Application of a rapid direct count method to deep-sea sediment bacteria
Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Bremen, Germany Journal of Microbiological Methods
(Impact Factor: 2.03).
07/2004; 57(3):351-67. DOI: 10.1016/j.mimet.2004.02.005
For the first time, a Live/Dead (L/D) Bacterial Viability Kit (BacLight ) protocol was adapted to marine sediments and applied to deep-sea sediment samples to assess the viability (based on membrane integrity) of benthic bacterial communities. Following a transect of nine stations in the Fram Strait (Arctic Ocean), we observed a decrease of both bacterial viability and abundance with increasing water (1250-5600 m) and sediment depth (0-5 cm). Percentage of viable (and thus potentially active) cells ranged between 20-60% within the first and 10-40% within the fifth centimetre of sediment throughout the transect, esterase activity estimations (FDA) similarly varied from highest (13.3+/-5.4 nmol cm(-3) h(-1)) to lowest values below detection limit down the sediment column. Allowing for different bottom depths and vertical sediment sections, bacterial viability was significantly correlated with FDA estimations (p<0.001), indicating that viability assessed by BacLight staining is a good indicator for bacterial activity in deep-sea sediments. Comparisons between total L/D and DAPI counts not only indicated a complete bacterial cell coverage, but a better ability of BacLight staining to detect cells under low activity conditions. Time course experiments confirmed the need of a rapid method for viability measurements of deep-sea sediment bacteria, since changes in pressure and temperature conditions caused a decrease in bacterial viability of up to 50% within the first 48 h after sample retrieval. The Bacterial Viability Kit proved to be easy to handle and to provide rapid and reliable information. It's application to deep-sea samples in absence of pressure-retaining gears is very promising, as short staining exposure time is assumed to lessen profound adverse effects on bacterial metabolism due to decompression.
Available from: Guenter Engling
- "FCM provides a direct, rapid and precise quantification of particle suspension (up to ten thousand particles per second). Recently, FCM combined with fluorescent dyes has been applied to various environmental samples, including estuarine water (Moreira-Turcq & Martin, 1998), drinking water (Boulos et al., 1999), deep-sea sediment (Quéric et al., 2004), activated sludge (Ziglio et al., 2002), and atmospheric aerosol (Chen & Li, 2005a, 2005b; Prigione et al., 2004). Furthermore, the FCM method has been discussed and compared with the epifluorescence microscopy method in a few studies (Prigione et al., 2004; Minor & Nallathamby, 2004). "
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ABSTRACT: Fungal spores constitute the most abundant fraction of biological aerosols in the atmosphere, influencing human health, the biosphere, atmospheric chemistry, and climate. However, the total abundance of fungal spores in the atmosphere is rather uncertain and likely underestimated to a large extent by traditional Colony Forming Units (CFU) assays. In this study, flow cytometry (FCM) was utilized in combination with fluorescent stains for the rapid counting of ambient fungal spores, with complementary quantification of two molecular tracers for fungal spores. The FCM results had significant positive correlation with the concentrations of the fungal tracers (R2 was 0.75 and 0.70 for arabitol and mannitol, respectively). During this study, total particle counts, fungal spore numbers and the fractions of fungal spores of the total particle numbers were in the range of 44,698–9,54,211 m−3, 8224–261,154 m−3 and 1.9–46.5%, respectively, at an urban location in northern China. Meteorological conditions were shown to have complex effects on the ambient concentrations of fungal spores: the number concentrations of fungal spores exhibited significant positive correlation with relative humidity and temperature, negative correlation with wind speed and no relationship with solar radiation during the sampling period.
