Fixation filter, device for the rapid in situ preservation of particulate samples

Taylor, Craig D.; Edgcomb, Virginia P.; Doherty, Kenneth W.; Engstrom, Ivory B.; Shanahan, T. M.; Pachiadaki, Maria; Molyneaux, Stephen J.; Honjo, Susumu

doi:10.1016/j.dsr.2014.09.006

Cited by 21 publications

(18 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, custom filter chambers with reservoirs (Taylor et al, 2013) (Figure 6d) were used to hold the preservative sucrose lysis buffer (SLB) until sample collection. The filter chambers were designed to be used with preservative such as glutaraldehyde, but because some preservative escapes the filter units into the lake and environmental preservation is of primary importance in the Dry Valleys, we chose to use SLB, which is nontoxic and is a superior preservative when used to preserve DNA for sequencing (Mitchell & Takacs-Vesbach, 2008).…”

Section: Ppsmentioning

confidence: 99%

Autonomous Year-Round Sampling and Sensing to Explore the Physical and Biological Habitability of Permanently Ice-Covered Antarctic Lakes

Winslow¹,

Dugan²,

Buelow³

et al. 2014

mar technol soc j

View full text Add to dashboard Cite

A B S T R A C TThe lakes of the McMurdo Dry Valleys, Antarctica, are some of the only systems on our planet that are perennially ice-covered and support year-round metabolism. As such, these ecosystems can provide important information on conditions and life in polar regions on Earth and on other icy worlds in our solar system. Working in these extreme environments of the Dry Valleys poses many challenges, particularly with respect to data collection during dark winter months when logistical constraints make fieldwork difficult. In this paper, we describe the motivation, design, and challenges for this recently deployed instrumentation in Lake Bonney, a lake that has been the subject of summer research efforts for more than 40 years. The instrumentation deployed includes autonomous water, phytoplankton, and sediment samplers as well as cable-mounted profiling platforms with dissolved gas and fluorometry sensors. Data obtained from these instruments will allow us, for the first time, to define the habitability of this environment during the polar night. We include lessons learned during deployment and recommendations for effective instrument operation in these extreme conditions.

show abstract

Section: Ppsmentioning

confidence: 99%

Autonomous Year-Round Sampling and Sensing to Explore the Physical and Biological Habitability of Permanently Ice-Covered Antarctic Lakes

Winslow¹,

Dugan²,

Buelow³

et al. 2014

mar technol soc j

View full text Add to dashboard Cite

show abstract

“…Other instrument platforms focus primarily on remote collection and fixation of biological samples for laboratory-based analyses. One such instrument is the Microbial Sampler-Submersible Incubation Device (MS-SID), which is based on the Submersible Incubation Device, a robotic instrument originally developed to carry out in situ incubation experiments [28] and the Fixation Filter system [29]. By pairing incubation capabilities with sample collection and fixation capabilities, this instrument promises to allow an examination of microbial gene expression profiles and/or community compositions associated with specific metabolic activities [30,31].…”

Section: Another Ecogenomic Sensor Under Development Is the Autonomoumentioning

confidence: 99%

Probing the living ocean with ecogenomic sensors

Ottesen

2016

Current Opinion in Microbiology

View full text Add to dashboard Cite

This review discusses the role of ecogenomic sensors in biological oceanography. Ecogenomic sensors are instruments that can autonomously collect biological samples and perform molecular analyses. This technology reduces logistical constraints on the length and duration of biological data collection. Autonomous, robotic performance of molecular assays shows particular promise in the field of public health. Recent applications include simultaneous detection of harmful algal species and fecal markers paired with same-day remote reporting of test results. Ecogenomic instruments are also showing promise for molecular ecological studies. Autonomous collection and preservation of biological samples is facilitating high-resolution ecological studies that are expanding our understanding of marine microbial ecology and dynamics. This review discusses recent applications of these instruments and makes recommendations for future developments.

show abstract

“…For example, rate measurements derived from in situ incubations differ from those derived from Niskin bottle samples (Taylor and Doherty ). Community gene expression profiles from Niskin bottle samples also differ from those obtained from in situ pumps (Feike et al ; Stewart et al ) or in situ preservation systems (Taylor et al ; Edgcomb et al ). However, because of their availability, ease of use and cost effectiveness, Niskin bottles are routinely used for microbiological measurements, particularly for microscopy, rate processes and rRNA‐ and DNA‐based methods.…”

mentioning

confidence: 98%

Niskin bottle sample collection aliases microbial community composition and biogeochemical interpretation

Suter

Scranton

Chow

et al. 2016

Limnology & Oceanography

View full text Add to dashboard Cite

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.

show abstract

Fixation filter, device for the rapid in situ preservation of particulate samples

Cited by 21 publications

References 43 publications

Autonomous Year-Round Sampling and Sensing to Explore the Physical and Biological Habitability of Permanently Ice-Covered Antarctic Lakes

Autonomous Year-Round Sampling and Sensing to Explore the Physical and Biological Habitability of Permanently Ice-Covered Antarctic Lakes

Probing the living ocean with ecogenomic sensors

Niskin bottle sample collection aliases microbial community composition and biogeochemical interpretation

Contact Info

Product

Resources

About