flavobacteria, the y-Proteobacteria subgroups Arctic96B16, Ant4D3 and SAR86, and the y-Proteobacteria clade. The uncultivated Marine Group II (MGII) Euryarchaeota are also thought to have a role in DON transformation, based on the recovery of protein degradation pathways in metagenomics data. However, direct evidence of their role in using dissolved proteins has not been demonstrated, and interactions between archaea and HWM organic matter are largely unexplored. A recent study found that some MGII were physically associated with particles, and their genome content suggested.


There is a direct link between phytoplanktonderived dissolved protein and several dominant, yet uncultivated, members of the bacterial and archaeal community. The activity of 77 uncultivated free-living microbial taxa is newly implicated in the cycling of dissolved proteins affiliated with the Verrucomicrobia, Planctomycetes, Actinobacteria and MGII Euryarchaeota.

Fewer sub-clades were found to be active in protein uptake in taxa such as y-Proteobacteria, SAR86 and Actinobacteria.

Some taxa found in particle-attached fractions were particularly active in protein assimilation (Flavobacteria, Verrucomicrobia and Planctomycetes), but their free-living counterparts were not. The utilization of dissolved HMW-DON by particle-attached bacteria and Euryarchaeota demonstrates that diverse particle-attached microbial communities can also act as a sink of important DON substrates over relatively short timescales (24 hours).

The researchers hypothesized that MGII archaea were actively involved in protein turnover, and that this activity would be enhanced in association with particles.

TonB-dependent receptors (TBDRs) are a potential mechanism used by certain marine microbes in utilization of dissolved protein. The number of taxa assimilating protein correlated with genomic representation of TBDR encoding genes. This finding warrants further investigation.


Seawater was collected aboard the R/V Western Flyer during Monterey Bay Aquarium Research Institute cruise CN13ID, 7–17 October 2013. The researchers performed the incubations at a station in the coastal transition zone of the Central California Current, where there is a rich contextual background on biogeochemistry and picoeukaryotic phytoplanker Micromonas pusilla is resident.

The researchers performed DNA stable-isotope probing (SIP), using isotopically labelled proteins (13C and 15N) from the M. pusilla. They coupled SIP with high-throughput Illumina sequencing of 16S small subunit ribosomal RNA genes in three different size fractions to identify protein assimilation by individual bacterial and archaeal operational taxonomic units.


The study provides the first direct link between MGII cells and protein recycling. Its results significantly expand the known microbial diversity mediating the cycling of dissolved protein in the ocean. 


Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean, Orsi, W.D. et al., ISME Journal, 8 March 2016)

Read the full brief