Ulloa
Osvaldo
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Osvaldo
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ArticlePotential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters(Springer Nature, 2020-11-16) Gazitúa, M. Consuelo ; Vik, Dean R. ; Roux, Simon ; Gregory, Ann C. ; Bolduc, Benjamin ; Widner, Brittany ; Mulholland, Margaret R. ; Hallam, Steven J. ; Ulloa, Osvaldo ; Sullivan, Matthew B.Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.
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ArticleSampling and processing methods impact microbial community structure and potential activity in a seasonally anoxic fjord: Saanich Inlet, British Columbia.(Frontiers Media, 2019-03-22) Torres-Beltrán, Mónica ; Mueller, Andreas ; Scofield, Melanie ; Pachiadaki, Maria G. ; Taylor, Craig D. ; Tyshchenko, Kateryna ; Michiels, Céline ; Lam, Phyllis ; Ulloa, Osvaldo ; Jürgens, Klaus ; Hyun, Jung-Ho ; Edgcomb, Virginia P. ; Crowe, Sean A. ; Hallam, Steven J.The Scientific Committee on Oceanographic Research (SCOR) Working Group 144 Microbial Community Responses to Ocean Deoxygenation workshop held in Vancouver, B.C on July 2014 had the primary objective of initiating a process to standardize operating procedures for compatible process rate and multi-omic (DNA, RNA, protein, and metabolite) data collection in marine oxygen minimum zones and other oxygen depleted waters. Workshop attendees participated in practical sampling and experimental activities in Saanich Inlet, British Columbia, a seasonally anoxic fjord. Experiments were designed to compare and cross-calibrate in situ versus bottle sampling methods to determine effects on microbial community structure and potential activity when using different filter combinations, filtration methods, and sample volumes. Resulting biomass was preserved for small subunit ribosomal RNA (SSU or 16S rRNA) and SSU rRNA gene (rDNA) amplicon sequencing followed by downstream statistical and visual analyses. Results from these analyses showed that significant community shifts occurred between in situ versus on ship processed samples. For example, Bacteroidetes, Alphaproteobacteria, and Opisthokonta associated with on-ship filtration onto 0.4 μm filters increased fivefold compared to on-ship in-line 0.22 μm filters or 0.4 μm filters processed and preserved in situ. In contrast, Planctomycetes associated with 0.4 μm in situ filters increased fivefold compared to on-ship filtration onto 0.4 μm filters and on-ship in-line 0.22 μm filters. In addition, candidate divisions and Chloroflexi were primarily recovered when filtered onto 0.4 μm filters in situ. Results based on rRNA:rDNA ratios for microbial indicator groups revealed previously unrecognized roles of candidate divisions, Desulfarculales, and Desulfuromandales in sulfur cycling, carbon fixation and fermentation within anoxic basin waters. Taken together, filter size and in situ versus on-ship filtration had the largest impact on recovery of microbial groups with the potential to influence downstream metabolic reconstruction and process rate measurements. These observations highlight the need for establishing standardized and reproducible techniques that facilitate cross-scale comparisons and more accurately assess in situ activities of microbial communities.
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ArticleA review of protist grazing below the photic zone emphasizing studies of oxygen-depleted water columns and recent applications of in situ approaches(Frontiers Media, 2017-04-26) Medina Faull, Luis E. ; Taylor, Craig D. ; Pachiadaki, Maria G. ; Henríquez-Castillo, Carlos ; Ulloa, Osvaldo ; Edgcomb, Virginia P.Little is still known of the impacts of protist grazing on bacterioplankton communities in the dark ocean. Furthermore, the accuracy of assessments of in situ microbial activities, including protist grazing, can be affected by sampling artifacts introduced during sample retrieval and downstream manipulations. Potential artifacts may be increased when working with deep-sea samples or samples from chemically unique water columns such as oxygen minimum zones (OMZs). OMZs are oxygen-depleted regions in the ocean, where oxygen concentrations can drop to <20 μM. These regions are typically located near eastern boundary upwelling systems and currently occur in waters occupying below about 8% of total ocean surface area, representing ~1% of the ocean's volume. OMZs have a profound impact not only on the distribution of marine Metazoa, but also on the composition and activities of microbial communities at the base of marine food webs. Here we present an overview of current knowledge of protist phagotrophy below the photic zone, emphasizing studies of oxygen-depleted waters and presenting results of the first attempt to implement new technology for conducting these incubation studies completely in situ (the Microbial Sampling- Submersible Incubation Device, MS-SID). We performed 24-h incubation experiments in the Eastern Tropical South Pacific (ETSP) OMZ. This preliminary study shows that up to 28% of bacterial biomass may be consumed by protists in waters where oxygen concentrations were down to ~4.8 μM and up to 13% at a station with nitrite accumulation where oxygen concentrations were undetectable. Results also show that shipboard measurements of grazing rates were lower than rates measured from the same water using the MS-SID, suggesting that in situ experiments help to minimize artifacts that may be introduced when conducting incubation studies using waters collected from below the photic zone, particularly from oxygen-depleted regions of the water column.
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ArticleLate Quaternary variability of sedimentary nitrogen isotopes in the eastern South Pacific Ocean(American Geophysical Union, 2007-05-01) De Pol-Holz, Ricardo ; Ulloa, Osvaldo ; Lamy, Frank ; Dezileau, Laurent ; Sabatier, Pierre ; Hebbeln, DierkWe present high-resolution bulk sedimentary δ 15N data from the southern edge of the present-day oxygen minimum zone of the eastern South Pacific. The record is interpreted as representing changes in water column nitrogen removal during the last 70,000 years. We found significant fluctuations in the isotopic signal that suggest major reorganizations of the oxygen minimum zone at millennial timescales. These fluctuations were not related to other millennial-scale changes like the Northern Hemisphere's Dansgaard-Oeschger climate swings or local changes in primary productivity, so appear to be dictated by the Southern Hemisphere's climate rhythm. This is preliminarily corroborated by an overall agreement between our δ 15N data and the sedimentary proxy of ice sheet dynamics in Patagonia, which is in turn correlated with surface water properties at the midlatitude subduction region of the eastern South Pacific intermediate waters. Finally, potential implications on late Quaternary changes in atmospheric CO2 concentrations are discussed.