title: Standard filtration practices may significantly distort planktonic microbial diversity estimates.
abstract: Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size) and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40 to 60% of prefilter datasets at low volumes (0.05-0.5 L) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes, and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold). Taxon richness (97% similarity clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.
authors.affiliation: School of Biology, Georgia Institute of Technology Atlanta, GA, USA.
authors.forename: Cory C
authors.initials: CC
authors.lastname: Padilla
authors.affiliation: School of Biology, Georgia Institute of Technology Atlanta, GA, USA.
authors.forename: Sangita
authors.initials: S
authors.lastname: Ganesh
authors.affiliation: School of Biology, Georgia Institute of Technology Atlanta, GA, USA.
authors.forename: Shelby
authors.initials: S
authors.lastname: Gantt
authors.affiliation: School of Biology, Georgia Institute of Technology Atlanta, GA, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Huhman
authors.affiliation: School of Biology, Georgia Institute of Technology Atlanta, GA, USA.
authors.forename: Darren J
authors.initials: DJ
authors.lastname: Parris
authors.affiliation: School of Biology, Georgia Institute of Technology Atlanta, GA, USA.
authors.forename: Neha
authors.initials: N
authors.lastname: Sarode
authors.affiliation: School of Biology, Georgia Institute of Technology Atlanta, GA, USA.
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Stewart
keywords: Vibrio; filter fractionation; marine bacteria; particle-associated; prefilter; richness