Niskin bottle sample collection aliases microbial community composition and biogeochemical interpretation

Abstract

Particles able to settle distances of approximately a meter in 1–2 h are undersampled in water traditionally collected in Niskin bottles. Gardner (Limnol Oceanogr, 22, 764–768, 1977) demonstrated that particles sink into the space below the spout of Niskin bottles on timescales relevant to sample processing. We examined this effect on measurements of microbial abundance, community composition, and transparent stainable particles across an oxygen‐sulfide gradient in the Cariaco Basin. Within 1 h, modestly sized micro‐aggregates (> 16 μm) were not detected in samples drawn from the spout, but were abundant in the waters below the spout. Total transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP) were at least twice as abundant in the below‐spout samples as in spout‐collected water. Below‐spout samples accounted for four times more total particle surface area per mL than spout samples. Approximately 10% of all microbes were particle‐associated, which led to only small enrichments of total microbes in the below‐spout samples. However, fluorescent in situ hybridization (FISH) revealed five of seven clades surveyed were significantly more enriched in water below the spout than total cells, indicating (1) a small bias when enumerating total particles and microbes from spout samples and (2) a very strong bias for particular phylogenetic groups that are more prevalent on particles than the total community. In particular, sulfate‐reducing δ‐proteobacteria were consistently enriched in below‐spout samples collected at depths along the oxygen‐sulfide transition. Abundance of this functional group has potentially been underestimated in the past. Consequently, microbial diversity results derived from Niskin bottle samples should be cautiously applied when interpreting biogeochemical cycling.

Transparent exopolymer particles (TEP) in the deep ocean: full-depth distribution patterns and contribution to the organic carbon pool

“…Finally, determination of TEP and POC from discrete water samples collected in N iskin bottles may suffer from biases associated with sampling and sample processing. A recent study showed that TEP concentration was underestimated by 1−13% due to settling of TEP in the space below the spout of Niskin bottles (Suter et al 2017). If this occurred during our sampling, we might have slightly to moderately underestimated TEP concentrations.…”

An autonomous, in situ light‐dark bottle device for determining community respiration and net community production

“…For example, the PHORCYS minimizes physical disturbances associated with seawater handling: Since the instrument takes seawater samples and then incubates them in place, the planktonic community is not subjected to rapid changes in temperature, pressure, and light associated with bringing water samples to the surface via hydrocast and preparing them for shipboard incubations (Calvo‐Díaz et al ). The PHORCYS also minimizes another potential bias that can arise when water containing marine microbes is sampled from Niskin bottles; Suter et al () found that variation in settling rates among marine particles can lead to an undersampling of microbial communities on faster‐sinking particles, which can fall below the bottles' spouts before aliquots can be drawn.…”

“…These can be generally divided into two categories: (1) those that result from the preparation for or act of incubating natural microbial populations and (2) errors inherent in the method used to determine the concentration of dissolved oxygen (e.g., Winkler titration, fluorescence‐quenching optode, or Clark electrode). The sources of uncertainty associated with bottle/chamber incubations span both categories and include (1) contamination, disruption, or bias introduced through the process of obtaining seawater samples from depth and preparing them for incubation (Tamburini et al ; Suter et al ); (2) unrepresentative incubation conditions that do not faithfully reproduce the variations in temperature, turbulence, and light inherent in natural systems; (3) so‐called “bottle effects” associated with low‐volume incubations which may limit nutrient availability (Furnas ) or induce unnatural changes in community structure (Venrick et al ; Calvo‐Díaz et al ); and (4), in the case of metabolic rate measurements extrapolated from Winker (1888) titrations, the lack of temporal resolution inherent in measurements based only on two endpoints. In any study where incubations are used, the choice of incubation methodology places inherent limits on the spatial and temporal resolution of the data collected (Karl et al ).…”

Deep Into Oceanic N2 Fixation

“…The precision of N 2 fixation rates may be affected by (i) a slower than theoretically assumed dissolution of the 15 N 2 bubble in seawater (Mohr et al, 2010;Großkopf et al, 2012), (ii) the contamination of 15 N 2 gas stocks with nitrogenous species other than N 2 (Dabundo et al, 2014), and (iii) failure to measure time zero δ 15 N values of the particulate nitrogen pool. As any other tracer method, 15 N 2 -based N 2 fixation rates are subject to a number of other sources of error, including variability in incubation and/or filtration time among replicates, sample particle size and its retention in filters varying with filter pore size (Bombar et al, 2018), as well as heterogeneous distribution of particles in Niskin bottles (Suter et al, 2017). Moreover, the vast majority of 15 N 2 -based published N 2 fixation measurements report net rates, whereas the leakage of 15 N-labeled dissolved organic nitrogen and/or ammonium can be significant in certain cases (e.g., Berthelot et al, 2017).…”