Alma Parada

All Publications

• Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota. Environmental microbiology Parada, A. E., Mayali, X., Weber, P. K., Wollard, J., Santoro, A. E., Fuhrman, J. A., Pett-Ridge, J., Dekas, A. E. 2022

  Abstract

  Marine Group I (MGI) Thaumarchaeota were originally described as chemoautotrophic nitrifiers, but molecular and isotopic evidence suggests heterotrophic and/or mixotrophic capabilities. Here, we investigated the quantity and composition of organic matter assimilated by individual, uncultured MGI cells from the Pacific Ocean to constrain their potential for mixotrophy and heterotrophy. We observed that most MGI cells did not assimilate carbon from any organic substrate provided (glucose, pyruvate, oxaloacetate, protein, urea, and amino acids). The minority of MGI cells that did assimilate it did so exclusively from nitrogenous substrates (urea, 15% of MGI; amino acids, 36% of MGI), and only as an auxiliary carbon source (<20% of that subset's total cellular carbon was derived from those substrates). At the population level, MGI assimilation of organic carbon comprised just 0.5-11% of total carbon. We observed extensive assimilation of inorganic carbon and urea- and amino acid-derived nitrogen (equal to that from ammonium), consistent with metagenomic and metatranscriptomic analyses performed here and previously showing a widespread potential for MGI to perform autotrophy and transport and degrade organic nitrogen. Our results constrain the quantity and composition of organic matter used by MGI and suggest they use it primarily to meet nitrogen demands for anabolism and nitrification. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1111/1462-2920.16299

  View details for PubMedID 36478085

• Single-cell view of deep-sea microbial activity and intracommunity heterogeneity ISME JOURNAL Arandia-Gorostidi, N., Parada, A. E., Dekas, A. E. 2022

  Abstract

  Microbial activity in the deep sea is cumulatively important for global elemental cycling yet is difficult to quantify and characterize due to low cell density and slow growth. Here, we investigated microbial activity off the California coast, 50-4000 m water depth, using sensitive single-cell measurements of stable-isotope uptake and nucleic acid sequencing. We observed the highest yet reported proportion of active cells in the bathypelagic (up to 78%) and calculated that deep-sea cells (200-4000 m) are responsible for up to 34% of total microbial biomass synthesis in the water column. More cells assimilated nitrogen derived from amino acids than ammonium, and at higher rates. Nitrogen was assimilated preferentially to carbon from amino acids in surface waters, while the reverse was true at depth. We introduce and apply the Gini coefficient, an established equality metric in economics, to quantify intracommunity heterogeneity in microbial anabolic activity. We found that heterogeneity increased with water depth, suggesting a minority of cells contribute disproportionately to total activity in the deep sea. This observation was supported by higher RNA/DNA ratios for low abundance taxa at depth. Intracommunity activity heterogeneity is a fundamental and rarely measured ecosystem parameter and may have implications for community function and resilience.

  View details for DOI 10.1038/s41396-022-01324-6

  View details for Web of Science ID 000864589800001

  View details for PubMedID 36202927

• Rates and physicochemical drivers of microbial anabolic activity in deep-sea sediments and implications for deep time. Environmental microbiology Meyer, N. R., Parada, A. E., Kapili, B. J., Fortney, J. L., Dekas, A. E. 2022

  Abstract

  Sediment microorganisms influence global climate and redox by altering rates of organic carbon burial. However, the activity and ecology of benthic microorganisms are poorly characterized, especially in the deep sea. Here, we conducted nearly 300 stable isotope tracer experiments in sediments from the Pacific and Atlantic Oceans (100-4500 m water depth) to determine the rates, spatial distribution, and physicochemical controls on microbial total anabolic activity, nitrogen fixation, and inorganic/organic carbon uptake. Using correlative and manipulative approaches, we find that total activity is limited primarily by organic carbon and/or energy. Activity correlates significantly with distance from shore, sediment depth, C:N ratios, and overlying chlorophyll concentrations, and is stimulated by carbon but not nitrogen additions. Consistent with this, nitrogen fixation was undetected despite relatively low concentrations of porewater ammonium and the previous detection of nifH genes. Inorganic carbon uptake accounted for 7-55% of carbon assimilation per sample (median 21%), suggesting chemoautotrophy is an important and unappreciated source of labile carbon in deep-sea sediments. Community 16S rRNA was dominated by Bacteria (<2% Archaea), primarily Desulfobacterales of the Deltaproteobacteria. Leveraging our findings, we modeled global benthic microbial activity through geologic time and find the potential for significant shifts in total activity with supercontinental cycles. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1111/1462-2920.16183

  View details for PubMedID 36054699

• Characterizing the "fungal shunt": Parasitic fungi on diatoms affect carbon flow and bacterial communities in aquatic microbial food webs. Proceedings of the National Academy of Sciences of the United States of America Klawonn, I., Van den Wyngaert, S., Parada, A. E., Arandia-Gorostidi, N., Whitehouse, M. J., Grossart, H., Dekas, A. E. 2021; 118 (23)

