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  • 1
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    Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum (2021)
    American Chemical Society
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.
    Description: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.
    Description: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.
    Keywords: Lipids ; Alkyls ; Bacteria ; Genetics ; Chromatography
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Towards a better understanding of microbial carbon flux in the sea (2011)
    Inter-Research
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    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2008. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 53 (2008): 21-38, doi:10.3354/ame01230.
    Description: We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas.
    Description: Our work was supported by the following grants: NSF grant 0217282 (H.D.), Spanish MEC grant MODIVUS (J.M.G.), the Swedish Science Council (J.P.), the IEO time-series RADIALES programme (X.A.G.M.), the Earth and Life Science Division of the Dutch Science Foundation, ARCHIMEDES project, #835.20.023 (G.J.H.).
    Keywords: Carbon flux ; Microbial ecology ; Ocean ; Bacteria ; Protists ; Light ; Genomics ; Chemoautotrophy ; Models
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Gradients in dimethylsulfide, dimethylsulfoniopropionate, dimethylsulfoxide, and bacteria near the sea surface (2011)
    Inter-Research
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    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2005. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Marine Ecology Progress Series 295 (2005): 33-42, doi:10.3354/meps295033.
    Description: Gradients of dimethylsulfide (DMS), dimethylsulfoniopropionate (DMSP), dimethylsulfoxide (DMSO), and bacterial numbers and diversity from the surface microlayer to 500 cm depth were assessed in coastal waters surrounding the Martha’s Vineyard Coastal Observatory, Massachusetts, USA. Microlayer samples were collected with a surface skimmer: a partially submerged, rotating glass cylinder (‘drum’) that allows the collection of a thin layer of water by adherence to the drum. A depletion of DMS towards the water surface (10 cm) was found at all sampling days, with largest gradients during rough sea surface conditions. The steep gradients show that gas fluxes and transfer velocities, based on the concentration disequilibrium between the water and the atmosphere, need to be based on near surface gas concentration values. Elevated DMSP, DMSO concentrations and bacterial numbers were found at the sea surface during calm conditions. Although degassing and photo-oxidation on the skimmer will bias the microlayer data, the results indicate stratification of DMSP, DMSO and bacteria during periods of smooth sea surface conditions.
    Description: We also thank the postdoctoral scholar program at the Woods Hole Oceanographic Institution, with funding provided by the J. Seward Johnson Fund.
    Keywords: Marine sulfur ; Bacteria ; Depth profiles ; Microlayer sampling ; Coastal waters ; DMS ; DMSP ; DMSO
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton (2015)
    Inter-Research
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    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2015. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 75 (2015): 129-137, doi:10.3354/ame01753.
    Description: High-throughput sequencing of small subunit ribosomal RNA (SSU rRNA) genes from marine environments is a widely applied method used to uncover the composition of microbial communities. We conducted an analysis of surface ocean waters with the commonly employed hypervariable 4 region SSU rRNA gene primers 515F and 806R, and found that bacteria belonging to the SAR11 clade of Alphaproteobacteria, a group typically making up 20 to 40% of the bacterioplankton in this environment, were greatly underrepresented and comprised 〈4% of the total community. Using the SILVA reference database, we found a single nucleotide mismatch to nearly all SAR11 subclades, and revised the 806R primer so that it increased the detection of SAR11 clade sequences in the database from 2.6 to 96.7%. We then compared the performance of the original and revised 806R primers in surface seawater samples, and found that SAR11 comprised 0.3 to 3.9% of sequences with the original primers and 17.5 to 30.5% of the sequences with the revised 806R primer. Furthermore, an investigation of seawater obtained from aquaria revealed that SAR11 sequences acquired with the revised 806R primer were more similar to natural cellular abundances of SAR11 detected using fluorescence in situ hybridization counts. Collectively, these results demonstrate that a minor adjustment to the 806R primer will greatly increase detection of the globally abundant SAR11 clade in marine and lake environments, and enable inclusion of this important bacterial lineage in experimental and environmental-based studies.
    Description: This project was supported by NSF award OCE-1233612 to A.A. with contributions from BIOS Grant in aid award to S.McN. and NSF Oceanic Microbial Observatory OCE-0801991 subcontract to BIOS managed by R.P.
    Keywords: SSU rRNA gene ; 16S ; SAR11 ; Bacteria ; Fluorescence in situ hybridization ; FISH
    Repository Name: Woods Hole Open Access Server
    Type: Article
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