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  • 1
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    Ancestral absence of electron transport chains in Patescibacteria and DPANN (2020)
    Frontiers Media
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beam, J. P., Becraft, E. D., Brown, J. M., Schulz, F., Jarett, J. K., Bezuidt, O., Poulton, N. J., Clark, K., Dunfield, P. F., Ravin, N. V., Spear, J. R., Hedlund, B. P., Kormas, K. A., Sievert, S. M., Elshahed, M. S., Barton, H. A., Stott, M. B., Eisen, J. A., Moser, D. P., Onstott, T. C., Woyke, T., & Stepanauskas, R. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology, 11, (2020): 1848, doi:10.3389/fmicb.2020.01848.
    Description: Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
    Description: This work was funded by the USA National Science Foundation grants 1441717, 1826734, and 1335810 (to RS); and 1460861 (REU site at Bigelow Laboratory for Ocean Sciences). RS was also supported by the Simons Foundation grant 510023. TW, FS, and JJ were funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231. NR group was funded by the Russian Science Foundation (grant 19-14-00245). SS was funded by USA National Science Foundation grants OCE-0452333 and OCE-1136727. BH was funded by NASA Exobiology grant 80NSSC17K0548.
    Keywords: Bacteria ; Archaea ; evolution ; genomics fermentation ; respiration ; oxidoreductases
    Repository Name: Woods Hole Open Access Server
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  • 2
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    The microbiological drivers of temporally dynamic Dimethylsulfoniopropionate cycling processes in Australian coastal shelf waters (2022)
    Frontiers Media
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    Publication Date: 2022-10-31
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in O’Brien, J., McParland, E. L., Bramucci, A. R., Ostrowski, M., Siboni, N., Ingleton, T., Brown, M. V., Levine, N. M., Laverock, B., Petrou, K., & Seymour, J. The microbiological drivers of temporally dynamic Dimethylsulfoniopropionate cycling processes in Australian coastal shelf waters. Frontiers in Microbiology, 13, (2022): 894026, https://doi.org/10.3389/fmicb.2022.894026.
    Description: The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2–2 μm and 〉2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.
    Description: This research was supported by the Australian Research Council Grants FT130100218 and DP180100838 awarded to JS and DP140101045 awarded to JS and KP, as well as an Australian Government Research Training Program Scholarship awarded to JO’B.
    Keywords: DMSP ; DMS ; DLA ; Phytoplankton ; Bacteria ; qPCR ; 16S rRNA gene ; 18S rRNA gene
    Repository Name: Woods Hole Open Access Server
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  • 3
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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
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  • 4
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    Diversity and distribution of prokaryotes within a shallow-water pockmark field (2016)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 941, doi:10.3389/fmicb.2016.00941.
    Description: Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.
    Description: This work was partially supported by a Postdoctoral Fellowship from the Center for Dark Energy Biosphere Investigations [C-DEBI, grant OCE-0939564] awarded to DG, by National Science Foundation grant OCE 11-24141 to CV, and European Science Foundation EuroDeep BIOFUN grant CTM2007-28739-E to EM. This article commits to EU HERMIONE [contract no. 226354] and CoCoNet [contract no. 287844] programs, and the Italian MIUR flag Ritmare within the National Research Program 2011–2013.
    Keywords: Pockmarks ; Cold seeps ; Hydrocarbons ; Prokaryotic diversity ; Bacteria ; Archaea ; Hydrocarbon degradation ; Microbial diversity
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Iron limitation of a springtime bacterial and phytoplankton community in the Ross Sea : implications for vitamin B12 nutrition (2014)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums. The definitive version was published in Frontiers in Microbiology 2 (2011): 160, doi:10.3389/fmicb.2011.00160.
