Osvaldo Ulloa

University of Concepción · Departamento de Oceanografía

Marine oxygen minimum zones (OMZs) are oxygen-starved regions of the ocean harboring diverse microbial communities that drive biogeochemical processes of global significance, particularly those associated with the nitrogen cycle, with resulting impacts on marine nutrient cycles and the climate system. OMZs appear to be expanding and intensifying du...

Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N 2) and nitrous oxide (N 2 O) gases. Anaerobic microbial processes, in...

Cryptic Sulfur Cycling Aerobic bacteria and ocean circulation patterns control the formation and distribution of oxygen-minimum zones at moderate depth in the oceans. These habitats host microorganisms that thrive on other metabolic substrates in the absence of oxygen—most commonly, metabolizing thermodynamically favorable nitrogen compounds like n...

Recent decadal trends of deoxygenation in the global ocean interior have resulted in the expansion and shoaling of oxygen minimum zones (OMZs). When the OMZs upper bound nears the euphotic zone a unique community of phytoplankton, residing in extremely low light (<0.1% surface irradiance) and dissolved oxygen concentrations (<1-2 μmol kg⁻¹), can ap...

Zooplankton diversity in the deep “midnight zone” (>1000 m), where sunlight does not reach, remains largely unknown. Uncovering such diversity has been challenging because of the major difficulties in sampling deep pelagic fauna and identifying many (unknown) species that belong to these complex swimmer assemblages. In this study, we evaluated zoop...

We use data collected by Biogeochemical Argo (BGC-Argo) float, over a 5-year period (2016-2021), to study the dynamics of a unique low-oxygen-adapted phytoplanktonic community in the eastern tropical North Pacific. We isolate this community using a model that partitions vertical profiles of chlorophyll a (Chl a) and particulate backscattering into...

Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and c...

It is commonly known that phytoplankton have a pivotal role in marine biogeochemistry and ecosystems as carbon fixers and oxygen producers, but their response to deoxygenation has scarcely been studied. Nonetheless, in the major oceanic oxygen minimum zones (OMZs), all surface phytoplankton groups, regardless of size, disappear and are replaced by...

Information on the intracellular content and functional diversity of phytoplankton pigments can provide valuable insight on the ecophysiological state of primary producers and the flow of energy within aquatic ecosystems. Combined global datasets of analytical flow cytometry (AFC) cell counts and High-Performance Liquid Chromatography (HPLC) pigmen...

Gammaproteobacteria of the genus Alteromonas are prominent members of pelagic marine microbial communities, playing critical roles in the aerobic degradation of particulate organic matter. Comparative genomic studies of these microorganisms have mainly focused on the metabolic and genomic plasticity of strains isolated primarily from oxygenated env...

Anoxic marine zones (AMZs) constitute pelagic systems distinguished from the oxygen minimum zones (OMZs) by the complete absence of detectable oxygen and the accumulation of nitrite in mid-waters. At the top of the oxygen-depleted layer and below the oxycline, nutrients are abundant; light intensity is very much reduced (<1% of incident light) and...

Respiration is a key process in the cycling of particulate matter and, therefore, an important control mechanism of carbon export to the ocean's interior. Most of the fixed carbon is lost in the upper ocean, and only a minor amount of organic material sustains life in the deep-sea. Conditions are particularly extreme in hadal trenches , and yet the...

Eurythenes S.I. Smith in Scudder, 1882 (Crustacea: Amphipoda) are prevalent scavengers of the benthopelagic community from bathyal to hadal depths. While a well-studied genus, molecular systematic studies have uncovered cryptic speciation and multiple undescribed lineages. Here, we apply an integrative taxonomic approach and describe the tenth spec...

Significance The marine unicellular cyanobacterium Prochlorococcus is the most abundant photosynthetic organism on Earth. Members of this genus are classically thought to be adapted to high-oxygen and nutrient-poor ocean conditions, with a principle divergence between high-light and low-light ecotypes. We show that the most basal Prochlorococcus li...

Euphausiids (krill) are important contributors to marine biomass and key players in marine pelagic trophic webs. Euphausiid stomachs represent a specific niche for microbes that participate in the digestion of the host’s dietary components. Methods for the study of the diversity and function of these microorganisms remain complex. Bacterial ribosoma...

Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here, we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic waters (<0.02 μmol/l O2) in the...

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...

The strong seasonal variability in physical-chemical conditions of the Eastern South Pacific Ocean creates an ideal setting to study spatiotemporal distribution of key marine microbial communities. We herein report a nearly 4-year-long time series of the variability in amoA gene counts of ammonia oxidizing archaea (AOA) and bacteria (betaproteobact...

