Biology subjects

Joye, S. B.

Publications and source records attributed to Joye, S. B..

5 recordsLinked to original sources

bioRxiv2024

Methane production from hydrocarbons by consortia dominated by ANME archaea

Understanding microbial production and consumption of methane, a potent greenhouse gas in the atmosphere, is critical for bridging knowledge gaps in global carbon cycling. In anoxic environments, methane is known to be produced through hydrogenotrophic, acetoclastic or methylotrophic mechanisms. Methane production from hydrocarbons may also be important, especially in hydrocarbon-rich environments, like the Gulf of California, but the mechanism of this hydrocarbonoclastic methanogenesis remains unclear. The activity of consortia of anaerobic methane oxidizing (ANME) archaea and bacteria limits the release of methane to the atmosphere by consuming methane in anoxic environments globally. Here we used isotopic-labeling to track the conversion of hydrocarbons (hexadecane and naphthalene) to methane in enrichments from hydrothermally impacted, hydrocarbon-rich sediments from the Gulf of California. Methane was produced directly from hexadecane and naphthalene, in both the presence and absence of sulfate. We reconstructed metagenomic assembled-genomes (MAGs) from these experiments which revealed a mixture of bacteria dominated by Desulfobacteriota and Bacteroidota, and archaea dominated by Aeinigmarchaeota, Thermoplasmatota, and ANME group 2c. The ANME-2c were the only MAGs that encoded methyl coenzyme M reductases (McrA) and complete Wood-Ljungdahl pathways (WLP). This suggests that ANME-2c archaea may be involved in the production of methane along the seafloor, and that our understanding of the roles of these globally important microbes is not yet fully appreciated.

microbiology↗

bioRxiv2024

Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems

Viruses are ubiquitous in deep-sea hydrothermal environments, where they exert a major influence on microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identified 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plumes, 40 deposits, and 2 diffuse flow), and reconstructed 5,708 viral metagenome-assembled genomes (vMAGs), the majority of which were bacteriophages. Hydrothermal viruses were largely endemic. However, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses often shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our study indicates that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism, and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.

microbiology↗

bioRxiv2024

A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide

Subsurface environments constitute one of Earths largest habitats for microbial life, yet differences between surface and subsurface microbiomes and between marine and terrestrial microbiomes remain unclear. We analyzed 478 archaeal and 1054 bacterial amplicon sequence datasets and 147 metagenomes from diverse and globally distributed surface and subsurface environments. Taxonomic analyses show that archaeal and bacterial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between marine and terrestrial microbiomes, suggesting a horizontal phylogenetic divide between sea and land that mirrors patterns in plant and animal diversity. In contrast, community composition overlapped from surface to subsurface environments indicating vertical diversity continua rather than a discrete subsurface biosphere. Diversity of terrestrial microbiomes decreases from surface to subsurface environments. Marine subsurface diversity and phylogenetic novelty rivaled (bacteria) or even exceeded (archaea) that of surface environments, suggesting that the marine subsurface holds a considerable and underestimated fraction of Earths archaeal and bacterial diversity. TeaserSubsurface ecosystems within Earths crust and seafloor harbor diverse and distinct microbiomes featuring many unknown lineages.

microbiology↗

bioRxiv2020

Colwellia and Marinobacter metapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities

Over 7 million liters of Corexit EC9500A and EC9527A were applied to the Gulf of Mexico in response to the Deepwater Horizon oil spill. The impacts of dispersants remain under debate and negative, positive, and inconclusive impacts have been reported. Here, metatrancriptomics was applied in the context of metapangenomes to microcosms that simulated environmental conditions comparable to the hydrocarbon-rich 1,100 m deep plume. Within this microcosm study, negative effects of dispersants on microbial hydrocarbon degradation were previously reported based on activity measurements and geochemical data. Transcriptional enrichment of Colwellia, a potential dispersant degrader, followed variable time-dependent trajectories due to interactions between oil, dispersants, and nutrients. The Colwellia metapangenome captured a mixture of environmental responses linked to the Colwellia psychrerythraea 34H genome and to the genomes of other members of the Colwellia genus. The activation of genes involved in lipid degradation, nitrogen metabolism, and membrane composition under oil or nutrient availability, suggested an opportunistic growth strategy for Colwellia. In contrast, transcripts of Marinobacter, a natural hydrocarbon degrader, increased only in oil treatments. Marinobacter transcripts largely recruited to the accessory metapangenome of Marinobacter sp. C18, the closest genomic reference. A complex response involving carbon and lipid metabolism, chemotaxis and a type IV secretion system suggested active energy-dependent processes in Marinobacter. These findings highlight chemistry-dependent responses in the metabolism of key hydrocarbon-degrading bacteria and underscore that dispersant-driven selection could temper the ability of the community to respond to hydrocarbon injection.

microbiology↗

bioRxiv2020

Deep-sea corals near cold seeps associate with chemoautotrophic bacteria that are related to the symbionts of cold seep and hydrothermal vent mussels.

Cnidarians are known for their symbiotic relationships, yet no known association exists between corals and chemoautotrophic microbes. Deep-sea corals, which support diverse animal communities in the Gulf of Mexico, are often found on authigenic carbonate in association with cold seeps. Sulfur-oxidizing chemoautotrophic bacteria of the SUP05 cluster are dominant symbionts of bathymodiolin mussels at cold seeps and hydrothermal vents around the world and have also been found in association with sponges. Therefore, we investigated whether other basal metazoans, corals, also associate with bacteria of the SUP05 cluster and report here that such associations are widespread. This was unexpected because it has been proposed that cnidarians would not form symbioses with chemoautotrophic bacteria due to their high oxygen demand and their lack of specialized respiratory structures. We screened corals, water, and sediment for SUP05 using 16S metabarcoding and found SUP05 phylotypes associated with corals at high relative abundance (10 - 91%). These coral-associated SUP05 phylotypes were coral host specific, absent in water samples, and rare or not detected in sediment samples. The genome of one SUP05 phylotype associated with Paramuricea sp. type B3, contained the genetic potential to oxidize reduced sulfur compounds and fix carbon and these pathways were transcriptionally active. Finally, the relative abundance of this SUP05 phylotype was positively correlated with chemoautotrophically-derived carbon and nitrogen input into the coral holobiont based on stable carbon and nitrogen isotopic compositions. We propose that SUP05 may supplement the diet of its host coral through chemoautotrophy or may provide nitrogen, essential amino acids, or vitamins. This is the first documented association between a chemoautotrophic symbiont and a cnidarian, broadening the known symbioses of corals and may represent a novel interaction between coral communities and cold seeps.

microbiology↗