Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface

Abstract

Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequences representing seven bacterial phyla. Two organisms, E01-9C-26 (Gammaproteobacteria), represented by four single cell genomes, and Opi.OSU.00C, an uncharacterized Verrucomicrobia, were the first of their types retrieved by single cell genome sequencing and were studied in detail. Metagenomic data showed that E01-9C-26 is found throughout the dark ocean, while Opi.OSU.00C was observed to bloom transiently in the nutrient-depleted euphotic zone of the late spring and early summer. The E01-9C-26 genomes had an estimated size of 4.76–5.05 Mbps, and contained “O” and “W”-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes. Metabolic reconstruction indicated E01-9C-26 are likely versatile methylotrophs capable of scavenging C1 compounds, methylated compounds, reduced sulfur compounds, and a wide range of amines, including D-amino acids. The genome sequences identified E01-9C-26 as a source of “O” and “W”-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes, but are of unknown function. In contrast, Opi.OSU.00C genomes encode genes for catabolizing carbohydrate compounds normally associated with eukaryotic phytoplankton. This exploration of optofluidics showed that it was effective for retrieving diverse single-cell bacterioplankton genomes and has potential advantages in microbiology applications that require working with small sample volumes or targeting cells by their morphology.

Macrofaunal control of microbial community structure in continental margin sediments

“…In addition, several metabolically diverse lineages correlate significantly with nonlocal mixing (N a ). The metabolisms of these lineages include nitrification [e.g., Nitrospinae ( 45 ), Nitrosomonadales of Betaproteobacteria ( 46 )], aerobic methylotrophy [E01-9C-26 of Gammaproteobacteria ( 47 )], aerobic organotrophy [ Arenicella of Gammaproteobacteria ( 48 )], anaerobic organotrophy [ Bacteroidia of Bacteroidetes ( 49 )], and sulfate reduction [Sva0485 of Deltaproteobacteria ( 50 )].…”

Characterization of sponge‐associated Verrucomicrobia: microcompartment‐based sugar utilization and enhanced toxin–antitoxin modules as features of host‐associated Opitutales

“…Freshwater and marine Verrucomicrobia play an important role in global carbon cycling, processing decaying organic materials and degrading various polysaccharides (Cardman et al ., 2014; Cabello‐Yeves et al ., 2017; He et al ., 2017; Sichert et al ., 2020). Genomic studies of marine planktonic Verrucomicrobia have revealed their specialization on certain types of polysaccharides and related their seasonal distribution to dissolved organic matter in seawater (Haro‐Moreno et al ., 2018; Landry et al ., 2018). Recently discovered ‘ Lentimonas ’ sp.…”

Cell Separations and Sorting

“…Another application of optofluidics was demonstrated by Landry et al 23 who developed a method for single-cell genome amplification from sorted via an optical trap bacterioplankton cells. The device retrieved diverse single-cell bacterioplankton genomes and offered utility in microbiology applications that required working with small sample volumes.…”