Oxygen minimum zones (OMZs) support ocean biogeochemical cycles of global importance. The OMZ off central Chile is characterized by seasonally variable oxygen concentrations due to upwelling events. Bacterial and archaeal communities from this area have been previously described; however, picoeukaryote communities remain largely unexplored. In orde...

Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of surface oxygenated to anoxic waters (< 0.02 μmol/L O...

Across boundary currents, zooplankton are subject to strong oceanographic gradients and hence strong selective pressures. How such gradients interact with the speciation process of pelagic organisms is still poorly understood in the open ocean realm. Here we report on genetic diversity within the pelagic copepod Pleuromamma abdominalis in the poorl...

Prochlorococcus and Synechococcus are the most abundant free‐living photosynthetic microorganisms in the ocean. Uncultivated lineages of these picocyanobacteria also thrive in the dimly illuminated upper part of oxygen‐deficient zones (ODZs), where an important portion of ocean nitrogen (N) loss takes place via denitrification and anaerobic ammoniu...

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 collec...

Significance Biological communities are conventionally described as assemblages of species, whose ecological roles are known or predictable from their observable morphology. In microbial ecology, such a taxonomic approach is hindered by limited capacity to discriminate among different microbes, which bear highly dynamic genomes and establish comple...

Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic di...

Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox...

Here we present ecophysiological studies of the anaerobic sulfide oxidizers considered critical to cryptic sulfur cycling in oceanic oxygen minimum zones (OMZs). We find that HS− oxidation rates by microorganisms in the Chilean OMZ offshore from Dichato are sufficiently rapid (18 nM h−1), even at HS− concentrations well below 100 nM, to oxidize all...

Anoxic marine zones (AMZs) impact biogeochemical cycles at the global scale, particularly the nitrogen cycle. Key microbial players from AMZs have been identified, but the majority remains unrecognized or uncharacterized. Thirty‐one single‐cell amplified genomes (SAGs) from the eastern tropical North and South Pacific AMZs were sequenced to gain in...

Bacterial community composition and its relationship to oxygen were investigated in the non-sulfidic shelf waters exposed to seasonal upwelling and oxygen deficiency off central Chile. Using 16S rRNA gene clone libraries, terminal restriction fragment length polymorphism (T-RFLP) and iTAG sequencing analyses of nearly 4 years of monthly sampling th...

Thaumarchaea are often abundant in low oxygen marine environments, and recent kinetic studies indicate a capacity for aerobic ammonia oxidation at vanishingly low oxygen levels (nM). However, molecular diversity surveys targeting this group to high sequencing coverage are limited, and how these populations are coupled to changes in dissolved oxygen...

Significance Anoxic marine zones (AMZs) create expansive habitats for microbes whose anaerobic metabolisms help drive global nutrient cycles, for example, by removing nitrogen from the oceans by producing N 2 gas. AMZ cycles may also be shaped by oxygen intrusion from outside the AMZ, creating opportunities for aerobic microbial metabolisms. Here w...

Seasonal wind-driven upwelling, high primary production in surface waters, and oxygen deficiency in subsurface waters characterize the coastal ecosystem of the subtropical eastern South Pacific (ESP), and shape the nature and dynamics of the microbial community structure and function. We investigated the diversity, abundance, and transcriptional le...

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 wh...

Marine oxygen deficient zones (ODZs) have long been identified as sites of fixed nitrogen (N) loss. However, the mechanisms and rates of N loss processes have been debated, and traditional methods for measuring these rates are labor-intensive and may miss hot spots in spatially and temporally variable environments. Here, we estimate rates of hetero...

Significance As an essential nutrient, nitrogen plays a critical role in regulating oceanic primary productivity. Nitrogen is cycled between bioavailable and nonavailable forms through a network of aerobic and anaerobic microbial processes. Expanding oxygen minimum zones are hot spots for such transformations. Using a highly sensitive oxygen-sensin...

The nosZ gene, which encodes for N2O reduction to N2, was used to study the structure of denitrifying communities in the oxygen minimum zone off Chilean and Peruvian coast throughout terminal restriction fragment length polymorphism (TRFLP) and cloning of nosZ genes. TRFLP analysis showed little diversity of nosZ genes at suboxic depths (Oxygen Min...

Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological inform...

Highly sensitive STOX O2 sensors were used for determination of in situ O2 distribution in the eastern tropical north and south Pacific oxygen minimum zones (ETN/SP OMZs), as well as for laboratory determination of O2 uptake rates of water masses at various depths within these OMZs. Oxygen was generally below the detection limit (few nmol L−1) in t...

Cáhuil Lagoon in central Chile harbors distinct microbial communities in various solar salterns that are arranged as interconnected ponds with increasing salt concentrations. Here, we report the metagenome of the 3.0- to 0.2-µm fraction of the microbial community present in a crystallizer pond with 34% salinity.

