Measuring Bacterial Production in Deep-Sea Sediments using 3H-Thymidine Incorporation: Ecological Significance

Abstract

Bacteria play a major role in the decomposition of organic matter arriving at the deep-sea floor, and hence there is a need to determine accurate rates of bacterial production associated with sediment particles. However, sediment-based procedures are not well defined and sampling deep-sea sediments is technically difficult, time consuming, and expensive, often only producing relatively small amounts of undisturbed sediment for analysis. We describe and test a small-scale method (requiring 0.25 ml sediment) for the examination of bacterial production in deep-sea calcium carbonate rich sediments. Time course experiments showed variation in the period of linear [3H]thymidine uptake between 1 and 3 hr depending on station depth. The average concentration of natural thymidine in deep-sea sediments was 0.61 nmol per 0.5 ml slurry sample. Isotope dilution was significant, ranging between 26 and 51%. There was substantial small-scale (0.2-1.0 m) variation in deep-sea benthic bacterial [3H]thymidine incorporation rates (39%). Deep-sea surficial sediment bacterial production (assuming zero isotope dilution due to its potential high variability) in surficial sediments of the deep NE Atlantic varied between 0.014 and 0.48 mg C g-1 d-1 (mean = 0.23 mg C g-1 d-1) over 3 locations of depths between 1,092 and 3,572 m and at 3 times. Bacterial biomass varied between 1.1 and 12 mg C g-1 (mean = 6.1 mg C g-1). Bacterial growth rate estimates in these deep-sea sediments varied between 0.003 and 0.13 d-1 (mean = 0.050 d-1) giving doubling times of 5.3-216 d (mean = 44.5 d); which are similar to those of bacteria inhabiting waters in the upper mixed layer (2-<40 m) of the water column (2.6-57.8 d). comparison with shallow and coastal sea sediments (0.13-116 d) indicates that deep-sea sediment bacteria in the NE Atlantic are able to grow at rates similar to those in shallow sediment systems given sufficient food. However, the range is broader for deep-sea sediment bacteria, which may indicate a more "feast" and "fast" life than their counterparts in shallower environments. waters >2,000 m cover 60% of the Earth's surface; thus bacterial production in deep-sea sediments must contribute an important fraction of oceanic and global bacterial production. It is therefore important to establish an accurate method of measuring bacterial production so that the full roles and controls of bacteria from this environment can be determined.

Large-Scale Distribution and Activity of Prokaryotes in Deep-Sea Surface Sediments of the Mediterranean Sea and the Adjacent Atlantic Ocean

“…This is supported by our measurements of HCP, which are high compared to other measurements made in surface sediments at similar depths [49,82], and which positively correlate with the PBM and active cells for the Mediterranean stations (Pearson moment correlation, r = 0.50, n = 60, p <0.001, and r = 0.54, n = 60, p <0.001, respectively). However, when we calculated the cell-specific activity at each Mediterranean station, this was comparable to those in the literature (e.g., [83] and references therein) and one order of magnitude lower on average than those reported by [79] for the Mediterranean Sea water column at similar depths. This observation suggests that sediment prokaryotes convert organic matter into biomass at a rate comparable to that for other oceans, despite the higher bottom temperature [79].…”

Marine actinobacteria: perspectives, challenges, future directions

“…[H-3] thymidine incorporation), the logistical difficulties of conducting experiments in the deep-sea per se usually results in ship-or shore-based experiments with collected material (e.g. Dixon and Turley 2001). Moreover, as (DeLong 2001) has pointed out 'when using these approaches, species composition and its variability (perhaps the most important parameters in a biogeochemical sense) remain unknown'.…”

Quantification of Viral and Prokaryotic Production Rates in Benthic Ecosystems: A Methods Comparison

“…Independent evidence indicate that viruses are abundant and active in benthic ecosystems, with current measurements of viral abundance typically ranging from 10 8 to 10 11 virus g -1 of dry sediment and viral production rates in the order of 10 6 to 10 8 virus g -1 h -1 ( Fischer et al, 2003 ; Hewson and Fuhrman, 2003 ; Middelboe et al, 2003 ; Glud and Middelboe, 2004 ; Mei and Danovaro, 2004 ; Danovaro et al, 2008a , b , 2015 ; Pinto et al, 2013 ). The same holds true for benthic prokaryotes, usually in the order of 10 7 to 10 9 cells g -1 of dry sediment and ranging in production rates from few nanograms to >1 μg of C g -1 h -1 ( van Duyl and Kop, 1994 ; Dixon and Turley, 2001 ; Danovaro et al, 2008a , b ). However, direct comparisons of values obtained across different studies has been hampered by the variety of methodological approaches used, as well as the array of environmental settings investigated.…”

“…The non-specific binding of 3 H-thymidine to the sediments was taken into account by analyzing replicate sediment sub-samples treated with 80% ethanol before 3 H-thymidine addition (i.e., sediment blanks). Prokaryotic C production was calculated assuming the CF previously reported for deep-sea sediments of 2 × 10 18 cells produced per mole thymidine incorporated and on the basis of the C content of prokaryotic cells ( Dixon and Turley, 2001 ).…”