Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur‐oxidizing micro‐organisms in particular. In this study, the thiosulfate‐oxidizing hydrothermal vent bacterium
Growth rates are central to understanding microbial interactions and community dynamics. Metagenomic growth estimators have been developed, specifically codon usage bias (CUB) for maximum growth rates and “peak-to-trough ratio” (PTR) for in situ rates. Both were originally tested with pure cultures, but natural populations are more heterogeneous, especially in individual cell histories pertinent to PTR. To test these methods, we compared predictors with observed growth rates of freshly collected marine prokaryotes in unamended seawater. We prefiltered and diluted samples to remove grazers and greatly reduce virus infection, so net growth approximated gross growth. We sampled over 44 h for abundances and metagenomes, generating 101 metagenome-assembled genomes (MAGs), including Actinobacteria, Verrucomicrobia, SAR406, MGII archaea, etc. We tracked each MAG population by cell-abundance-normalized read recruitment, finding growth rates of 0 to 5.99 per day, the first reported rates for several groups, and used these rates as benchmarks. PTR, calculated by three methods, rarely correlated to growth (r ~−0.26–0.08), except for rapidly growing γ-Proteobacteria (r ~0.63–0.92), while CUB correlated moderately well to observed maximum growth rates (r = 0.57). This suggests that current PTR approaches poorly predict actual growth of most marine bacterial populations, but maximum growth rates can be approximated from genomic characteristics.
more » « less- Award ID(s):
- 1737409
- NSF-PAR ID:
- 10192911
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- The ISME Journal
- Volume:
- 15
- Issue:
- 1
- ISSN:
- 1751-7362
- Format(s):
- Medium: X Size: p. 183-195
- Size(s):
- ["p. 183-195"]
- Sponsoring Org:
- National Science Foundation
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Abstract Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04–1.9 mM) and high pressure (5–10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed‐system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O2was 0.25 hr−1. This is comparable to theμ max(0.28 hr−1) observed at low pH (<6) at ambient pressure whenT. thermophila produces the same mix of sulfur species. The half‐saturation constant for O2() estimated from this study was 0.2 mM (at a cell density of 105cells/ml) and was robust at all pressures tested (0.4–10 MPa), consistent with piezotolerant behavior of this strain. The cell‐specific was determined to be 1.5 pmol O2/cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell‐specific and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats). -
Glass, Jennifer B. (Ed.)ABSTRACT Standard methods for calculating microbial growth rates (μ) through the use of proxies, such as in situ fluorescence, cell cycle, or cell counts, are critical for determining the magnitude of the role bacteria play in marine carbon (C) and nitrogen (N) cycles. Taxon-specific growth rates in mixed assemblages would be useful for attributing biogeochemical processes to individual species and understanding niche differentiation among related clades, such as found in Synechococcus and Prochlorococcus . We tested three novel DNA sequencing-based methods (iRep, bPTR, and GRiD) for evaluating the growth of light-synchronized Synechococcus cultures under different light intensities and temperatures. In vivo fluorescence and cell cycle analysis were used to obtain standard estimates of growth rate for comparison with those of the sequence-based methods (SBM). None of the SBM values were correlated with growth rates calculated by standard techniques despite the fact that all three SBM were correlated with the percentage of cells in S phase (DNA replication) over the diel cycle. Inaccuracy in determining the time of maximum DNA replication is unlikely to account entirely for the absence of a relationship between SBM and growth rate, but the fact that most microbes in the surface ocean exhibit some degree of diel cyclicity is a caution for application of these methods. SBM correlate with DNA replication but cannot be interpreted quantitatively in terms of growth rate. IMPORTANCE Small but abundant, cyanobacterial strains such as the photosynthetic Synechococcus spp. are important because they contribute significantly to primary productivity in the ocean. These bacteria generate oxygen and provide biologically available carbon, which is essential for organisms at higher trophic levels. The small size and diversity of natural microbial assemblages mean that taxon-specific activities (e.g., growth rate) are difficult to obtain in the field. It has been suggested that sequence-based methods (SBM) may be able to solve this problem. We find, however, that SBM can detect DNA replication and are correlated with phases of the cell cycle but cannot be interpreted in terms of absolute growth rate for Synechococcus cultures growing under a day-night cycle, like that experienced in the ocean.more » « less