    Description: The Ross Sea is home to some of the largest phytoplankton blooms in the Southern Ocean. Primary production in this system has previously been shown to be iron limited in the summer and periodically iron and vitamin B12 colimited. In this study, we examined trace metal limitation of biological activity in the Ross Sea in the austral spring and considered possible implications for vitamin B12 nutrition. Bottle incubation experiments demonstrated that iron limited phytoplankton growth in the austral spring while B12, cobalt, and zinc did not. This is the first demonstration of iron limitation in a Phaeocystis antarctica-dominated, early season Ross Sea phytoplankton community. The lack of B12 limitation in this location is consistent with previous Ross Sea studies in the austral summer, wherein vitamin additions did not stimulate P. antarctica growth and B12 was limiting only when bacterial abundance was low. Bottle incubation experiments and a bacterial regrowth experiment also revealed that iron addition directly enhanced bacterial growth. B12 uptake measurements in natural water samples and in an iron fertilized bottle incubation demonstrated that bacteria serve not only as a source for vitamin B12, but also as a significant sink, and that iron additions enhanced B12 uptake rates in phytoplankton but not bacteria. Additionally, vitamin uptake rates did not become saturated upon the addition of up to 95 pM B12. A rapid B12 uptake rate was observed after 13 min, which then decreased to a slower constant uptake rate over the next 52 h. Results from this study highlight the importance of iron availability in limiting early season Ross Sea phytoplankton growth and suggest that rates of vitamin B12 production and consumption may be impacted by iron availability.
    Description: This research was supported by NSF grants OCE-0752291, OPP-0440840, OPP-0338097, OPP-0338164, ANT-0732665, OCE-0452883, and OCE-1031271, the Center for Microbial Oceanography Research and Education (CMORE) and a National Science Foundation (NSF) Graduate Research Fellowship (2007037200) and an Environmental Protection Agency STAR Fellowship to EMB (F6E20324).
    Keywords: Iron limitation ; Vitamin B12 ; Ross Sea ; Colimitation ; Bacteria ; Phytoplankton ; Iron fertilization
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Soil salinity and pH drive soil bacterial community composition and diversity along a lateritic slope in the Avon River critical zone observatory, Western Australia. (2019)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in O'Brien, F. J. M., Almaraz, M., Foster, M. A., Hill, A. F., Huber, D. P., King, E. K., Langford, H., Lowe, M., Mickan, B. S., Miller, V. S., Moore, O. W., Mathes, F., Gleeson, D., & Leopold, M. Soil salinity and pH drive soil bacterial community composition and diversity along a lateritic slope in the Avon River critical zone observatory, Western Australia. Frontiers in Microbiology, 10, (2019): 1486, doi:10.3389/fmicb.2019.01486.
    Description: Soils are crucial in regulating ecosystem processes, such as nutrient cycling, and supporting plant growth. To a large extent, these functions are carried out by highly diverse and dynamic soil microbiomes that are in turn governed by numerous environmental factors including weathering profile and vegetation. In this study, we investigate geophysical and vegetation effects on the microbial communities of iron-rich lateritic soils in the highly weathered landscapes of Western Australia (WA). The study site was a lateritic hillslope in southwestern Australia, where gradual erosion of the duricrust has resulted in the exposure of the different weathering zones. High-throughput amplicon sequencing of the 16S rRNA gene was used to investigate soil bacterial community diversity, composition and functioning. We predicted that shifts in the microbial community would reflect variations in certain edaphic properties associated with the different layers of the lateritic profile and vegetation cover. Our results supported this hypothesis, with electrical conductivity, pH and clay content having the strongest correlation with beta diversity, and many of the differentially abundant taxa belonging to the phyla Actinobacteria and Proteobacteria. Soil water repellence, which is associated with Eucalyptus vegetation, also affected beta diversity. This enhanced understanding of the natural system could help to improve future crop management in WA since the physicochemical properties of the agricultural soils in this region are inherited from laterites via the weathering and pedogenesis processes.
    Description: This work was funded by the WUN and the individual authors’ institutions. MA and MF were funded by the Critical Zone Observatory Program, NSF ICER 1445346.
    Keywords: Soil microbial ; Community ; Bacteria ; Laterite ; Critical zone ; Western Australia
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Bacterial and archaeal specific-predation in the North Atlantic Basin (2019)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Tuorto, S., McGuinness, L. R., Gong, D., & Kerkhof, L. J. Bacterial and archaeal specific-predation in the North Atlantic Basin. Frontiers in Marine Science, 6, (2019): 555, doi:10.3389/fmars.2019.00555.