  Abstract

  Microbial interactions in aquatic environments profoundly affect global biogeochemical cycles, but the role of microparasites has been largely overlooked. Using a model pathosystem, we studied hitherto cryptic interactions between microparasitic fungi (chytrid Rhizophydiales), their diatom host Asterionella, and cell-associated and free-living bacteria. We analyzed the effect of fungal infections on microbial abundances, bacterial taxonomy, cell-to-cell carbon transfer, and cell-specific nitrate-based growth using microscopy (e.g., fluorescence in situ hybridization), 16S rRNA gene amplicon sequencing, and secondary ion mass spectrometry. Bacterial abundances were 2 to 4 times higher on individual fungal-infected diatoms compared to healthy diatoms, particularly involving Burkholderiales. Furthermore, taxonomic compositions of both diatom-associated and free-living bacteria were significantly different between noninfected and fungal-infected cocultures. The fungal microparasite, including diatom-associated sporangia and free-swimming zoospores, derived 100% of their carbon content from the diatom. By comparison, transfer efficiencies of photosynthetic carbon were lower to diatom-associated bacteria (67 to 98%), with a high cell-to-cell variability, and even lower to free-living bacteria (32%). Likewise, nitrate-based growth for the diatom and fungi was synchronized and faster than for diatom-associated and free-living bacteria. In a natural lacustrine system, where infection prevalence reached 54%, we calculated that 20% of the total diatom-derived photosynthetic carbon was shunted to the parasitic fungi, which can be grazed by zooplankton, thereby accelerating carbon transfer to higher trophic levels and bypassing the microbial loop. The herein termed "fungal shunt" can thus significantly modify the fate of photosynthetic carbon and the nature of phytoplankton-bacteria interactions, with implications for diverse pelagic food webs and global biogeochemical cycles.

  View details for DOI 10.1073/pnas.2102225118

  View details for PubMedID 34074785

• Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP. Frontiers in microbiology Dekas, A. E., Parada, A. E., Mayali, X., Fuhrman, J. A., Wollard, J., Weber, P. K., Pett-Ridge, J. 2019; 10: 2682

  Abstract

  Characterizing and quantifying in situ metabolisms remains both a central goal and challenge for environmental microbiology. Here, we used a single-cell, multi-isotope approach to investigate the anabolic activity of marine microorganisms, with an emphasis on natural populations of Thaumarchaeota. After incubating coastal Pacific Ocean water with 13C-bicarbonate and 15N-amino acids, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to isotopically screen 1,501 individual cells, and 16S rRNA amplicon sequencing to assess community composition. We established isotopic enrichment thresholds for activity and metabolic classification, and with these determined the percentage of anabolically active cells, the distribution of activity across the whole community, and the metabolic lifestyle-chemoautotrophic or heterotrophic-of each cell. Most cells (>90%) were anabolically active during the incubation, and 4-17% were chemoautotrophic. When we inhibited bacteria with antibiotics, the fraction of chemoautotrophic cells detected via nanoSIMS increased, suggesting archaea dominated chemoautotrophy. With fluorescence in situ hybridization coupled to nanoSIMS (FISH-nanoSIMS), we confirmed that most Thaumarchaeota were living chemoautotrophically, while bacteria were not. FISH-nanoSIMS analysis of cells incubated with dual-labeled (13C,15N-) amino acids revealed that most Thaumarchaeota cells assimilated amino-acid-derived nitrogen but not carbon, while bacteria assimilated both. This indicates that some Thaumarchaeota do not assimilate intact amino acids, suggesting intra-phylum heterogeneity in organic carbon utilization, and potentially their use of amino acids for nitrification. Together, our results demonstrate the utility of multi-isotope nanoSIMS analysis for high-throughput metabolic screening, and shed light on the activity and metabolism of uncultured marine archaea and bacteria.

  View details for DOI 10.3389/fmicb.2019.02682

  View details for PubMedID 31920997

  View details for PubMedCentralID PMC6927911

• Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP FRONTIERS IN MICROBIOLOGY Dekas, A. E., Parada, A. E., Mayali, X., Fuhrman, J. A., Wollard, J., Weber, P. K., Pett-Ridge, J. 2019; 10

  View details for DOI 10.3389/fmicb.2019.02682

  View details for Web of Science ID 000505025200001

• Microbial Community Composition in Deep‐Subsurface Reservoir Fluids Reveals Natural Interwell Connectivity Water Resources Research Zhang, Y., Dekas, A., Hawkins, A., Parada, A., Gorbatenko, O., Li, K., Horne, R. 2019

  View details for DOI 10.1029/2019WR025916

• High-quality genome sequences of uncultured microbes by assembly of read clouds. Nature biotechnology Bishara, A., Moss, E. L., Kolmogorov, M., Parada, A. E., Weng, Z., Sidow, A., Dekas, A. E., Batzoglou, S., Bhatt, A. S. 2018

  Abstract

  Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (>200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20*) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which were complete (>90% complete, <5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.

  View details for PubMedID 30320765