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Abstract. Oceanic emissions of dimethyl sulfide (CH3SCH3,DMS) have long been recognized to impact aerosol particle composition andsize, the concentration of cloud condensation nuclei (CCN), and Earth'sradiation balance. The impact of oceanic emissions of methanethiol(CH3SH, MeSH), which is produced by the same oceanic precursor as DMS,on the volatile sulfur budget of the marine atmosphere is largelyunconstrained. Here we present direct flux measurements of MeSH oceanicemissions using the eddy covariance (EC) method with a high-resolutionproton-transfer-reaction time-of-flight mass spectrometer (PTR-ToFMS)detector and compare them to simultaneous flux measurements of DMS emissionsfrom a coastal ocean site. Campaign mean mixing ratios of DMS and MeSH were72 ppt (28–90 ppt interquartile range) and 19.1 ppt (7.6–24.5 pptinterquartile range), respectively. Campaign mean emission fluxes of DMS (FDMS) and MeSH (FMeSH) were 1.13 ppt m s−1 (0.53–1.61 ppt m s−1 interquartile range) and 0.21 ppt m s−1 (0.10–0.31 ppt m s−1 interquartile range), respectively. Linear least squares regression of observed MeSH and DMS flux indicates the emissions are highly correlatedwith each other (R2=0.65) over the course of the campaign,consistent with a shared oceanic source. The campaign mean DMS to MeSH fluxratio (FDMS:FMeSH) was 5.5 ± 3.0, calculated from the ratio of 304 individual coincident measurements of FDMS and FMeSH. Measured FDMS:FMeSH was weakly correlated (R2=0.15) withocean chlorophyll concentrations, with FDMS:FMeSH reaching a maximumof 10.8 ± 4.4 during a phytoplankton bloom period. No other volatilesulfur compounds were observed by PTR-ToFMS to have a resolvable emissionflux above their flux limit of detection or to have a gas-phase mixing ratio consistently above their limit of detection during the study period,suggesting DMS and MeSH are the dominant volatile organic sulfur compoundsemitted from the ocean at this site. The impact of this MeSH emission source on atmospheric budgets of sulfurdioxide (SO2) was evaluated by implementing observed emissions in a coupled ocean–atmosphere chemical box model using a newly compiled MeSHoxidation mechanism. Model results suggest that MeSH emissions lead toafternoon instantaneous SO2 production of 2.5 ppt h−1, which results in a 43 % increase in total SO2 production compared to a casewhere only DMS emissions are considered and accounts for 30% of theinstantaneous SO2 production in the marine boundary layer at the meanmeasured FDMS and FMeSH. This contribution of MeSH to SO2production is driven by a higher effective yield of SO2 from MeSHoxidation and the shorter oxidation lifetime of MeSH compared to DMS. Thislarge additional source of marine SO2 has not been previouslyconsidered in global models of marine sulfur cycling. The field measurementsand modeling results presented here demonstrate that MeSH is an importantcontributor to volatile sulfur budgets in the marine atmosphere and must be measured along with DMS in order to constrain marine sulfur budgets. Thislarge additional source of marine–reduced sulfur from MeSH will contribute to particle formation and growth and CCN abundance in the marine atmosphere, with subsequent impacts on climate.more » « less
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Nitrogen fixers (diazotrophs) are often an important nitrogen source to phytoplankton nutrient budgets in N-limited marine environments. Diazotrophic symbioses between cyanobacteria and diatoms can dominate nitrogen-fixation regionally, particularly in major river plumes and in open ocean mesoscale blooms. This study reports the successful isolation and growth in monocultures of multiple strains of a diatom-cyanobacteria symbiosis from the Gulf of Mexico using a modified artificial seawater medium. We document the influence of light and nutrients on nitrogen fixation and growth rates of the host diatom Hemiaulus hauckii Grunow together with its diazotrophic endosymbiont Richelia intracellularis Schmidt, as well as less complete results on the Hemiaulus membranaceus - R. intracellularis symbiosis. The symbioses rates reported here are for the joint diatom-cyanobacteria unit. Symbiont diazotrophy was sufficient to support both the host diatom and cyanobacteria symbionts, and the entire symbiosis replicated and grew without added nitrogen. Maximum growth rates of multiple strains of H. hauckii symbioses in N-free medium with N 2 as the sole N source were 0.74–0.93 div d −1 . Growth rates followed light saturation kinetics in H. hauckii symbioses with a growth compensation light intensity (E C ) of 7–16 µmol m −2 s −1 and saturation light level (E K ) of 84–110 µmol m −2 s −1 . Nitrogen fixation rates by the symbiont while within the host followed a diel pattern where rates increased from near-zero in the scotophase to a maximum 4–6 h into the photophase. At the onset of the scotophase, nitrogen-fixation rates declined over several hours to near-zero values. Nitrogen fixation also exhibited light saturation kinetics. Maximum N 2 fixation rates (84 fmol N 2 heterocyst −1 h −1 ) in low light adapted cultures (50 µmol m −2 s − 1) were approximately 40–50% of rates (144–154 fmol N 2 heterocyst −1 h −1 ) in high light (150 and 200 µmol m −2 s −1 ) adapted cultures. Maximum laboratory N 2 fixation rates were ~6 to 8-fold higher than literature-derived field rates of the H. hauckii symbiosis. In contrast to published results on the Rhizosolenia-Richelia symbiosis, the H. hauckii symbiosis did not use nitrate when added, although ammonium was consumed by the H. hauckii symbiosis. Symbiont-free host cell cultures could not be established; however, a symbiont-free H. hauckii strain was isolated directly from the field and grown on a nitrate-based medium that would not support DDA growth. Our observations together with literature reports raise the possibility that the asymbiotic H. hauckii are lines distinct from an obligately symbiotic H. hauckii line. While brief descriptions of successful culture isolation have been published, this report provides the first detailed description of the approaches, handling, and methodologies used for successful culture of this marine symbiosis. These techniques should permit a more widespread laboratory availability of these important marine symbioses.more » « less