Journal of Aerosol Science 12/2013; 66:179–186. DOI:10.1016/j.jaerosci.2013.08.013 · 2.24 Impact Factor
Available from: Alban Ramette
- "The most northern stations (N3 and N4) as well as the deepest station sampled in this study (HG-VI) were partly ice covered during sampling. TV-MUC cores were sub-sampled using modified 10-ml syringes (2 cm in diameter), sub-divided into 1-cm layers and only the uppermost centimeter representing the most active community was analyzed in this study . Necessary permits for sampling were obtained from the Norwegian authorities (Fisheries directorate). "
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ABSTRACT: Knowledge on spatial scales of the distribution of deep-sea life is still sparse, but highly relevant to the understanding of dispersal, habitat ranges and ecological processes. We examined regional spatial distribution patterns of the benthic bacterial community and covarying environmental parameters such as water depth, biomass and energy availability at the Arctic Long-Term Ecological Research (LTER) site HAUSGARTEN (Eastern Fram Strait). Samples from 13 stations were retrieved from a bathymetric (1,284-3,535 m water depth, 54 km in length) and a latitudinal transect (∼ 2,500 m water depth; 123 km in length). 454 massively parallel tag sequencing (MPTS) and automated ribosomal intergenic spacer analysis (ARISA) were combined to describe both abundant and rare types shaping the bacterial community. This spatial sampling scheme allowed detection of up to 99% of the estimated richness on phylum and class levels. At the resolution of operational taxonomic units (97% sequence identity; OTU3%) only 36% of the Chao1 estimated richness was recovered, indicating a high diversity, mostly due to rare types (62% of all OTU3%). Accordingly, a high turnover of the bacterial community was also observed between any two sampling stations (average replacement of 79% of OTU3%), yet no direct correlation with spatial distance was observed within the region. Bacterial community composition and structure differed significantly with increasing water depth along the bathymetric transect. The relative sequence abundance of Verrucomicrobia and Planctomycetes decreased significantly with water depth, and that of Deferribacteres increased. Energy availability, estimated from phytodetrital pigment concentrations in the sediments, partly explained the variation in community structure. Overall, this study indicates a high proportion of unique bacterial types on relatively small spatial scales (tens of kilometers), and supports the sampling design of the LTER site HAUSGARTEN to study bacterial community shifts in this rapidly changing area of the world's oceans.
PLoS ONE 09/2013; 8(9):e72779. DOI:10.1371/journal.pone.0072779 · 3.23 Impact Factor
Available from: Elena Manini
- "Prokaryotic distribution, abundance and community composition are controlled by environmental and trophic variables [17,36–40]. To date, only regional and local scale driving factors have been investigated, and although depth-related trends in prokaryotic abundance distribution have been reported [41–43], the enduring controlling factors of the variability of prokaryotic parameters (i.e., abundance, biomass, activity) appear to be the amount and availability of organic matter that settles to the seafloor [36–38,44–46]. In deep-sea sediments, the quantity and quality of organic matter is largely dependent upon seasonal deposition and burial of organic matter produced in the photic layer, as well as the complex biochemical transformations of the particles as they sink down the water column . "
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ABSTRACT: The deep-sea represents a substantial portion of the biosphere and has a major influence on carbon cycling and global biogeochemistry. Benthic deep-sea prokaryotes have crucial roles in this ecosystem, with their recycling of organic matter from the photic zone. Despite this, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments. To assess the influence of environmental and trophic variables on the large-scale distribution of prokaryotes, we investigated the prokaryotic assemblage composition (Bacteria to Archaea and Euryarchaeota to Crenarchaeota ratio) and activity in the surface deep-sea sediments of the Mediterranean Sea and the adjacent North Atlantic Ocean. Prokaryotic abundance and biomass did not vary significantly across the Mediterranean Sea; however, there were depth-related trends in all areas. The abundance of prokaryotes was positively correlated with the sedimentary concentration of protein, an indicator of the quality and bioavailability of organic matter. Moving eastwards, the Bacteria contribution to the total prokaryotes decreased, which appears to be linked to the more oligotrophic conditions of the Eastern Mediterranean basins. Despite the increased importance of Archaea, the contributions of Crenarchaeota Marine Group I to the total pool was relatively constant across the investigated stations, with the exception of Matapan-Vavilov Deep, in which Euryarchaeota Marine Group II
dominated. Overall, our data suggest that deeper areas of the Mediterranean Sea share more similar communities
with each other than with shallower sites. Freshness and quality of sedimentary organic matter were identified
through Generalized Additive Model analysis as the major factors for describing the variation in the prokaryotic
community structure and activity in the surface deep-sea sediments. Longitude was also important in explaining the
observed variability, which suggests that the overlying water masses might have a critical role in shaping the benthic
PLoS ONE 08/2013; 8(8):e72996. DOI:10.1371/journal.pone.0072996 · 3.23 Impact Factor
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