    Description: Stable isotope probing (SIP) was used to track prokaryotic and eukaryotic carbon uptake along a meridional transect (Long. 52°W) in the North Atlantic to assess if 13C-resource partitioning between bacteria and archaea and 13C-labeled eukaryotic predators could be detected. One-liter SIP microcosms were amended with 13C-acetate or 13C-urea and incubated for 48 h. Our data indicated archaea often outcompeted bacteria for 13C-urea while both archaea and bacteria could incorporate 13C-acetate. This 13C label could also be tracked into eukaryotic microbes. The largest number of 13C-labeled eukaryotic OTUs, and the greatest percentage of eukaryotic 13C signal, were observed in conjunction with both archaeal and bacterial 13C incorporation, suggesting that most eukaryotic predators do not distinguish between archaeal and bacterial prey. However, other 13C-eukaryotic OTUs were exclusively associated with either 13C-archaeal or 13C-bacterial OTUs. These archaeal-specific and bacterial-specific 13C-eukaryotic OTUs were related to known bactivorous predators including Ancyromonas, Amastigomonas, Cafeteria, and Caecitellus. Our SIP findings suggest both resource partitioning between bacteria and TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota) archaea and selective predation by eukaryotic predators. Determining the equalizing mechanisms for co-existence in the marine environment can help map predator/prey interactions to better estimate carbon flow in the deep ocean.
    Description: This research was made possible through the support of the U.S Global Ocean Carbon and Repeat Hydrography Program and NSF Ocean Technology and Interdisciplinary Program grant (#1131022) to LK.
    Keywords: Archaea ; Bacteria ; Predation ; Competition ; Stable isotope probing ; Deep ocean
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Ancient metabolisms of a thermophilic subseafloor bacterium (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Smith, A. R., Mueller, R., Fisk, M. R., & Colwell, F. S. Ancient metabolisms of a thermophilic subseafloor bacterium. Frontiers in Microbiology, 12, (2021): 764631, https://doi.org/10.3389/fmicb.2021.764631.
    Description: The ancient origins of metabolism may be rooted deep in oceanic crust, and these early metabolisms may have persisted in the habitable thermal anoxic aquifer where conditions remain similar to those when they first appeared. The Wood–Ljungdahl pathway for acetogenesis is a key early biosynthetic pathway with the potential to influence ocean chemistry and productivity, but its contemporary role in oceanic crust is not well established. Here, we describe the genome of a novel acetogen from a thermal suboceanic aquifer olivine biofilm in the basaltic crust of the Juan de Fuca Ridge (JdFR) whose genome suggests it may utilize an ancient chemosynthetic lifestyle. This organism encodes the genes for the complete canonical Wood–Ljungdahl pathway, but is potentially unable to use sulfate and certain organic carbon sources such as lipids and carbohydrates to supplement its energy requirements, unlike other known acetogens. Instead, this organism may use peptides and amino acids for energy or as organic carbon sources. Additionally, genes involved in surface adhesion, the import of metallic cations found in Fe-bearing minerals, and use of molecular hydrogen, a product of serpentinization reactions between water and olivine, are prevalent within the genome. These adaptations are likely a reflection of local environmental micro-niches, where cells are adapted to life in biofilms using ancient chemosynthetic metabolisms dependent on H2 and iron minerals. Since this organism is phylogenetically distinct from a related acetogenic group of Clostridiales, we propose it as a new species, Candidatus Acetocimmeria pyornia.
    Description: Metagenome sequencing was made possible by the Deep Carbon Observatory Census of Deep Life supported by the Alfred P. Sloan Foundation and was performed at the Marine Biological Laboratory (Woods Hole, MA, United States). This work was funded by NASA grant NNX08AO22G and a graduate fellowship from the NSF Center for Dark Energy Biosphere Investigations. The flow cells were funded under J0972A from the U.S. Science Support Program of Joint Oceanographic Institutions.
    Keywords: Metabolism ; Carbon fixation ; Acetogenesis ; Bacteria ; Seafloor ; Hydrogen ; Amino acid ; Clostridia
    Repository Name: Woods Hole Open Access Server
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