Biology subjects

Salcedo, R. S. R.

Publications and source records attributed to Salcedo, R. S. R..

4 recordsLinked to original sources

bioRxiv2026

Anaerobic methane oxidation by ANME-2a at two molar chloride in Orca Basin

Anaerobic methane oxidation, typically mediated by consortia of archaea and bacteria, is a key process in the global methane cycle, but little is known about its upper salinity limits. We characterized the microbial methane cycle in the anoxic, hypersaline Orca Basin using metagenomics, metatranscriptomics, fluorescence in situ hybridization, and geochemical measurements at sub-meter resolution. In the brine, we detected transcriptional activity of the halophilic methylotrophic methanogen Methanohalophilus, consistent with a biological source for Orca Basin methane. In the particle-rich halocline ([~]2 M Cl-; [~]2235 meters depth), high mcrA transcription by a novel ANME-2a species was co-located with a positive shift in {delta}13C-CH4 indicative of anaerobic oxidation of methane. ANME-2a also transcribed genes for biosynthesis of the osmolyte N({varepsilon})-acetyl-{beta}-L-lysine, supporting adaptation for hypersaline conditions. At the same depth, consortia of sarcina-like archaea, likely ANME-2a, were observed in association with vibrioid and filamentous bacteria, potentially members of a halotolerant genus in the order Desulfobulbales (family SURF-16, which includes the previously identified ANME partner Seep-DBB) that were active at the same depth. At and above the oxic-anoxic interface, aerobic methane oxidation appears to be mediated by three genera of uncultivated Methylococcales bacteria. Our results double the upper salinity range of ANME-2a to [~]2 M Cl- and reveal the key microbial players in the methane bio-filter between the Orca Basin brine and overlying seawater.

microbiology↗

bioRxiv2026

Substantial genetic potential for deep-sea chemoautotrophy extends beyond nitrifiers

I.Microbial chemoautotrophy in the deep sea has the potential to sustain ecosystems at depth, contribute to global carbon sequestration, and ameliorate the currently unbalanced deep-sea carbon budget. However, an understanding of its mechanisms and feasibility is still emerging, particularly beyond that fueled by nitrification. Here, we conduct both a gene-based and genome-resolved analysis of 28 metagenomes in the Northeast Pacific Ocean to investigate the prevalence, distribution, and phylogenetic and metabolic diversity of deep-sea chemoautotrophs. We find that organisms encoding marker genes for dissolved inorganic carbon (DIC) fixation are abundant and widespread at our study site, comprising 11-26% of microbial communities from 150-4000 m water depth. Marker genes for the Calvin cycle and 3-Hydroxypropionate (3HP) bi-cycles are more prevalent than those for the 3-Hydroxypropionate/4-Hydroxybutyrate (3HP/4HB) and reverse Tricarboxylic Acid (rTCA) cycles, the latter two of which are encoded by organisms conducting nitrification. We construct and identify 128 putatively chemoautotrophic metagenome-assembled genomes, spanning 14 phyla including the Proteobacteria, Actinobacteria, SAR324, and the Thermoproteota. They contained genes for the oxidation of carbon monoxide (77.3%), sulfur (68.8%), ammonia (5.5%), and/or methane (3.1%), suggesting diverse catabolisms fuel deep-sea DIC fixation and an underappreciated potential role for aerobic carbon monoxide oxidation. Fifty percent of these genomes encoded multiple inorganic catabolic pathways and 99% included genes for organic matter transport, suggesting catabolic flexibility and potentially facultative autotrophy, respectively. We create an inclusive inventory and map of potential chemoautotrophs at our study site, expanding their known phylogenetic breadth, metabolic repertoires, and potential to impact the carbon cycle. ImportanceThe deep-sea carbon cycle plays a central role regulating marine ecosystem productivity and the global climate. Chemoautotrophy, the microbial conversion of inorganic carbon (e.g., CO2 or HCO-3) into cellular biomass, is an understudied process with the potential to significantly shift models of the marine carbon budget. While some deep-sea chemoautotrophs are known, a wholistic analysis of organisms with the genetic potential for chemoautotrophy in the dark water column is lacking. Here, we find that microorganisms with the genetic potential for chemoautotrophy are widespread and abundant, and that they are more phylogenetically and metabolically diverse than previously appreciated. In particular, the prevalence of genes involved in CO oxidation suggests a currently unrecognized role in fueling deep-sea chemoautotrophy. By identifying the potential microbial mediators and coupled energy sources, our results allow for more accurate predictions of when, where, and how deep-sea chemoautotrophy occurs, and therefore its potential role in carbon cycling.

microbiology↗

bioRxiv2024

Urea assimilation and oxidation supports the activity of a phylogenetically diverse microbial community in the dark ocean

Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary ion mass spectrometry (nanoSIMS). We find that the majority (>60%) of active cells across all samples assimilated urea-derived N, and that cell-specific nitrogen-incorporation rates from urea were higher than that from ammonium. Both urea concentrations and assimilation rates relative to ammonium generally increased below the euphotic zone. We detected ammonia- and urea-based nitrification at all depths at one of two sites analyzed, demonstrating their potential to support chemoautotrophy in the mesopelagic and bathypelagic regions. Using newly generated metagenomes we find that the ureC gene, encoding the catalytic subunit of urease, is found within 39% of deep-sea cells in this region, including the Nitrosophaerota (likely for nitrification) as well as thirteen other phyla such as Proteobacteria, Verrucomicrobia, Plantomycetota, Nitrospinota, and Chloroflexota (likely for assimilation). Analysis of public metagenomes revealed ureC within 10-46% of deep-sea cells around the world, with higher prevalance below the photic zone, suggesting urea is widely available to the deep-sea microbiome globally. Our results demonstrate that urea is a nitrogen source to abundant and diverse microorganisms in the dark ocean, as well as a significant contributor to deep-sea nitrification and therefore fuel for chemoautotrophy.

microbiology↗

bioRxiv2024

Abundant and metabolically flexible lineages within the SAR324 and gammaproteobacteria dominate the potential for rubisco-mediated carbon fixation in the dark ocean

BackgroundRubisco is among the most abundant enzymes on Earth and is a critical conduit for inorganic carbon into the biosphere. Despite this, the full extent of rubisco diversity and the biology of organisms that employ it for carbon fixation are still emerging, particularly in unlit ecosystems like the deep sea. ResultsHere, we generate fifteen deeply-sequenced metagenomes along a spatially-resolved transect off the California coast, and combine them with globally-distributed public data to examine the diversity, distribution, and metabolic features of rubisco-encoding organisms from the dark water column. Organisms with rubisco were detected in the vast majority of all samples, spanning over 1,000 species groups and together comprising up to [~]20% of the total microbial community. At 150 meters and below, potential for carbon fixation via rubisco was dominated by just two orders of gammaproteobacteria and SAR324, encoding either the form I or II rubisco. Many of these organisms also possessed genes for the oxidation of reduced sulfur compounds, which may energetically support carbon fixation. Transcriptomic profiling in the epi- and mesopelagic suggested that all major forms of rubisco can be highly expressed in the deep water column, but are not done so constitutively, consistent with metabolic flexibility. ConclusionOur results demonstrate that the genetic potential to fix carbon via rubisco is significant and spatially widespread in the dark ocean. We identify several rubisco-encoding species groups that are particularly abundant and cosmopolitan, highlighting the key role they may play in deep-sea chemoautotrophy and the global marine carbon cycle.

microbiology↗