Biology subjects

Gazitua, M. C.

Publications and source records attributed to Gazitua, M. C..

3 recordsLinked to original sources

bioRxiv2020

Genome-resolved viral ecology in a marine oxygen minimum zone (OMZ)

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 mol/L O2) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46,127 viral populations (>5 kb), which augments the known viruses at this site by 10-fold. ETSP viral communities clustered into 6 groups that correspond to oceanographic features, with 3 clusters representing samples from suboxic to anoxic waters. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. Viruses were largely endemic as few (6% of viruses from this study) were found in at least another marine metagenome, and of those, most (77%) were restricted to other OMZs. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate-critical environments. Originality-Significance StatementMarine oxygen minimum zones (OMZs) are unique and important ocean ecosystems where microbes drive climate-altering nutrient transformations. This study provides a baseline, deeply sequenced viral metagenomic dataset and reference viral genomes to assess ecological change and drivers across the oxygenated surface to de-oxygenated deep waters of the Eastern Tropical South Pacific (ETSP) OMZ. Community ecological assessment of the ETSP viromes reveals a relatively low diversity viral community with a high degree of endemic populations in the OMZ waters.

microbiology↗

bioRxiv2020

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Microbial and viral communities transform the chemistry of Earths ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles, and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

microbiology↗

bioRxiv2020

Glacier ice archives fifteen-thousand-year-old viruses

While glacier ice cores provide climate information over tens to hundreds of thousands of years, study of microbes is challenged by ultra-low-biomass conditions, and virtually nothing is known about co-occurring viruses. Here we establish ultra-clean microbial and viral sampling procedures and apply them to two ice cores from the Guliya ice cap (northwestern Tibetan Plateau, China) to study these archived communities. This method reduced intentionally contaminating bacterial, viral, and free DNA to background levels in artificial-ice-core control experiments, and was then applied to two authentic ice cores to profile their microbes and viruses. The microbes differed significantly across the two ice cores, presumably representing the very different climate conditions at the time of deposition that is similar to findings in other cores. Separately, viral particle enrichment and ultra-low-input quantitative viral metagenomic sequencing from [~]520 and [~]15,000 years old ice revealed 33 viral populations (i.e., species-level designations) that represented four known genera and likely 28 novel viral genera (assessed by gene-sharing networks). In silico host predictions linked 18 of the 33 viral populations to co-occurring abundant bacteria, including Methylobacterium, Sphingomonas, and Janthinobacterium, indicating that viruses infected several abundant microbial groups. Depth-specific viral communities were observed, presumably reflecting differences in the environmental conditions among the ice samples at the time of deposition. Together, these experiments establish a clean procedure for studying microbial and viral communities in low-biomass glacier ice and provide baseline information for glacier viruses, some of which appear to be associated with the dominant microbes in these ecosystems. ImportanceThis study establishes ultra-clean microbial and viral sampling procedures for glacier ice, which complements prior in silico decontamination methods and expands, for the first time, the clean procedures to viruses. Application of these methods to glacier ice confirmed prior common microbiological findings for a new ice core climate record, and provides a first window into viral genomes and their ecology from glacier ice across two time horizons, and emphasizes their likely impact on abundant microbial groups. Together these efforts provide clean sampling approaches and foundational datasets that should enable simultaneous access to an archived virosphere in glacier ice.

ecology↗