Unlabelled: A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O2 and the sensitivity of the anaerobic N2-producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O2 at nanomolar levels affects anammox and denitrifica...

We investigated anammox, denitrification and dissimilatory reduction of nitrite to ammonium (DNRA) activity in the Eastern Tropical South Pacific oxygen minimum zone (OMZ) off northern Chile, at high-depth resolution through the oxycline into the anoxic OMZ core. This was accompanied by high-resolution nutrient and oxygen profiles to link changes i...

Sulfur-oxidizing γ-proteobacteria are abundant in marine oxygen-deficient waters, and appear to play a key role in a previously unrecognized cryptic sulfur cycle. Metagenomic analyses of members of the uncultured SUP05 lineage in the Canadian seasonally anoxic fjord Saanich Inlet (SI), hydrothermal plumes in the Guaymas Basin (GB) and single cell g...

Anaerobic ammonium oxidizers contribute to the removal of fixed nitrogen in oxygen-deficient marine ecosystems such as oxygen minimum zones (OMZ). Here we surveyed for the first time the occurrence and diversity of anammox bacteria in the Colombian Pacific, a transition area between the prominent South and North Pacific OMZs. Anammox bacteria were...

Microbial activity is a fundamental component of oceanic nutrient cycles. Photosynthetic microbes, collectively termed phytoplankton, are responsible for the vast majority of primary production in marine waters. The availability of nutrients in the upper ocean frequently limits the activity and abundance of these organisms. Experimental data have r...

a b s t r a c t Phytoplankton community structure was analysed in the Subantarctic sector of the eastern South Pacific, a high-nutrient, low-chlorophyll (HNLC) region, during a period of deep vertical mixing (austral winter Aug–Oct, 2005) when Antarctic Intermediate Water (AAIW) gets formed, and during a period of water-column stratification charac...

Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and biodiversity, and contribute to ocean nitrogen loss and greenhouse gas emissions. Here we describe the viral communities associated with the Eastern Tropical South Pacific (ETSP) OMZ off Iquique, Chile for the first time through abundance estimates and viral m...

The smallest marine phytoplankton, collectively termed picophytoplankton, have been routinely enumerated by flow cytometry since the late 1980s during cruises throughout most of the world ocean. We compiled a database of 40 946 data points, with separate abundance entries for Prochlorococcus , Synechococcus and picoeukaryotes. We use average conver...

Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic d...

Relationship between numbers of reads assigned to each B. prasinos RCC1105 chromosome based on BLASTX-based analysis of contigs (see Materials and Methods for details) or direct assembly with Geneious. (TIF)

Percent of false assignment of O. ‘lucimarinus ’ proteins based on Best BLAST hit (BBH, blue line) or after filtration with gene-specific thresholds for identity and alignment length (FA, red line) as a function of read length (see Materials and Methods for details). (TIF)

Similarity between specific genes from selected gene classes of B. prasinos RCC1105 genome and T142 and T149 Newbler contigs (see Materials and Methods for details). (PDF)

Assignment of Geneious contigs for samples T142 and T149 to specific chromosomes of B. prasinos RCC1105 based on a BLASTX-based algorithm (see Materials and Methods for details). An estimate of coverage was computed as the ratio between the total length of contigs assigned to one chromosome and the length of this chromosome. This value may exceed 1...

Estimation of the number of major haplotypes and of their frequency for selected regions of genes with a high read coverage in both samples. (PDF)

Genotype variability within the 5,646 bp rRNA operon. Positions are given along chromosome 11. Localisation of helix 3 of ITS2 follows Marin and Melkonian [39]. (PDF)

Structure of the rRNA operon. (A) Alignment of the B. prasinos RCC1105 rRNA operon (forward copy) with the two contigs T142_109 and T149_486 that contain it. Both contigs do not contain the 433 bp SSU rRNA gene intron that characterizes RCC1105. Contig T149_486 appears to contain a 468 bp intron at the end of the LSU rRNA gene. (B) Detail of the pu...

Assignment of reads and Geneious contigs for samples T142 and T149 to phylogenetic groups based on BLASTN search of a subset of the nr GenBank database, analyzed by MEGAN (see Materials and Methods for details). The contribution of the best represented groups and of the eukaryotic groups expected to be present in the samples are detailed. (PDF)

Assignment of reads for Pacific picoeukaryote samples T142 to individual chromosomes of O.’ lucimarinus’ using Geneious Assembler (see Materials and Methods for details). (PDF)

Genotypic variability of the rRNA operon. T142 and T149 reads were directly assembled with Geneious to the B. prasinos RCC1105 rRNA operon. (A) Individual reads for sample T142 in the region of the SSU rRNA intron present in the genome of RCC 1105. The arrow points to a read with a sequence nearly identical to the intron sequence. (B) Individual re...